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Respiratory Viruses Surveillance – Revilux

La surveillance SENTINELLE des infections respiratoires aiguës est une collaboration entre le Laboratoire national de santé (LNS), la Direction de la Santé et un réseau de médecins-généralistes et de pédiatres répartis à travers tout le Luxembourg. Ce rapport hebdomadaire est publié par le département de microbiologie du LNS dans le cadre de ses missions de surveillance, de vigileance et d’alerte dans les domaines de la santé publique, de l’analyse des données rapportant l’activité clinique dans la Sentinelle et les données virologiques à l’appui.

Pour recevoir des informations supplémentaires à ce sujet, veuillez nous contacter via email à l’adresse sentinelle@lns.etat.lu

The LNS processes the data collected for the purpose of sending documentation related to its activities. To learn more about the management of personal data and to exercise your rights, you can refer to the data protection policy on the LNS website at the following address: https://lns.lu/donnees-personnelles/ and more particularly in the section “In the context of LNS communication operations and its website”. If you no longer wish to receive these communications, you can unsubscribe to the newsletter. To do so, please send an email to revilux@lns.etat.lu


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  • Semaine 46

    Respiratory Viruses in Luxembourg (ReViLux)

    Weekly report (15 – 21 November 2021)

    Executive Summary

    The Sentinel Surveillance Network identified 8 cases of influenza-like illness, thus remaining below the recommended threshold for the epidemic season.

    Regarding SARS-CoV-2 genomic surveillance, the Laboratoire national de santé analysed 635 specimens from residents in Luxembourg in week 46/2021 (from 1897 total cases in the Grand Duchy of Luxembourg, 33,7%). This exceeds the minimum sample size (456) recommended by the ECDC to detect emerging variants reaching a 2,5% proportion.

    All specimens were assigned to the Delta variant, no Omicron cases were detected. Community surveillance showed that the AY.43 lineage continues to be the most frequent one (43,0%), followed by AY.98.1 (8,6%) and B.1.617.2 (8,3%). Regarding target groups (hospital and vaccine-breaktrhough cases), the same three lineages were found to be the most frequent ones during the last 10 weeks, with no notable differences between reference groups. As for the mutations under surveillance, they revealed no outstanding behaviour, remaining in agreement with the lineages observed.

    Introduction

    The Laboratoire national de santé, as National Reference Laboratory for Acute Respiratory Infections in Luxembourg, performs close surveillance on respiratory viruses, with a special focus on SARS-CoV-2. There are currently two active projects on which the ReViLux provides updates:

    The Sentinel Surveillance Network. It provides a broad picture of respiratory diseases affecting the Luxembourgish population, based on its double monitoring system (syndromic and virological).

    The National SARS-COV-2 Genomic Surveillance Program. It enables detailed observation of SARS-CoV-2 mutations and variants through time and space, and also monitoring specific groups of interest.

    Sentinel Surveillance Network

    The Sentinel Surveillance Network aims at monitoring the circulating respiratory viruses, including SARS-CoV-2, and hence underpin public health actions. Following the World Health Organization (WHO) and European Centre for Disease Prevention and Control (ECDC) guidance, it focuses on cases of acute respiratory infection (ARI) and influenza-like illness (ILI).

    Week 40 marked the beginning of the new influenza season 2021-2022. Results of syndromic surveillance during the last four weeks are displayed in Table 1 and the history of ILI consultations since the 2019-2020 season is shown in Figure 1. Eight cases of ILI were identified in week 46 (out of 409 consultations); therefore, the percentage of ILI (1,96%) remains below the threshold for the epidemic season (2,59%), according to the ECDC.

    Regarding the virological surveillance, a partnership among the CNS, private laboratories and the LNS recently started and will enable us to monitor the presence of several respiratory viruses. Results from the first analyses will be published soon.

    SARS-CoV-2 Genomic Surveillance

    The current sequencing strategy

    The National Reference Laboratory for Acute Respiratory Infections at LNS receives SARS-CoV-2 positive samples (nasopharyngeal or oropharyngeal swabs analysed by RT-PCR) from national laboratories and proceeds as follows:

    Sequencing all specimens from hospital cases.
    Sequencing all specimens from post-vaccination cases.
    Sequencing specimens from clusters with high transmission.
    Sequencing a representative sample of community cases.

    The representative sample of community cases is a systematic selection from all SARS-CoV-2 positive cases registered in Luxembourg to detect emerging variants and early increases in their incidence and transmission within the community in Luxembourg. This sample is selected according to the ECDC guidelines.

    Due to the emergence of the new Omicron variant of concern, as well as the high incidence rates in the European context, the LNS is currently carrying a complementary sequencing effort to provide real-time monitoring of the circulating SARS-CoV-2 variants in the country. A flash sequencing and reporting will be implemented for strategic samples: unusual transmission events (e.g. increased transmission despite the interventions in place), unexpected disease presentation/severity, vaccine-breakthrough infections and patients with known epidemiologic link to settings where the Omicron variant is already circulating. Additionally, the genomic and molecular microbiology unit (LUX-GEMM) at LNS will introduce a screening strategy based on the S-gene target failure RT-PCR to enable faster detection and identification of any potential Omicron variant cases.

    The LNS shares its sequencing results with GISAID EpiCov database periodically. SARS-CoV-2 lineages have been assigned based on Rambaut et al. using the Phylogenetic Assignment of Named Global Outbreak LINeages (pangolin) software (v3.1.16, pangoLEARN 2021-11-09). The Pango nomenclature is used in addition to the WHO nomenclature to enable easier visualization of links between any evolving variants and their ancestor (See nomenclature equivalences in Appendix 1). Delta lineages nomenclature is in constant review. The original Delta B.1.617.2 lineage is being re-classified into more specific AY lineages in order to enable a more precise tracing of the cases. This report is based on the latest nomenclature, and previously assigned lineages might have been updated to remain consistent with the latest nomenclature.

    Sequenced specimens

    In week 46, 1897 new cases were registered in Luxembourg; hence, the minimum sample size required to detect emerging variants at a 2.5% incidence is estimated to be 456 specimens (24%).

    As shown in Figure 2, last week the microbial genomics unit at the LNS analysed 830 specimens from week 46, with 635 specimens having been collected in week 46 from residents (33.5% coverage of the 1897 total cases registered in Luxembourg; see coverage trend in Figure 2). This exceeds the minimum sample size (456) to detect a 2.5% incidence recommended by the ECDC. The representative sample of community cases is built by systematic selection.

    Circulating lineage detection

    The distribution of successfully assigned lineages within the representative sample is shown in Figure 3. The selection of lineages displayed is based on their pevalence during the last 10 weeks (min. 1%). This distribution is further detailed for the last 2 weeks in Table 2. The lineage AY.43 continues to be the most frequent one (43,0%), followed by AY.98.1 (8,6%) and B.1.617.2 (8,3%).

    Mutation surveillance

    In addition to the surveillance of SARS-CoV-2 variants, the LNS monitors the occurrence of SARS-CoV-2 mutations reported to have a clinical and epidemiological relevance. This complementary surveillance enables us to detect unexpected mutations among the specimens sequenced. It is expected that VOC defining mutations share the same distribution as their corresponding VOCs. However, newly acquired mutations may occur and their early detection might be key to expect changes in the epidemic evolution.

    Following ECDC guidance, the LNS is currently monitoring 14 mutations to the spike protein frequently associated to VOCs (plus 28 additional mutations linked to the Omicron variant that are currently being analysed). Table 3 provides the cumulative frequencies of these mutations, detected in the lineage-assignable genome sequences since 1 Sep 2020 (N = 23 151), as well as the frequencies for the last 3 weeks.

    In broad terms, the mutations identified were expected according to the lineages assigned during this week. No mutation showed a remarkable behaviour.

    References

    Centers for Disease Control and Prevention. SARS-CoV-2 Variant Classifications and Definitions. Retrieved 30 November 2021, from https://www.cdc.gov/coronavirus/2019-ncov/variants/variant-info.html

    COVID-19 Data Portal – accelerating scientific research through data. (2021). Retrieved 30 November 2021, from https://www.covid19dataportal.org/sequences

    European Centre for Disease Prevention and Control. Guidance for representative and targeted genomic SARS-CoV-2 monitoring – 3 May 2021. ECDC : Stockholm ; 2021

    European Centre for Disease Prevention and Control. SARS-CoV-2 variants of concern. Retrieved 30 November 2021, from https://www.ecdc.europa.eu/en/covid-19/variants-concern

    Genomic sequencing of SARS-CoV-2: a guide to implementation for maximum impact on public health. Geneva: World Health Organization; 2021.

    GitHub – cov-lineages/pangolin: Software package for assigning SARS-CoV-2 genome sequences to global lineages. (2021). Retrieved 30 November 2021, from https://github.com/cov-lineages/pangolin

    Hadfield J., Megill C., Bell S., Huddleston J., Potter B., Callender C. et al. (2018). Nextstrain: real-time tracking of pathogen evolution. Bioinformatics, 34(23), 4121-4123. doi: 10.1093/bioinformatics/bty407

    Pango Network. New AY lineages. Retrieved 30 November 2021, from: https://www.pango.network/new-ay-lineages/

    Pango Network. New AY lineages. Retrieved 30 November 2021, from: https://www.pango.network/new-ay-lineages-and-an-update-to-ay-4-ay-12/

    Rambaut A., Holmes E., O’Toole Á., Hill V., McCrone J., Ruis C. et al. (2020). A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nature Microbiology, 5(11), 1403-1407. doi: 10.1038/s41564-020-0770-5

    Appendices

    Appendix 1: SARS-CoV-2 variants of concern

    According to the ECDC

    References:

    1. Madhi SA, Baillie V, Cutland CL, Voysey M, Koen AL, Fairlie L, et al. Efficacy of the ChAdOx1 nCoV-19 Covid-19 Vaccine against the B.1.351 Variant. New England Journal of Medicine. 2021.
    2. Cele S, Gazy I, Jackson L, Hwa S-H, Tegally H, Lustig G, et al. Escape of SARS-CoV-2 501Y.V2 from neutralization by convalescent plasma. Nature. 2021.
    3. Pearson CA. Estimates of severity and transmissibility of novel South Africa SARS-CoV-2 variant 501Y.V2 [Available from: https://cmmid.github.io/topics/covid19/reports/sa-novel-variant/2021_01_11_Transmissibility_and_severity_of_501Y_V2_in_SA.pdf
    4. Funk T, Pharris A, Spiteri G, Bundle N, Melidou A, Carr M, et al. Characteristics of SARS-CoV-2 variants of concern B.1.1.7, B.1.351 or P.1: data from seven EU/EEA countries, weeks 38/2020 to 10/2021. Eurosurveillance. 2021;26(16):2100348.
    5. Faria NR, Mellan TA, Whittaker C, Claro IM, Candido DdS, Mishra S, et al. Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil. Science. 2021.
    6. Dejnirattisai W, Zhou D, Supasa P, Liu C, Mentzer AJ, Ginn HM, et al. Antibody evasion by the P.1 strain of SARS-CoV-2. Cell. 2021.
    7. Public Health England. SARS-CoV-2 variants of concern and variants under investigation in England Technical briefing 12 2021 [Available from: https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/988619/Variants_of_Concern_VOC_Technical_Briefing_12_England.pdf
    8. Jamie Lopez Bernal NA, Charlotte Gower, Eileen Gallagher, Dr Ruth Simmons, Simon Thelwall, Julia Stowe, Elise Tessier, Natalie Groves, Gavin Dabrera, Richard Myers, Vanessa Saliba, Shamez Ladhani, Coli, Campbell, Gayatri Amirthalingam, Matt Edmunds, Maria Zambon, Kevin Brown, Susan Hopkins, Meera Chand, Mary Ramsay. Effectiveness of COVID-19 vaccines against the B.1.617.2 variant 2021 [Available from: https://khub.net/documents/135939561/430986542/Effectiveness+of+COVID-19+vaccines+against+the+B.1.617.2+variant.pdf/204c11a4-e02e-11f2-db19-b3664107ac42
    9. Sheikh A, McMenamin J, Taylor B, Robertson C. SARS-CoV-2 Delta VOC in Scotland: demographics, risk of hospital admission, and vaccine effectiveness. The Lancet.
    10. Stowe J, Andrews N, Gower C, Gallagher E, Utsi L, Simmons R, et al. Effectiveness of COVID-19 vaccines against hospital admission with the Delta (B.1.617.2) variant 2021 [Available from: https://khub.net/documents/135939561/479607266/Effectiveness+of+COVID-19+vaccines+against+hospital+admission+with+the+Delta+%28B.1.617.2%29+variant.pdf/1c213463-3997-ed16-2a6f-14e5deb0b997?t=1623689315431
    11. Public Health England. SARS-CoV-2 variants of concern and variants under investigation in England Technical briefing 16 2021 [Available from: https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/997414/Variants_of_Concern_VOC_Technical_Briefing_16.pdf

    According to the WHO

  • Semaine 45

    Respiratory Viruses in Luxembourg (ReViLux)

    Weekly report (8 – 14 November 2021)

    Executive Summary

    The Sentinel Surveillance Network identified 9 cases of influenza-like illness, thus remaining below the recommended threshold for the new epidemic season, according to the European Center for Disease Prevention and Control (ECDC) guidelines.

    Regarding SARS-CoV-2 genomic surveillance, the Laboratoire national de santé analysed 596 specimens from residents in Luxembourg in week 45/2021 (from 1444 total cases in the Grand Duchy of Luxembourg, 41,3%). This exceeds the minimum sample size (424) recommended by the ECDC to detect emerging variants of a 2,5% proportion.

    All specimens were assigned to the Delta variant. Community surveillance showed that the AY.43 lineage continues to be the most frequent one (38,0%), followed by B.1.617.2 (12,3%) and AY.98.1 (7,1%). Regarding target groups, the same three lineages were found to be the most frequent ones, both within hospital specimens and post-vaccination breakthrough cases. As for the mutations under surveillance, they revealed no outstanding behaviour, remaining in agreement with the lineages observed.

    Introduction

    The Laboratoire national de santé, as National Reference Laboratory for Acute Respiratory Infections in Luxembourg, performs close surveillance on respiratory viruses, with a special focus on SARS-CoV-2. There are currently two active projects on which the ReViLux provides updates:

    The Sentinel Surveillance Network. It provides a broad picture of respiratory diseases affecting the Luxembourgish population, based on its double monitoring system (syndromic and virological).

    The National SARS-COV-2 Genomic Surveillance Program. It enables detailed observation of SARS-CoV-2 mutations and variants through time and space, and also monitoring specific groups of interest.

    Sentinel Surveillance Network

    The Sentinel Surveillance Network aims at monitoring the circulating respiratory viruses, including SARS-CoV-2, and hence underpin public health actions. Following the World Health Organization (WHO) and European Centre for Disease Prevention and Control (ECDC) guidance, it focuses on cases of acute respiratory infection (ARI) and influenza-like illness (ILI).

    Week 40 marked the beginning of the new influenza season 2021-2022. Results of syndromic surveillance during week 44 are displayed in Table 1 and the history of ILI consultations since the 2019-2020 season is shown in Figure 1. Nine cases of ILI were identified in week 45 (out of 492 consultations); therefore, the percentage of ILI (1,83%) remains below the threshold for the epidemic season (2,59%), according to the ECDC.

    Regarding the virological surveillance, a partnership among the CNS, private laboratories and the LNS recently started and will enable us to monitor the presence of several respiratory viruses. Results from the first analyses will be published soon.

    SARS-CoV-2 Genomic Surveillance

    The current sequencing strategy

    The National Reference Laboratory for Acute Respiratory Infections at LNS receives SARS-CoV-2 positive samples (nasopharyngeal or oropharyngeal swabs analysed by RT-PCR) from the national network of laboratories and proceeds as follows:

    Sequencing all specimens from hospital cases.
    Sequencing all specimens from post-vaccination cases.
    Sequencing specimens from clusters with high transmission.
    Sequencing a representative sample of community cases.

    The representative sample of community cases is a systematic selection from all SARS-CoV-2 positive cases registered in Luxembourg to detect emerging variants and early increases in their incidence and transmission within the community in Luxembourg. This sample is selected according to the ECDC guidelines.

    The LNS shares its sequencing results with GISAID EpiCov database (www.gisaid.org) periodically. SARS-CoV-2 lineages (variants) have been assigned based on Rambaut et al. using the Phylogenetic Assignment of Named Global Outbreak LINeages (pangolin) software (v3.1.16, pangoLEARN 2021-11-09). Delta lineages nomenclature is under constant review. The original Delta B.1.617.2 lineage is being re-classified into more specific AY lineages in order to enable a more precise tracing of the cases. This report is based on the latest nomenclature, and previously assigned lineages have been updated to remain consistent with the latest nomenclature.

    The ReViLux continues to use the Pango nomenclature, in addition to the WHO nomenclature, to allow easier visualization of links between any evolving variants and their ancestor (https://cov-lineages.org). See nomenclature equivalences in Appendix 1.

    Methodological notes

    Alpha variant is no longer considered as a variant of concern by the ECDC, due to both its low circulation and the high effectiveness of vaccines in controlling it. Therefore, specimens assigned to this variant are no longer reported separately.

    Sequenced specimens

    In week 45, 1444 new cases were registered in Luxembourg; hence, the minimum sample size required to detect emerging variants at a 2,5% incidence is estimated to be 424 specimens (29,4%).

    As shown in Figure 2, last week the microbial genomics unit at the LNS analysed 732 specimens from week 45, with 596 specimens having been collected in week 45 from residents (41,3% coverage of the 1444 total cases registered in Luxembourg; see coverage trend in Figure 2). This exceeds the minimum sample size (424) to detect a 2,5% incidence recommended by the ECDC. The representative sample of community cases is built by systematic selection.

    Circulating lineage detection

    The distribution of successfully assigned lineages within the representative sample is shown in Figure 3. The selection of displayed lineages is based on their prevalence during the last 10 weeks (min. 1%). This distribution is further detailed for the last 2 weeks in Table 2. The lineage AY.43 continues to be the most frequent one (38,0%), followed by B.1.617.2 (12,3%), while the remaining lineages show frequencies lower than 10%.

    Mutation surveillance

    In addition to the surveillance of SARS-CoV-2 variants, the LNS monitors the occurrence of SARS-CoV-2 mutations reported to have a clinical and epidemiological relevance. This complementary surveillance enables us to detect unexpected mutations among the specimens sequenced. It is expected that VOC defining mutations share the same distribution as their corresponding VOCs. However, newly acquired mutations may occur and their early detection might be key to expect changes in the epidemic evolution.

    Following ECDC guidance, the LNS is currently monitoring 15 mutations to the spike protein frequently associated to VOCs and variants of interest (VOIs). Table 3 provides the cumulative frequencies of these mutations, detected in the lineage-assignable genome sequences since 1 Sep 2020 (N = 21 506), as well as the frequencies for the last 3 weeks.

    In broad terms, the mutations identified were expected according to the lineages assigned during this week. No mutation showed an outstanding behaviour.

    References

    Centers for Disease Control and Prevention. SARS-CoV-2 Variant Classifications and Definitions. Retrieved 22 November 2021, from https://www.cdc.gov/coronavirus/2019-ncov/variants/variant-info.html

    COVID-19 Data Portal – accelerating scientific research through data. (2021). Retrieved 22 November 2021, from https://www.covid19dataportal.org/sequences

    European Centre for Disease Prevention and Control. Guidance for representative and targeted genomic SARS-CoV-2 monitoring – 3 May 2021. ECDC : Stockholm ; 2021

    European Centre for Disease Prevention and Control. SARS-CoV-2 variants of concern. Retrieved 22 November 2021, from https://www.ecdc.europa.eu/en/covid-19/variants-concern

    Genomic sequencing of SARS-CoV-2: a guide to implementation for maximum impact on public health. Geneva: World Health Organization; 2021.

    GitHub – cov-lineages/pangolin: Software package for assigning SARS-CoV-2 genome sequences to global lineages. (2021). Retrieved 22 November 2021, from https://github.com/cov-lineages/pangolin

    Hadfield J., Megill C., Bell S., Huddleston J., Potter B., Callender C. et al. (2018). Nextstrain: real-time tracking of pathogen evolution. Bioinformatics, 34(23), 4121-4123. doi: 10.1093/bioinformatics/bty407

    Pango Network. New AY lineages. Retrieved 22 November 2021, from: https://www.pango.network/new-ay-lineages/

    Pango Network. New AY lineages. Retrieved 22 November 2021, from: https://www.pango.network/new-ay-lineages-and-an-update-to-ay-4-ay-12/

    Rambaut A., Holmes E., O’Toole Á., Hill V., McCrone J., Ruis C. et al. (2020). A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nature Microbiology, 5(11), 1403-1407. doi: 10.1038/s41564-020-0770-5

    Appendices

    Appendix 1: SARS-CoV-2 variants of concern

    According to the ECDC

    References:

    1. Madhi SA, Baillie V, Cutland CL, Voysey M, Koen AL, Fairlie L, et al. Efficacy of the ChAdOx1 nCoV-19 Covid-19 Vaccine against the B.1.351 Variant. New England Journal of Medicine. 2021.
    2. Cele S, Gazy I, Jackson L, Hwa S-H, Tegally H, Lustig G, et al. Escape of SARS-CoV-2 501Y.V2 from neutralization by convalescent plasma. Nature. 2021.
    3. Pearson CA. Estimates of severity and transmissibility of novel South Africa SARS-CoV-2 variant 501Y.V2 [Available from: https://cmmid.github.io/topics/covid19/reports/sa-novel-variant/2021_01_11_Transmissibility_and_severity_of_501Y_V2_in_SA.pdf
    4. Funk T, Pharris A, Spiteri G, Bundle N, Melidou A, Carr M, et al. Characteristics of SARS-CoV-2 variants of concern B.1.1.7, B.1.351 or P.1: data from seven EU/EEA countries, weeks 38/2020 to 10/2021. Eurosurveillance. 2021;26(16):2100348.
    5. Faria NR, Mellan TA, Whittaker C, Claro IM, Candido DdS, Mishra S, et al. Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil. Science. 2021.
    6. Dejnirattisai W, Zhou D, Supasa P, Liu C, Mentzer AJ, Ginn HM, et al. Antibody evasion by the P.1 strain of SARS-CoV-2. Cell. 2021.
    7. Public Health England. SARS-CoV-2 variants of concern and variants under investigation in England Technical briefing 12 2021 [Available from: https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/988619/Variants_of_Concern_VOC_Technical_Briefing_12_England.pdf
    8. Jamie Lopez Bernal NA, Charlotte Gower, Eileen Gallagher, Dr Ruth Simmons, Simon Thelwall, Julia Stowe, Elise Tessier, Natalie Groves, Gavin Dabrera, Richard Myers, Vanessa Saliba, Shamez Ladhani, Coli, Campbell, Gayatri Amirthalingam, Matt Edmunds, Maria Zambon, Kevin Brown, Susan Hopkins, Meera Chand, Mary Ramsay. Effectiveness of COVID-19 vaccines against the B.1.617.2 variant 2021 [Available from: https://khub.net/documents/135939561/430986542/Effectiveness+of+COVID-19+vaccines+against+the+B.1.617.2+variant.pdf/204c11a4-e02e-11f2-db19-b3664107ac42
    9. Sheikh A, McMenamin J, Taylor B, Robertson C. SARS-CoV-2 Delta VOC in Scotland: demographics, risk of hospital admission, and vaccine effectiveness. The Lancet.
    10. Stowe J, Andrews N, Gower C, Gallagher E, Utsi L, Simmons R, et al. Effectiveness of COVID-19 vaccines against hospital admission with the Delta (B.1.617.2) variant 2021 [Available from: https://khub.net/documents/135939561/479607266/Effectiveness+of+COVID-19+vaccines+against+hospital+admission+with+the+Delta+%28B.1.617.2%29+variant.pdf/1c213463-3997-ed16-2a6f-14e5deb0b997?t=1623689315431
    11. Public Health England. SARS-CoV-2 variants of concern and variants under investigation in England Technical briefing 16 2021 [Available from: https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/997414/Variants_of_Concern_VOC_Technical_Briefing_16.pdf

    According to the WHO

     

     

  • Semaine 44

    Respiratory Viruses in Luxembourg (ReViLux)

    Weekly report (1– 7 November 2021)

    Executive Summary

    The Sentinel Surveillance Network identified 3 cases of influenza-like illness, thus remaining below the recommended threshold for the new epidemic season, according to the European Center for Disease Prevention and Control (ECDC) guidelines.

    Regarding SARS-CoV-2 genomic surveillance, the Laboratoire national de santé analysed 557 specimens from residents in Luxembourg in week 44/2021 (from 1211 total cases in the Grand Duchy of Luxembourg, 46,0%). This exceeds the minimum sample size (401) recommended by the ECDC to detect emerging variants at a 2.5% incidence at the epidemic situation in the country.

    All specimens were assigned to the Delta variant. Community surveillance showed that the AY.43 lineage continues to be the most frequent one (38,4%), followed by B.1.617.2 (26,7%). In respect to target groups, AY lineages were found in 70,7% of hospital specimens and 74,3% of post-vaccination breakthrough cases. As for the mutations under surveillance, they revealed no outstanding behaviour, remaining in agreement with the lineages observed.

    Introduction

    The Laboratoire national de santé, as National Reference Laboratory for Acute Respiratory Infections in Luxembourg, performs close surveillance on respiratory viruses, with a special focus on SARS-CoV-2. There are currently two active projects on which the ReViLux provides updates:

    The Sentinel Surveillance Network. It provides a broad picture of respiratory diseases affecting the Luxembourgish population, based on its double monitoring system (syndromic and virological).

    The National SARS-COV-2 Genomic Surveillance Program. It enables detailed observation of SARS-CoV-2 mutations and variants through time and space, and also monitoring specific groups of interest.

    Sentinel Surveillance Network

    The Sentinel Surveillance Network aims at monitoring the circulating respiratory viruses, including SARS-CoV-2, and hence underpin public health actions. Following the World Health Organization (WHO) and European Centre for Disease Prevention and Control (ECDC) guidance, it focuses on cases of acute respiratory infection (ARI) and influenza-like illness (ILI).

    Week 40 marked the beginning of the new influenza season 2021-2022. Results of syndromic surveillance during week 44 are displayed in Table 1 and the history of ILI consultations since the 2019-2020 season is shown in Figure 1. Three cases of ILI were identified in week 44 (out of 234 consultations); therefore, the percentage of ILI (1,28%) remains below the threshold for the epidemic season (2,59%), according to the ECDC.

    Regarding the virological surveillance, a partnership among the CNS, private laboratories and the LNS recently started and will enable us to monitor the presence of several respiratory viruses. Results from the first analyses will be published soon.

    SARS-CoV-2 Genomic Surveillance

    The current sequencing strategy

    The National Reference Laboratory for Acute Respiratory Infections at LNS receives SARS-CoV-2 positive samples (nasopharyngeal or oropharyngeal swabs analysed by RT-PCR) from the national network of laboratories and proceeds as follows:

    Sequencing all specimens from hospital cases.
    Sequencing all specimens from reinfection and post-vaccination cases.
    Sequencing all specimens from cluster cases.
    Sequencing a representative sample of community cases.

    The representative sample of community cases is a systematic selection from all SARS-CoV-2 positive cases registered in Luxembourg to detect emerging variants and early increases in their incidence and transmission within the community in Luxembourg. This sample is selected according to the ECDC guidelines.

    The LNS shares its sequencing results with GISAID EpiCov database (www.gisaid.org) periodically. SARS-CoV-2 lineages (variants) have been assigned based on Rambaut et al. using Phylogenetic Assignment of Named Global Outbreak LINeages (pangolin) software  (v3.1.16, pangoLEARN 2021-10-18). The ReViLux continues to use the Pango nomenclature, in addition to the WHO nomenclature, to allow easier visualization of links between any evolving variants and their ancestor (https://cov-lineages.org). See nomenclature equivalences in the Appendices.

    Methodological notes

    Since 3 September 2021, the ECDC no longer considers B.1.1.7 and B.1.1.7+E484K lineages (Alpha variant) as variants of concern. This decision is based on both their low circulation and the high effectiveness of vaccines in controlling them.

    Delta sublineages nomenclature is in constant review. This report is based on the pangoLEARN version v2021-10-18. Previously assigned lineages might differ after retrospective analysis of the sequences, based on the updated pangoLEARN version.

    Sequenced specimens

    In week 44, 1211 new cases were registered in Luxembourg; hence, the minimum sample size required to detect emerging variants at a 2,5% incidence is estimated to be 401 specimens (33,1%).

    As shown in Figure 2, last week the microbial genomics unit at the LNS sequenced 673 specimens from week 44, with 557 specimens having been collected in week 44 from residents (46,0% coverage of the 1211 total cases registered in Luxembourg; see coverage trend in Figure 2). This exceeds the minimum sample size (401) to detect a 2.5% incidence recommended by the ECDC. The representative sample of community cases is built by systematic selection.

    Circulating lineage detection

    In week 44/2021, only Delta variant cases were detected among all specimens sequenced (target groups, clusters and non-residents comprised), as shown in Figure 3. The distribution of successfully assigned lineages is displayed in Table 2. The lineage AY.43 continues to be the most frequent one (38,4%), followed by B.1.617.2 (26,7%).

    Mutation surveillance

    In addition to the surveillance of SARS-CoV-2 variants, the LNS monitors the occurrence of SARS-CoV-2 mutations reported to have a clinical and epidemiological relevance. This complementary surveillance enables us to detect unexpected mutations among the specimens sequenced. It is expected that VOC defining mutations share the same distribution as their corresponding VOCs. However, newly acquired mutations may occur and their early detection might be key to expect changes in the epidemic evolution.

    Following ECDC guidance, the LNS is currently monitoring 15 mutations to the spike protein frequently associated to VOCs and variants of interest (VOIs). Table 3 provides the cumulative frequencies of these mutations, detected in the lineage-assignable genome sequences since 1 Sep 2020 (N = 21 942), as well as the frequencies for the last 3 weeks.

    In broad terms, the mutations identified were expected according to the lineages assigned during this week. No mutation showed an outstanding behaviour.

    References

    Centers for Disease Control and Prevention. SARS-CoV-2 Variant Classifications and Definitions. Retrieved 15 November 2021, from https://www.cdc.gov/coronavirus/2019-ncov/variants/variant-info.html

    COVID-19 Data Portal – accelerating scientific research through data. (2021). Retrieved 15 November 2021, from https://www.covid19dataportal.org/sequences

    European Centre for Disease Prevention and Control. Guidance for representative and targeted genomic SARS-CoV-2 monitoring – 3 May 2021. ECDC : Stockholm ; 2021

    European Centre for Disease Prevention and Control. SARS-CoV-2 variants of concern. Retrieved 15 November 2021, from https://www.ecdc.europa.eu/en/covid-19/variants-concern

    Genomic sequencing of SARS-CoV-2: a guide to implementation for maximum impact on public health. Geneva: World Health Organization; 2021.

    GitHub – cov-lineages/pangolin: Software package for assigning SARS-CoV-2 genome sequences to global lineages. (2021). Retrieved 15 November 2021, from https://github.com/cov-lineages/pangolin

    Hadfield J., Megill C., Bell S., Huddleston J., Potter B., Callender C. et al. (2018). Nextstrain: real-time tracking of pathogen evolution. Bioinformatics, 34(23), 4121-4123. doi: 10.1093/bioinformatics/bty407

    Pango Network. New AY lineages. Retrieved 15 November 2021, from: https://www.pango.network/new-ay-lineages/

    Pango Network. New AY lineages. Retrieved 15 November 2021, from: https://www.pango.network/new-ay-lineages-and-an-update-to-ay-4-ay-12/

    Rambaut A., Holmes E., O’Toole Á., Hill V., McCrone J., Ruis C. et al. (2020). A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nature Microbiology, 5(11), 1403-1407. doi: 10.1038/s41564-020-0770-5

    Appendices

    Appendix 1: SARS-CoV-2 variants of concern according to the ECDC

     

    References:

    1. Madhi SA, Baillie V, Cutland CL, Voysey M, Koen AL, Fairlie L, et al. Efficacy of the ChAdOx1 nCoV-19 Covid-19 Vaccine against the B.1.351 Variant. New England Journal of Medicine. 2021.
    2. Cele S, Gazy I, Jackson L, Hwa S-H, Tegally H, Lustig G, et al. Escape of SARS-CoV-2 501Y.V2 from neutralization by convalescent plasma. Nature. 2021.
    3. Pearson CA. Estimates of severity and transmissibility of novel South Africa SARS-CoV-2 variant 501Y.V2 [Available from: https://cmmid.github.io/topics/covid19/reports/sa-novel-variant/2021_01_11_Transmissibility_and_severity_of_501Y_V2_in_SA.pdf
    4. Funk T, Pharris A, Spiteri G, Bundle N, Melidou A, Carr M, et al. Characteristics of SARS-CoV-2 variants of concern B.1.1.7, B.1.351 or P.1: data from seven EU/EEA countries, weeks 38/2020 to 10/2021. Eurosurveillance. 2021;26(16):2100348.
    5. Faria NR, Mellan TA, Whittaker C, Claro IM, Candido DdS, Mishra S, et al. Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil. Science. 2021.
    6. Dejnirattisai W, Zhou D, Supasa P, Liu C, Mentzer AJ, Ginn HM, et al. Antibody evasion by the P.1 strain of SARS-CoV-2. Cell. 2021.
    7. Public Health England. SARS-CoV-2 variants of concern and variants under investigation in England Technical briefing 12 2021 [Available from: https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/988619/Variants_of_Concern_VOC_Technical_Briefing_12_England.pdf
    8. Jamie Lopez Bernal NA, Charlotte Gower, Eileen Gallagher, Dr Ruth Simmons, Simon Thelwall, Julia Stowe, Elise Tessier, Natalie Groves, Gavin Dabrera, Richard Myers, Vanessa Saliba, Shamez Ladhani, Coli, Campbell, Gayatri Amirthalingam, Matt Edmunds, Maria Zambon, Kevin Brown, Susan Hopkins, Meera Chand, Mary Ramsay. Effectiveness of COVID-19 vaccines against the B.1.617.2 variant 2021 [Available from: https://khub.net/documents/135939561/430986542/Effectiveness+of+COVID-19+vaccines+against+the+B.1.617.2+variant.pdf/204c11a4-e02e-11f2-db19-b3664107ac42
    9. Sheikh A, McMenamin J, Taylor B, Robertson C. SARS-CoV-2 Delta VOC in Scotland: demographics, risk of hospital admission, and vaccine effectiveness. The Lancet.
    10. Stowe J, Andrews N, Gower C, Gallagher E, Utsi L, Simmons R, et al. Effectiveness of COVID-19 vaccines against hospital admission with the Delta (B.1.617.2) variant 2021 [Available from: https://khub.net/documents/135939561/479607266/Effectiveness+of+COVID-19+vaccines+against+hospital+admission+with+the+Delta+%28B.1.617.2%29+variant.pdf/1c213463-3997-ed16-2a6f-14e5deb0b997?t=1623689315431
    11. Public Health England. SARS-CoV-2 variants of concern and variants under investigation in England Technical briefing 16 2021 [Available from: https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/997414/Variants_of_Concern_VOC_Technical_Briefing_16.pdf

    Appendix 2: SARS-CoV-2 variants of concern according to the WHO

     

     

     

     

     

  • Semaine 43

    Respiratory Viruses in Luxembourg (ReViLux)

    Weekly report (25 – 31 October 2021)

    Executive Summary

    The Sentinel Surveillance Network identified 14 cases of influenza-like illness, thus exceeding the recommended threshold for the new epidemic season, according to the European Center for Disease Prevention and Control (ECDC) guidelines.

    Regarding SARS-CoV-2 genomic surveillance, the Laboratoire national de santé analysed 497 specimens from residents in Luxembourg in week 43/2021 (from 1118 total cases in the Grand Duchy of Luxembourg, 44,5%). This exceeds the minimum sample size (391) recommended by the ECDC to detect emerging variants at a 2.5% incidence at the epidemic situation in the country.

    All specimens were assigned to the Delta variant. Community surveillance showed that the lineage AY.43 is the most frequent one (35,5%), followed by B.1.617.2 (28,9%) and AY.25 (11,0%). In respect to target groups, AY lineages were found in 67,1% of hospital specimens and 69,0% of post-vaccination breakthrough cases. As for the mutations under surveillance, they revealed no outstanding behaviour, remaining in agreement with the lineages observed.

    Introduction

    The Laboratoire national de santé, as National Reference Laboratory for Acute Respiratory Infections in Luxembourg, performs close surveillance on respiratory viruses, with a special focus on SARS-CoV-2. There are currently two active projects on which the ReViLux provides updates:

    The Sentinel Surveillance Network. It provides a broad picture of respiratory diseases affecting the Luxembourgish population, based on its double monitoring system (syndromic and virological).

    The National SARS-COV-2 Genomic Surveillance Program. It enables detailed observation of SARS-CoV-2 mutations and variants through time and space, and also monitoring specific groups of interest.

    Sentinel Surveillance Network

    The Sentinel Surveillance Network aims at monitoring the circulating respiratory viruses, including SARS-CoV-2, and hence underpin public health actions. Following the World Health Organization (WHO) and European Centre for Disease Prevention and Control (ECDC) guidance, it focuses on cases of acute respiratory infection (ARI) and influenza-like illness (ILI).

    Week 40 marked the beginning of the new influenza season 2021-2022. Results of syndromic surveillance during week 43 are displayed in Table 1 and the history of ILI consultations since the 2019-2020 season is shown in Figure 1. Fourteen cases of ILI were identified in week 43 (out of 504 consultations); therefore, the percentage of ILI (2,78%) is slightly above the threshold for the epidemic season (2,59%), according to the ECDC.

    Regarding the virological surveillance, a partnership among the CNS, private laboratories and the LNS recently started and will enable us to monitor the presence of several respiratory viruses. Results from the first analyses will be published soon.

    SARS-CoV-2 Genomic Surveillance

    The current sequencing strategy

    The National Reference Laboratory for Acute Respiratory Infections at LNS receives SARS-CoV-2 positive samples (nasopharyngeal or oropharyngeal swabs analysed by RT-PCR) from the national network of laboratories and proceeds as follows:

    Sequencing all specimens from hospital cases.
    Sequencing all specimens from reinfection and post-vaccination cases.
    Sequencing all specimens from cluster cases.
    Sequencing a representative sample of community cases.

    The representative sample of community cases is a systematic selection from all SARS-CoV-2 positive cases registered in Luxembourg to detect emerging variants and early increases in their incidence and transmission within the community in Luxembourg. This sample is selected according to the ECDC guidelines.

    The LNS shares its sequencing results with GISAID EpiCov database (www.gisaid.org) periodically. SARS-CoV-2 lineages (variants) have been assigned based on Rambaut et al. using Phylogenetic Assignment of Named Global Outbreak LINeages (pangolin) software  (v3.1.16, pangoLEARN 2021-10-18). The ReViLux continues to use the Pango nomenclature, in addition to the WHO nomenclature, to allow easier visualization of links between any evolving variants and their ancestor (https://cov-lineages.org). See nomenclature equivalences in the Appendices.

    Methodological notes

    Since 3 September 2021, the ECDC no longer considers B.1.1.7 and B.1.1.7+E484K lineages (Alpha variant) as variants of concern. This decision is based in both their low circulation and the high effectiveness of vaccines in controlling them.

    Delta sublineages nomenclature is in constant review. This report is based on the pangoLEARN version v2021-10-18, which included a reclassification into lineage AY.43 of many specimens previously assigned the parental lineage B.1.617.2. Previously reported lineage distributions might differ after retrospective analysis of the sequences, based on the updated pangoLEARN version.

    Sequenced specimens

    In week 43, 1118 new cases were registered in Luxembourg; hence, the minimum sample size required to detect emerging variants at a 2.5% incidence is estimated to be 391 specimens (35%).

    As shown in Figure 2, last week the microbial genomics unit at the LNS sequenced 568 specimens from week 43, with 497 specimens having been collected in week 43 from residents (44,5% coverage of the 1118 total cases registered in Luxembourg; see coverage trend in Figure 2). This exceeds the minimum sample size (391) to detect a 2.5% incidence recommended by the ECDC. The representative sample of community cases is built by systematic selection.

    Circulating lineage detection

    In week 43/2021, only Delta variant cases were detected among all specimens sequenced in the representative sample of community cases, including 20 Delta subtypes. The distribution of VOCs is displayed in Table 2 and their evolution over the weeks is shown in Figure 3. The lineage AY.43 was the most frequent one (35,5%), followed by B.1.617.2 (29,6%) and AY.25 (10,2%). The distribution of lineages for week 43 displayed in this report differs from the one published in the previous one due to an update to the source software (more details in the Methodological note).

    Mutation surveillance

    In addition to the surveillance of SARS-CoV-2 variants, the LNS monitors the occurrence of SARS-CoV-2 mutations reported to have a clinical and epidemiological relevance. This complementary surveillance enables us to detect unexpected mutations among the specimens sequenced. It is expected that VOC defining mutations share the same distribution as their corresponding VOCs. However, newly acquired mutations may occur and their early detection might be key to expect changes in the epidemic evolution.

    Following ECDC guidance, the LNS is currently monitoring 15 mutations to the spike protein frequently associated to VOCs and variants of interest (VOIs). Table 3 provides the cumulative frequencies of these mutations, detected in the lineage-assignable genome sequences since 1 Sep 2020 (N = 21 310), as well as the frequencies for the last 3 weeks.

    In broad terms, the mutations identified were expected according to the lineages assigned during this week. No mutation showed an outstanding behaviour.

    References

    Centers for Disease Control and Prevention. SARS-CoV-2 Variant Classifications and Definitions. Retrieved 8 November 2021, from https://www.cdc.gov/coronavirus/2019-ncov/variants/variant-info.html

    COVID-19 Data Portal – accelerating scientific research through data. (2021). Retrieved 8 November 2021, from https://www.covid19dataportal.org/sequences

    European Centre for Disease Prevention and Control. Guidance for representative and targeted genomic SARS-CoV-2 monitoring – 3 May 2021. ECDC : Stockholm ; 2021

    European Centre for Disease Prevention and Control. SARS-CoV-2 variants of concern. Retrieved 8 November 2021, from https://www.ecdc.europa.eu/en/covid-19/variants-concern

    Genomic sequencing of SARS-CoV-2: a guide to implementation for maximum impact on public health. Geneva: World Health Organization; 2021.

    GitHub – cov-lineages/pangolin: Software package for assigning SARS-CoV-2 genome sequences to global lineages. (2021). Retrieved 8 November 2021, from https://github.com/cov-lineages/pangolin

    Hadfield J., Megill C., Bell S., Huddleston J., Potter B., Callender C. et al. (2018). Nextstrain: real-time tracking of pathogen evolution. Bioinformatics, 34(23), 4121-4123. doi: 10.1093/bioinformatics/bty407

    Pango Network. New AY lineages. Retrieved 8 November 2021, from: https://www.pango.network/new-ay-lineages/

    Pango Network. New AY lineages. Retrieved 8 November 2021, from: https://www.pango.network/new-ay-lineages-and-an-update-to-ay-4-ay-12/

    Rambaut A., Holmes E., O’Toole Á., Hill V., McCrone J., Ruis C. et al. (2020). A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nature Microbiology, 5(11), 1403-1407. doi: 10.1038/s41564-020-0770-5

    Appendices

    Appendix 1: SARS-CoV-2 variants of concern according to the ECDC

    References:

    1. Madhi SA, Baillie V, Cutland CL, Voysey M, Koen AL, Fairlie L, et al. Efficacy of the ChAdOx1 nCoV-19 Covid-19 Vaccine against the B.1.351 Variant. New England Journal of Medicine. 2021.
    2. Cele S, Gazy I, Jackson L, Hwa S-H, Tegally H, Lustig G, et al. Escape of SARS-CoV-2 501Y.V2 from neutralization by convalescent plasma. Nature. 2021.
    3. Pearson CA. Estimates of severity and transmissibility of novel South Africa SARS-CoV-2 variant 501Y.V2 [Available from: https://cmmid.github.io/topics/covid19/reports/sa-novel-variant/2021_01_11_Transmissibility_and_severity_of_501Y_V2_in_SA.pdf
    4. Funk T, Pharris A, Spiteri G, Bundle N, Melidou A, Carr M, et al. Characteristics of SARS-CoV-2 variants of concern B.1.1.7, B.1.351 or P.1: data from seven EU/EEA countries, weeks 38/2020 to 10/2021. Eurosurveillance. 2021;26(16):2100348.
    5. Faria NR, Mellan TA, Whittaker C, Claro IM, Candido DdS, Mishra S, et al. Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil. Science. 2021.
    6. Dejnirattisai W, Zhou D, Supasa P, Liu C, Mentzer AJ, Ginn HM, et al. Antibody evasion by the P.1 strain of SARS-CoV-2. Cell. 2021.
    7. Public Health England. SARS-CoV-2 variants of concern and variants under investigation in England Technical briefing 12 2021 [Available from: https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/988619/Variants_of_Concern_VOC_Technical_Briefing_12_England.pdf
    8. Jamie Lopez Bernal NA, Charlotte Gower, Eileen Gallagher, Dr Ruth Simmons, Simon Thelwall, Julia Stowe, Elise Tessier, Natalie Groves, Gavin Dabrera, Richard Myers, Vanessa Saliba, Shamez Ladhani, Coli, Campbell, Gayatri Amirthalingam, Matt Edmunds, Maria Zambon, Kevin Brown, Susan Hopkins, Meera Chand, Mary Ramsay. Effectiveness of COVID-19 vaccines against the B.1.617.2 variant 2021 [Available from: https://khub.net/documents/135939561/430986542/Effectiveness+of+COVID-19+vaccines+against+the+B.1.617.2+variant.pdf/204c11a4-e02e-11f2-db19-b3664107ac42
    9. Sheikh A, McMenamin J, Taylor B, Robertson C. SARS-CoV-2 Delta VOC in Scotland: demographics, risk of hospital admission, and vaccine effectiveness. The Lancet.
    10. Stowe J, Andrews N, Gower C, Gallagher E, Utsi L, Simmons R, et al. Effectiveness of COVID-19 vaccines against hospital admission with the Delta (B.1.617.2) variant 2021 [Available from: https://khub.net/documents/135939561/479607266/Effectiveness+of+COVID-19+vaccines+against+hospital+admission+with+the+Delta+%28B.1.617.2%29+variant.pdf/1c213463-3997-ed16-2a6f-14e5deb0b997?t=1623689315431
    11. Public Health England. SARS-CoV-2 variants of concern and variants under investigation in England Technical briefing 16 2021 [Available from: https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/997414/Variants_of_Concern_VOC_Technical_Briefing_16.pdf

    Appendix 2: SARS-CoV-2 variants of concern according to the WHO

     

  • Semaine 42

    Respiratory Viruses in Luxembourg (ReViLux)

    Weekly report (18 – 24 October 2021)

    Executive Summary

    The Sentinel Surveillance Network identified 9 cases of influenza-like illness, thus remaining below the recommended threshold for the new epidemic season, according to the European Center for Disease Prevention and Control (ECDC) guidelines.

    Regarding SARS-CoV-2 genomic surveillance, the Laboratoire national de santé analysed 481 specimens from residents in Luxembourg in week 42/2021 (from 981 total cases in the Grand Duchy of Luxembourg, 49,0%). This exceeds the minimum sample size (373) recommended by the ECDC to detect emerging variants at a 2.5% incidence at the epidemic situation in the country.

    All specimens were assigned to the Delta variant. Community surveillance showed that parental lineage B.1.617.2 continues to be the most frequent one (62,5%), followed by AY.25 (8,8%) and AY.34 (7,2%). In respect to target groups, AY lineages were found in 55,6% of hospital specimens and 38,7% of post-vaccination breakthrough cases. As for the mutations under surveillance, they revealed no outstanding behaviour, remaining in agreement with the lineages observed.

    Introduction

    The Laboratoire national de santé, as National Reference Laboratory for Acute Respiratory Infections in Luxembourg, performs close surveillance on respiratory viruses, with a special focus on SARS-CoV-2. There are currently two active projects on which the ReViLux provides updates:

    The Sentinel Surveillance Network. It provides a broad picture of respiratory diseases affecting the Luxembourgish population, based on its double monitoring system (syndromic and virological).

    The National SARS-COV-2 Genomic Surveillance Program. It enables detailed observation of SARS-CoV-2 mutations and variants through time and space, and also monitoring specific groups of interest.

    Sentinel Surveillance Network

    The Sentinel Surveillance Network aims at monitoring the circulating respiratory viruses, including SARS-CoV-2, and hence underpin public health actions. Following the World Health Organization (WHO) and European Centre for Disease Prevention and Control (ECDC) guidance, it focuses on cases of acute respiratory infection (ARI) and influenza-like illness (ILI).

    Week 40 marked the beginning of the new influenza season 2021-2022. Results of syndromic surveillance during week 42 are displayed in Table 1 and the history of ILI consultations since the 2019-2020 season is shown in Figure 1. Nine cases of ILI were identified in week 42 (out of 529 consultations); therefore, the percentage of ILI (1,70%) remains below the threshold for the epidemic season (2,59%), according to the ECDC.

    Regarding the virological surveillance, a partnership among the CNS, private laboratories and the LNS recently started and will enable us to monitor the presence of several respiratory viruses. Results from the first analyses will be published soon.

    SARS-CoV-2 Genomic Surveillance

    The current sequencing strategy

    The National Reference Laboratory for Acute Respiratory Infections at LNS receives SARS-CoV-2 positive samples (nasopharyngeal or oropharyngeal swabs analysed by RT-PCR) from the national network of laboratories and proceeds as follows:

    Sequencing all specimens from hospital cases.
    Sequencing all specimens from reinfection and post-vaccination cases.
    Sequencing all specimens from cluster cases.
    Sequencing a representative sample of community cases.

    The representative sample of community cases is a systematic selection from all SARS-CoV-2 positive cases registered in Luxembourg to detect emerging variants and early increases in their incidence and transmission within the community in Luxembourg. This sample is selected according to the ECDC guidelines.

    The LNS shares its sequencing results with GISAID EpiCov database (www.gisaid.org) periodically. SARS-CoV-2 lineages (variants) have been assigned based on Rambaut et al. using Phylogenetic Assignment of Named Global Outbreak LINeages (pangolin) software (v3.1.14, pangoLEARN 2021-10-13). The ReViLux continues to use the Pango nomenclature, in addition to the WHO nomenclature, to allow easier visualization of links between any evolving variants and their ancestor (https://cov-lineages.org). See nomenclature equivalences in the Appendices.

    Methodological notes

    Since 3 September 2021, the ECDC no longer considers B.1.1.7 and B.1.1.7+E484K lineages (Alpha variant) as variants of concern. This decision is based in both their low circulation and the high effectiveness of vaccines in controlling them.

    Delta sublineages nomenclature is in constant review. This report is based on the pangoLEARN version v2021-10-13. Previously assigned lineages might differ after retrospective analysis of the sequences, based on the updated pangoLEARN version.

    Sequenced specimens

    In week 42, 981 new cases were registered in Luxembourg; hence, the minimum sample size required to detect emerging variants at a 2.5% incidence is estimated to be 373 specimens (38%).

    As shown in Figure 2, last week the microbial genomics unit at the LNS sequenced 611 specimensfrom week 42, with 481 specimens having been collected in week 42 from residents (49% coverage of the 981 total cases registered in Luxembourg; see coverage trend in Figure 2). This exceeds the minimum sample size (373) to detect a 2.5% incidence recommended by the ECDC. The representative sample of community cases is built by systematic selection.

    Circulating lineage detection

    In week 42/2021, only Delta variant cases were detected among all specimens sequenced in the representative sample of community cases, including 12 Delta subtypes. The distribution of VOCs is displayed in Table 2 and their evolution over the weeks is shown in Figure 3. The parental lineage B.1.617.2 continues to be the most frequent one (62,5%), followed by AY.25 (8,8%) and AY.34 (7,2%). The distribution of lineages for week 40 displayed in this report differs from the one published in the previous one due to an update of the source software (more details in the Methodological note).

    Mutation surveillance

    In addition to the surveillance of SARS-CoV-2 variants, the LNS monitors the occurrence of SARS-CoV-2 mutations reported to have a clinical and epidemiological relevance. This complementary surveillance enables us to detect unexpected mutations among the specimens sequenced. It is expected that VOC defining mutations share the same distribution as their corresponding VOCs. However, newly acquired mutations may occur and their early detection might be key to expect changes in the epidemic evolution.

    Following ECDC guidance, the LNS is currently monitoring 15 mutations to the spike protein frequently associated to VOCs and variants of interest (VOIs). Table 3 provides the cumulative frequencies of these mutations, detected in the lineage-assignable genome sequences since 1 Sep 2020 (N = 20 753), as well as the frequencies for the last 3 weeks.

    In broad terms, the mutations identified were expected according to the lineages assigned during this week. No mutation showed an outstanding behaviour.

    References

    Centers for Disease Control and Prevention. SARS-CoV-2 Variant Classifications and Definitions. Retrieved 3 November 2021, from https://www.cdc.gov/coronavirus/2019-ncov/variants/variant-info.html

    COVID-19 Data Portal – accelerating scientific research through data. (2021). Retrieved 3 November 2021, from https://www.covid19dataportal.org/sequences

    European Centre for Disease Prevention and Control. Guidance for representative and targeted genomic SARS-CoV-2 monitoring – 3 May 2021. ECDC : Stockholm ; 2021

    European Centre for Disease Prevention and Control. SARS-CoV-2 variants of concern. Retrieved 3 November 2021, from https://www.ecdc.europa.eu/en/covid-19/variants-concern

    Genomic sequencing of SARS-CoV-2: a guide to implementation for maximum impact on public health. Geneva: World Health Organization; 2021.

    GitHub – cov-lineages/pangolin: Software package for assigning SARS-CoV-2 genome sequences to global lineages. (2021). Retrieved 3 November 2021, from https://github.com/cov-lineages/pangolin

    Hadfield J., Megill C., Bell S., Huddleston J., Potter B., Callender C. et al. (2018). Nextstrain: real-time tracking of pathogen evolution. Bioinformatics, 34(23), 4121-4123. doi: 10.1093/bioinformatics/bty407

    Pango Network. New AY lineages. Retrieved 3 November 2021, from: https://www.pango.network/new-ay-lineages/

    Pango Network. New AY lineages. Retrieved 3 November 2021, from: https://www.pango.network/new-ay-lineages-and-an-update-to-ay-4-ay-12/

    Rambaut A., Holmes E., O’Toole Á., Hill V., McCrone J., Ruis C. et al. (2020). A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nature Microbiology, 5(11), 1403-1407. doi: 10.1038/s41564-020-0770-5

    Appendices

    Appendix 1: SARS-CoV-2 variants of concern according to the ECDC

    References:

    1. Madhi SA, Baillie V, Cutland CL, Voysey M, Koen AL, Fairlie L, et al. Efficacy of the ChAdOx1 nCoV-19 Covid-19 Vaccine against the B.1.351 Variant. New England Journal of Medicine. 2021.
    2. Cele S, Gazy I, Jackson L, Hwa S-H, Tegally H, Lustig G, et al. Escape of SARS-CoV-2 501Y.V2 from neutralization by convalescent plasma. Nature. 2021.
    3. Pearson CA. Estimates of severity and transmissibility of novel South Africa SARS-CoV-2 variant 501Y.V2 [Available from: https://cmmid.github.io/topics/covid19/reports/sa-novel-variant/2021_01_11_Transmissibility_and_severity_of_501Y_V2_in_SA.pdf
    4. Funk T, Pharris A, Spiteri G, Bundle N, Melidou A, Carr M, et al. Characteristics of SARS-CoV-2 variants of concern B.1.1.7, B.1.351 or P.1: data from seven EU/EEA countries, weeks 38/2020 to 10/2021. Eurosurveillance. 2021;26(16):2100348.
    5. Faria NR, Mellan TA, Whittaker C, Claro IM, Candido DdS, Mishra S, et al. Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil. Science. 2021.
    6. Dejnirattisai W, Zhou D, Supasa P, Liu C, Mentzer AJ, Ginn HM, et al. Antibody evasion by the P.1 strain of SARS-CoV-2. Cell. 2021.
    7. Public Health England. SARS-CoV-2 variants of concern and variants under investigation in England Technical briefing 12 2021 [Available from: https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/988619/Variants_of_Concern_VOC_Technical_Briefing_12_England.pdf
    8. Jamie Lopez Bernal NA, Charlotte Gower, Eileen Gallagher, Dr Ruth Simmons, Simon Thelwall, Julia Stowe, Elise Tessier, Natalie Groves, Gavin Dabrera, Richard Myers, Vanessa Saliba, Shamez Ladhani, Coli, Campbell, Gayatri Amirthalingam, Matt Edmunds, Maria Zambon, Kevin Brown, Susan Hopkins, Meera Chand, Mary Ramsay. Effectiveness of COVID-19 vaccines against the B.1.617.2 variant 2021 [Available from: https://khub.net/documents/135939561/430986542/Effectiveness+of+COVID-19+vaccines+against+the+B.1.617.2+variant.pdf/204c11a4-e02e-11f2-db19-b3664107ac42
    9. Sheikh A, McMenamin J, Taylor B, Robertson C. SARS-CoV-2 Delta VOC in Scotland: demographics, risk of hospital admission, and vaccine effectiveness. The Lancet.
    10. Stowe J, Andrews N, Gower C, Gallagher E, Utsi L, Simmons R, et al. Effectiveness of COVID-19 vaccines against hospital admission with the Delta (B.1.617.2) variant 2021 [Available from: https://khub.net/documents/135939561/479607266/Effectiveness+of+COVID-19+vaccines+against+hospital+admission+with+the+Delta+%28B.1.617.2%29+variant.pdf/1c213463-3997-ed16-2a6f-14e5deb0b997?t=1623689315431
    11. Public Health England. SARS-CoV-2 variants of concern and variants under investigation in England Technical briefing 16 2021 [Available from: https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/997414/Variants_of_Concern_VOC_Technical_Briefing_16.pdf

    Appendix 2: SARS-CoV-2 variants of concern according to the WHO

     

  • Semaine 41

    Respiratory Viruses in Luxembourg (ReViLux)

    Weekly report (11– 17 October 2021)

    Executive Summary

    The Sentinel Surveillance Network identified 12 cases of influenza-like illness, thus remaining below the recommended threshold for the new epidemic season, according to the European Center for Disease Prevention and Control (ECDC) guidelines.

    Regarding SARS-CoV-2 genomic surveillance, the Laboratoire national de santé analysed 434 specimens from residents in Luxembourg in week 41/2021 (from 786 total cases in the Grand Duchy of Luxembourg, 55,2% sequencing coverage). This exceeds the minimum sample size (341) recommended by the ECDC to detect emerging variants at a 2.5% incidence at the epidemic situation in the country.

    All specimens were assigned to the Delta variant. Community surveillance showed that parental lineage B.1.617.2 continues to be the most frequent one (65,1%), followed by AY.25 (7,9%) and AY.34 (6,7%). In respect to target groups, AY lineages were found in 36,2% of hospital specimens and 33,6% of post-vaccination breakthrough cases. As for the mutations under surveillance, they revealed no outstanding behaviour, remaining in agreement with the lineages observed.

    Introduction

    The Laboratoire national de santé, as National Reference Laboratory for Acute Respiratory Infections in Luxembourg, performs close surveillance on respiratory viruses, with a special focus on SARS-CoV-2. There are currently three active projects:

    The Sentinel Surveillance Network. It provides a broad picture of respiratory diseases affecting the Luxembourgish population, based on its double monitoring system (syndromic and virological).

    The National SARS-COV-2 Genomic Surveillance Program. It enables detailed observation of SARS-CoV-2 mutations and variants through time and space, and also monitoring specific groups of interest.

    The COVVAC Serology Project. It assesses the post-vaccination serological status in long-term care facilities and its evolution over time.

    The ReViLux provides updates on the first two projects.

    Sentinel Surveillance Network

    The Sentinel Surveillance Network aims at monitoring the circulating respiratory viruses, including SARS-CoV-2, and hence underpin public health actions. Following the World Health Organization (WHO) and European Centre for Disease Prevention and Control (ECDC) guidance, it focuses on cases of acute respiratory infection (ARI) and influenza-like illness (ILI).

    Week 40 marked the beginning of the new influenza season 2021-2022. Results of syndromic surveillance during week 41 are displayed in Table 1 and the history of ILI consultations since the 2019-2020 season is shown in Figure 1. Twelve cases of ILI were identified in week 41 (out of 535 consultations); therefore, the percentage of ILI (2,24%) remains below the threshold for the epidemic season (2,59%), according to the ECDC.

    Regarding the virological surveillance, a partnership among the CNS, private laboratories and the LNS recently started and will enable us to monitor the presence of several respiratory viruses. Results from the first analyses will be published soon.

    SARS-CoV-2 Genomic Surveillance

    The current sequencing strategy

    The National Reference Laboratory for Acute Respiratory Infections at LNS receives SARS-CoV-2 positive samples (nasopharyngeal or oropharyngeal swabs analysed by RT-PCR) from the national network of laboratories and proceeds as follows:

    Sequencing all specimens from hospital cases.
    Sequencing all specimens from reinfection and post-vaccination cases.
    Sequencing all specimens from cluster cases.
    Sequencing a representative sample of community cases.

    The representative sample of community cases is a systematic selection from all SARS-CoV-2 positive cases registered in Luxembourg to detect emerging variants and early increases in their incidence and transmission within the community in Luxembourg. This sample is selected according to the ECDC guidelines.

    The LNS shares its sequencing results with GISAID EpiCov database (www.gisaid.org) periodically. SARS-CoV-2 lineages (variants) have been assigned based on Rambaut et al. using Phylogenetic Assignment of Named Global Outbreak LINeages (pangolin) software  (v3.1.14, pangoLEARN 2021-10-13). The ReViLux continues to use the Pango nomenclature, in addition to the WHO nomenclature, to allow easier visualization of links between any evolving variants and their ancestor (https://cov-lineages.org). See nomenclature equivalences in the Annex 1.

    Methodological notes

    Since 3 September 2021, the ECDC no longer considers B.1.1.7 and B.1.1.7+E484K lineages (Alpha variant) as variants of concern. This decision is based in both their low circulation and the high effectiveness of vaccines in controlling them.

    Delta sublineages nomenclature is in constant review. This report is based on the pangoLEARN version v2021-10-13. Previously assigned lineages might differ after retrospective analysis of the sequences, based on the updated pangoLEARN version.

    Sequenced specimens

    In week 41, 786 new cases were registered in Luxembourg; hence, the minimum sample size required to detect emerging variants at a 2.5% incidence is estimated to be 341 specimens (43,4%).

    The microbial genomics unit at the LNS sequenced 474 specimens from week 41, with 434 specimens having been collected in week 41 from residents (55,2% coverage of the 786 total cases registered in Luxembourg; see coverage trend in Figure 2). This exceeds the minimum sample size (341) to detect a 2.5% incidence recommended by the ECDC. The representative sample of community cases is built by systematic selection.

    Circulating lineage detection

    In week 41/2021, only Delta variant cases were detected among all specimens sequenced in the representative sample of community cases, including 12 Delta subtypes. The distribution of VOCs is displayed in Table 2 and their evolution over the weeks is shown in Figure 3. The parental lineage B.1.617.2 continues to be the most frequent one (65,1%), followed by AY.25 (7,9%) and AY.34 (6,7%). The distribution of lineages for week 40 displayed in this report differs from the one published in the previous one due to an update of the source software (more details in the Methodological note).

    Mutation surveillance

    In addition to the surveillance of SARS-CoV-2 variants, the LNS monitors the occurrence of SARS-CoV-2 mutations reported to have a clinical and epidemiological relevance. This complementary surveillance enables us to detect unexpected mutations among the specimens sequenced. It is expected that VOC defining mutations share the same distribution as their corresponding VOCs. However, newly acquired mutations may occur and their early detection might be key to expect changes in the epidemic evolution.

    Following ECDC guidance, the LNS is currently monitoring 15 mutations to the spike protein frequently associated to VOCs and variants of interest (VOIs). Table 3 provides the cumulative frequencies of these mutations, detected in the lineage-assignable genome sequences since 1 Sep 2020 (N = 20 483), as well as the frequencies for the last 3 weeks.

    In broad terms, the mutations identified were expected according to the lineages assigned during this week. No mutation showed an outstanding behaviour.

    References

    Centers for Disease Control and Prevention. SARS-CoV-2 Variant Classifications and Definitions. Retrieved 25 October 2021, from https://www.cdc.gov/coronavirus/2019-ncov/variants/variant-info.html

    COVID-19 Data Portal – accelerating scientific research through data. (2021). Retrieved 25 October 2021, from https://www.covid19dataportal.org/sequences

    European Centre for Disease Prevention and Control. Guidance for representative and targeted genomic SARS-CoV-2 monitoring – 3 May 2021. ECDC : Stockholm ; 2021

    European Centre for Disease Prevention and Control. SARS-CoV-2 variants of concern. Retrieved 25 October 2021, from https://www.ecdc.europa.eu/en/covid-19/variants-concern

    Genomic sequencing of SARS-CoV-2: a guide to implementation for maximum impact on public health. Geneva: World Health Organization; 2021.

    GitHub – cov-lineages/pangolin: Software package for assigning SARS-CoV-2 genome sequences to global lineages. (2021). Retrieved 25 October 2021, from https://github.com/cov-lineages/pangolin

    Hadfield J., Megill C., Bell S., Huddleston J., Potter B., Callender C. et al. (2018). Nextstrain: real-time tracking of pathogen evolution. Bioinformatics, 34(23), 4121-4123. doi: 10.1093/bioinformatics/bty407

    Pango Network. New AY lineages. Retrieved 25 October 2021, from: https://www.pango.network/new-ay-lineages/

    Pango Network. New AY lineages. Retrieved 25 October 2021, from: https://www.pango.network/new-ay-lineages-and-an-update-to-ay-4-ay-12/

    Rambaut A., Holmes E., O’Toole Á., Hill V., McCrone J., Ruis C. et al. (2020). A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nature Microbiology, 5(11), 1403-1407. doi: 10.1038/s41564-020-0770-5

    Annexes

    Annex 1. SARS-CoV-2 variants naming

    Adapted from ECDC – SARS-CoV-2 variants of concern (https://www.ecdc.europa.eu/en/covid-19/variants-concern)

    References:

    1. Madhi SA, Baillie V, Cutland CL, Voysey M, Koen AL, Fairlie L, et al. Efficacy of the ChAdOx1 nCoV-19 Covid-19 Vaccine against the B.1.351 Variant. New England Journal of Medicine. 2021.
    2. Cele S, Gazy I, Jackson L, Hwa S-H, Tegally H, Lustig G, et al. Escape of SARS-CoV-2 501Y.V2 from neutralization by convalescent plasma. Nature. 2021.
    3. Pearson CA. Estimates of severity and transmissibility of novel South Africa SARS-CoV-2 variant 501Y.V2 [Available from: https://cmmid.github.io/topics/covid19/reports/sa-novel-variant/2021_01_11_Transmissibility_and_severity_of_501Y_V2_in_SA.pdf
    4. Funk T, Pharris A, Spiteri G, Bundle N, Melidou A, Carr M, et al. Characteristics of SARS-CoV-2 variants of concern B.1.1.7, B.1.351 or P.1: data from seven EU/EEA countries, weeks 38/2020 to 10/2021. Eurosurveillance. 2021;26(16):2100348.
    5. Faria NR, Mellan TA, Whittaker C, Claro IM, Candido DdS, Mishra S, et al. Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil. Science. 2021.
    6. Dejnirattisai W, Zhou D, Supasa P, Liu C, Mentzer AJ, Ginn HM, et al. Antibody evasion by the P.1 strain of SARS-CoV-2. Cell. 2021.
    7. Public Health England. SARS-CoV-2 variants of concern and variants under investigation in England Technical briefing 12 2021 [Available from: https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/988619/Variants_of_Concern_VOC_Technical_Briefing_12_England.pdf
    8. Jamie Lopez Bernal NA, Charlotte Gower, Eileen Gallagher, Dr Ruth Simmons, Simon Thelwall, Julia Stowe, Elise Tessier, Natalie Groves, Gavin Dabrera, Richard Myers, Vanessa Saliba, Shamez Ladhani, Coli, Campbell, Gayatri Amirthalingam, Matt Edmunds, Maria Zambon, Kevin Brown, Susan Hopkins, Meera Chand, Mary Ramsay. Effectiveness of COVID-19 vaccines against the B.1.617.2 variant 2021 [Available from: https://khub.net/documents/135939561/430986542/Effectiveness+of+COVID-19+vaccines+against+the+B.1.617.2+variant.pdf/204c11a4-e02e-11f2-db19-b3664107ac42
    9. Sheikh A, McMenamin J, Taylor B, Robertson C. SARS-CoV-2 Delta VOC in Scotland: demographics, risk of hospital admission, and vaccine effectiveness. The Lancet.
    10. Stowe J, Andrews N, Gower C, Gallagher E, Utsi L, Simmons R, et al. Effectiveness of COVID-19 vaccines against hospital admission with the Delta (B.1.617.2) variant 2021 [Available from: https://khub.net/documents/135939561/479607266/Effectiveness+of+COVID-19+vaccines+against+hospital+admission+with+the+Delta+%28B.1.617.2%29+variant.pdf/1c213463-3997-ed16-2a6f-14e5deb0b997?t=1623689315431
    11. Public Health England. SARS-CoV-2 variants of concern and variants under investigation in England Technical briefing 16 2021 [Available from: https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/997414/Variants_of_Concern_VOC_Technical_Briefing_16.pdf

     

  • Semaine 40

    Respiratory Viruses in Luxembourg (ReViLux)

    Weekly report (4 – 10 October 2021)

    Executive Summary

    The Sentinel Surveillance Network identified 5 cases of influenza-like illness, thus remaining below the recommended threshold for the new epidemic season, according to the European Center for Disease Prevention and Control (ECDC) guidelines.

    Regarding SARS-CoV-2 genomic surveillance, the Laboratoire national de santé analysed 493 specimens from residents in Luxembourg in week 40/2021 (from 675 total cases in the Grand Duchy of Luxembourg, 73,0% sequencing coverage). This exceeds the minimum sample size (318) recommended by the ECDC to detect emerging variants at a 2.5% incidence at the epidemic situation in the country.

    All specimens were assigned to the Delta variant. Community surveillance showed that parental lineage B.1.617.2 continues to be the most frequent one (61,3%), followed by AY.4 (15,4%) and AY.34 (10,1%). In respect to target groups, AY lineages were found in 36,8% of hospital specimens and 50,0% of post-vaccination breakthrough cases. As for the mutations under surveillance, they reveiled no outstanding behaviour, remaining in agreement with the lineages observed.

    Introduction

    The Laboratoire national de santé, as National Reference Laboratory for Acute Respiratory Infections in Luxembourg, performs close surveillance on respiratory viruses, with a special focus on SARS-CoV-2. There are currently three active projects:

    The Sentinel Surveillance Network. It provides a broad picture of respiratory diseases affecting the Luxembourgish population, based on its double monitoring system (syndromic and virological).

    The National SARS-COV-2 Genomic Surveillance Program. It enables detailed observation of SARS-CoV-2 mutations and variants through time and space, and also monitoring specific groups of interest.

    The COVVAC Serology Project. It assesses the post-vaccination serological status in long-term care facilities and its evolution over time.

    The objective of the ReViLux is to inform public health actions in Luxembourg.

    Sentinel Surveillance Network

    The Sentinel Surveillance Network aims at monitoring the circulating respiratory viruses, including SARS-CoV-2, and hence underpin public health actions. Following the World Health Organization (WHO) and European Centre for Disease Prevention and Control (ECDC) guidance, it focuses on cases of acute respiratory infection (ARI) and influenza-like illness (ILI).

    Week 40 marks the beginning of the new influenza season 2021-2022. Results of syndromic surveillance during this first week are displayed in Table 1 and the history of ILI consultations since the 2019-2020 season is shown in Figure 1. Five cases of ILI were identified in week 40 (out of 320 consultations); therefore, the percentage of ILI (1,56%) remains below the threshold for the epidemic season in Luxembourg (2,59%), according to the ECDC.

    Regarding the virological surveillance, a partnership between the CNS, private laboratories and the LNS recently was established and will enable to monitor the presence of several respiratory viruses. Results from the first analysis will be published soon.

    SARS-CoV-2 Genomic Surveillance

    The current sequencing strategy

    The National Reference Laboratory for Acute Respiratory Infections at LNS receives SARS-CoV-2 positive samples (nasopharyngeal or oropharyngeal swabs analysed by RT-PCR) from the national network of laboratories and proceeds as follows:

    Sequencing all specimens from hospital cases.
    Sequencing all specimens from reinfection and post-vaccination cases.
    Sequencing all specimens from cluster cases.
    Sequencing a representative sample of community cases.

    The representative sample of community cases is a systematic selection from all SARS-CoV-2 positive cases registered in Luxembourg to detect emerging variants and early increases in their incidence and transmission within the community in Luxembourg. This sample is selected according to the ECDC guidelines.

    The LNS shares its sequencing results with GISAID EpiCov database (www.gisaid.org) periodically. SARS-CoV-2 lineages (variants) have been assigned based on Rambaut et al. using Phylogenetic Assignment of Named Global Outbreak LINeages (pangolin) software  (v3.1.14, pangoLEARN 2021-09-28). The ReViLux continues to use the Pango nomenclature, in addition to the WHO nomenclature, to allow easier visualization of links between any evolving variants and their ancestor (https://cov-lineages.org). See nomenclature equivalences in the Appendices.

    Methodological notes

    Since 3 September 2021, the ECDC no longer considers B.1.1.7 and B.1.1.7+E484K lineages (Alpha variant) as variants of concern. This decision is based in both their low circulation and the high effectiveness of vaccines in controlling them.

    Delta sublineages nomenclature is in constant review. This report is based on the pangoLEARN version (v2021-09-28). Previously assigned lineages might differ after retrospective analysis of the sequences, based on the updated pangoLEARN version.

    Sequenced specimens

    In week 40, 675 new cases were registered in Luxembourg; hence, the minimum sample size required to detect emerging variants at a 2.5% incidence is estimated to be 318 specimens (47.1%).

    The microbial genomics unit at the LNS sequenced 665 specimens from week 40, with 493 specimens having been collected in week 40 from residents (73% coverage of the 675 total cases registered in Luxembourg; see coverage trend in Figure 2). This exceeds the minimum sample size (318) to detect a 2.5% incidence recommended by the ECDC. The representative sample of community cases is built by systematic selection.

    Circulating lineage detection

    In week 40/2021, only Delta variant cases were detected among all specimens sequenced in the representative sample of community cases, including 10 Delta subtypes. The distribution of VOCs is displayed in Table 2, and their evolution over the weeks is shown in Figure 3. The parental lineage B.1.617.2 continues to be the most frequent one (61,3%), followed by AY.4 (15,4%) and AY.34 (10,1%).

    Mutation surveillance

    In addition to the surveillance of SARS-CoV-2 variants, the LNS monitors the occurrence of SARS-CoV-2 mutations reported to have a clinical and epidemiological relevance. This complementary surveillance enables us to detect unexpected mutations among the specimens sequenced. It is expected that VOC defining mutations share the same distribution as their corresponding VOCs. However, newly acquired mutations may occur and their early detection might be key to expect changes in the epidemic evolution.

    Following ECDC guidance, the LNS is currently monitoring 15 mutations to the spike protein frequently associated to VOCs and variants of interest (VOIs). Table 3 provides the cumulative frequencies of these mutations, detected in the lineage-assignable genome sequences since 1 Sep 2020 (N = 20 007), as well as the frequencies for the last 3 weeks.

    In broad terms, the mutations identified were expected according to the lineages assigned during this week. No mutation showed an outstanding behaviour.

    References

    Centers for Disease Control and Prevention. SARS-CoV-2 Variant Classifications and Definitions. Retrieved 19 October 2021, from https://www.cdc.gov/coronavirus/2019-ncov/variants/variant-info.html

    COVID-19 Data Portal – accelerating scientific research through data. (2021). Retrieved 19 October 2021, from https://www.covid19dataportal.org/sequences

    European Centre for Disease Prevention and Control. Guidance for representative and targeted genomic SARS-CoV-2 monitoring – 3 May 2021. ECDC : Stockholm ; 2021

    European Centre for Disease Prevention and Control. SARS-CoV-2 variants of concern. Retrieved 19 October 2021, from https://www.ecdc.europa.eu/en/covid-19/variants-concern

    Genomic sequencing of SARS-CoV-2: a guide to implementation for maximum impact on public health. Geneva: World Health Organization; 2021.

    GitHub – cov-lineages/pangolin: Software package for assigning SARS-CoV-2 genome sequences to global lineages. (2021). Retrieved 19 October 2021, from https://github.com/cov-lineages/pangolin

    Pango Network. New AY lineages. Retrieved 19 October 2021, from: https://www.pango.network/new-ay-lineages/

    Pango Network. New AY lineages. Retrieved 19 October 2021, from: https://www.pango.network/new-ay-lineages-and-an-update-to-ay-4-ay-12/

    Rambaut A., Holmes E., O’Toole Á., Hill V., McCrone J., Ruis C. et al. (2020). A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nature Microbiology, 5(11), 1403-1407. doi: 10.1038/s41564-020-0770-5

    Appendices:

    Appendix 1: SARS-CoV-2 variants of concern according to the ECDC

    References:

    1. Madhi SA, Baillie V, Cutland CL, Voysey M, Koen AL, Fairlie L, et al. Efficacy of the ChAdOx1 nCoV-19 Covid-19 Vaccine against the B.1.351 Variant. New England Journal of Medicine. 2021.
    2. Cele S, Gazy I, Jackson L, Hwa S-H, Tegally H, Lustig G, et al. Escape of SARS-CoV-2 501Y.V2 from neutralization by convalescent plasma. Nature. 2021.
    3. Pearson CA. Estimates of severity and transmissibility of novel South Africa SARS-CoV-2 variant 501Y.V2 [Available from: https://cmmid.github.io/topics/covid19/reports/sa-novel-variant/2021_01_11_Transmissibility_and_severity_of_501Y_V2_in_SA.pdf
    4. Funk T, Pharris A, Spiteri G, Bundle N, Melidou A, Carr M, et al. Characteristics of SARS-CoV-2 variants of concern B.1.1.7, B.1.351 or P.1: data from seven EU/EEA countries, weeks 38/2020 to 10/2021. Eurosurveillance. 2021;26(16):2100348.
    5. Faria NR, Mellan TA, Whittaker C, Claro IM, Candido DdS, Mishra S, et al. Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil. Science. 2021.
    6. Dejnirattisai W, Zhou D, Supasa P, Liu C, Mentzer AJ, Ginn HM, et al. Antibody evasion by the P.1 strain of SARS-CoV-2. Cell. 2021.
    7. Public Health England. SARS-CoV-2 variants of concern and variants under investigation in England Technical briefing 12 2021 [Available from: https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/988619/Variants_of_Concern_VOC_Technical_Briefing_12_England.pdf
    8. Jamie Lopez Bernal NA, Charlotte Gower, Eileen Gallagher, Dr Ruth Simmons, Simon Thelwall, Julia Stowe, Elise Tessier, Natalie Groves, Gavin Dabrera, Richard Myers, Vanessa Saliba, Shamez Ladhani, Coli, Campbell, Gayatri Amirthalingam, Matt Edmunds, Maria Zambon, Kevin Brown, Susan Hopkins, Meera Chand, Mary Ramsay. Effectiveness of COVID-19 vaccines against the B.1.617.2 variant 2021 [Available from: https://khub.net/documents/135939561/430986542/Effectiveness+of+COVID-19+vaccines+against+the+B.1.617.2+variant.pdf/204c11a4-e02e-11f2-db19-b3664107ac42
    9. Sheikh A, McMenamin J, Taylor B, Robertson C. SARS-CoV-2 Delta VOC in Scotland: demographics, risk of hospital admission, and vaccine effectiveness. The Lancet.
    10. Stowe J, Andrews N, Gower C, Gallagher E, Utsi L, Simmons R, et al. Effectiveness of COVID-19 vaccines against hospital admission with the Delta (B.1.617.2) variant 2021 [Available from: https://khub.net/documents/135939561/479607266/Effectiveness+of+COVID-19+vaccines+against+hospital+admission+with+the+Delta+%28B.1.617.2%29+variant.pdf/1c213463-3997-ed16-2a6f-14e5deb0b997?t=1623689315431
    11. Public Health England. SARS-CoV-2 variants of concern and variants under investigation in England Technical briefing 16 2021 [Available from: https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/997414/Variants_of_Concern_VOC_Technical_Briefing_16.pdf

    Appendix 2: SARS-CoV-2 variants of concern according to the WHO

  • Semaine 39

    Respiratory Viruses in Luxembourg (ReViLux)

    Weekly report (27 Sept – 3 Oct 2021)

    Executive Summary

    The Sentinel Surveillance Network identified no cases of influenza-like illness, thus remaining below the recommended threshold for the interepidemic season, according to the European Center for Disease Prevention and Control (ECDC) guidelines.

    Regarding SARS-CoV-2 genomic surveillance, the Laboratoire national de santé analysed 380 specimens from residents in Luxembourg in week 39/2021 (from 591 total cases in the Grand Duchy of Luxembourg, 60,7% sequencing coverage). This exceeds the minimum sample size (288) recommended by the ECDC to detect emerging variants at a 2.5% incidence at the current epidemic situation in the country.

    All specimens were assigned to the Delta variant. Community surveillance showed that parental lineage B.1.617.2 continues to be the most frequent one (60,4%), followed by AY.4 (14,4%) and AY.34 (11,7%). In respect to target groups, AY lineages were found in similar proportions: 40,0% of hospital specimens and 44,1% of post-vaccination breakthrough cases. As for the mutations under surveillance, they reveiled no outstanding behaviour, remaining in agreement with the lineages observed.

    Introduction

    The Laboratoire national de santé, as National Reference Laboratory for Acute Respiratory Infections in Luxembourg, performs close surveillance on respiratory viruses, with a special focus on SARS-CoV-2. There are currently three active projects:

    The Sentinel Surveillance Network. It provides a broad picture of respiratory diseases affecting the Luxembourgish population, based on its double monitoring system (syndromic and virological).

    The National SARS-COV-2 Genomic Surveillance Program. It enables detailed observation of SARS-CoV-2 mutations and variants through time and space, and also monitoring specific groups of interest.

    The COVVAC Serology Project. It assesses the post-vaccination serological status in long-term care facilities and its evolution over time.

    The objective of the ReViLux is to inform public health actions in Luxembourg.

    Sentinel Surveillance Network

    The Sentinel Surveillance Network aims at monitoring the circulating respiratory viruses, including SARS-CoV-2, and hence underpin public health actions. Following the World Health Organization (WHO) and European Centre for Disease Prevention and Control (ECDC) guidance, it focuses on cases of acute respiratory infection (ARI) and influenza-like illness (ILI).

    Results of syndromic surveillance during week 39 are displayed in Table 1 and the history of ILI consultations since the 2018-2019 season is shown in Figure 1. No cases of ILI were identified in week 36 (out of 339 consultations); therefore, the percentage of ILI remains below the threshold for the interepidemic season (1,14%), according to the ECDC.

    Regarding the virological surveillance, no data is available for week 39.

     

    SARS-CoV-2 Genomic Surveillance

    The current sequencing strategy

    The National Reference Laboratory for Acute Respiratory Infections at LNS receives SARS-CoV-2 positive samples (nasopharyngeal or oropharyngeal swabs analysed by RT-PCR) from the national network of laboratories and proceeds as follows:

    Sequencing all specimens from hospital cases.
    Sequencing all specimens from reinfection and post-vaccination cases.
    Sequencing all specimens from cluster cases.
    Sequencing a representative sample of community cases.

    The representative sample of community cases is a systematic selection from all SARS-CoV-2 positive cases registered in Luxembourg to detect emerging variants and early increases in their incidence and transmission within the community in Luxembourg. This sample is selected according to the ECDC guidelines.

    The LNS shares its sequencing results with GISAID EpiCov database (www.gisaid.org) periodically. SARS-CoV-2 lineages (variants) have been assigned based on Rambaut et al. using Phylogenetic Assignment of Named Global Outbreak LINeages (pangolin) software  (v3.1.14, pangoLEARN 2021-09-28). The ReViLux continues to use the Pango nomenclature, in addition to the WHO nomenclature, to allow easier visualization of links between any evolving variants and their ancestor (https://cov-lineages.org). See nomenclature equivalences in Annex 1.

    Methodological notes

    Since 3 September 2021, the ECDC no longer considers B.1.1.7 and B.1.1.7+E484K lineages (Alpha variant) as variants of concern. This decision is based in both their low circulation and the high effectiveness of vaccines in controlling them.

    Delta sublineages nomenclature is in constant review. This report is based on the pangoLEARN version (v2021-09-28). Previously assigned lineages might differ after retrospective analysis of the sequences, based on the updated pangoLEARN version.

    Sequenced specimens

    In week 39, 591 new cases were registered in Luxembourg; hence, the minimum sample size required to detect emerging variants at a 2.5% incidence is estimated to be 298 specimens (50.4%).

    The microbial genomics unit at the LNS sequenced 380 specimens from week 39, with 359 specimens having been collected in week 39 from residents (60,7% coverage of the 591 total cases registered in Luxembourg; see coverage trend in Figure 2). This exceeds the minimum coverage (10%) and minimum sample size (298) to detect a 2.5% incidence, recommended by the ECDC. The representative sample of community cases is built by systematic selection.

    Circulating lineage detection

    In week 39/2021, only Delta variant cases were detected among all specimens sequenced in the representative samle of community cases, including 11 Delta subtypes. The distribution of VOCs is displayed in Table 2, and their evolution over the weeks  sis shown in Figure 3. The parental lineage B.1.617.2 continues to be the most frequent one (60,4%), followed by AY.4 (14,4%) and AY.34 (11,7%).

     

    Mutation surveillance

    In addition to the surveillance of SARS-CoV-2 variants, the LNS monitors the occurrence of SARS-CoV-2 mutations reported to have a clinical and epidemiological relevance. This complementary surveillance enables us to detect unexpected mutations among the specimens sequenced. It is expected that VOC defining mutations share the same distribution as their corresponding VOCs. However, newly acquired mutations may occur and their early detection might be key to expect changes in the epidemic evolution.

    Following ECDC guidance, the LNS is currently monitoring 15 mutations to the spike protein frequently associated to VOCs and variants of interest (VOIs). Table 3 provides the cumulative frequencies of these mutations, detected in the lineage-assignable genome sequences since 1 Sep 2020 (N = 19 401), as well as the frequencies for the last 3 weeks.

    In broad terms, the mutations identified were expected according to the lineages assigned during this week.

    References

    Centers for Disease Control and Prevention. SARS-CoV-2 Variant Classifications and Definitions. Retrieved 11 October 2021, from https://www.cdc.gov/coronavirus/2019-ncov/variants/variant-info.html

    COVID-19 Data Portal – accelerating scientific research through data. (2021). Retrieved 11 October 2021, from https://www.covid19dataportal.org/sequences

    European Centre for Disease Prevention and Control. Guidance for representative and targeted genomic SARS-CoV-2 monitoring – 3 May 2021. ECDC : Stockholm ; 2021

    European Centre for Disease Prevention and Control. SARS-CoV-2 variants of concern. Retrieved 11 October 2021, from https://www.ecdc.europa.eu/en/covid-19/variants-concern

    Pango Network. New AY lineages. Retrieved 11 October 2021, from: https://www.pango.network/new-ay-lineages/

    Pango Network. New AY lineages. Retrieved 11 October 2021, from: https://www.pango.network/new-ay-lineages-and-an-update-to-ay-4-ay-12/

    Rambaut A., Holmes E., O’Toole Á., Hill V., McCrone J., Ruis C. et al. (2020). A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nature Microbiology, 5(11), 1403-1407. doi: 10.1038/s41564-020-0770-5

    Annexes

    Annex 1. SARS-CoV-2 variants naming

    References:

    1. Madhi SA, Baillie V, Cutland CL, Voysey M, Koen AL, Fairlie L, et al. Efficacy of the ChAdOx1 nCoV-19 Covid-19 Vaccine against the B.1.351 Variant. New England Journal of Medicine. 2021.
    2. Cele S, Gazy I, Jackson L, Hwa S-H, Tegally H, Lustig G, et al. Escape of SARS-CoV-2 501Y.V2 from neutralization by convalescent plasma. Nature. 2021.
    3. Pearson CA. Estimates of severity and transmissibility of novel South Africa SARS-CoV-2 variant 501Y.V2 [Available from: https://cmmid.github.io/topics/covid19/reports/sa-novel-variant/2021_01_11_Transmissibility_and_severity_of_501Y_V2_in_SA.pdf
    4. Funk T, Pharris A, Spiteri G, Bundle N, Melidou A, Carr M, et al. Characteristics of SARS-CoV-2 variants of concern B.1.1.7, B.1.351 or P.1: data from seven EU/EEA countries, weeks 38/2020 to 10/2021. Eurosurveillance. 2021;26(16):2100348.
    5. Faria NR, Mellan TA, Whittaker C, Claro IM, Candido DdS, Mishra S, et al. Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil. Science. 2021.
    6. Dejnirattisai W, Zhou D, Supasa P, Liu C, Mentzer AJ, Ginn HM, et al. Antibody evasion by the P.1 strain of SARS-CoV-2. Cell. 2021.
    7. Public Health England. SARS-CoV-2 variants of concern and variants under investigation in England Technical briefing 12 2021 [Available from: https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/988619/Variants_of_Concern_VOC_Technical_Briefing_12_England.pdf
    8. Jamie Lopez Bernal NA, Charlotte Gower, Eileen Gallagher, Dr Ruth Simmons, Simon Thelwall, Julia Stowe, Elise Tessier, Natalie Groves, Gavin Dabrera, Richard Myers, Vanessa Saliba, Shamez Ladhani, Coli, Campbell, Gayatri Amirthalingam, Matt Edmunds, Maria Zambon, Kevin Brown, Susan Hopkins, Meera Chand, Mary Ramsay. Effectiveness of COVID-19 vaccines against the B.1.617.2 variant 2021 [Available from: https://khub.net/documents/135939561/430986542/Effectiveness+of+COVID-19+vaccines+against+the+B.1.617.2+variant.pdf/204c11a4-e02e-11f2-db19-b3664107ac42
    9. Sheikh A, McMenamin J, Taylor B, Robertson C. SARS-CoV-2 Delta VOC in Scotland: demographics, risk of hospital admission, and vaccine effectiveness. The Lancet.
    10. Stowe J, Andrews N, Gower C, Gallagher E, Utsi L, Simmons R, et al. Effectiveness of COVID-19 vaccines against hospital admission with the Delta (B.1.617.2) variant 2021 [Available from: https://khub.net/documents/135939561/479607266/Effectiveness+of+COVID-19+vaccines+against+hospital+admission+with+the+Delta+%28B.1.617.2%29+variant.pdf/1c213463-3997-ed16-2a6f-14e5deb0b997?t=1623689315431
    11. Public Health England. SARS-CoV-2 variants of concern and variants under investigation in England Technical briefing 16 2021 [Available from: https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/997414/Variants_of_Concern_VOC_Technical_Briefing_16.pdf

  • Semaine 38

    Respiratory Viruses in Luxembourg (ReViLux)

    Weekly report (20 – 26 September 2021)

    Executive Summary

    The Sentinel Surveillance Network identified 1 case of influenza-like illness, thus remaining below the recommended threshold for the interepidemic season, according to the European Center for Disease Prevention and Control (ECDC) guidelines.

    Regarding SARS-CoV-2 genomic surveillance, the Laboratoire national de santé analysed 435 specimens from residents in Luxembourg in week 38/2021 (out of 590 total cases in the Grand Duchy of Luxembourg, 73,7% sequencing coverage). This exceeds the minimum coverage (10%) and minimum sample size (298) recommended by the ECDC.

    All specimens were assigned to the Delta variant. Community surveillance showed that parental lineage B.1.617.2 continues to be the most frequent one (57,7%), followed by AY.34 (14,1%) and AY.4 (10,7%). In respect to target groups, AY lineages were found in 44,4% of post-vaccination breakthrough cases. As for the mutations under surveillance, they reveiled no outstanding behaviour, remaining in agreement with the lineages observed.

    Introduction

    The Laboratoire national de santé, as National Reference Laboratory for Acute Respiratory Infections in Luxembourg, performs close surveillance on respiratory viruses, with a special focus on SARS-CoV-2. There are currently three active projects:

    The Sentinel Surveillance Network. It provides a broad picture of respiratory diseases affecting the Luxembourgish population, based on its double monitoring system (syndromic and virological).

    The National SARS-COV-2 Genomic Surveillance Program. It enables detailed observation of SARS-CoV-2 mutations and variants through time and space, and also monitoring specific groups of interest.

    The COVVAC Serology Project. It assesses the post-vaccination serological status in long-term care facilities and its evolution over time.

    The ReViLux provides updates on the first two projects.

    Sentinel Surveillance Network

    The Sentinel Surveillance Network aims at monitoring the circulating respiratory viruses, including SARS-CoV-2, and hence underpin public health actions. Following the World Health Organization (WHO) and European Centre for Disease Prevention and Control (ECDC) guidance, it focuses on cases of acute respiratory infection (ARI) and influenza-like illness (ILI).

    Results of syndromic surveillance during week 38 are displayed in Table 1 and the history of ILI consultations since the 2018-2019 season is shown in Figure 1. One case of ILI was identified in week 38 (out of 710 consultations); therefore, the percentage of ILI (0,14%) remains below the threshold for the interepidemic season (1,14%), according to the ECDC.

    Regarding the virological surveillance, no data is available for week 38.

    SARS-CoV-2 Genomic Surveillance

    The current sequencing strategy

    The National Reference Laboratory for Acute Respiratory Infections at LNS receives SARS-CoV-2 positive samples (nasopharyngeal or oropharyngeal swabs analysed by RT-PCR) from the national network of laboratories and proceeds as follows:

    Sequencing all specimens from hospital cases.
    Sequencing all specimens from reinfection and post-vaccination cases.
    Sequencing all specimens from cluster cases.
    Sequencing a representative sample of community cases.

    The representative sample of community cases is a systematic selection from all SARS-CoV-2 positive cases registered in Luxembourg to detect emerging variants and early increases in their incidence and transmission within the community in Luxembourg. This sample is selected according to the ECDC guidelines.

    The LNS shares its sequencing results with GISAID EpiCov database (www.gisaid.org) periodically. SARS-CoV-2 lineages (variants) have been assigned based on Rambaut et al. using Phylogenetic Assignment of Named Global Outbreak LINeages (pangolin) software  (v3.1.14, pangoLEARN 2021-09-28). The ReViLux continues to use the Pango nomenclature, in addition to the WHO nomenclature, to allow easier visualization of links between any evolving variants and their ancestor (https://cov-lineages.org). See nomenclature equivalences in Annex 1.

    Methodological notes

    Since 3 September 2021, the ECDC no longer considers B.1.1.7 and B.1.1.7+E484K lineages (Alpha variant) as variants of concern. This decision is based in both their low circulation and the high effectiveness of vaccines in controlling them.

    An updated pangoLEARN version (v2021-09-28) has been used in this report, hence including new AY subtypes, up to AY.38. Previously assigned lineages might differ after retrospective analysis of the sequences, based on the updated pangoLEARN version.

    Sequenced specimens

    In week 38, 590 new cases were registered in Luxembourg; hence, the minimum sample size required to detect emerging variants at a 2.5% incidence is estimated to be 298 specimens (50.5%).

    The microbial genomics unit at the LNS sequenced 570 specimens from week 38, with 435 specimens having been collected in week 38 from residents (73,7% coverage of the 590 total cases registered in Luxembourg; see coverage trend in Figure 2). This exceeds the minimum coverage (10%) and minimum sample size (298) to detect a 2.5% incidence recommended by the ECDC. The representative sample of community cases is built by systematic selection.

    Circulating lineage detection

    The evolution of variants over the weeks is shown in Figure 3.

    In week 38/2021, only Delta variant cases were detected among all specimens sequenced in the representative sample of community cases, including 11 Delta subtypes. The distribution of VOCs is displayed in Table 2, and their evolution over the weeks is shown in Figure 4. The parental lineage B.1.617.2 continues to be the most frequent one (57,7%), followed by AY.34 (14,1%) and AY.4 (10,7%).

    Mutation surveillance

    In addition to the surveillance of SARS-CoV-2 variants, the LNS monitors the occurrence of SARS-CoV-2 mutations reported to have a clinical and epidemiological relevance. This complementary surveillance enables us to detect unexpected mutations among the specimens sequenced. It is expected that VOC defining mutations share the same distribution as their corresponding VOCs. However, newly acquired mutations may occur and their early detection might be key to expect changes in the epidemic evolution.

    Following ECDC guidance, the LNS is currently monitoring 15 mutations to the spike protein frequently associated to VOCs and variants of interest (VOIs). Table 3 provides the cumulative frequencies of these mutations, detected in the lineage-assignable genome sequences since 1 Sep 2020 (N = 19 051), as well as the frequencies for the last 3 weeks.

    In broad terms, the mutations identified were expected according to the lineages assigned during this week.

    References

    Centers for Disease Control and Prevention. SARS-CoV-2 Variant Classifications and Definitions. Retrieved 4 October 2021, from https://www.cdc.gov/coronavirus/2019-ncov/variants/variant-info.html

    COVID-19 Data Portal – accelerating scientific research through data. (2021). Retrieved 4 October 2021, from https://www.covid19dataportal.org/sequences

    European Centre for Disease Prevention and Control. Guidance for representative and targeted genomic SARS-CoV-2 monitoring – 3 May 2021. ECDC : Stockholm ; 2021

    European Centre for Disease Prevention and Control. SARS-CoV-2 variants of concern. Retrieved 4 October 2021, from https://www.ecdc.europa.eu/en/covid-19/variants-concern

    Genomic sequencing of SARS-CoV-2: a guide to implementation for maximum impact on public health. Geneva: World Health Organization; 2021.

    GitHub – cov-lineages/pangolin: Software package for assigning SARS-CoV-2 genome sequences to global lineages. (2021). Retrieved 4 October 2021, from https://github.com/cov-lineages/pangolin

    Hadfield J., Megill C., Bell S., Huddleston J., Potter B., Callender C. et al. (2018). Nextstrain: real-time tracking of pathogen evolution. Bioinformatics, 34(23), 4121-4123. doi: 10.1093/bioinformatics/bty407

    Pango Network. New AY lineages. Retrieved 4 October 2021, from: https://www.pango.network/new-ay-lineages/

    Pango Network. New AY lineages. Retrieved 4 October 2021, from: https://www.pango.network/new-ay-lineages-and-an-update-to-ay-4-ay-12/

    Rambaut A., Holmes E., O’Toole Á., Hill V., McCrone J., Ruis C. et al. (2020). A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nature Microbiology, 5(11), 1403-1407. doi: 10.1038/s41564-020-0770-5

    Annexes

    Annex 1. SARS-CoV-2 variants naming

    References:

    1. Madhi SA, Baillie V, Cutland CL, Voysey M, Koen AL, Fairlie L, et al. Efficacy of the ChAdOx1 nCoV-19 Covid-19 Vaccine against the B.1.351 Variant. New England Journal of Medicine. 2021.
    2. Cele S, Gazy I, Jackson L, Hwa S-H, Tegally H, Lustig G, et al. Escape of SARS-CoV-2 501Y.V2 from neutralization by convalescent plasma. Nature. 2021.
    3. Pearson CA. Estimates of severity and transmissibility of novel South Africa SARS-CoV-2 variant 501Y.V2 [Available from: https://cmmid.github.io/topics/covid19/reports/sa-novel-variant/2021_01_11_Transmissibility_and_severity_of_501Y_V2_in_SA.pdf
    4. Funk T, Pharris A, Spiteri G, Bundle N, Melidou A, Carr M, et al. Characteristics of SARS-CoV-2 variants of concern B.1.1.7, B.1.351 or P.1: data from seven EU/EEA countries, weeks 38/2020 to 10/2021. Eurosurveillance. 2021;26(16):2100348.
    5. Faria NR, Mellan TA, Whittaker C, Claro IM, Candido DdS, Mishra S, et al. Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil. Science. 2021.
    6. Dejnirattisai W, Zhou D, Supasa P, Liu C, Mentzer AJ, Ginn HM, et al. Antibody evasion by the P.1 strain of SARS-CoV-2. Cell. 2021.
    7. Public Health England. SARS-CoV-2 variants of concern and variants under investigation in England Technical briefing 12 2021 [Available from: https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/988619/Variants_of_Concern_VOC_Technical_Briefing_12_England.pdf
    8. Jamie Lopez Bernal NA, Charlotte Gower, Eileen Gallagher, Dr Ruth Simmons, Simon Thelwall, Julia Stowe, Elise Tessier, Natalie Groves, Gavin Dabrera, Richard Myers, Vanessa Saliba, Shamez Ladhani, Coli, Campbell, Gayatri Amirthalingam, Matt Edmunds, Maria Zambon, Kevin Brown, Susan Hopkins, Meera Chand, Mary Ramsay. Effectiveness of COVID-19 vaccines against the B.1.617.2 variant 2021 [Available from: https://khub.net/documents/135939561/430986542/Effectiveness+of+COVID-19+vaccines+against+the+B.1.617.2+variant.pdf/204c11a4-e02e-11f2-db19-b3664107ac42
    9. Sheikh A, McMenamin J, Taylor B, Robertson C. SARS-CoV-2 Delta VOC in Scotland: demographics, risk of hospital admission, and vaccine effectiveness. The Lancet.
    10. Stowe J, Andrews N, Gower C, Gallagher E, Utsi L, Simmons R, et al. Effectiveness of COVID-19 vaccines against hospital admission with the Delta (B.1.617.2) variant 2021 [Available from: https://khub.net/documents/135939561/479607266/Effectiveness+of+COVID-19+vaccines+against+hospital+admission+with+the+Delta+%28B.1.617.2%29+variant.pdf/1c213463-3997-ed16-2a6f-14e5deb0b997?t=1623689315431
    11. Public Health England. SARS-CoV-2 variants of concern and variants under investigation in England Technical briefing 16 2021 [Available from: https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/997414/Variants_of_Concern_VOC_Technical_Briefing_16.pdf

     

     

  • Semaine 37

    Respiratory Viruses in Luxembourg (ReViLux)

    Weekly report (13 – 19 September 2021)

    Executive Summary

    The Sentinel Surveillance Network identified no case of influenza-like illness this week, thus remaining below the recommended threshold for the interepidemic season, according to the European Center for Disease Prevention and Control (ECDC) guidelines.

    Regarding SARS-CoV-2 genomic surveillance, the Laboratoire national de santé analysed 360 specimens from residents in Luxembourg in week 37/2021 (from 542 total cases in the Grand Duchy of Luxembourg, 66,4%). This exceeds the minimum coverage (10%) and minimum sample size (285) recommended by the ECDC.

    All specimens were assigned to the Delta variant. Community surveillance showed that parental lineage B.1.617.2 continues to be the most frequent one (81,4%), followed by AY.4 (4,6%). In respect to target groups, AY lineages were found in 29,5% of post-vaccination breakthrough cases.

    Introduction

    The Laboratoire national de santé, as National Reference Laboratory for Acute Respiratory Infections in Luxembourg, performs close surveillance on respiratory viruses, with a special focus on SARS-CoV-2. There are currently three active projects:

    The Sentinel Surveillance Network. It provides a broad picture of respiratory diseases affecting the Luxembourgish population, based on its double monitoring system (syndromic and virological).

    The National SARS-COV-2 Genomic Surveillance Program. It enables detailed observation of SARS-CoV-2 mutations and variants through time and space, and also monitoring specific groups of interest.

    The COVVAC Serology Project. It assesses the post-vaccination serological status in long-term care facilities and its evolution over time.

    The ReViLux provides updates on the first two projects.

    Sentinel Surveillance Network

    The Sentinel Surveillance Network aims at monitoring the circulating respiratory viruses, including SARS-CoV-2, and hence underpin public health actions. Following the World Health Organization (WHO) and European Centre for Disease Prevention and Control (ECDC) guidance, it focuses on cases of acute respiratory infection (ARI) and influenza-like illness (ILI).

    Results of syndromic surveillance during week 37 are displayed in Table 1 and the history of ILI consultations since the 2018-2019 season is shown in Figure 1. No case of ILI was identified in week 37 (out of 289 consultations); therefore, the percentage of ILI (0,0%) remains below the threshold for the interepidemic season (1,14%), according to the ECDC.

    Regarding the virological surveillance, no data is available for week 37.

    SARS-CoV-2 Genomic Surveillance

    The current sequencing strategy

    The National Reference Laboratory for Acute Respiratory Infections at LNS receives SARS-CoV-2 positive samples (nasopharyngeal or oropharyngeal swabs analysed by RT-PCR) from the national network of laboratories and proceeds as follows:

    Sequencing all specimens from hospital cases.
    Sequencing all specimens from reinfection and post-vaccination cases.
    Sequencing all specimens from cluster cases.
    Sequencing a representative sample of community cases.

    The representative sample of community cases is a systematic selection from all SARS-CoV-2 positive cases registered in Luxembourg to detect emerging variants and early increases in their incidence and transmission within the community in Luxembourg. This sample is selected according to the ECDC guidelines.

    The LNS shares its sequencing results with GISAID EpiCov database (www.gisaid.org) periodically. SARS-CoV-2 lineages (variants) have been assigned based on Rambaut et al. using Phylogenetic Assignment of Named Global Outbreak LINeages (pangolin) software  (v3.1.11, pangoLEARN 2021-08-24). The ReViLux continues to use the Pango nomenclature, in addition to the WHO nomenclature, to allow easier visualization of links between any evolving variants and their ancestor (https://cov-lineages.org). See nomenclature equivalences in Annex 1.

    Methodological note on Delta subtypes

    Since 3 September 2021, the ECDC no longer considers B.1.1.7 and B.1.1.7+E484K lineages (Alpha variant) as variants of concern. This decision is based in both their low circulation and the high effectiveness of vaccines in controlling them.

    Since 24 August 2021, the Phylogenetic Assignment of Named Global Outbreak Lineages (PANGOLIN) software uses a new version of its reference library, which includes additional Delta lineages (AY). Both B.1.617.2 and AY lineages are classified as Delta variant by international Public Health institutions (WHO, ECDC).

    Sequenced specimens

    In week 37, 542 new cases were registered in Luxembourg; hence, the minimum sample size required to detect emerging variants at a 2.5% incidence is estimated to be 285 specimens (52.6%).

    The microbial genomics unit at the LNS sequenced 380 specimens from week 37, with 360 specimens having been collected in week 37 from residents (66.4% coverage of the 542 total cases registered in Luxembourg; see coverage trend in Figure 2). This exceeds the minimum coverage (10%) and minimum sample size (285) to detect a 2.5% incidence recommended by the ECDC. The representative sample of community cases is built by systematic selection.

    Circulating lineage detection

    The evolution of variants over the weeks is shown in Figure 3.

    In week 37/2021, only Delta variant cases were detected among all specimens sequenced in the representative sample of community cases, including 9 Delta subtypes. The distribution of VOCs is displayed in Table 2, and their evolution over the weeks is shown in Figure 4.

    Mutation surveillance

    In addition to the surveillance of SARS-CoV-2 variants, the LNS monitors the occurrence of SARS-CoV-2 mutations reported to have a clinical and epidemiological relevance. This complementary surveillance enables us to detect unexpected mutations among the specimens sequenced. It is expected that VOC defining mutations share the same distribution as their corresponding VOCs. However, newly acquired mutations may occur and their early detection might be key to expect changes in the epidemic evolution.

    Following ECDC guidance, the LNS is currently monitoring 15 mutations to the spike protein frequently associated to VOCs and variants of interest (VOIs). Table 3 provides the cumulative frequencies of these mutations, detected in the lineage-assignable genome sequences since 1 Sep 2020 (N = 18 562), as well as the frequencies for the last 3 weeks. Figure 9 displays their distribution over the weeks.

    References

    Centers for Disease Control and Prevention. SARS-CoV-2 Variant Classifications and Definitions. Retrieved 1 October 2021, from https://www.cdc.gov/coronavirus/2019-ncov/variants/variant-info.html

    COVID-19 Data Portal – accelerating scientific research through data. (2021). Retrieved 1 October 2021, from https://www.covid19dataportal.org/sequences

    European Centre for Disease Prevention and Control. Guidance for representative and targeted genomic SARS-CoV-2 monitoring – 3 May 2021. ECDC : Stockholm ; 2021

    European Centre for Disease Prevention and Control. SARS-CoV-2 variants of concern. Retrieved 1 October 2021, from https://www.ecdc.europa.eu/en/covid-19/variants-concern

    Genomic sequencing of SARS-CoV-2: a guide to implementation for maximum impact on public health. Geneva: World Health Organization; 2021.

    GitHub – cov-lineages/pangolin: Software package for assigning SARS-CoV-2 genome sequences to global lineages. (2021). Retrieved 1 October 2021, from https://github.com/cov-lineages/pangolin

    Hadfield J., Megill C., Bell S., Huddleston J., Potter B., Callender C. et al. (2018). Nextstrain: real-time tracking of pathogen evolution. Bioinformatics, 34(23), 4121-4123. doi: 10.1093/bioinformatics/bty407

    Pango Network. New AY lineages. Retrieved 1 October 2021, from: https://www.pango.network/new-ay-lineages/

    Pango Network. New AY lineages. Retrieved 1 October 2021, from: https://www.pango.network/new-ay-lineages-and-an-update-to-ay-4-ay-12/

    Rambaut A., Holmes E., O’Toole Á., Hill V., McCrone J., Ruis C. et al. (2020). A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nature Microbiology, 5(11), 1403-1407. doi: 10.1038/s41564-020-0770-5

    Annexes

    Annex 1. SARS-CoV-2 variants naming

    References:

    1. Madhi SA, Baillie V, Cutland CL, Voysey M, Koen AL, Fairlie L, et al. Efficacy of the ChAdOx1 nCoV-19 Covid-19 Vaccine against the B.1.351 Variant. New England Journal of Medicine. 2021.
    2. Cele S, Gazy I, Jackson L, Hwa S-H, Tegally H, Lustig G, et al. Escape of SARS-CoV-2 501Y.V2 from neutralization by convalescent plasma. Nature. 2021.
    3. Pearson CA. Estimates of severity and transmissibility of novel South Africa SARS-CoV-2 variant 501Y.V2 [Available from: https://cmmid.github.io/topics/covid19/reports/sa-novel-variant/2021_01_11_Transmissibility_and_severity_of_501Y_V2_in_SA.pdf
    4. Funk T, Pharris A, Spiteri G, Bundle N, Melidou A, Carr M, et al. Characteristics of SARS-CoV-2 variants of concern B.1.1.7, B.1.351 or P.1: data from seven EU/EEA countries, weeks 38/2020 to 10/2021. Eurosurveillance. 2021;26(16):2100348.
    5. Faria NR, Mellan TA, Whittaker C, Claro IM, Candido DdS, Mishra S, et al. Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil. Science. 2021.
    6. Dejnirattisai W, Zhou D, Supasa P, Liu C, Mentzer AJ, Ginn HM, et al. Antibody evasion by the P.1 strain of SARS-CoV-2. Cell. 2021.
    7. Public Health England. SARS-CoV-2 variants of concern and variants under investigation in England Technical briefing 12 2021 [Available from: https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/988619/Variants_of_Concern_VOC_Technical_Briefing_12_England.pdf
    8. Jamie Lopez Bernal NA, Charlotte Gower, Eileen Gallagher, Dr Ruth Simmons, Simon Thelwall, Julia Stowe, Elise Tessier, Natalie Groves, Gavin Dabrera, Richard Myers, Vanessa Saliba, Shamez Ladhani, Coli, Campbell, Gayatri Amirthalingam, Matt Edmunds, Maria Zambon, Kevin Brown, Susan Hopkins, Meera Chand, Mary Ramsay. Effectiveness of COVID-19 vaccines against the B.1.617.2 variant 2021 [Available from: https://khub.net/documents/135939561/430986542/Effectiveness+of+COVID-19+vaccines+against+the+B.1.617.2+variant.pdf/204c11a4-e02e-11f2-db19-b3664107ac42
    9. Sheikh A, McMenamin J, Taylor B, Robertson C. SARS-CoV-2 Delta VOC in Scotland: demographics, risk of hospital admission, and vaccine effectiveness. The Lancet.
    10. Stowe J, Andrews N, Gower C, Gallagher E, Utsi L, Simmons R, et al. Effectiveness of COVID-19 vaccines against hospital admission with the Delta (B.1.617.2) variant 2021 [Available from: https://khub.net/documents/135939561/479607266/Effectiveness+of+COVID-19+vaccines+against+hospital+admission+with+the+Delta+%28B.1.617.2%29+variant.pdf/1c213463-3997-ed16-2a6f-14e5deb0b997?t=1623689315431
    11. Public Health England. SARS-CoV-2 variants of concern and variants under investigation in England Technical briefing 16 2021 [Available from: https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/997414/Variants_of_Concern_VOC_Technical_Briefing_16.pdf
  • Semaine 36

    Respiratory Viruses in Luxembourg (ReViLux)

    Weekly report (6 – 12 September 2021)

    Executive Summary

    The Sentinel Surveillance Network identified 2 cases of influenza-like illness, thus remaining below the recommended threshold for the interepidemic season, according to the European Center for Disease Prevention and Control (ECDC) guidelines.

    Regarding SARS-CoV-2 genomic surveillance, the Laboratoire national de santé analysed 366 specimens from residents in Luxembourg in week 36/2021 (from 553 total cases in the Grand Duchy of Luxembourg, 66,2%). This exceeds the minimum coverage (10%) and minimum sample size (288) recommended by the ECDC.

    All specimens from week 36/2021 but one were assigned to the Delta variant, the remaining being Alpha variant. Community surveillance showed that parental lineage B.1.617.2 continues to be the most frequent one (77,1%), followed by AY.12 (11,1%). In respect to target groups, AY lineages were found in 25,8% of post-vaccination breakthrough cases.

    Introduction

    The Laboratoire national de santé, as National Reference Laboratory for Acute Respiratory Infections in Luxembourg, performs close surveillance on respiratory viruses, with a special focus on SARS-CoV-2. There are currently three active projects:

    The Sentinel Surveillance Network. It provides a broad picture of respiratory diseases affecting the Luxembourgish population, based on its double monitoring system (syndromic and virological).

    The National SARS-COV-2 Genomic Surveillance Program. It enables detailed observation of SARS-CoV-2 mutations and variants through time and space, and also monitoring specific groups of interest.

    The COVVAC Serology Project. It assesses the post-vaccination serological status in long-term care facilities and its evolution over time.

    The ReViLux provides updates on the first two projects.

    Sentinel Surveillance Network

    The Sentinel Surveillance Network aims at monitoring the circulating respiratory viruses, including SARS-CoV-2, and hence underpin public health actions. Following the World Health Organization (WHO) and European Centre for Disease Prevention and Control (ECDC) guidance, it focuses on cases of acute respiratory infection (ARI) and influenza-like illness (ILI).

    Results of syndromic surveillance during week 36 are displayed in Table 1 and the history of ILI consultations since the 2018-2019 season is shown in Figure 1. Two cases of ILI were identified in week 36 (out of 476 consultations); therefore, the percentage of ILI (0,42%) remains below the threshold for the interepidemic season (1,14%), according to the ECDC.

    Regarding the virological surveillance, no data is available for week 36.

     

    SARS-CoV-2 Genomic Surveillance

    The current sequencing strategy

    The National Reference Laboratory for Acute Respiratory Infections at LNS receives SARS-CoV-2 positive samples (nasopharyngeal or oropharyngeal swabs analysed by RT-PCR) from the national network of laboratories and proceeds as follows:

    * Sequencing all specimens from hospital cases.
    * Sequencing all specimens from reinfection and post-vaccination cases.
    * Sequencing all specimens from cluster cases.
    * Sequencing a representative sample of community cases.

    The representative sample of community cases is a systematic selection from all SARS-CoV-2 positive cases registered in Luxembourg to detect emerging variants and early increases in their incidence and transmission within the community in Luxembourg. This sample is selected according to the ECDC guidelines.

    The LNS shares its sequencing results with GISAID EpiCov database (www.gisaid.org) periodically. SARS-CoV-2 lineages (variants) have been assigned based on Rambaut et al. using Phylogenetic Assignment of Named Global Outbreak LINeages (pangolin) software  (v3.1.11, pangoLEARN 2021-08-24). The ReViLux continues to use the Pango nomenclature, in addition to the WHO nomenclature, to allow easier visualization of links between any evolving variants and their ancestor (https://cov-lineages.org). See nomenclature equivalences in Annex 1.

    Methodological note on Delta subtypes

    Since 3 September 2021, the ECDC no longer considers B.1.1.7 and B.1.1.7+E484K lineages (Alpha variant) as variants of concern. This decision is based in both their low circulation and the high effectiveness of vaccines in controlling them.

    Since 24 August 2021, the Phylogenetic Assignment of Named Global Outbreak Lineages (PANGOLIN) software uses a new version of its reference library (pango-designation v1.2.66), which includes 13 additional Delta lineages (AY.13 to AY.25). Both B.1.617.2 and AY lineages are classified as Delta variant by the World Health Organization.

    Sequenced specimens

    In week 36, 553 new cases were registered in Luxembourg; hence, the minimum sample size required to detect emerging variants at a 2.5% incidence is estimated to be 288 specimens (52.1%).

    The microbial genomics unit at the LNS sequenced 475 specimens from week 36, with 366 specimens having been collected in week 36 from residents (66,2% coverage of the 553 total cases registered in Luxembourg; see coverage in Figure 2). This exceeds the minimum coverage (10%) and minimum sample size (288) to detect a 2.5% incidence recommended by the ECDC. The representative sample of community cases is built by systematic selection.

    Circulating lineage detection

    The evolution of variants over the weeks is shown in Figure 3.

    In week 36/2021, only Delta variant cases were detected among all specimens sequenced in the representative sample of community cases, including 9 Delta subtypes. The distribution of VOCs is displayed in Table 2, and their evolution over the weeks is shown in Figure 4.

    Mutation surveillance

    In addition to the surveillance of SARS-CoV-2 variants, the LNS monitors the occurrence of SARS-CoV-2 mutations reported to have a clinical and epidemiological relevance. This complementary surveillance enables us to detect unexpected mutations among the specimens sequenced. It is expected that VOC defining mutations share the same distribution as their corresponding VOCs. However, newly acquired mutations may occur and their early detection might be key to expect changes in the epidemic evolution.

    Following ECDC guidance, the LNS is currently monitoring 15 mutations to the spike protein frequently associated to VOCs and variants of interest (VOIs). Table 3 provides the cumulative frequencies of these mutations, detected in the lineage-assignable genome sequences since 1 Sep 2020 (N = 18 231), as well as the frequencies over the last 3 weeks.

    References

    Centers for Disease Control and Prevention. SARS-CoV-2 Variant Classifications and Definitions. Retrieved 20 September 2021, from https://www.cdc.gov/coronavirus/2019-ncov/variants/variant-info.html

    COVID-19 Data Portal – accelerating scientific research through data. (2021). Retrieved 20 September 2021, from https://www.covid19dataportal.org/sequences

    European Centre for Disease Prevention and Control. Guidance for representative and targeted genomic SARS-CoV-2 monitoring – 3 May 2021. ECDC : Stockholm ; 2021

    European Centre for Disease Prevention and Control. SARS-CoV-2 variants of concern. Retrieved 20 September 2021, from https://www.ecdc.europa.eu/en/covid-19/variants-concern

    Genomic sequencing of SARS-CoV-2: a guide to implementation for maximum impact on public health. Geneva: World Health Organization; 2021.

    GitHub – cov-lineages/pangolin: Software package for assigning SARS-CoV-2 genome sequences to global lineages. (2021). Retrieved 20 September 2021, from https://github.com/cov-lineages/pangolin

    Hadfield J., Megill C., Bell S., Huddleston J., Potter B., Callender C. et al. (2018). Nextstrain: real-time tracking of pathogen evolution. Bioinformatics, 34(23), 4121-4123. doi: 10.1093/bioinformatics/bty407

    Pango Network. New AY lineages. Retrieved 20 September 2021, from: https://www.pango.network/new-ay-lineages/

    Pango Network. New AY lineages. Retrieved 20 September 2021, from: https://www.pango.network/new-ay-lineages-and-an-update-to-ay-4-ay-12/

    Rambaut A., Holmes E., O’Toole Á., Hill V., McCrone J., Ruis C. et al. (2020). A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nature Microbiology, 5(11), 1403-1407. doi: 10.1038/s41564-020-0770-5

    Annexes

    Annex 1. SARS-CoV-2 variants naming

    References:

    1. Madhi SA, Baillie V, Cutland CL, Voysey M, Koen AL, Fairlie L, et al. Efficacy of the ChAdOx1 nCoV-19 Covid-19 Vaccine against the B.1.351 Variant. New England Journal of Medicine. 2021.
    2. Cele S, Gazy I, Jackson L, Hwa S-H, Tegally H, Lustig G, et al. Escape of SARS-CoV-2 501Y.V2 from neutralization by convalescent plasma. Nature. 2021.
    3. Pearson CA. Estimates of severity and transmissibility of novel South Africa SARS-CoV-2 variant 501Y.V2 [Available from: https://cmmid.github.io/topics/covid19/reports/sa-novel-variant/2021_01_11_Transmissibility_and_severity_of_501Y_V2_in_SA.pdf
    4. Funk T, Pharris A, Spiteri G, Bundle N, Melidou A, Carr M, et al. Characteristics of SARS-CoV-2 variants of concern B.1.1.7, B.1.351 or P.1: data from seven EU/EEA countries, weeks 38/2020 to 10/2021. Eurosurveillance. 2021;26(16):2100348.
    5. Faria NR, Mellan TA, Whittaker C, Claro IM, Candido DdS, Mishra S, et al. Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil. Science. 2021.
    6. Dejnirattisai W, Zhou D, Supasa P, Liu C, Mentzer AJ, Ginn HM, et al. Antibody evasion by the P.1 strain of SARS-CoV-2. Cell. 2021.
    7. Public Health England. SARS-CoV-2 variants of concern and variants under investigation in England Technical briefing 12 2021 [Available from: https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/988619/Variants_of_Concern_VOC_Technical_Briefing_12_England.pdf
    8. Jamie Lopez Bernal NA, Charlotte Gower, Eileen Gallagher, Dr Ruth Simmons, Simon Thelwall, Julia Stowe, Elise Tessier, Natalie Groves, Gavin Dabrera, Richard Myers, Vanessa Saliba, Shamez Ladhani, Coli, Campbell, Gayatri Amirthalingam, Matt Edmunds, Maria Zambon, Kevin Brown, Susan Hopkins, Meera Chand, Mary Ramsay. Effectiveness of COVID-19 vaccines against the B.1.617.2 variant 2021 [Available from: https://khub.net/documents/135939561/430986542/Effectiveness+of+COVID-19+vaccines+against+the+B.1.617.2+variant.pdf/204c11a4-e02e-11f2-db19-b3664107ac42
    9. Sheikh A, McMenamin J, Taylor B, Robertson C. SARS-CoV-2 Delta VOC in Scotland: demographics, risk of hospital admission, and vaccine effectiveness. The Lancet.
    10. Stowe J, Andrews N, Gower C, Gallagher E, Utsi L, Simmons R, et al. Effectiveness of COVID-19 vaccines against hospital admission with the Delta (B.1.617.2) variant 2021 [Available from: https://khub.net/documents/135939561/479607266/Effectiveness+of+COVID-19+vaccines+against+hospital+admission+with+the+Delta+%28B.1.617.2%29+variant.pdf/1c213463-3997-ed16-2a6f-14e5deb0b997?t=1623689315431
    11. Public Health England. SARS-CoV-2 variants of concern and variants under investigation in England Technical briefing 16 2021 [Available from: https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/997414/Variants_of_Concern_VOC_Technical_Briefing_16.pdf

     

  • Semaine 35

    Respiratory Viruses in Luxembourg (ReViLux)

    Weekly report (30 August – 5 Septembre 2021)

    Executive Summary

    The Sentinel Surveillance Network identified two cases of influenza-like illness, thus remaining below the recommended threshold for the interepidemic season, according to the European Center for Disease Prevention and Control (ECDC) guidelines.

    Regarding SARS-CoV-2 genomic surveillance, the Laboratoire national de santé analysed 302 Luxembourgish specimens in week 35/2021 (from 573 total cases in the Grand Duchy of Luxembourg, 52,7%). This exceeds the minimum coverage (10%) and sample size (293) recommended by the ECDC.

    All specimens from week 35/2021 were assigned to the Delta variant. Community surveillance showed that the parental lineage B.1.617.2 continues to be the most frequent one (73,4%), followed by AY.12 (9,9%). In respect to target groups, AY lineages were found in 23,5% of post-vaccination breakthrough cases.

    Introduction

    The Laboratoire national de santé, as National Reference Laboratory for Acute Respiratory Infections in Luxembourg, performs close surveillance on respiratory viruses, with a special focus on SARS-CoV-2. There are currently three active projects:

    The Sentinel Surveillance Network. It provides a broad picture of respiratory diseases affecting the Luxembourgish population, based on its double monitoring system (syndromic and virological).

    The National SARS-COV-2 Genomic Surveillance Program. It enables detailed observation of SARS-CoV-2 mutations and variants through time and space, and also monitoring specific groups of interest.

    The COVVAC Serology Project. It assesses the post-vaccination serological status in long-term care facilities and its evolution over time.

    The ReViLux provides updates on the first two projects.

    Sentinel Surveillance Network

    The Sentinel Surveillance Network aims at monitoring the circulating respiratory viruses, including SARS-CoV-2, and hence underpin public health actions. Following the World Health Organization (WHO) and European Centre for Disease Prevention and Control (ECDC) guidance, it focuses on cases of acute respiratory infection (ARI) and influenza-like illness (ILI).

    Results of syndromic surveillance during week 35 are displayed in Table 1 and the history of ILI consultations since the 2018-2019 season is shown in Figure 1. Two cases of ILI were identified in week 35 (out of 332 consultations); therefore, the percentage of ILI (0,60%) remains below the threshold for the interepidemic season (1,14%), according to the ECDC.

    Regarding the virological surveillance, no data is available for week 35.

    SARS-CoV-2 Genomic Surveillance

    The current sequencing strategy

    The National Reference Laboratory for Acute Respiratory Infections at LNS receives SARS-CoV-2 -positive samples (nasopharyngeal or oropharyngeal swabs analysed by RT-PCR) from the national network of laboratories and proceeds as follows:

    -Sequencing all specimens from hospital cases.
    -Sequencing all specimens from reinfection and post-vaccination cases.
    -Sequencing all specimens from cluster cases.
    -Sequencing a representative sample of community cases.

    The representative sample of community cases is a systematic selection from all SARS-CoV-2 positive cases registered in Luxembourg to detect emerging variants and early increases in their incidence and transmission within the community in Luxembourg. This sample is selected according to the ECDC guidelines.

    The LNS shares its sequencing results with GISAID EpiCov database (www.gisaid.org) periodically. SARS-CoV-2 lineages (variants) have been assigned based on Rambaut et al. using Phylogenetic Assignment of Named Global Outbreak LINeages (pangolin) software  (v3.1.11, pangoLEARN 2021-08-24). The ReViLux continues to use the Pango nomenclature, in addition to the WHO nomenclature, to allow easier visualization of links between any evolving variants and their ancestor (https://cov-lineages.org). See nomenclature equivalences in Annex 1.

    Methodological note on Delta subtypes

    The ECDC no longer considers B.1.1.7 and B.1.1.7+E484K lineages (Alpha variant) as variants of concern. This decision is based in both their low circulation and the high effectiveness of vaccines in controlling them.

    Since 24 August 2021, the Phylogenetic Assignment of Named Global Outbreak Lineages (PANGOLIN) software uses a new version of its reference library (pango-designation v1.2.66), which includes 13 additional Delta lineages (AY.13 to AY.25). Both B.1.617.2 and AY lineages are classified as Delta variant by the World Health Organization.

    Sequenced specimens

    In week 35, 573 new cases were registered in Luxembourg; hence, the minimum sample size required to detect emerging variants at a 2.5% incidence is estimated to be 293 specimens (51.1%).

    The microbial genomics unit at the LNS sequenced 380 specimens, with 302 specimens having been collected in week 35 from residents (52,7% coverage of the 573 total cases registered in Luxembourg; see coverage trend in Figure 2). This exceeds the minimum coverage (10%) and minimum sample size (293) to detect a 2.5% incidence recommended by the ECDC. The representative sample of community cases is based on a systematic selection.

    Circulating lineage detection

    The evolution of variants over the weeks is shown in Figure 3.

    In week 35/2021, only Delta variant cases were detected among all specimens sequenced (target groups, clusters and non-residents comprised), including 5 Delta subtypes. The distribution of VOCs is displayed in Table 2, and their evolution over the weeks is shown in Figure 4.

    Mutation surveillance

    In addition to the surveillance of SARS-CoV-2 variants, the LNS monitors the occurrence of SARS-CoV-2 mutations assumed to have a clinical and epidemiological relevance. These results are being updated and will be presented next week.

    References

    Centers for Disease Control and Prevention. SARS-CoV-2 Variant Classifications and Definitions. Retrieved 13 September 2021, from https://www.cdc.gov/coronavirus/2019-ncov/variants/variant-info.html

    COVID-19 Data Portal – accelerating scientific research through data. (2021). Retrieved 13 September 2021, from https://www.covid19dataportal.org/sequences

    European Centre for Disease Prevention and Control. Guidance for representative and targeted genomic SARS-CoV-2 monitoring – 3 May 2021. ECDC : Stockholm ; 2021

    European Centre for Disease Prevention and Control. SARS-CoV-2 variants of concern. Retrieved 13 September 2021, from https://www.ecdc.europa.eu/en/covid-19/variants-concern

    Genomic sequencing of SARS-CoV-2: a guide to implementation for maximum impact on public health. Geneva: World Health Organization; 2021.

    GitHub – cov-lineages/pangolin: Software package for assigning SARS-CoV-2 genome sequences to global lineages. (2021). Retrieved 13 September 2021, from https://github.com/cov-lineages/pangolin

    Hadfield J., Megill C., Bell S., Huddleston J., Potter B., Callender C. et al. (2018). Nextstrain: real-time tracking of pathogen evolution. Bioinformatics, 34(23), 4121-4123. doi: 10.1093/bioinformatics/bty407

    Pango Network. New AY lineages. Retrieved 13 September 2021, from: https://www.pango.network/new-ay-lineages/

    Pango Network. New AY lineages. Retrieved 13 September 2021, from: https://www.pango.network/new-ay-lineages-and-an-update-to-ay-4-ay-12/

    Rambaut A., Holmes E., O’Toole Á., Hill V., McCrone J., Ruis C. et al. (2020). A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nature Microbiology, 5(11), 1403-1407. doi: 10.1038/s41564-020-0770-5

    Annexes

    Annex 1. SARS-CoV-2 variants naming

    The ReViLux continues to use the Pango nomenclature, in addition to the WHO nomenclature, to allow easier visualization of links between any evolving variants and their ancestor. Equivalence for VOC are shown in Table A1 (adapted from WHO).

  • Semaine 34

    Respiratory Viruses in Luxembourg (ReViLux)

    Weekly report (23 – 29 August 2021)

    Executive Summary

    The Sentinel Surveillance Network identified one case of influenza-like illness, thus remaining below the recommended threshold for the interepidemic season, according to the European Center for Disease Prevention and Control (ECDC) guidelines.

    Regarding SARS-CoV-2 genomic surveillance, the Laboratoire national de santé analysed 270 Luxembourgish specimens from week 34/2021 (from 542 total cases in the Grand Duchy of Luxembourg, 49,8%). This exceeds the minimum coverage (10%), but does not reach the minimum sample size (285) allowing to detect a 2.5% incidence, as recommended by the ECDC.

    All specimens from week 34/2021 were assigned to Delta variant. Community surveillance showed that the parental lineage B.1.617.2 continues to be the most frequent one (85,7%), followed by AY.4 (10,5%). In respect to target group surveillance, all cases analysed, including 32 reinfection and post-vaccination breakthrough cases, were identified as Delta variant.

    Introduction

    The Laboratoire national de santé, as National Reference Laboratory for Acute Respiratory Infections in Luxembourg, performs close surveillance on respiratory viruses, with a special focus on SARS-CoV-2. There are currently three active projects:

    The Sentinel Surveillance Network. It provides a broad picture of respiratory diseases affecting the Luxembourgish population, based on its double monitoring system (syndromic and virological).

    The National SARS-COV-2 Genomic Surveillance Program. It enables detailed observation of SARS-CoV-2 mutations and variants through time and space, and also monitoring specific groups of interest.

    The COVVAC Serology Project. It assesses the post-vaccination serological status in long-term care facilities and its evolution over time.

    The ReViLux provides updates on the first two projects.

    Sentinel Surveillance Network

    The Sentinel Surveillance Network aims at monitoring the circulating respiratory viruses, including SARS-CoV-2, and hence underpin public health actions. Following the World Health Organization (WHO) and European Centre for Disease Prevention and Control (ECDC) guidance, it focuses on cases of acute respiratory infection (ARI) and influenza-like illness (ILI).

    Results of syndromic surveillance during week 34 are displayed in Table 1 and the history of ILI consultations since the 2018-2019 season is shown in Figure 1. One case of ILI was identified in week 34 (out of 394 consultations); therefore, the percentage of ILI (0,25%) remains below the threshold for the interepidemic season (1,14%), according to the ECDC.

    Regarding the virological surveillance, no data is available for week 34.

    SARS-CoV-2 Genomic Surveillance

    The current sequencing strategy

    The National Reference Laboratory for Acute Respiratory Infections at LNS receives SARS-CoV-2 -positive samples for (nasopharyngeal or oropharyngeal swabs analysed by RT-PCR) from the national network of laboratories and proceeds as follows:

    – Sequencing all specimens from hospital cases.
    – Sequencing all specimens from reinfection and post-vaccination cases.
    – Sequencing all specimens from cluster cases.
    – Sequencing a representative sample of community cases.

    The representative sample of community cases is a systematic selection from all SARS-CoV-2 positive cases registered in Luxembourg to detect emerging variants and early increases in their incidence and transmission within the community in Luxembourg. This sample is selected according to the ECDC guidelines.

    The LNS shares its sequencing results with GISAID EpiCov database (www.gisaid.org) periodically. SARS-CoV-2 lineages (variants) have been assigned based on Rambaut et al. using the Phylogenetic Assignment of Named Global Outbreak LINeages (pangolin) software  (v3.1.11, pangoLEARN 2021-08-09). The ReViLux continues to use the Pango nomenclature, in addition to the WHO nomenclature, to allow easier visualization of links between any evolving variants and their ancestor (https://cov-lineages.org). See nomenclature equivalences in Annex 1.

    Methodological note

    Since 3 September 2021, the ECDC no longer considers B.1.1.7 and B.1.1.7+E484K lineages (Alpha variant) as variants of concern. This decision is based in both their low circulation and the high effectiveness of vaccines in controlling them.

    Since 24 August 2021, the Phylogenetic Assignment of Named Global Outbreak Lineages (PANGOLIN) software uses a new version of its reference library (pango-designation v1.2.66), which includes 13 additional Delta lineages (AY.13 to AY.25). Both B.1.617.2 and AY lineages are classified as Delta variant by the World Health Organization.

    Sequenced specimens

    In week 34, 542 new cases were registered in Luxembourg; hence, the minimum sample size required to detect emerging variants at a 2.5% incidence is estimated to be 285 specimens (52,6%).

    The microbial genomics unit at the LNS sequenced 285 specimens, with 270 specimens having been collected in week 34 from residents (49,8% coverage of the 542 total cases registered in Luxembourg; see coverage trend in Figure 2). This exceeds the minimum coverage (10%), but does not reach the minimum sample size (285) to detect a 2.5% incidence, as recommended by ECDC. The representative sample of community cases is based on a systematic selection.

    Circulating lineage detection

    The evolution of variants over the weeks is shown in Figure 3.

    In week 34/2021, only Delta variant cases were detected within our population sequencing pool (after removal of cluster and non-resident specimens), including 5 Delta subtypes. The distribution of VOCs is displayed in Table 2, and their evolution over the weeks is shown in Figure 4.

    Mutation surveillance

    In addition to the surveillance of SARS-CoV-2 variants, the LNS monitors the occurrence of SARS-CoV-2 mutations assumed to have a clinical and epidemiological relevance.

    Table 3 provides the overall frequencies of these mutations, detected in the lineage-assignable genome sequences, analyzed since 1 Sep 2020 (N = 17469), as well as the frequencies in week 34/2021.

    References

    Centers for Disease Control and Prevention. SARS-CoV-2 Variant Classifications and Definitions. Retrieved 6 September 2021, from https://www.cdc.gov/coronavirus/2019-ncov/variants/variant-info.html

    COVID-19 Data Portal – accelerating scientific research through data. (2021). Retrieved 6 September 2021, from https://www.covid19dataportal.org/sequences

    European Centre for Disease Prevention and Control. Guidance for representative and targeted genomic SARS-CoV-2 monitoring – 3 May 2021. ECDC : Stockholm ; 2021

    Genomic sequencing of SARS-CoV-2: a guide to implementation for maximum impact on public health. Geneva: World Health Organization; 2021.

    GitHub – cov-lineages/pangolin: Software package for assigning SARS-CoV-2 genome sequences to global lineages. (2021). Retrieved 6 September 2021, from https://github.com/cov-lineages/pangolin

    Hadfield J., Megill C., Bell S., Huddleston J., Potter B., Callender C. et al. (2018). Nextstrain: real-time tracking of pathogen evolution. Bioinformatics, 34(23), 4121-4123. doi: 10.1093/bioinformatics/bty407

    Pango Network. New AY lineages. Retrieved 6 September 2021, from: https://www.pango.network/new-ay-lineages/

    Pango Network. New AY lineages. Retrieved 6 September 2021, from: https://www.pango.network/new-ay-lineages-and-an-update-to-ay-4-ay-12/

    Rambaut A., Holmes E., O’Toole Á., Hill V., McCrone J., Ruis C. et al. (2020). A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nature Microbiology, 5(11), 1403-1407. doi: 10.1038/s41564-020-0770-5

    Annexes

    Annex 1. SARS-CoV-2 variants naming

    The ReViLux continues to use the Pango nomenclature, in addition to the WHO nomenclature, to allow easier visualization of links between any evolving variants and their ancestor. Equivalence for VOC are shown in Table A1 (adapted from WHO).

  • Semaine 33

    Respiratory Viruses in Luxembourg (ReViLux)

    Weekly report (16 – 22 August 2021)

    Executive Summary

    The Sentinel Surveillance Network identified no cases of influenza-like illness, thus remaining below the recommended threshold for the interepidemic season, according to the European Center for Disease Prevention and Control (ECDC) guidelines.

    Regarding SARS-CoV-2 genomic surveillance, the Laboratoire national de santé analysed 244 Luxembourgish specimens in week 33/2021 (from 440 total cases in the Grand Duchy of Luxembourg, 55,5%). This exceeds the minimum coverage (10%) but does not reach the minimum sample size (254) recommended by the ECDC.

    Community surveillance showed that Delta variant continues to be the dominant one in Luxembourg (99,1%), with low prevalence of the Gamma (0,9%). In respect to target group surveillance, all cases analysed were identified as VOC cases, and 15 post-vaccination breakthrough cases were assigned to Delta variant.

    Introduction

    The Laboratoire national de santé, as National Reference Laboratory for Acute Respiratory Infections in Luxembourg, performs close surveillance on respiratory viruses, with a special focus on SARS-CoV-2. There are currently three active projects:

    The Sentinel Surveillance Network. It provides a broad picture of respiratory diseases affecting the Luxembourgish population, based on its double monitoring system (syndromic and virological).

    The National SARS-COV-2 Genomic Surveillance Program. It enables detailed observation of SARS-CoV-2 mutations and variants through time and space, and also monitoring specific groups of interest.

    The COVVAC Serology Project. It assesses the post-vaccination serological status in long-term care facilities and its evolution over time.

    The ReViLux provides updates on the first two projects.

    Sentinel Surveillance Network

    The Sentinel Surveillance Network aims at monitoring the circulating respiratory viruses, including SARS-CoV-2, and hence underpin public health actions. Following the World Health Organization (WHO) and European Centre for Disease Prevention and Control (ECDC) guidance, it focuses on cases of acute respiratory infection (ARI) and influenza-like illness (ILI).

    Results of syndromic surveillance during week 33 (16 August 2021 – 22 August 2021) are displayed in Table 1 and the history of ILI consultations since the 2018-2019 season is shown in Figure 1. No cases of ILI were identified in week 33; therefore, the percentage of ILI is below the threshold for the interepidemic season (1,14%), according to the ECDC.

    Regarding the virological surveillance, no data is available for week 33.

    SARS-CoV-2 Genomic Surveillance

    The current sequencing strategy

    The National Reference Laboratory for Acute Respiratory Infections at LNS receives SARS-CoV-2 -positive samples for (nasopharyngeal or oropharyngeal swabs analysed by RT-PCR) from the national network of laboratories and proceeds as follows:

    – Sequencing all specimens from hospital cases.
    – Sequencing all specimens from reinfection and post-vaccination cases.
    – Sequencing all specimens from cluster cases.
    – Sequencing a sample of community cases.

    The sample of community cases is a selection from all cases to detect emerging SARS-CoV-2 variants and early increases in their incidence and transmission within the community in Luxembourg. This sample is selected according to the ECDC guidelines.

    The LNS shares its sequencing results with GISAID EpiCov database (www.gisaid.org) periodically. SARS-CoV-2 lineages (variants) have been assigned based on Rambaut et al. using Phylogenetic Assignment of Named Global Outbreak LINeages (pangolin) software  (v3.1.11, pangoLEARN 2021-08-09). The ReViLux continues to use the Pango nomenclature, in addition to the WHO nomenclature, to allow easier visualization of links between any evolving variants and their ancestor (https://cov-lineages.org). See nomenclature equivalences in Annex 1.

    Methodological note on Delta subtypes

    The latest version of the pangoLEARN software included new lineages AY.4-AY.12. These are sublineages within B.1.617.2 (Delta variant), and were previously assigned to the B.1.617.2 lineage. However, due to their different geographic backgrounds they are now identified separately in order to allow a more detailed tracking. They are all classified as Delta variant by the World Health Organization.

    Sequenced specimens

    In week 33, 440 new cases were registered in Luxembourg; hence, the minimum sample size required to detect a 2.5% incidence is estimated to be 254 specimens (57,7%).

    The microbial genomics unit at the LNS sequenced 319 specimens, with 244 specimens having been collected in week 33 from residents (55,5% coverage of the 440 total cases registered in Luxembourg; see coverage trend in Figure 2). This exceeds the minimum coverage (10%) but does not reach the minimum sample size (254) recommended by ECDC. The community sample size in week 33, after removal of 17 additional cluster cases, was 227.

    Circulating lineage detection

    The evolution of variants over the weeks is shown in Figure 3.

    In week 33/2021, only Gamma and Delta variants (including 3 Delta subtypes) were detected within our population sequencing pool, after removal of cluster specimens, and excluding specimens collected from non-residents, as shown in Figure 4. The most prevalent variants are displayed in Table 2.

    Mutation surveillance

    In addition to the surveillance of SARS-CoV-2 variants, the LNS monitors the occurrence of SARS-CoV-2 mutations assumed to have a clinical and epidemiological relevance.

    Table 3 provides the overall frequencies of these mutations, detected in the lineage-assignable genome sequences, analyzed since 1 Sep 2020 (N=17166), as well as the frequencies in week 33/2021.

    References

    Centers for Disease Control and Prevention. SARS-CoV-2 Variant Classifications and Definitions. Retrieved 3 September 2021, from https://www.cdc.gov/coronavirus/2019-ncov/variants/variant-info.html

    COVID-19 Data Portal – accelerating scientific research through data. (2021). Retrieved 3 September 2021, from https://www.covid19dataportal.org/sequences

    European Centre for Disease Prevention and Control. Guidance for representative and targeted genomic SARS-CoV-2 monitoring – 3 May 2021. ECDC : Stockholm ; 2021

    Genomic sequencing of SARS-CoV-2: a guide to implementation for maximum impact on public health. Geneva: World Health Organization; 2021.

    GitHub – cov-lineages/pangolin: Software package for assigning SARS-CoV-2 genome sequences to global lineages. (2021). Retrieved 3 September 2021, from https://github.com/cov-lineages/pangolin

    Hadfield J., Megill C., Bell S., Huddleston J., Potter B., Callender C. et al. (2018). Nextstrain: real-time tracking of pathogen evolution. Bioinformatics, 34(23), 4121-4123. doi: 10.1093/bioinformatics/bty407

    Pango Network. New AY lineages. Retrieved 3 September 2021, from: https://www.pango.network/new-ay-lineages/

    Rambaut A., Holmes E., O’Toole Á., Hill V., McCrone J., Ruis C. et al. (2020). A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nature Microbiology, 5(11), 1403-1407. doi: 10.1038/s41564-020-0770-5

    Annexes

    Annex 1. SARS-CoV-2 variants naming

    The ReViLux continues to use the Pango nomenclature, in addition to the WHO nomenclature, to allow easier visualization of links between any evolving variants and their ancestor. Equivalence for VOC are shown in Table A1 (adapted from WHO).

     

     

     

  • Semaine 32

    Respiratory Viruses in Luxembourg (ReViLux)

    Weekly report (09 – 15 August 2021)

    Executive Summary

    The Sentinel Surveillance Network identified no cases of influenza-like illness, thus remaining below the recommended threshold for the interepidemic season, according to the European Center for Disease Prevention and Control (ECDC) guidelines.

    Regarding SARS-CoV-2 genomic surveillance, the Laboratoire national de santé analysed 178 Luxembourgish specimens in week 32/2021 (from 295 total cases in the Grand Duchy of Luxembourg, 60,4%). This exceeds the minimum coverage (10%) but does not reach the minimum sample size (198) recommended by the ECDC.

    Community surveillance showed that Delta variant continues to be the dominant one in Luxembourg (96,7%), with low prevalence of Gamma variant (3,3%).

    In respect to target group surveillance, all cases analysed were identified as VOC cases and 11 post-vaccination breakthrough cases were identified as Delta variant cases (including 2 AY.4 cases and 1 AY.7 case).

    Introduction

    The Laboratoire national de santé, as National Reference Laboratory for Acute Respiratory Infections in Luxembourg, performs close surveillance on respiratory viruses, with a special focus on SARS-CoV-2. There are currently three active projects:

    The Sentinel Surveillance Network. It provides a broad picture of respiratory diseases affecting the Luxembourgish population, based on its double monitoring system (syndromic and virological).

    The National SARS-COV-2 Genomic Surveillance Program. It enables detailed observation of SARS-CoV-2 mutations and variants through time and space, and also monitoring specific groups of interest.

    The COVVAC Serology Project. It assesses the post-vaccination serological status in long-term care facilities and its evolution over time.

    The ReViLux provides updats on the first two projects.

    Sentinel Surveillance Network

    The Sentinel Surveillance Network aims at monitoring the circulating respiratory viruses, including SARS-CoV-2, and hence underpin public health actions. Following the World Health Organization (WHO) and European Centre for Disease Prevention and Control (ECDC) guidance, it focuses on cases of acute respiratory infection (ARI) and influenza-like illness (ILI).

    Results of syndromic surveillance during week 32 (9 August 2021 – 15 August 2021) are displayed in Table 1 and the history of ILI consultations since the 2018-2019 season is shown in Figure 1. No cases of ILI were identified in week 32; therefore, the percentage of ILI is below the threshold for the interepidemic season (1,14%), according to the ECDC.

    Regarding the virological surveillance, no data is available for week 32.

    SARS-CoV-2 Genomic Surveillance

    The current sequencing strategy

    The National Reference Laboratory for Acute Respiratory Infections at LNS receives SARS-CoV-2 -positive samples for (nasopharyngeal or oropharyngeal swabs analysed by RT-PCR) from the national network of laboratories and proceeds as follows:

    Sequencing all specimens from hospital cases.
    Sequencing all specimens from reinfection and post-vaccination cases.
    Sequencing all specimens from cluster cases.
    Sequencing a sample of community cases.

    The sample of community cases is a selection from all cases to detect emerging SARS-CoV-2 variants and early increases in their incidence and transmission within the community in Luxembourg. This sample is selected according to the ECDC guidelines.

    The LNS shares its sequencing results with GISAID EpiCov database (www.gisaid.org) periodically. SARS-CoV-2 lineages (variants) have been assigned based on Rambaut et al. using Phylogenetic Assignment of Named Global Outbreak LINeages (pangolin) software  (v3.1.11, pangoLEARN 2021-08-09). The ReViLux continues to use the Pango nomenclature, in addition to the WHO nomenclature, to allow easier visualization of links between any evolving variants and their ancestor (https://cov-lineages.org). See nomenclature equivalences in Annex 1.

    Methodological note on Delta subtypes

    The latest version of the pangoLEARN software included new lineages AY.4-AY.12. These are sublineages within B.1.617.2 (Delta variant), and were previously assigned to the B.1.617.2 lineage. However, due to their different geographic backgrounds, they are now identified separately in order to allow a more detailed tracking. No functional difference from the parental lineage B.1.617.2 has yet been described, to the best of our knowledge. The Centers for Disease Control and Prevention (CDC) and the ECDC have already classified these new lineages as Delta variant, and the ReViLux will adopt the same classification.

    Sequenced specimens

    In week 32, 295 new cases were registered in Luxembourg; hence, the minimum sample size required to detect a 2.5% incidence is estimated to be 198 specimens (67,1%).

    The microbial genomics unit at the LNS sequenced 285 specimens, with 178 specimens having been collected in week 32 from residents (60,4% coverage of the 295 total cases registered in Luxembourg; see coverage trend in Figure 2). This exceeds the minimum coverage (10%) but does not reach the minimum sample size (198) recommended by ECDC. The community sample size in week 32, after removal of 20 additional cluster cases, was 158.

    Circulating lineage detection

    The evolution of variants over the weeks is shown in Figure 3.

    In week 32/2021, only Gamma and Delta variants were detected within our population sequencing pool (after removal of cluster and non-resident specimens), including 5 Delta subtypes. The distribution of VOCs is displayed in Table 2, and their evolution over the weeks is shown in Figure 4.

     

    Mutation surveillance

    In addition to the surveillance of SARS-CoV-2 variants, the LNS monitors the occurrence of SARS-CoV-2 mutations assumed to have a clinical and epidemiological relevance. Currently, 13 mutations are being observed, and this list is updated continually.

    Table 3 provides the overall frequencies of these mutations, detected in the lineage-assignable genome sequences, analyzed since 1 Sep 2020 (N=16879), as well as the frequencies in week 32/2021.

    References

    Centers for Disease Control and Prevention. SARS-CoV-2 Variant Classifications and Definitions. Retrieved 24 August 2021, from https://www.cdc.gov/coronavirus/2019-ncov/variants/variant-info.html

    COVID-19 Data Portal – accelerating scientific research through data. (2021). Retrieved 23 August 2021, from https://www.covid19dataportal.org/sequences

    European Centre for Disease Prevention and Control. Guidance for representative and targeted genomic SARS-CoV-2 monitoring – 3 May 2021. ECDC : Stockholm ; 2021

    Genomic sequencing of SARS-CoV-2: a guide to implementation for maximum impact on public health. Geneva: World Health Organization; 2021.

    GitHub – cov-lineages/pangolin: Software package for assigning SARS-CoV-2 genome sequences to global lineages. (2021). Retrieved 23 August 2021, from https://github.com/cov-lineages/pangolin

    Hadfield J., Megill C., Bell S., Huddleston J., Potter B., Callender C. et al. (2018). Nextstrain: real-time tracking of pathogen evolution. Bioinformatics, 34(23), 4121-4123. doi: 10.1093/bioinformatics/bty407

    Pango Network. New AY lineages. Retrieved 24 August 2021, from: https://www.pango.network/new-ay-lineages/

    Rambaut A., Holmes E., O’Toole Á., Hill V., McCrone J., Ruis C. et al. (2020). A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nature Microbiology, 5(11), 1403-1407. doi: 10.1038/s41564-020-0770-5

    Annexe

    SARS-CoV-2 variants naming

    The ReViLux continues to use the Pango nomenclature, in addition to the WHO nomenclature, to allow easier visualization of links between any evolving variants and their ancestor. Equivalence for VOC are shown in Table A1 (adapted from WHO).

     

     

  • Semaine 31

    Respiratory Viruses in Luxembourg (ReViLux)

    Weekly report (2 – 8 August 2021)

    Executive Summary

    The Sentinel Surveillance Network identified one case of influenza-like illness, which reaches the threshold that is applicable to the interepidemic season, according to the European Center for Disease Prevention and Control (ECDC) guidelines.

    Regarding SARS-CoV-2 genomic surveillance, the Laboratoire national de santé analysed 221 specimens in week 31/2021 (from 404 total cases in the Grand Duchy of Luxembourg, 54,7%), including 180 non-targeted specimens (44,6%). This exceeds the minimum coverage (10%) but does not reach the minimum sample size (242) recommended by the ECDC.

    Community surveillance showed that Delta variant continues to be the dominant one in Luxembourg (94,4%), with low presence of the Gamma (4,4%) and other variants (1,1%).

    In respect to target group surveillance, all cases analysed were identified as VOC cases and 16 post-vaccination breakthrough cases were identified as VOCs.

    Introduction

    The Laboratoire national de santé, as National Reference Laboratory for Acute Respiratory Infections in Luxembourg, performs close surveillance on respiratory viruses, with a special focus on SARS-CoV-2. There are currently three active projects:

    The Sentinel Surveillance Network. It provides a broad picture of respiratory diseases affecting the Luxembourgish population, based on its double monitoring system (syndromic and virological).

    The National SARS-COV-2 Genomic Surveillance Program. It enables detailed observation of SARS-CoV-2 mutations and variants through time and space, and also monitoring specific groups of interest.

    The COVVAC Serology Project. It assesses the post-vaccination serological status in long-term care facilities and its evolution over time.

    The ReViLux provides updates on the first two projects.

    Sentinel Surveillance Network

    The Sentinel Surveillance Network aims at monitoring the circulating respiratory viruses, including SARS-CoV-2, and hence underpin public health actions. Following the World Health Organization (WHO) and European Centre for Disease Prevention and Control (ECDC) guidance, it focuses on cases of acute respiratory infection (ARI) and influenza-like illness (ILI).

    Results of syndromic surveillance during week 31 (02 August 2021 – 08 August 2021) are displayed in Table 1 and the history of ILI consultations since the 2018-2019 season is shown in Figure 1. Only 1 case of ILI was identified, but as the number of consultations dropped to 87, the proportion of ILI cases in week 31 exceeds the threshold for the interepidemic season (1,14%) according to the ECDC. A close look will be kept at the evolution of ILI cases next week.

    Regarding the virological surveillance, no data is available for week 31.

    SARS-CoV-2 Genomic Surveillance

    The current sequencing strategy

    The National Reference Laboratory for Acute Respiratory Infections at LNS receives SARS-CoV-2 -positive samples for (nasopharyngeal or oropharyngeal swabs analysed by RT-PCR) from the national network of laboratories and proceeds as follows:

    Sequencing all specimens from hospitalized cases.

    Sequencing all specimens from reinfection and post-vaccination cases.

    Sequencing all specimens from cluster cases.

    Sequencing a sample of community cases.

    The sample of community cases is a selection from all cases to detect emerging SARS-CoV-2 variants and early increases in their incidence and transmission within the community in Luxembourg. This sample is selected according to the ECDC guidelines.

    In week 31, 404 new cases were registered in Luxembourg; hence, the minimum sample size required to detect a 2.5% incidence is estimated to be 242 specimens (59,9%). The number of non-targeted specimens from Luxembourgish residents, successfully sequenced this week was 180 (44,6%), which exceeds the minimum coverage (10%) but does not reach the minimum sample size (242) recommended by ECDC.

    The LNS shares its sequencing results with GISAID EpiCov database (www.gisaid.org) periodically. SARS-CoV-2 lineages (variants) have been assigned based on Rambaut et al. using Phylogenetic Assignment of Named Global Outbreak LINeages (pangolin) software  (v3.1.10, pangoLEARN 2021-07-28). The ReViLux continues to use the Pango nomenclature, in addition to the WHO nomenclature, to allow easier visualization of links between any evolving variants and their ancestor (https://cov-lineages.org). See nomenclature equivalences in Annex 1.

    Sequenced specimens

    Last week, the microbial genomics platform at the LNS sequenced 252 specimens, with 248 having been collected in week 31/2021. Among the latter, 61 specimens were reported to be part of a cluster or non-residents. The number of non-targeted specimens from Luxembourgish residents successfully sequenced this week was 180 (44,6% coverage of 404 total cases) (see coverage trend in Figure 2).

    Circulating lineage detection

    The evolution of variants over the weeks is shown in Figure 3.

    In week 31/2021, 5 circulating SARS-CoV-2 variants were detected within our population sequencing pool, after removal of cluster specimens, and excluding specimens collected from non-residents, as shown in Figure 4. The most prevalent lineages are displayed in Table 2 and information about the lineages is provided in Annex 2.

    Mutation surveillance

    In addition to the surveillance of SARS-CoV-2 variants by whole genome sequencing, the LNS monitors the occurrence of SARS-CoV-2 mutations assumed to have a clinical and epidemiological relevance. Currently, 13 mutations are being observed, and this list is updated continually.

    Table 3 provides the overall frequencies of these mutations, detected in the lineage-assignable genome sequences, analyzed since 1 Sep 2020 (N=16679), as well as the frequencies in week 31/2021.

    References

    COVID-19 Data Portal – accelerating scientific research through data. (2021). Retrieved 2 August 2021, from https://www.covid19dataportal.org/sequences

    European Centre for Disease Prevention and Control. Guidance for representative and targeted genomic SARS-CoV-2 monitoring – 3 May 2021. ECDC : Stockholm ; 2021

    Genomic sequencing of SARS-CoV-2: a guide to implementation for maximum impact on public health. Geneva: World Health Organization; 2021.

    GitHub – cov-lineages/pangolin: Software package for assigning SARS-CoV-2 genome sequences to global lineages. (2021). Retrieved 2 August 2021, from https://github.com/cov-lineages/pangolin

    Hadfield J., Megill C., Bell S., Huddleston J., Potter B., Callender C. et al. (2018). Nextstrain: real-time tracking of pathogen evolution. Bioinformatics, 34(23), 4121-4123. doi: 10.1093/bioinformatics/bty407

    Rambaut A., Holmes E., O’Toole Á., Hill V., McCrone J., Ruis C. et al. (2020). A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nature Microbiology, 5(11), 1403-1407. doi: 10.1038/s41564-020-0770-5

    Annexes

    Annex 1. SARS-CoV-2 variants naming

    The ReViLux continues to use the (Pango) system to allow easier visualisation of links between any evolving variants and their ancestor. Equivalence for most frequently used VOC nomenclatures are shown in Table A1 (adapted from WHO).

    Annex 2. Summary of evidence regarding the most frequently detected variants in the Great Duchy of Luxembourg

    Lineage B.1.1.7 is characterized by several spike protein mutations, including N501Y, H69/V70del and P861H. The variant seems to have a considerable epidemiological impact, as it has a higher transmissibility rate.

    Lineage B.1.351 holds numerous spike protein mutations, of which three are located in the receptor binding domain (K417N, E484K and N501Y), and are therefore relevant for antibody binding. As for B.1.1.7, a higher transmissibility rate and viral loads seem to be associated with this variant. Due to the K417N and E484K mutations, an impact on vaccination efficacy and possibility of reinfection is subject to scientific investigation.

    Lineage P.1 (descendent of B.1.1.28), initially found in the Amazon region, has a similar mutation profile as the South African variant, including E484K and N501Y. Concerns are, as for the South African variant, higher transmissibility and a decreased protection by neutralizing antibodies.

    Lineage B.1.525 carries several mutations of biological significance, including E484K, Q677H and F888L. It does not carry N501Y, but a set of deletions similar to the B.1.1.7 variant.

    Lineage B.1.617 is a variant first detected in India and was designated “Under Investigation” on 1st  April 2021 by Public Health England. It contains a number of spike mutations associated with antigenic escape or found in other variants of concern, including L452R, E484Q and P681R. Subtype B.1.617.2 does not carry S:E484Q and seems to be more transmissible than B.1.1.7 (increasing confidence). Neutralization studies show reductions in cross-neutralizing activity between B.1.1.7 and B.1.351.

  • Semaine 30

    Respiratory Viruses in Luxembourg (ReViLux)

    Weekly report (Period 26/07/-01/08/2021)

    Executive Summary

    The Sentinel Surveillance Network identified no cases of influenza-like illness, thus Luxembourg remains below the recommended threshold for the interepidemic season, according to the European Center for Disease Prevention and Control (ECDC) guidelines.

    Regarding SARS-CoV-2 genomic surveillance, the Laboratoire national de santé analysed 266 Luxembourgish specimens in week 30/2021 (from 439 total cases in the Grand Duchy of Luxembourg, 60,6%), including 226 non-targeted specimens (51,5%), which exceeds the minimum coverage (10%) but does not reach the minimum sample size recommended by ECDC (which is 254 in our current epidemiological situation).

    Community surveillance revealed a decrease in all VOC cases, including Delta variant; yet, this remains the dominant one in Luxembourg (81%). The other two variants are the Gamma (18,1%) and Alpha (0,9%) ones.

    In respect to target group surveillance, all cases analysed were identified as VOC cases, and 9 post-vaccination breakthrough cases were identified as VOCs.

    Introduction

    The Laboratoire national de santé, as National Reference Laboratory for Acute Respiratory Infections in Luxembourg, performs close surveillance on respiratory viruses, with a special focus on SARS-CoV-2. There are currently three active projects:

    The Sentinel Surveillance Network. It provides a broad picture of respiratory diseases affecting the Luxembourgish population, based on its double monitoring system (syndromic and virological).

    The National SARS-COV-2 Genomic Surveillance Program. It enables detailed observation of SARS-CoV-2 mutations and variants through time and space, and also monitoring specific groups of interest.

    The COVVAC Serology Project. It assesses the post-vaccination serological status in long-term care facilities and its evolution over time.

    The ReViLux provides updates on the first two projects.

    Sentinel Surveillance Network

    The Sentinel Surveillance Network aims at monitoring the circulating respiratory viruses, including SARS-CoV-2, and hence underpin public health actions. Following the World Health Organization (WHO) and European Centre for Disease Prevention and Control (ECDC) guidance, it focuses on cases of acute respiratory infection (ARI) and influenza-like illness (ILI).

    Results of syndromic surveillance during week 30 (26 July 2021 – 1 August 2021) are displayed in Table 1 and the history of ILI consultations since the 2018-2019 season is shown in Figure 1. No cases of ILI were detected during week 30.

    Regarding the virological surveillance, no data is available for week 30.

    SARS-CoV-2 Genomic Surveillance

    The current sequencing strategy

    The National Reference Laboratory for Acute Respiratory Infections at LNS receives SARS-CoV-2 -positive samples (nasopharyngeal or oropharyngeal swabs, analysed by RT-PCR) from the national network of laboratories and proceeds as follows:

    • Sequencing all specimens from hospitalized cases.
    • Sequencing all specimens from reinfection and post-vaccination cases.
    • Sequencing all specimens from cluster cases.
    • Sequencing a sample of community cases.

    The sample of community cases is a selection from all cases to detect emerging SARS-CoV-2 variants and early increases in their incidence and transmission within the community in Luxembourg. This sample is selected according to the ECDC guidelines.

    In week 30, 439 new cases were registered in Luxembourg; hence, the minimum sample size required to detect a 2.5% incidence is estimated to be 254 specimens (57,9%). The number of non-targeted specimens from Luxembourgish residents, successfully sequenced this week was 226 (51,5%), which exceeds the minimum coverage (10%) but does not reach the minimum sample size (254) recommended by ECDC.

    The LNS shares its sequencing results with GISAID EpiCov database (www.gisaid.org) periodically. SARS-CoV-2 lineages (variants) have been assigned based on Rambaut et al. using Phylogenetic Assignment of Named Global Outbreak LINeages (pangolin) software  (v3.1.7, pangoLEARN version 2021-07-09). The ReViLux continues to use the Pango nomenclature, in addition to the WHO nomenclature, to allow easier visualization of links between any evolving variants and their ancestor (https://cov-lineages.org). See nomenclature equivalences in Annex 1.

    Sequenced specimens

    Last week, the microbial genomics platform at the LNS sequenced 314 specimens, with 284 having been collected in week 30/2021. Among the latter, 49 specimens were reported to be part of a cluster or vaccine failure investigation, and 18 specimens were from non-residents (9 specimens overlapping). The number of non-targeted specimens from Luxembourgish residents successfully sequenced this week was 226 (51,5% coverage of 439 total cases) (see coverage trend in Figure 2).

    Circulating lineage detection

    The evolution of variants over the weeks is shown in Figure 3. The number of cases decreased for all VOCs, but Delta variant remains the dominant one.

    In week 30/2021, 3 circulating SARS-CoV-2 variants were detected within our population sequencing pool, after removal of cluster specimens, and excluding specimens collected from non-residents, as shown in Figure 4. The most prevalent lineages are displayed in Table 2 and information about the lineages is provided in Annex 2.

    Mutation surveillance

    In addition to the surveillance of SARS-CoV-2 variants, the LNS monitors the occurrence of SARS-CoV-2 mutations assumed to have a clinical and epidemiological relevance. Currently, 13 mutations are being observed, and this list is updated continually.

    Table 3 provides the overall frequencies of these mutations, detected in the lineage-assignable genome sequences, analyzed between 1 Sep 2020 and 01 Aug 2021 (N=16423), as well as the frequencies in week 30/2021.

    References

    COVID-19 Data Portal – accelerating scientific research through data. (2021). Retrieved 2 August 2021, from https://www.covid19dataportal.org/sequences

    European Centre for Disease Prevention and Control. Guidance for representative and targeted genomic SARS-CoV-2 monitoring – 3 May 2021. ECDC : Stockholm ; 2021

    Genomic sequencing of SARS-CoV-2: a guide to implementation for maximum impact on public health. Geneva: World Health Organization; 2021.

    GitHub – cov-lineages/pangolin: Software package for assigning SARS-CoV-2 genome sequences to global lineages. (2021). Retrieved 2 August 2021, from https://github.com/cov-lineages/pangolin

    Hadfield J., Megill C., Bell S., Huddleston J., Potter B., Callender C. et al. (2018). Nextstrain: real-time tracking of pathogen evolution. Bioinformatics, 34(23), 4121-4123. doi: 10.1093/bioinformatics/bty407

    Rambaut A., Holmes E., O’Toole Á., Hill V., McCrone J., Ruis C. et al. (2020). A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nature Microbiology, 5(11), 1403-1407. doi: 10.1038/s41564-020-0770-5

    Annexes

    Annex 1. SARS-CoV-2 variants naming

    The ReViLux continues to use the (Pango) system to allow easier visualisation of links between any evolving variants and their ancestor. Equivalence for most frequently used VOC nomenclatures are shown in Table A1 (adapted from WHO).

    Annex 2. Summary of evidence regarding the most frequently detected variants in the Great Duchy of Luxembourg

    Lineage B.1.1.7 is characterized by several spike protein mutations, including N501Y, H69/V70del and P861H. The variant seems to have a considerable epidemiological impact, as it has a higher transmissibility rate.

    Lineage B.1.351 holds numerous spike protein mutations, of which three are located in the receptor binding domain (K417N, E484K and N501Y), and are therefore relevant for antibody binding. As for B.1.1.7, a higher transmissibility rate and viral loads seem to be associated with this variant. Due to the K417N and E484K mutations, an impact on vaccination efficacy and possibility of reinfection is subject to scientific investigation.

    Lineage P.1 (descendent of B.1.1.28), initially found in the Amazon region, has a similar mutation profile as the South African variant, including E484K and N501Y. Concerns are, as for the South African variant, higher transmissibility and a decreased protection by neutralizing antibodies.

    Lineage B.1.525 carries several mutations of biological significance, including E484K, Q677H and F888L. It does not carry N501Y, but a set of deletions similar to the B.1.1.7 variant.

    Lineage B.1.617 is a variant first detected in India and was designated “Under Investigation” on 1st  April 2021 by Public Health England. It contains a number of spike mutations associated with antigenic escape or found in other variants of concern, including L452R, E484Q and P681R. Subtype B.1.617.2 does not carry S:E484Q and seems to be more transmissible than B.1.1.7 (increasing confidence). Neutralization studies show reductions in cross-neutralizing activity between B.1.1.7 and B.1.351.

     

  • Semaine 29

    Respiratory Viruses in Luxembourg (ReViLux)

    Weekly report (Period 19/07/-25/07/2021)

    Executive Summary

    The Sentinel Surveillance Network identified no cases of influenza-like illness, thus remaining below the recommended threshold for the interepidemic season, according to the European Center for Disease Prevention and Control (ECDC) guidelines.

    Regarding SARS-CoV-2 genomic surveillance, the Laboratoire national de santé analysed 356 specimens in week 29/2021 (from 566 total cases in the Grand Duchy of Luxembourg, 62,9%). This exceeds the minimum coverage (10%) and sample size recommended by the ECDC (which is 292 in our current epidemiological situation).

    Community surveillance revealed a sharp fall of Gamma cases (-65,0% compared to week 28) and a mild increase of Delta variant cases, which remains on an increasing trend since week 24. Currently, the Delta variant continues to be the dominant variant in Luxembourg.

    In respect to target group surveillance, all cases analysed were identified as VOC cases, and 13 post-vaccination breakthrough cases were identified as VOCs.

    Introduction

    The Laboratoire national de santé, as National Reference Laboratory for Acute Respiratory Infections in Luxembourg, performs close surveillance on respiratory viruses, with a special focus on SARS-CoV-2. There are currently three active projects:

    The Sentinel Surveillance Network. It provides a broad picture of respiratory diseases affecting the Luxembourgish population, based on its double monitoring system (syndromic and virological).

    The National SARS-COV-2 Genomic Surveillance Program. It enables detailed observation of SARS-CoV-2 mutations and variants through time and space, and also monitoring specific groups of interest.

    The COVVAC Serology Project. It assesses the post-vaccination serological status in long-term care facilities and its evolution over time.

    The ReViLux provides updates on the first two projects.

    Sentinel Surveillance Network

    The Sentinel Surveillance Network aims at monitoring the circulating respiratory viruses, including SARS-CoV-2, and hence underpin public health actions. Following the World Health Organization (WHO) and European Centre for Disease Prevention and Control (ECDC) guidance, it focuses on cases of acute respiratory infection (ARI) and influenza-like illness (ILI).

    Results of syndromic surveillance during week 29 (19 July 2021 – 25 July 2021) are displayed in Table 1 and the history of ILI consultations since the 2018-2019 season is shown in Figure 1. The percentage of ILI remains below the threshold for the interepidemic season, according to the ECDC.

    Regarding the virological surveillance, no data is available for week 29.

    SARS-CoV-2 Genomic Surveillance

    The current sequencing strategy

    The National Reference Laboratory for Acute Respiratory Infections at LNS receives SARS-CoV-2 -positive samples for (nasopharyngeal or oropharyngeal swabs analysed by RT-PCR) from the national network of laboratories and proceeds as follows:

    • Sequencing all specimens from hospitalized cases.
    • Sequencing all specimens from reinfection and post-vaccination cases.
    • Sequencing all specimens from cluster cases.
    • Sequencing a representative sample of community cases.

    The representative sample of community cases is a selection from all cases to detect emerging SARS-CoV-2 variants and early increases in their incidence and transmission within the community in Luxembourg. This sample is selected according to the ECDC guidelines.

    In week 29, 566 new cases were registered in Luxembourg; hence, the minimum sample size required to detect a 2.5% incidence is estimated to be 292 specimens (51,6%). The number of non-targeted specimens from Luxembourgish residents successfully sequenced this week was 297 (52,5%), which exceeds the minimum coverage (10%) and minimum sample size (292) recommended by ECDC.

    The LNS shares its sequencing results with GISAID EpiCov database (www.gisaid.org) periodically. SARS-CoV-2 lineages (variants) have been assigned based on Rambaut et al. using Phylogenetic Assignment of Named Global Outbreak LINeages (pangolin) software  (v3.1.7, pangoLEARN version 2021-07-09). The ReViLux continues to use the Pango nomenclature, in addition to the WHO nomenclature, to allow easier visualization of links between any evolving variants and their ancestor (https://cov-lineages.org). See nomenclature equivalences in Annex 1.

    Sequenced specimens

    Last week, the microbial genomics platform at the LNS sequenced 588 specimens, with 391 having been collected in week 29/2021. Among the latter, 74 specimens were reported to be part of a cluster or vaccine failure investigation, and 35 specimens were from non-residents (15 specimens overlapping). The number of non-targeted specimens from Luxembourgish residents successfully sequenced this week was 297 (52,5% coverage of 566 total cases) (see coverage trend in Figure 2).

    Circulating lineage detection

    The evolution of variants over the weeks is shown in Figure 3. Delta variant showed a constant increase, in absolute values, during the last seven weeks, and remains the dominant variant.

    In week 29/2021, 4 circulating SARS-CoV-2 variants were detected within our representative sequencing pool, after removal of cluster specimens, and excluding specimens collected from non-residents, as shown in Figure 4. The most prevalent lineages are displayed in Table 2 and information about the lineages is provided in Annex 2.

    Mutation surveillance

    In addition to the surveillance of SARS-CoV-2 variants, the LNS monitors the occurrence of SARS-CoV-2 mutations assumed to have a clinical and epidemiological relevance. Currently, 13 mutations are being observed, and this list is updated continually.

    Table 3 provides the overall frequencies of these mutations, detected in the lineage-assignable genome sequences, analyzed between 1 Sep 2020 and 25 Jul 2021 (N=16080), as well as the frequencies in week 29/2021.

    References

    COVID-19 Data Portal – accelerating scientific research through data. (2021). Retrieved 2 August 2021, from https://www.covid19dataportal.org/sequences

    European Centre for Disease Prevention and Control. Guidance for representative and targeted genomic SARS-CoV-2 monitoring – 3 May 2021. ECDC : Stockholm ; 2021

    Genomic sequencing of SARS-CoV-2: a guide to implementation for maximum impact on public health. Geneva: World Health Organization; 2021.

    GitHub – cov-lineages/pangolin: Software package for assigning SARS-CoV-2 genome sequences to global lineages. (2021). Retrieved 2 August 2021, from https://github.com/cov-lineages/pangolin

    Hadfield, J., Megill, C., Bell, S., Huddleston, J., Potter, B., & Callender, C. et al. (2018). Nextstrain: real-time tracking of pathogen evolution. Bioinformatics, 34(23), 4121-4123. doi: 10.1093/bioinformatics/bty407

    Rambaut A., Holmes E., O’Toole Á., Hill V., McCrone J., Ruis C. et al. (2020). A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nature Microbiology, 5(11), 1403-1407. doi: 10.1038/s41564-020-0770-5

    Annexes

    Annex 1. SARS-CoV-2 variants naming

    The ReViLux continues to use the (Pango) system to allow easier visualisation of links between any evolving variants and their ancestor. Equivalence for most frequently used VOC nomenclatures are shown in Table A1 (adapted from WHO).

    Annex 2. Summary of evidence regarding the most frequently detected variants in the Great Duchy of Luxembourg

    Lineage B.1.1.7 is characterized by several spike protein mutations, including N501Y, H69/V70del and P861H. The variant seems to have a considerable epidemiological impact, as it has a higher transmissibility rate.

    Lineage B.1.351 holds numerous spike protein mutations, of which three are located in the receptor binding domain (K417N, E484K and N501Y), and are therefore relevant for antibody binding. As for B.1.1.7, a higher transmissibility rate and viral loads seem to be associated with this variant. Due to the K417N and E484K mutations, an impact on vaccination efficacy and possibility of reinfection is subject to scientific investigation.

    Lineage P.1 (descendent of B.1.1.28), initially found in the Amazon region, has a similar mutation profile as the South African variant, including E484K and N501Y. Concerns are, as for the South African variant, higher transmissibility and a decreased protection by neutralizing antibodies.

    Lineage B.1.525 carries several mutations of biological significance, including E484K, Q677H and F888L. It does not carry N501Y, but a set of deletions similar to the B.1.1.7 variant.

    Lineage B.1.617 is a variant first detected in India and was designated “Under Investigation” on 1st  April 2021 by Public Health England. It contains a number of spike mutations associated with antigenic escape or found in other variants of concern, including L452R, E484Q and P681R. Subtype B.1.617.2 does not carry S:E484Q and seems to be more transmissible than B.1.1.7 (increasing confidence). Neutralization studies show reductions in cross-neutralizing activity between B.1.1.7 and B.1.351.

  • Semaine 28

    Respiratory Viruses in Luxembourg (ReViLux)

    Weekly report (Period 12/07/-18/07/2021)

    Executive Summary

    The Sentinel Surveillance Network identified 2 cases of influenza-like illnesses, which remains below the recommended threshold for the interepidemic season, according to the European Center for Disease Prevention and Control (ECDC) guidelines.

    Regarding SARS-CoV-2 genomic surveillance, the Laboratoire national de santé analysed 454 specimens in week 28/2021 (from 727 total cases in the Great Duchy of Luxembourg, 62,4%). This exceeds the minimum coverage (10%) and sample size recommended by the ECDC (which is 45,3% in our current epidemiological situation).

    Community case surveillance revealed an increase of Delta variant cases, which have been on an increasing trend over the last five weeks. Currently, the Delta variant remains the dominant variant in Luxembourg.

    Target group surveillance showed 49 VOCs within hospitalized cases (51,0% Delta and 46,9% Gamma) and all cluster cases were linked to VOCs (80,6% Delta, 19,4% Gamma). Additionally, 14 reinfection or post-vaccination breakthrough cases linked to VOCs were identified.

    Introduction

    The Laboratoire national de santé, as National Reference Laboratory for Acute Respiratory Infections in Luxembourg, performs close surveillance on respiratory viruses, with a special focus on SARS-CoV-2. There are currently three projects:

    • The Sentinel Surveillance Network. It provides a broad picture of respiratory diseases affecting the Luxembourgish population, based on its double monitoring system (syndromic and virological).
    • The National SARS-COV-2 Genomic Surveillance Program. It enables dynamic detailed observation of SARS-CoV-2 mutations and variants, but also monitoring specific groups of interest.
    • The COVVAC Serology Project. It assesses the post-vaccination serological status in Long-term care facilities and its evolution over time.

    The ReViLux provides updates on the first two projects.

    Sentinel Surveillance Network

    The Sentinel Surveillance Network aims at monitoring the circulating respiratory viruses, including SARS-CoV-2, and hence underpin public health actions. Following the WHO[1] and ECDC[2] guidance, it focuses on cases of acute respiratory infection (ARI) and influenza-like illness (ILI).

    Results of syndromic surveillance during week 28 (12 July 2021 – 18 July 2021) are displayed in Table 1 and the history of ILI consultations since the 2018-2019 season is shown in Figure 1. The percentage of ILI remains below the threshold for the interepidemic season, according to the ECDC.

    Regarding the virological surveillance, no data is available for week 28.

    [1] World Health Organization

    [2] European Centre for Disease Prevention and Control

     

    SARS-CoV-2 Genomic Surveillance

    The current sequencing strategy

    The National Reference Laboratory for Acute Respiratory Infections at LNS receives SARS-CoV-2 -positive samples for (nasopharyngeal or oropharyngeal swabs analysed by RT-PCR) from the national network of laboratories and proceeds as follows:

    1. Sequencing all specimens from hospitalized cases.
    2. Sequencing all specimens from reinfection and post-vaccination cases.
    3. Sequencing all specimens from cluster cases.
    4. Sequencing a representative sample of community cases.

    The representative sample of community cases is a selection from all cases to detect emerging SARS-CoV-2 variants and early increases in their incidence and transmission within the community in Luxembourg. This sample is selected according to ECDC guidelines.

    In week 28, 727 new cases were registered in Luxembourg; hence, the minimum sample size required to detect a 2.5% incidence is estimated to be 329 specimens (45,3%). The number of non-targeted specimens from Luxembourgish residents successfully sequenced this week was 425 (58,5%), which exceeds the minimum coverage (10%) and minimum sample size (329) recommended by ECDC.

    The LNS shares its sequencing results with GISAID EpiCov database (www.gisaid.org) periodically. SARS-CoV-2 lineages (variants) have been assigned based on Rambaut et al. using Phylogenetic Assignment of Named Global Outbreak LINeages (pangolin) software  (v3.1.5, pangoLEARN version 2021-06-15). The ReViLux continues to use the Pango nomenclature, in addition to the WHO nomenclature, to allow easier visualization of links between any evolving variants and their ancestor (https://cov-lineages.org). See nomenclature equivalences in Annex 1.

    Sequenced specimens

    Last week, the microbial genomics platform at the LNS sequenced 559 specimens, with 475 having been collected in week 28/2021. Among the latter, 31 specimens were reported to be part of a cluster or vaccine failure investigation, and 21 specimens were from non-residents (2 specimens overlapping). The number of non-targeted specimens from Luxembourgish residents successfully sequenced this week was 425 (58,5% coverage of 727 total cases) (see coverage trend in Figure 2).

    Circulating lineage detection

    The evolution of variants over the weeks is shown in Figure 3. Delta variant showed a constant increase, in absolute values, during the last five weeks, and has become again the dominant variant.

    In week 28/2021, 5 circulating SARS-CoV-2 variants were detected within our representative sequencing pool, after removal of cluster specimens, and excluding specimens collected from non-residents, as shown in Figure 4. The most prevalent lineages are displayed in Table 2 and information about the lineages is provided in Annex 2.

     

     

    Mutation surveillance

    In addition to the surveillance of SARS-CoV-2 variants, the LNS monitors the occurrence of SARS-CoV-2 mutations assumed to have a clinical and epidemiological relevance. Currently, 13 mutations are being observed, and this list is updated continually.

    Table 3 provides the overall frequencies of these mutations, detected in the lineage-assignable genome sequences, analyzed between 1 Sep 2020 and 11 Jul 2021 (N=14977), as well as the frequencies in week 28/2021.

    References

    COVID-19 Data Portal – accelerating scientific research through data. (2021). Retrieved 21 July 2021, from https://www.covid19dataportal.org/sequences

    European Centre for Disease Prevention and Control. Guidance for representative and targeted genomic SARS-CoV-2 monitoring – 3 May 2021. ECDC : Stockholm ; 2021

    Genomic sequencing of SARS-CoV-2: a guide to implementation for maximum impact on public health. Geneva: World Health Organization; 2021.

    GitHub – cov-lineages/pangolin: Software package for assigning SARS-CoV-2 genome sequences to global lineages. (2021). Retrieved 21 July 2021, from https://github.com/cov-lineages/pangolin

    Hadfield, J., Megill, C., Bell, S., Huddleston, J., Potter, B., & Callender, C. et al. (2018). Nextstrain: real-time tracking of pathogen evolution. Bioinformatics, 34(23), 4121-4123. doi: 10.1093/bioinformatics/bty407

    Instituto Nacional de Saúde Doutor Ricardo Jorge. Diversidade genética do novo coronavírus SARS-CoV-2 (COVID-19) em Portugal. Retrieved 26 July 2021, from https://insaflu.insa.pt/covid19/

    Rambaut, A., Holmes, E., O’Toole, Á., Hill, V., McCrone, J., & Ruis, C. et al. (2020). A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nature Microbiology, 5(11), 1403-1407. doi: 10.1038/s41564-020-0770-5

    Robert Koch Institut. Aktueller Lage-/Situationsbericht des RKI zu COVID-19. Retrieved 26 July 2021, from https://www.rki.de/DE/Content/InfAZ/N/Neuartiges_Coronavirus/Situationsberichte/Gesamt.html;jsessionid=69BC18053F9591C56EB148E463103DB7.internet101

    Santé publique France. Enquêtes Flash : évaluation de la circulation des variants du SARS-CoV-2 en France. Retrieved 26 July 2021, from https://www.santepubliquefrance.fr/etudes-et-enquetes/enquetes-flash-evaluation-de-la-circulation-des-variants-du-sars-cov-2-en-france

    Sciensano. COVID-19 – Bulletin épidémiologique hebdomadaire (23 juillet 2021). Retrieved 26 July 2021, from https://covid-19.sciensano.be/fr/covid-19-situation-epidemiologique

    Annexes

    Annex 1. SARS-CoV-2 variants naming

    The ReViLux continues to use the (Pango) system to allow easier visualisation of links between any evolving variants and their ancestor. Equivalence for most frequently used VOC nomenclatures are shown in Table A1 (adapted from WHO).

     

    Annex 2. Summary of information regarding the most frequently detected variants in the Great Duchy of Luxembourg

    Lineage B.1.1.7 is characterized by several spike protein mutations, including N501Y, H69/V70del and P861H. The variant seems to have a considerable epidemiological impact, as it has a higher transmissibility rate.

    Lineage B.1.351 holds numerous spike protein mutations, of which three are located in the receptor binding domain (K417N, E484K and N501Y), and are therefore relevant for antibody binding. As for B.1.1.7, a higher transmissibility rate and viral loads seem to be associated with this variant. Due to the K417N and E484K mutations, an impact on vaccination efficacy and possibility of reinfection is subject to scientific investigation.

    Lineage P.1 (descendent of B.1.1.28), initially found in the Amazon region, has a similar mutation profile as the South African variant, including E484K and N501Y. Concerns are, as for the South African variant, higher transmissibility and a decreased protection by neutralizing antibodies.

    Lineage B.1.525 carries several mutations of biological significance, including E484K, Q677H and F888L. It does not carry N501Y, but a set of deletions similar to the B.1.1.7 variant.

    Lineage B.1.617 is a variant first detected in India and was designated “Under Investigation” on 1st  April 2021 by Public Health England. It contains a number of spike mutations associated with antigenic escape or found in other variants of concern, including L452R, E484Q and P681R. Subtype B.1.617.2 does not carry S:E484Q and seems to be more transmissible than B.1.1.7 (increasing confidence). Neutralization studies show reductions in cross-neutralizing activity between B.1.1.7 and B.1.351.

     

  • Semaine 27

    Respiratory Viruses in Luxembourg (ReViLux)

    Weekly report (Period 05/07/-11/07/2021)

    Executive Summary

    The aim of the “Sentinel” national surveillance program is to monitor the circulating respiratory viruses, including SARS-CoV-2 variants, and hence underpin public health actions.

    In week 27/2021, the variant P.1 (Gamma) remains the dominant one with an overall frequency of 60% (CI 56% – 64%, p<0,05) in all sequenced specimens, followed by the B.1.617.2 (Delta) variant with 34,8% (CI 30,9% – 38,7%, p<0,05) and the B.1.1.7 (Alpha) variant with 4,1% (CI 2,5% – 5,7%, p<0,05).

    The representative sample size was estimated, based on the number of positive cases in Luxembourg for week 27 (828). The minimum sample size required to detect prevalence of P.1 (71,5%) reported in week 26, with an error margin of 5%, was estimated to be 228 specimens. This number corresponds to a coverage of 27,5%, which exceeds the minimum coverage recommended by ECDC (10%). The sequencing results of week 24 are not representative of the circulating variants in Luxembourg with an error margin of 5%.

    The total number of sequences performed this week was 682, with 580 specimens having been collected in the time frame of week 27/2021. The sequencing coverage – based on sequenced samples collected in week 27 and corresponding to Luxembourg residents – was 67,3% of all positive cases in Luxembourg.

    Clinical Surveillance

    The “Sentinel” surveillance network reported 293 consultations in week 27 (05/JULY/2021 – 11/JULY/2021). Four cases of ILI1 have been reported, which is 1,4% of consultantions, as shown in Figure 1. The number of consultations for ARI2 was 30, which represents 10,2%.

    SARS-CoV-2 Genomic Surveillance

    The current sequencing strategy

    The National Reference Laboratory for Acute Respiratory Infections at LNS continues to improve the representativeness of the pool of sequenced specimens to reach real-time epidemiology, by implementing the following weekly sequencing activities:

    -Sequencing specimens from all hospitalized positive cases
    -Sequencing specimens from all positive cases from Airport testing program
    -Sequencing specimens from all outbreaks and identified clusters
    -Systematic sequencing of specimens from reinfections and post-vaccination-infections
    -Population sequencing of specimens from representative regions and age groups, to follow the evolution of the different variants in the Luxembourg population.

    The representative sequencing sample was based on the minimum number of specimens required to extrapolate prevalence of VOC variants with error rate of 5%. The representative sample was estimated based on the number of positive cases in Luxembourg in week 27 (828). The minimum sample size required to detect prevalence of P.1 (71,5%) reported in week 26 with an error margin of 5% was estimated to be 228 specimens. The calculation was based on a sample size calculation tool that uses the expected prevalence of the variant in the total population. (Population Proportion – Sample Size – Select Statistical Consultants (select-statistics.co.uk). This number represented a coverage of 27,5%, which exceeds the minimum coverage recommended by ECDC (10%). The number of non-targeted specimens from Luxembourgish residents sequenced this week was 490. Therefore, our sequencing results this week are representative of the circulating variants in Luxembourg.

    The starting material used for sequencing is respiratory specimens (nasopharyngeal or oropharyngeal swabs) that have already been tested positive by RT PCR.

    The LNS sequencing data sharing strategy includes sharing of the sequencing data with GISAID EpiCov database (www.gisaid.org ) on a periodic basis.

    Sequenced specimens

    Last week the microbial genomics platform at the LNS sequenced 682 specimens, with 580 collected in week 27/2021. The sequencing pool referring to Luxembourgish residents represents 67,3% of new infections reported in Luxembourg in week 27/2021. Among these 580 specimens, 68 specimens were reported to be part of a cluster or vaccine failure investigation, and 23 specimens were from non-residents (1 specimen overlapping). This leads to 490 specimens, collected in week 27, and being a representative population sequencing sample. In the population representative sample of residents, the frequency for P.1 was 61%, while the frequency for B.1.617.2 and B.1.1.7, was 33,7% and 4,3% respectively.

    The population sequencing coverage in week 27/2021 was 59,2% (Figure 2). Based on statistical inference, the frequency of the reported variants in week 27/2021 is representative of the circulating variants in Luxembourg with a margin of error of 5%.

    Circulating lineage detection

    Lineages (variants) have been assigned based on Rambaut et al by means of Phylogenetic Assignment of Named Global Outbeak LINeages (pangolin) software  (v3.1.5, pangoLEARN version 2021-06-15).

    The lineage nomenclature system that we use is the one proposed by Rambaut et al. that focuses on actively circulating virus lineages (https://cov-lineages.org ).

    In week 27/2021, in the population representative sample, after removal of cluster samples, and excluding specimens collected from non-residents, there were 8 circulating SARS-CoV-2 variants, with the main three variants being the P.1 (61%, CI 56,7% – 65,3%), B.1.617.2 (33,7%, CI 29,5% – 37,9%) and B.1.1.7 (4,3%, CI 2,5% – 6,1%) as shown in Figure 3.

    Variants of Concern tracker (B.1.1.7, B.1.351, P.1, B.1.525, B.1.617.2)

    In week 27/2021, 348 new cases (60%) of the Gamma (P.1) variant have been detected (by comparison, the week 26/2021 pool had shown 71,5% of this variant). The total case count of sequenced Gamma variant was 887 by week 27/2021.

    In week 27/2021, 202 additional cases (34,8%) of the Delta variant B.1.617.2 have been detected (by comparison, the week 26/2021 pool had shown a frequency of 26,4% of this variant). The case count by week 27 for B.1.617.2 rose to 627.

    Among specimens collected within the week 27/2021, 24 cases of the Alpha (B.1.1.7) variant have been detected, representing 4,1% of the specimens in the week’s sequencing pool (by comparison, the week 26/2021 pool had shown a frequency of 1,1% of this variant). The total case count of sequenced variant Alpha was 6952 by week 27/2021.

    In the collection period of week 27/2021, 1 case of the Beta (B.1.351) variant has been detected, representing 0,2% (by comparison, the week 26/2021 pool had shown 0,4% of this variant). The total case count of sequenced variant B.1.351 was 1196 by week 27/2021.

    In week 27/2021, no new case of B.1.525 has been detected. The case count by week 27 for B.1.525 remains 50 (Figure 4).

    Lineage B.1.1.7 is characterized by several spike protein mutations, including N501Y, H69/V70del and P861H. The variant seems to have a considerable epidemiological impact, as it has a higher transmissibility rate.

    Lineage B.1.351 holds numerous spike protein mutations, of which three are located in the receptor binding domain (K417N, E484K and N501Y), and are therefore relevant for antibody binding. As for B.1.1.7, a higher transmissibility rate and viral loads seem to be associated with this variant. Due to the K417N and E484K mutations, an impact on vaccination efficacy and possibility of reinfection is subject to scientific investigation.

    Lineage P.1 (descendent of B.1.1.28), initially found in the Amazon region, has a similar mutation profile as the South African variant, including E484K and N501Y. Concerns are, as for the South African variant, higher transmissibility and a decreased protection by neutralizing antibodies.

    Lineage B.1.525 carries several mutations of biological significance, including E484K, Q677H and F888L. It does not carry N501Y, but a set of deletions similar to the B.1.1.7 variant.

    Lineage B.1.617 is a variant first detected in India and was designated “Under Investigation” on 1st  April 2021 by Public Health England. It contains a number of spike mutations associated with antigenic escape or found in other variants of concern, including L452R, E484Q and P681R. Subtype B.1.617.2 does not carry S:E484Q and seems to be more transmissible than B.1.1.7 (increasing confidence). Neutralization studies show reductions in cross-neutralizing activity between B.1.1.7 and B.1.351.

    WHO nomeculature to track VOC

    The ReViLux will continue to use the (Pango) system to allow easier visualisation of links between any evolving variants and their ancestor (Figure 5).

    Clinically relevant mutations

    Currently the LNS genomic surveillance program – independently from lineage calling – notes the occurrence of 13 different known SARS-CoV-2 mutations, assumed to have clinical and epidemiological relevance. The list of observed mutations is being updated continually, based on the appearance and prevalence of SARS-CoV-2 variants.

    The following table provides the overall frequencies of these mutations, detected in the lineage-assignable genome sequences, analyzed between 01/SEP/2020 and 11/JULY/2021 (N=14977), as well as the frequencies in week 27/2021.

    References

    Genomic sequencing of SARS-CoV-2. A guide to implementation for maximum impact on public health. WHO, 8 January 2021.

    COVID-19 data portal. 2020 (https://www.covid19dataportal.org/sequences )

    J Hadfield et al. Nextstrain: real-time tracking of pathogen evolution. Bioinformatics 2018;34:4121-4123

    A Rambaut et al. A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nat Microbiol 2020;5:1403-1407

    https://github.com/cov-lineages/pangolin

    For more information on lineages visit: https://cov-lineages.org
    For more information and statistics on Covid-19 infections in Luxembourg visit: https://covid19.public.lu/en.html

  • Semaine 26

    Respiratory Viruses in Luxembourg (ReViLux)

    Weekly report (Period 28/06/-04/07/2021)

    Executive Summary

    The aim of the “Sentinel” national surveillance program is to monitor the circulating respiratory viruses, including SARS-CoV-2 variants, and hence underpin public health actions.

    In week 26/2021, the variant P.1 (Gamma) became the dominant one with an overall frequency of 72,4% (CI 68,6% – 76,2%, p<0,05) in all sequenced specimens, followed by the B.1.617.2 (Delta) variant with 25,4% (CI 21,7% – 29,1%, p<0,05) and the B.1.1.7 (Alpha) variant with 1,1% (CI 0,2% – 2%, p<0,05).

    The representative sample size was estimated, based on the number of positive cases in Luxembourg for week 26 (787). The minimum sample size required to detect prevalence of B.1.617.2 (60,8%) reported in week 25, with an error margin of 5%, was estimated to be 251 specimens. This number corresponds to a coverage of 31,9%, which exceeds the minimum coverage recommended by ECDC (10%). The sequencing results of week 24 are not representative of the circulating variants in Luxembourg with an error margin of 5%.

    The total number of sequences performed this week was 637, with 540 specimens having been collected in the time frame of week 26/2021. The sequencing coverage – based on sequenced samples collected in week 26 and corresponding to Luxembourg residents – was 65,1% of all positive cases in Luxembourg.

     

    Clinical Surveillance

    The “Sentinel” surveillance network reported 290 consultations in week 26 (28/JUNE/2021 – 04/JULY/2021). No cases of ILI1 have been reported as shown in Figure 1. The number of consultations for ARI2 was 25, which represents 8,6%.

     

    SARS-CoV-2 Genomic Surveillance

    The current sequencing strategy

    The National Reference Laboratory for Acute Respiratory Infections at LNS continues to improve the representativeness of the pool of sequenced specimens to reach real-time epidemiology, by implementing the following weekly sequencing activities:

    • Sequencing specimens from all hospitalized positive cases
    • Sequencing specimens from all positive cases from Airport testing program
    • Sequencing specimens from all outbreaks and identified clusters
    • Systematic sequencing of specimens from reinfections and post-vaccination-infections
    • Population sequencing of specimens from representative regions and age groups, to follow the evolution of the different variants in the Luxembourg population.

    The representative sequencing sample was based on the minimum number of specimens required to extrapolate prevalence of VOC variants with error rate of 5%. The representative sample was estimated based on the number of positive cases in Luxembourg in week 26 (787). The minimum sample size required to detect prevalence of B.1.617.2 (60,8%) reported in week 25 with an error margin of 5% was estimated to be 251 specimens. The calculation was based on a sample size calculation tool that uses the expected prevalence of the variant in the total population. (Population Proportion – Sample Size – Select Statistical Consultants (select-statistics.co.uk). This number represented a coverage of 31,9%, which exceeds the minimum coverage recommended by ECDC (10%). The number of non-targeted specimens from Luxembourgish residents sequenced this week was 315. Therefore, our sequencing results this week are representative of the circulating variants in Luxembourg.

    The starting material used for sequencing is respiratory specimens (nasopharyngeal or oropharyngeal swabs) that have already been tested positive by RT PCR.

    The LNS sequencing data sharing strategy includes sharing of the sequencing data with GISAID EpiCov database (www.gisaid.org ) on a periodic basis.

    Sequenced specimens

    Last week the microbial genomics platform at the LNS sequenced 637 specimens, with 540 collected in week 26/2021. The sequencing pool referring to Luxembourgish residents represents 65,1% of new infections reported in Luxembourg in week 26/2021. Among these 540 specimens, 200 specimens were reported to be part of a cluster or outbreak investigation, and 28 specimens were from non-residents (3 specimen overlapping). This leads to 315 specimens, collected in week 26, and being a representative population sequencing sample. In the population representative sample of residents, the frequency for P.1 was 74,3%, while the frequency for B.1.617.2 and B.1.1.7, was 24,4% and 0,95% respectively.

    The population sequencing coverage in week 26/2021 was 40% (Figure 2). Based on statistical inference, the frequency of the reported variants in week 26/2021 is representative of the circulating variants in Luxembourg with a margin of error of 5%.

     

    Circulating lineage detection

    Lineages (variants) have been assigned based on Rambaut et al by means of Phylogenetic Assignment of Named Global Outbeak LINeages (pangolin) software  (v3.1.5, pangoLEARN version 2021-06-15).

    The lineage nomenclature system that we use is the one proposed by Rambaut et al. that focuses on actively circulating virus lineages (https://cov-lineages.org ).

    In week 26/2021, in the population representative sample, after removal of cluster samples, and excluding specimens collected from non-residents, there were 4 circulating SARS-CoV-2 variants, the P.1 (74,3%, CI 69,5% – 79,1%), B.1.617.2 (24,4%, CI 19,7% – 29,1%), B.1.1.7 (0,95%, CI 0% – 2%) and B.1.612 (0,3%, CI 0% – 0,9%) as shown in Figure 3.

     

     

    Variants of Concern tracker (B.1.1.7, B.1.351, P.1, B.1.525, B.1.617.2)

    While an overall 8-fold increase of new infections has been detected, the Gamma (P.1) variant showed a 20-fold increase in case numbers, with 391 new cases (72,4%) in week 26/2021 (by comparison, the week 25/2021 pool had shown 24,1% of this variant). The total case count of sequenced Gamma variant was 537 by week 26/2021.

    In week 26/2021, 137 additional cases of the Delta variant B.1.617.2 have been detected. The case count by week 26 for B.1.617.2 rose to 416.

    Among specimens collected within the week 26/2021, 6 cases of the Alpha (B.1.1.7) variant have been detected, representing 1,1% of the specimens in the week’s sequencing pool (by comparison, the week 25/2021 pool had shown a frequency of 10,1% of this variant). The total case count of sequenced variant Alpha was 6904 by week 26/2021.

    In the collection period of week 26/2021, 2 cases of the Beta (B.1.351) variant have been detected, representing 0,37% (by comparison, the week 25/2021 pool had shown 2,5% of this variant). The total case count of sequenced variant B.1.351 was 1192 by week 26/2021.

    In week 26/2021, one new case of B.1.525 has been detected. The case count by week 26 for B.1.525 was 50 (Figure 4).

    Lineage B.1.1.7 is characterized by several spike protein mutations, including N501Y, H69/V70del and P861H. The variant seems to have a considerable epidemiological impact, as it has a higher transmissibility rate.

    Lineage B.1.351 holds numerous spike protein mutations, of which three are located in the receptor binding domain (K417N, E484K and N501Y), and are therefore relevant for antibody binding. As for B.1.1.7, a higher transmissibility rate and viral loads seem to be associated with this variant. Due to the K417N and E484K mutations, an impact on vaccination efficacy and possibility of reinfection is subject to scientific investigation.

    Lineage P.1 (descendent of B.1.1.28), initially found in the Amazon region, has a similar mutation profile as the South African variant, including E484K and N501Y. Concerns are, as for the South African variant, higher transmissibility and a decreased protection by neutralizing antibodies.

    Lineage B.1.525 carries several mutations of biological significance, including E484K, Q677H and F888L. It does not carry N501Y, but a set of deletions similar to the B.1.1.7 variant.

    Lineage B.1.617 is a variant first detected in India and was designated “Under Investigation” on 1st  April 2021 by Public Health England. It contains a number of spike mutations associated with antigenic escape or found in other variants of concern, including L452R, E484Q and P681R. Subtype B.1.617.2 does not carry S:E484Q and seems to be more transmissible than B.1.1.7 (increasing confidence). Neutralization studies show reductions in cross-neutralizing activity between B.1.1.7 and B.1.351.

     

    By week 26/2021, 99,4 % of the variants detected in the sequenced specimen pool are declared as Variants of Concern, including the P.1 (Gamma), the B.1.617.2 (Delta), the B.1.1.7 (Alpha) and B.1.351 (Beta) variants.

    WHO nomeculature to track VOC

    The ReViLux will continue to use the (Pango) system to allow easier visualisation of links between any evolving variants and their ancestor (Figure 5).

    Clinically relevant mutations

    Currently the LNS genomic surveillance program – independently from lineage calling – notes the occurrence of 13 different known SARS-CoV-2 mutations, assumed to have clinical and epidemiological relevance. The list of observed mutations is being updated continually, based on the appearance and prevalence of SARS-CoV-2 variants.

    The following table provides the overall frequencies of these mutations, detected in the lineage-assignable genome sequences, analyzed between 01/SEP/2020 and 04/JULY/2021 (N=14284), as well as the frequencies in week 26/2021.

     

    References

    Genomic sequencing of SARS-CoV-2. A guide to implementation for maximum impact on public health. WHO, 8 January 2021.

    COVID-19 data portal. 2020 (https://www.covid19dataportal.org/sequences )

    J Hadfield et al. Nextstrain: real-time tracking of pathogen evolution. Bioinformatics 2018;34:4121-4123

    A Rambaut et al. A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nat Microbiol 2020;5:1403-1407

    https://github.com/cov-lineages/pangolin

    For more information on lineages visit: https://cov-lineages.org
    For more information and statistics on Covid-19 infections in Luxembourg visit: https://covid19.public.lu/en.html

  • Semaine 25

    Respiratory Viruses in Luxembourg (ReViLux)

    Weekly report (Period 21/06/-27/06/2021)

    Executive Summary

    The aim of the “Sentinel” national surveillance program is to monitor the circulating respiratory viruses, including SARS-CoV-2 variants, and hence underpin public health actions.

    In week 25/2021, the variant B.1.617.2 (Delta) remained the dominant one in Luxembourg with an overall frequency of 60,1% (CI 49,3% – 70,9%, p<0,05) in all sequenced specimens, followed by the P.1 (Gamma) variant with 24,1% (CI 14,7% – 33,5%, p<0,05), the B.1.1.7 (Alpha) variant with 10,1% (CI 3.5% – 16,7%, p<0,05) and one case of the B.1.351 (Bêta) variant.

    The representative sample size was estimated, based on the number of positive cases in Luxembourg for week 25 (107). The minimum sample size required to detect prevalence of B.1.617.2 (59%) reported in week 24, with an error margin of 5%, was estimated to be 84 specimens. This number corresponds to a coverage of 78,5 %, which exceeds the minimum coverage recommended by ECDC (10%). The sequencing results of week 24 are not representative of the circulating variants in Luxembourg with an error margin of 5%.

    The total number of sequences performed this week was 581, with 79 specimens having been collected in the time frame of week 25/2021. The sequencing coverage – based on sequenced samples collected in week 25 and corresponding to Luxembourg residents – was 69,2% of all positive cases in Luxembourg.

    Clinical Surveillance

    The “Sentinel” surveillance network reported 268 consultations in week 25 (21/JUNE/2021 – 27/JUNE/2021) and accordingly there were 0 cases of ILI1 and 31cases ARI2 as shown in Figure 1. The number of consultations for ARI2 was 31, which represents 11,6% of the consultations.

    Virological Surveillance

    Covid Consultation Centres have been closed since 16/May/2021. We are currently working on an alternative in partnership with private laboratories.

    SARS-CoV-2 Genomic Surveillance

    The current sequencing strategy

    The National Reference Laboratory for Acute Respiratory Infections at LNS continues to improve the representativeness of the pool of sequenced specimens to reach real-time epidemiology, by implementing the following weekly sequencing activities:

    • Sequencing specimens from all hospitalized positive cases
    • Sequencing specimens from all positive cases from Airport testing program
    • Sequencing specimens from all outbreaks and identified clusters
    • Systematic sequencing of specimens from reinfections and post-vaccination-infections
    • Population sequencing of specimens from representative regions and age groups, to follow the evolution of the different variants in the Luxembourg population.

    The representative sequencing sample was based on the minimum number of specimens required to extrapolate prevalence of VOC variants with error rate of 5%. The representative sample was estimated based on the number of positive cases in Luxembourg in week 25 (107). The minimum sample size required to detect prevalence of B.1.617.2 (59%) reported in week 24 with an error margin of 5% was estimated to be 84 specimens. The calculation was based on a sample size calculation tool that uses the expected prevalence of the variant in the total population. (Population Proportion – Sample Size – Select Statistical Consultants (select-statistics.co.uk). This number represented a coverage of 78,5%, which exceeds the minimum coverage recommended by ECDC (10%). The number of non-targeted specimens from Luxembourgish residents sequenced this week was 41. Therefore, our sequencing results this week are not representative of the circulating variants in Luxembourg.

    The starting material used for sequencing is respiratory specimens (nasopharyngeal or oropharyngeal swabs) that have already been tested positive by RT PCR.

    The LNS sequencing data sharing strategy includes sharing of the sequencing data with GISAID EpiCov database (www.gisaid.org ) on a periodic basis.

    Sequenced specimens

    Last week the microbial genomics platform at the LNS sequenced 581 specimens, with 79 collected in week 25/2021. The sequencing pool referring to Luxembourgish residents represents 69,2% of new infections reported in Luxembourg in week 25/2021. Among these 79 specimens, 35 specimens were reported to be part of a cluster or outbreak investigation, and 5 specimens were from non-residents (2 specimen overlapping). This leads to 41 specimens, collected in week 25, and not being a representative population sequencing sample. In the population sample of residents, the frequency for B.1.617.2 was 61%, while the frequency for P.1 and B.1.1.7, was 19,5% and 14,6% respectively.

    The population sequencing coverage in week 25/2021 was 38,3% (Figure 2). Based on statistical inference, the frequency of the reported variants in week 25/2021 is not representative of the circulating variants in Luxembourg with a margin of error of 5%.

    Circulating lineage detection

    Lineages (variants) have been assigned based on Rambaut et al by means of Phylogenetic Assignment of Named Global Outbeak LINeages (pangolin) software  (v3.0.3, pangoLEARN version 2021-05-27).

    The lineage nomenclature system that we use is the one proposed by Rambaut et al. that focuses on actively circulating virus lineages (https://cov-lineages.org ).

    In week 25/2021, in the population sample, after removal of cluster samples, and excluding specimens collected from non-residents, there were 5 circulating SARS-CoV-2 variants, with the main three variants being B.1.617.2 (61%, CI 46,1% – 75,9%), P.1 (19,5%, CI 7,4% – 31,6%) and B.1.1.7 (14,6%, CI 3,8% – 25,4%), as shown in Figure 3.

    Variants of Concern tracker (B.1.1.7, B.1.351, P.1, B.1.525, B.1.617.2)

    Among specimens collected within the week 25/2021, 8 cases of the Alpha (B.1.1.7) variant have been detected, representing 10,1% of the specimens in the week’s sequencing pool (by comparison, the week 24/2021 pool had shown a frequency of 29,7% of this variant, including additional specimens having been sequenced from previous weeks). The total case count of sequenced variant Alpha was 6882 by week 25/2021.

    In the collection period of week 25/2021, 2 cases of the Beta (B.1.351) variant have been detected, representing 2,5% (by comparison, the week 24/2021 pool had shown 1,5% of this variant). The total case count of sequenced variant B.1.351 was 1177 by week 25/2021. A strong increase in case numbers has been detected for the Gamma (P.1) variant, with 19 new cases (24,1%) in week 25/2021. Since week 51/2020, the highest proportion the Gamma variant ever represented was in week 18 with 4,5%. The last case detected in the sequencing pool before week 25 is dated back to June 9th. The total case count of sequenced Gamma variant was 145 by week 25/2021.

    In week 25/2021, no new case of B.1.525 has been detected. The case count by week 25 for B.1.525 is 49 (including additional sequencing of previous weeks).

    In week 25/2021, 48 additional cases of the Delta variant B.1.617.2 have been detected. The case count by week 25 for B.1.617.1 remained 9, and for B.1.617.2 it rose to 279. Since  May 6th, B.1.617.2 has been escalated by Public Health England from a variant under investigation to a variant of concern (Figure 4).

    Lineage B.1.1.7 is characterized by several spike protein mutations, including N501Y, H69/V70del and P861H. The variant seems to have a considerable epidemiological impact, as it has a higher transmissibility rate.

    Lineage B.1.351 holds numerous spike protein mutations, of which three are located in the receptor binding domain (K417N, E484K and N501Y), and are therefore relevant for antibody binding. As for B.1.1.7, a higher transmissibility rate and viral loads seem to be associated with this variant. Due to the K417N and E484K mutations, an impact on vaccination efficacy and possibility of reinfection is subject to scientific investigation.

    Lineage P.1 (descendent of B.1.1.28), initially found in the Amazon region, has a similar mutation profile as the South African variant, including E484K and N501Y. Concerns are, as for the South African variant, higher transmissibility and a decreased protection by neutralizing antibodies.

    Lineage B.1.525 carries several mutations of biological significance, including E484K, Q677H and F888L. It does not carry N501Y, but a set of deletions similar to the B.1.1.7 variant.

    Lineage B.1.617 is a variant first detected in India and was designated “Under Investigation” on 1st  April 2021 by Public Health England. It contains a number of spike mutations associated with antigenic escape or found in other variants of concern, including L452R, E484Q and P681R. Subtype B.1.617.2 does not carry S:E484Q and seems to more transmissible as B.1.1.7 (increasing confidence). Neutralization studies show reductions in cross-neutralizing activity between B.1.1.7 and B.1.351.

    By week 25/2021, 97,5 % of the variants detected in the sequenced specimen pool are declared as Variants of Concern, including the B.1.617.2 (Delta), the P.1 (Gamma), the B.1.1.7 (Alpha) and B.1.351 (Beta) variants.

    WHO nomeculature to track VOC

    The ReViLux will continue to use the (Pango) system to allow easier visualisation of links between any evolving variants and their ancestor (Figure 5).

    Clinically relevant mutations

    Currently the LNS genomic surveillance program – independently from lineage calling – notes the occurrence of 13 different known SARS-CoV-2 mutations, assumed to have clinical and epidemiological relevance. The list of observed mutations is being updated continually, based on the appearance and prevalence of SARS-CoV-2 variants.

    The following table provides the overall frequencies of these mutations, detected in the lineage-assignable genome sequences, analyzed between 01/SEP/2020 and 27/JUNE/2021 (N=13739), as well as the frequencies in week 25/2021.

    References

    Genomic sequencing of SARS-CoV-2. A guide to implementation for maximum impact on public health. WHO, 8 January 2021.

    COVID-19 data portal. 2020 (https://www.covid19dataportal.org/sequences )

    J Hadfield et al. Nextstrain: real-time tracking of pathogen evolution. Bioinformatics 2018;34:4121-4123

    A Rambaut et al. A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nat Microbiol 2020;5:1403-1407

    https://github.com/cov-lineages/pangolin

    For more information on lineages visit: https://cov-lineages.org
    For more information and statistics on Covid-19 infections in Luxembourg visit: https://covid19.public.lu/en.html

  • Semaine 24

    Respiratory Viruses in Luxembourg (ReViLux)

    Weekly report (Period 14/06/-20/06/2021)

    Executive Summary

    The aim of the “Sentinel” national surveillance program is to monitor the circulating respiratory viruses, including SARS-CoV-2 variants, and hence underpin public health actions.

    In week 24/2021, the variant B.1.617.2 became the dominant one in Luxembourg with an overall frequency of 59,4% (CI 47,4% – 71,4%, p<0,05), while the B.1.1.7 variant frequency dropped to 29,7% (CI 18,5% – 40,9%, p<0,05). One case of SARS-CoV-2 B.1.351 (1,5%, CI 0% – 4,5%, p<0,05) and no case of the P.1 variant were detected.

    The representative sample size was estimated, based on the number of positive cases in Luxembourg for week 24 (90). The minimum sample size required to detect prevalence of B.1.617.2 (34%) reported in week 23, with an error margin of 5%, was estimated to be 72 specimens. This number corresponds to a coverage of 80 %, which exceeds the minimum coverage recommended by ECDC (10%). The sequencing results of week 24 are not representative of the circulating variants in Luxembourg with an error margin of 5%.

    The total number of sequences performed this week was 284, with 64 specimens having been collected in the time frame of week 24/2021. The sequencing coverage – based on sequenced samples collected in week 24 and corresponding to Luxembourg residents – was 66,7% of all positive cases in Luxembourg.

    Clinical Surveillance

    The “Sentinel” surveillance network reported 374 consultations in week 24 (14/JUNE/2021 – 20/JUNE/2021). There were 3 cases of ILI1, corresponding to 0,8% of the consultations, as shown in Figure 1. The number of consultations for ARI2 was 37, which represents 9,9% of the consultations.

    Virological Surveillance

    Covid Consultation Centres have been closed since 16/May/2021. We are currently working on an alternative in partnership with private laboratories.

    SARS-CoV-2 Genomic Surveillance

    The current sequencing strategy

    The National Reference Laboratory for Acute Respiratory Infections at LNS continues to improve the representativeness of the pool of sequenced specimens to reach real-time epidemiology, by implementing the following weekly sequencing activities:

    • Sequencing specimens from all hospitalized positive cases
    • Sequencing specimens from all positive cases from Airport testing program
    • Sequencing specimens from all outbreaks and identified clusters
    • Systematic sequencing of specimens from reinfections and post-vaccination-infections
    • Population sequencing of specimens from representative regions and age groups, to follow the evolution of the different variants in the Luxembourg population.

    The representative sequencing sample was based on the minimum number of specimens required to extrapolate prevalence of VOC variants with error rate of 5%. The representative sample was estimated based on the number of positive cases in Luxembourg in week 24 (90). The minimum sample size required to detect prevalence of B.1.617.2 (34%) reported in week 23 with an error margin of 5% was estimated to be 72 specimens. The calculation was based on a sample size calculation tool that uses the expected prevalence of the variant in the total population. (Population Proportion – Sample Size – Select Statistical Consultants (select-statistics.co.uk). This number represented a coverage of 80%, which exceeds the minimum coverage recommended by ECDC (10%). The number of non-targeted specimens from Luxembourgish residents sequenced this week was 35. Therefore, our sequencing results this week are not representative of the circulating variants in Luxembourg.

    The starting material used for sequencing is respiratory specimens (nasopharyngeal or oropharyngeal swabs) that have already been tested positive by RT PCR.

    The LNS sequencing data sharing strategy includes sharing of the sequencing data with GISAID EpiCov database (www.gisaid.org ) on a periodic basis.

    Sequenced specimens

    Last week the microbial genomics platform at the LNS sequenced 284 specimens, with 64 collected in week 24/2021. The sequencing pool referring to Luxembourgish residents represents 66,7% of new infections reported in Luxembourg in week 24/2021. Among these 68 specimens, 25 specimens were reported to be part of a cluster or outbreak investigation, and 6 specimens were from non-residents (2 specimen overlapping). This leads to 35 specimens, collected in week 24, and not being a representative population sequencing sample. In the population sample of residents, the frequency of B.1.617.2 was 54,3%, while the frequency for B.1.1.7 was 34,3%. One case has been detected for the B.1.351 variant, representing 2,9%.

    The population sequencing coverage in week 24/2021 was 38,9% (Figure 2). Based on statistical inference, the frequency of the reported variants in week 24/2021 is not representative of the circulating variants in Luxembourg with a margin of error of 5%.

    Circulating lineage detection

    Lineages (variants) have been assigned based on Rambaut et al by means of Phylogenetic Assignment of Named Global Outbeak LINeages (pangolin) software  (v3.0.3, pangoLEARN version 2021-05-27).

    The lineage nomenclature system that we use is the one proposed by Rambaut et al. that focuses on actively circulating virus lineages (https://cov-lineages.org ).

    In week 24/2021, in the population sample, after removal of cluster samples, and excluding specimens collected from non-residents, there were 5 circulating SARS-CoV-2 variants, with the main three variants being B.1.617.2 (54,3%, CI 37,8% – 70,8%), B.1.1.7 (34,3%, CI 18,6% – 50%) and B (5,7%, CI 0% – 13,4%), as shown in Figure 3.

    Variants of Concern tracker (B.1.1.7, B.1.351, P.1, B.1.525, B.1.617.2)

    Among specimens collected within the week 24/2021, 19 cases of the B.1.1.7 variant have been detected, representing 29.7% of the specimens in the week’s sequencing pool (by comparison, the week 23/2021 pool had shown a frequency of 51.6% of this variant, including additional specimens having been sequenced from previous weeks). The total case count of sequenced variant B.1.1.7 (Alpha) was 6696 by week 24/2021.

    In the collection period of week 24/2021, 1 case of the South African variant B.1.351(Bêta) has been detected, representing 1.6% (by comparison, the week 23/2021 pool had shown 0.8% of this variant). The total case count of sequenced variant B.1.351 was 1123 by week 24/2021.

    No new case of the P.1 variant has been detected in week 24/2021.The total case count of sequenced variant P.1(Gamma) was 126 by week 24/2021 (including additional sequencing of previous weeks).

    In week 24/2021, no new case of B.1.525 has been detected. The case count by week 24 for B.1.525 is 48 (including additional sequencing of previous weeks).

    In week 24/2021, 38 additional cases of the Delta variant B.1.617.2 have been detected (latest sampling date 20/JUNE/2021). The case count by week 24 for B.1.617.1 increases by retrospective sequencing to 9, and for B.1.617.2 it raises to 231. Since  May 6th, B.1.617.2 has been escalated by Public Health England from a variant under investigation to a variant of concern (Figure 4).

    Lineage B.1.1.7 is characterized by several spike protein mutations, including N501Y, H69/V70del and P861H. The variant seems to have a considerable epidemiological impact, as it has a higher transmissibility rate.

    Lineage B.1.351 holds numerous spike protein mutations, of which three are located in the receptor binding domain (K417N, E484K and N501Y), and are therefore relevant for antibody binding. Similarly to B.1.1.7, a higher transmissibility rate and viral loads seem to be associated with this variant. Due to the K417N and E484K mutations, an impact on vaccination efficacy and possibility of reinfection is subject to scientific investigation.

    Lineage P.1 (descendent of B.1.1.28), initially found in the Amazon region, has a similar mutation profile as the South African variant, including E484K and N501Y. Concerns are, as for the South African variant, higher transmissibility and a decreased protection by neutralizing antibodies.

    Lineage B.1.525 carries several mutations of biological significance, including E484K, Q677H and F888L. It does not carry N501Y, but a set of deletions similar to the B.1.1.7 variant.

    Lineage B.1.617 is a variant first detected in India and was designated “Under Investigation” on 1st  April 2021 by Public Health England. It contains a number of spike mutations associated with antigenic escape or found in other variants of concern, including L452R, E484Q and P681R. Subtype B.1.617.2 does not carry S:E484Q and seems to be more transmissible, as B.1.1.7 (increasing confidence). Neutralization studies show reductions in cross-neutralizing activity between B.1.1.7 and B.1.351.

    By week 24/2021, 90.6 % of the variants detected in the sequenced specimen pool are declared as Variants of Concern, including the B.1.617.2, B.1.1.7 and B.1.351 variants.

    WHO nomeculature to track VOC

    The ReViLux will continue to use the (Pango) system to allow easier visualisation of links between any evolving variants and their ancestor (Figure 5).

    Clinically relevant mutations

    Currently the LNS genomic surveillance program – independently from lineage calling – notes the occurrence of 13 different known SARS-CoV-2 mutations, assumed to have clinical and epidemiological relevance. The list of observed mutations is being updated continually, based on the appearance and prevalence of SARS-CoV-2 variants.

    The following table provides the overall frequencies of these mutations, detected in the lineage-assignable genome sequences, analyzed between 01/SEP/2020 and 20/JUNE/2021 (N=13149), as well as the frequencies in week 24/2021.

    References

    Genomic sequencing of SARS-CoV-2. A guide to implementation for maximum impact on public health. WHO, 8 January 2021.

    COVID-19 data portal. 2020 (https://www.covid19dataportal.org/sequences )

    J Hadfield et al. Nextstrain: real-time tracking of pathogen evolution. Bioinformatics 2018;34:4121-4123

    A Rambaut et al. A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nat Microbiol 2020;5:1403-1407

    https://github.com/cov-lineages/pangolin

    For more information on lineages visit: https://cov-lineages.org
    For more information and statistics on Covid-19 infections in Luxembourg visit: https://covid19.public.lu/en.html

  • Semaine 23

    Respiratory Viruses in Luxembourg (ReViLux)

    Weekly report (Period 07/06/-13/06/2021)

    Executive Summary

    The aim of the “Sentinel” national surveillance program is to monitor the circulating respiratory viruses, including SARS-CoV-2 variants, and hence underpin public health actions.

    In week 23/2021, the overall frequency of the SARS-CoV-2 B.1.1.7 variant in all sequenced specimens slightly increased to 50,5% (CI 40,8% – 60,2%, p<0,05). One case of SARS-CoV-2 B.1.351 (1%, CI 0% – 2,9%, p<0,05) and 4 cases of P.1 variant (3,9%, CI 0% – 7,6%, p<0,05) were detected, while the frequency of the variant B.1.617.2 increased slightly to 36% (CI 26,7% – 45,3%, p<0,05).

    The representative sample size was estimated, based on the number of positive cases in Luxembourg for week 23 (189). The minimum sample size required to detect prevalence of B.1.1.7 (47%) reported in week 22, with an error margin of 5%, was estimated to be 127 specimens. This number corresponds to a coverage of 67,2 %, which exceeds the minimum coverage recommended by ECDC (10%). The sequencing results of week 23 are not representative of the circulating variants in Luxembourg with an error margin of 5%.

    The total number of sequences performed this week was 283, with 103 specimens having been collected in the time frame of week 23/2021. The sequencing coverage – based on sequenced samples collected in week 23 and corresponding to Luxembourg residents and to non-targeted collections – was 36% of all positive cases in Luxembourg.

    Clinical Surveillance

    The “Sentinel” surveillance network reported 375 consultations in week 23 (07/JUNE/2021 – 13/JUNE/2021). There were 4 cases of ILI1, corresponding to 1,1% of the consultations, as shown in Figure 1. The number of consultations for ARI2 was 35, which represents 9,3% of the consultations.

    Virological Surveillance

    Covid Consultation Centres have been closed since 16/May/2021. We are currently working on an alternative in partnership with private laboratories.

    SARS-CoV-2 Genomic Surveillance

    The current sequencing strategy

    The National Reference Laboratory for Acute Respiratory Infections at LNS continues to improve the representativeness of the pool of sequenced specimens to reach real-time epidemiology, by implementing the following weekly sequencing activities:

    • Sequencing specimens from all hospitalized positive cases
    • Sequencing specimens from all positive cases from Airport testing program
    • Sequencing specimens from all outbreaks and identified clusters
    • Systematic sequencing of specimens from reinfections and post-vaccination-infections
    • Population sequencing of specimens from representative regions and age groups, to follow the evolution of the different variants in the Luxembourg population.

    The representative sequencing sample was based on the minimum number of specimens required to extrapolate prevalence of VOC variants with error rate of 5%. The representative sample was estimated based on the number of positive cases in Luxembourg in week 23 (189). The minimum sample size required to detect prevalence of B.1.1.7 (47%) reported in week 22 with an error margin of 5% was estimated to be 127 specimens. The calculation was based on a sample size calculation tool that uses the expected prevalence of the variant in the total population. (Population Proportion – Sample Size – Select Statistical Consultants (select-statistics.co.uk). This number represented a coverage of 67,2% which exceeds the minimum coverage recommended by ECDC (10%). The number of non-targeted specimens from Luxembourgish residents sequenced this week was 68. Therefore, our sequencing results this week are not representative of the circulating variants in Luxembourg.

    The starting material used for sequencing is respiratory specimens (nasopharyngeal or oropharyngeal swabs) that have already been tested positive by RT PCR.

    The LNS sequencing data sharing strategy includes sharing of the sequencing data with GISAID EpiCov database (www.gisaid.org ) on a periodic basis.

    Sequenced specimens

    Last week the microbial genomics platform at the LNS sequenced 283 specimens, with 103 collected in week 23/2021. The sequencing pool referring to Luxembourgish residents represents 52,4% of new infections reported in Luxembourg in week 23/2021. Among these 103 specimens, 34 specimens were reported to be part of a cluster or outbreak investigation, and 5 specimens were from non-residents (4 specimen overlapping). This leads to 68 specimens, collected in week 23, and not being a representative population sequencing sample. In the population sample of residents, the frequency of B.1.1.7 was 58,8%, while the frequency for B.1.617.2 was 30,9%. Two cases have been detected for the P1 and 1 case for the B.1.351 variant, representing 2,9% and 1,5% respectively.

    The population sequencing coverage in week 23/2021 was 36% (Figure 2). Based on statistical inference, the frequency of the reported variants in week 23/2021 is not representative of the circulating variants in Luxembourg with a margin of error of 5%.

    Circulating lineage detection

    Lineages (variants) have been assigned based on Rambaut et al by means of Phylogenetic Assignment of Named Global Outbeak LINeages (pangolin) software  (v3.0.3, pangoLEARN version 2021-05-27).

    The lineage nomenclature system that we use is the one proposed by Rambaut et al. that focuses on actively circulating virus lineages (https://cov-lineages.org ).

    In week 23/2021, in the population sample, after removal of cluster samples, and excluding specimens collected from non-residents, there were 7 circulating SARS-CoV-2 variants, with the main three variants being B.1.1.7 (58,8%, CI 47,1% – 70,5%), B.1.617.2 (30,9%, CI 19,9% – 41,9%) and P.1 (2,9%, CI 0% – 6,9%), as shown in Figure 3.

    Variants of Concern tracker (B.1.1.7, B.1.351, P.1, B.1.525, B.1.617.2)

    Among specimens collected within the week 23/2021, 52 cases of the B.1.1.7 variant have been detected, representing 50,5% of the specimens in the week’s sequencing pool (by comparison, the week 22/2021 pool had shown a frequency of 47,4% of this variant, including additional specimens having been sequenced from previous weeks). The total case count of sequenced variant B.1.1.7 was 6460 by week 23/2021.

    In the collection period of week 23/2021, 1 case of the South African variant B.1.351 has been detected, representing 1% (by comparison, the week 22/2021 pool had shown 0% of this variant). The total case count of sequenced variant B.1.351 was 1079 by week 23/2021.

    Four new cases of the P.1 variant have been detected in week 23/2021, corresponding to 3,9%, while the previous week no case had been detected. The total case count of sequenced variant P.1 was 122 by week 23/2021.

    In week 23/2021, no new case of B.1.525 has been detected. The case count by week 23 for B.1.525 is 46.

    In week 23/2021, 36 additional cases of the Delta variant B.1.617.2 have been detected (latest sampling date 11/JUNE/2021). The case count by week 23 for B.1.617.1 increases by retrospective sequencing to 8, and for B.1.617.2 it raises to 186. Since  May 6th B.1.617.2 has been escalated by Public Health England from a variant under investigation to a variant of concern (Figure 4).

    Lineage B.1.1.7 is characterized by several spike protein mutations, including N501Y, H69/V70del and P861H. The variant seems to have a considerable epidemiological impact, as it has a higher transmissibility rate.

    Lineage B.1.351 holds numerous spike protein mutations, of which three are located in the receptor binding domain (K417N, E484K and N501Y), and are therefore relevant for antibody binding. As for B.1.1.7, a higher transmissibility rate and viral loads seem to be associated with this variant. Due to the K417N and E484K mutations, an impact on vaccination efficacy and possibility of reinfection is subject to scientific investigation.

    Lineage P.1 (descendent of B.1.1.28), initially found in the Amazon region, has a similar mutation profile as the South African variant, including E484K and N501Y. Concerns are, as for the South African variant, higher transmissibility and a decreased protection by neutralizing antibodies.

    Lineage B.1.525 carries several mutations of biological significance, including E484K, Q677H and F888L. It does not carry N501Y, but a set of deletions similar to the B.1.1.7 variant.

    Lineage B.1.617 is a variant first detected in India and was designated “Under Investigation” on 1st  April 2021 by Public Health England. It contains a number of spike mutations associated with antigenic escape or found in other variants of concern, including L452R, E484Q and P681R. Subtype B.1.617.2 does not carry S:E484Q and seems to more transmissible as B.1.1.7 (increasing confidence). Neutralization studies show reductions in cross-neutralizing activity between B.1.1.7 and B.1.351.

    By week 23/2021, 89,3 % of the variants detected in the sequenced specimen pool are declared as either Variants of Concern, including the B.1.1.7, the B.1.617.2 (increasing trend) and P.1 variant.

    WHO nomeculature to track VOC

    The ReViLux will continue to use the (Pango) system to allow easier visualisation of links between any evolving variants and their ancestor (Figure 5).

    Clinically relevant mutations

    Currently the LNS genomic surveillance program – independently from lineage calling – notes the occurrence of 13 different known SARS-CoV-2 mutations, assumed to have clinical and epidemiological relevance. The list of observed mutations is being updated continually, based on the appearance and prevalence of SARS-CoV-2 variants.

    The following table provides the overall frequencies of these mutations, detected in the lineage-assignable genome sequences, analyzed between 01/SEP/2020 and 13/JUNE/2021 (N=12723), as well as the frequencies in week 23/2021.

    References

    Genomic sequencing of SARS-CoV-2. A guide to implementation for maximum impact on public health. WHO, 8 January 2021.

    COVID-19 data portal. 2020 (https://www.covid19dataportal.org/sequences )

    J Hadfield et al. Nextstrain: real-time tracking of pathogen evolution. Bioinformatics 2018;34:4121-4123

    A Rambaut et al. A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nat Microbiol 2020;5:1403-1407

    https://github.com/cov-lineages/pangolin

    For more information on lineages visit: https://cov-lineages.org
    For more information and statistics on Covid-19 infections in Luxembourg visit: https://covid19.public.lu/en.html

  • Semaine 22

    Respiratory Viruses in Luxembourg (ReViLux)

    Weekly report (Period 31/05/-06/06/2021)

    Executive Summary

    The aim of the “Sentinel” national surveillance program is to monitor the circulating respiratory viruses, including SARS-CoV-2 variants, and hence underpin public health actions.

    In week 22/2021, the overall frequency of the SARS-CoV-2 B.1.1.7 variant in all sequenced specimens decreased to 47,4% (CI 40,4% – 54,4%, p<0,05). No case was detected for the SARS-CoV-2 B.1.351 and P.1 variant, while the frequency the variant B.1.617.2 doubled to 30,9% (CI 24,4% – 37,4%, p<0,05).

    The representative sample was estimated, based on the number of positive cases in Luxembourg for week 22 (324). The minimum sample size required to detect prevalence of B.1.1.7 (66%) reported in week 21, with an error margin of 5%, was estimated to be 168 specimens. This number corresponds to a coverage of 51,8 %, which exceeds the minimum coverage recommended by ECDC (10%). The sequencing results of week 22 are not representative of the circulating variants in Luxembourg with a margin of error of 5%.

    The total number of sequences performed this week was 371, with 194 specimens having been collected in the time frame of week 22/2021. The sequencing coverage – based on sequenced samples collected in week 22 and corresponding to Luxembourg residents and to non-targeted collections – was 45,1% of all positive cases in Luxembourg.

    Clinical Surveillance

    The “Sentinel” surveillance network reported 222 consultations in week 22 (31/MAY/2021 – 06/June/2021). There was 1 case of ILI1, corresponding to 0,5% of the consultations, as shown in Figure 1. The number of consultations for ARI2 was 18, which represents 8,1% of the consultations.

    Virological Surveillance

    Covid Consultation Centres have been closed by 16/May/2021. We are currently working on an alternative in partnership with private laboratories.

    SARS-CoV-2 Genomic Surveillance

    The current sequencing strategy

    The National Reference Laboratory for Acute Respiratory Infections at LNS continues to improve the representativeness of the pool of sequenced specimens to reach real-time epidemiology, by implementing the following weekly sequencing activities:

    • Sequencing specimens from all hospitalized positive cases
    • Sequencing specimens from all positive cases from Airport testing program
    • Sequencing specimens from all outbreaks and identified clusters
    • Systematic sequencing of specimens from reinfections and post-vaccination-infections
    • Population sequencing of specimens from representative regions and age groups, to follow the evolution of the different variants in the Luxembourg population.

    The representative sequencing sample was based on the minimum number of specimens required to extrapolate prevalence of VOC variants with error rate of 5%. The representative sample was estimated based on the number of positive cases in Luxembourg in week 22 (324). The minimum sample size required to detect prevalence of B.1.1.7 (66%) reported in week 20 with an error margin of 5% was estimated to be 168 specimens. The calculation was based on a sample size calculation tool that uses the expected prevalence of the variant in the total population. (Population Proportion – Sample Size – Select Statistical Consultants (select-statistics.co.uk). This number represented a coverage of 51,8% which exceeds the minimum coverage recommended by ECDC (10%). The number of non-targeted specimens from Luxembourgish residents sequenced this week was 146. Therefore, our sequencing results this week are not representative of the circulating variants in Luxembourg.

    The starting material used for sequencing is respiratory specimens (nasopharyngeal or oropharyngeal swabs) that have already been tested positive by RT PCR.

    In parallel, we continue to evaluate commercial PCR screening, using the same starting material, to detect the Variants of Concern (VOCs), with specific PCR. This will enable a faster investigation time of any outbreak and allow us to screen 100% of positive cases referred to LNS, including those that do not pass the quality criteria for sequencing. Specimens that are not eligible for sequencing can thus be used in a PCR to detect the presence of variants of concern.

    The LNS sequencing data sharing strategy includes sharing of the sequencing data with GISAID EpiCov database (www.gisaid.org ) on a periodic basis.

    Sequenced specimens

    Last week the microbial genomics platform at the LNS sequenced 371 specimens, with 194 collected in week 22/2021. The sequencing pool referring to Luxembourgish residents represents 52,8% of new infections reported in Luxembourg in week 22/2021. Among these 194 specimens, 40 specimens were reported to be part of a cluster or outbreak investigation, and 23 specimens were from non-residents (15 specimen overlapping). This leads to 146 specimens, collected in week 22, and being the representative population sequencing sample. In the population representative sample of residents, the frequencies of B.1.1.7 and  B.1.617.2 were 46,6% and 30,8% respectively. No cases have been detected for the B.1.351 and P.1 variants.

    The population sequencing coverage in week 22/2021 was 45,1% (Figure 2). Based on statistical inference, the frequency of the reported variants in week 22/2021 is not representative of the circulating variants in Luxembourg with a margin of error of 5%.

    Circulating lineage detection

    Lineages (variants) have been assigned based on Rambaut et al by means of Phylogenetic Assignment of Named Global Outbeak LINeages (pangolin) software  (v3.0.3, pangoLEARN version 2021-05-27).

    The lineage nomenclature system that we use is the one proposed by Rambaut et al. that focuses on actively circulating virus lineages (https://cov-lineages.org ).

    In the week 22/2021, in the population representative sample, after removal of cluster specimens, and excluding specimens collected from non-residents, there were 13 circulating SARS-CoV-2 variants, with the main three variants being  B.1.1.7 (46,6%, CI 38,5% – 54,7%), B.1.617.2 (30,8%, CI 23,3% – 38,3%) and B.1.1 (5,5%, CI 1,8% – 9,2%), as shown in Figure 3.

    Variants of Concern tracker (B.1.1.7, B.1.351, P.1, B.1.525, B.1.617.2)

    Among specimens collected within the week 22/2021, 92 cases of the B.1.1.7 variant have been detected, representing 47,4% of the specimens in the week’s sequencing pool (by comparison, the week 21/2021 pool had shown a frequency of 65,2% of this variant, including additional specimens having been sequenced from previous weeks). The total case count of sequenced variant B.1.1.7 was 6230 by week 22/2021.

    In the collection period of week 22/2021, no case of the South African variant B.1.351 has been detected (by comparison, the week 20/2021 pool had shown 3,1% of this variant, including additional specimens having been sequenced from previous weeks). The total case count of sequenced variant B.1.351 was 1048 by week 22/2021. The earliest collection date for this variant remains 11/JAN/2021 and the latest is 29/MAY/2021.

    In week 22/2021, no new case of B.1.525 and P.1 has been detected. The case count by week 22 for B.1.525 remains 45 (latest sampling date 17/MAY/2021) and for P.1 the case count increases due to retrospective sequencing to 112 (latest sampling date 30/MAY/2021).

    In week 22/2021, 60 additional cases of the Delta variant B.1.617.2 have been detected (latest sampling date 06/June/2021). The case count by week 22 for B.1.617.1 remains 6, and for B.1.617.2 it raises to 149. Since  May 6th B.1.617.2 has been escalated by Public Health England from a variant under investigation to a variant of concern (Figure 4).

    Lineage B.1.1.7 is characterized by several spike protein mutations, including N501Y, H69/V70del and P861H. The variant seems to have a considerable epidemiological impact, as it has a higher transmissibility rate.

    Lineage B.1.351 holds numerous spike protein mutations, of which three are located in the receptor binding domain (K417N, E484K and N501Y), and are therefore relevant for antibody binding. As for B.1.1.7, a higher transmissibility rate and viral loads seem to be associated with this variant. Due to the K417N and E484K mutations, an impact on vaccination efficacy and possibility of reinfection is subject to scientific investigation.

    Lineage P.1 (descendent of B.1.1.28), initially found in the Amazon region, has a similar mutation profile as the South African variant, including E484K and N501Y. Concerns are, as for the South African variant, higher transmissibility and a decreased protection by neutralizing antibodies.

    Lineage B.1.525 carries several mutations of biological significance, including E484K, Q677H and F888L. It does not carry N501Y, but a set of deletions similar to the B.1.1.7 variant.

    Lineage B.1.617 is a variant first detected in India and was designated “Under Investigation” on 1st  April 2021 by Public Health England. It contains a number of spike mutations associated with antigenic escape or found in other variants of concern, including L452R, E484Q and P681R. Subtype B.1.617.2 does not carry S:E484Q and seems to more transmissible as B.1.1.7 (increasing confidence). Neutralization studies show reductions in cross-neutralizing activity between B.1.1.7 and B.1.351.

    By week 22/2021, 78,3 % of the variants detected in the sequenced specimen pool are declared as either Variants of Concern. These include B.1.1.7, which is continuously decreasing, apparently being displaced by B.1.617.2.

    WHO nomeculature to track VOC

    The ReViLux will continue to use the “Pango” nomenclature system to allow easier links to any evolving variants with their ancestor (Figure 5).

    Clinically relevant mutations

    Currently the LNS genomic surveillance program – independently from lineage calling – notes the occurrence of 13 different known SARS-CoV-2 mutations, assumed to have clinical and epidemiological relevance. The list of observed mutations is being updated continually, based on the appearance and prevalence of SARS-CoV-2 variants.

    The following table provides the overall frequencies of these mutations, detected in the lineage-assignable genome sequences, analyzed between 01/SEP/2020 and 30/MAY/2021 (N=12080), as well as the frequencies in week 22/2021.

    References

    Genomic sequencing of SARS-CoV-2. A guide to implementation for maximum impact on public health. WHO, 8 January 2021.

    COVID-19 data portal. 2020 (https://www.covid19dataportal.org/sequences )

    J Hadfield et al. Nextstrain: real-time tracking of pathogen evolution. Bioinformatics 2018;34:4121-4123

    A Rambaut et al. A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nat Microbiol 2020;5:1403-1407

    https://github.com/cov-lineages/pangolin

    For more information on lineages visit: https://cov-lineages.org
    For more information and statistics on Covid-19 infections in Luxembourg visit: https://covid19.public.lu/en.html

     

  • Semaine 21

    Respiratory Viruses in Luxembourg (ReViLux)

    Weekly report (Period 24/05/-30/05/2021)

    Executive Summary

    The aim of the “Sentinel” national surveillance program is to monitor the circulating respiratory viruses, including SARS-CoV-2 variants, and hence underpin public health actions.

    In week 21/2021, the overall frequency of the SARS-CoV-2 B.1.1.7 variant in all sequenced specimens decreased to 66% (CI 59,6% – 72,4%, p<0,05). For the SARS-CoV-2 B.1.351 and P.1 variant, we found for each an overall frequency of 2,8% (CI 0,6% – 5%, p<0,05) within the sequenced sample. The frequency detected for the variant B.1.617.2 doubled to 14.6% (CI 9,8% – 19,3%, p<0,05).

    The representative sample was estimated, based on the number of positive cases in Luxembourg for week 21 (354). The minimum sample size required to detect prevalence of B.1.1.7 (76%) reported in week 20, with an error margin of 5%, was estimated to be 157 specimens. This number corresponds to a coverage of 44.3 %, which exceeds the minimum coverage recommended by ECDC (10%). The sequencing results of week 16 are representative of the circulating variants in Luxembourg with a margin of error of 5%.

    The total number of sequences performed this week was 293, with 212 specimens having been collected in the time frame of week 21/2021. The sequencing coverage this week was 55,4% from all positive cases in Luxembourg (based on sequenced samples collected in the time frame of week 21 and corresponding to Luxembourg residents).

    Clinical Surveillance

    The “Sentinel” surveillance network reported 187 consultations in week 21 (24/MAY/2021 – 30/MAY/2021). There were 2 cases of ILI1, corresponding to 1,1% of the consultations, as shown in Figure 1. The number of consultations for ARI2 was 34, which represents 18.2% of the consultations.

    Virological Surveillance

    Covid Consultation Centres have been closed by 16/May/2021. We are currently working on an alternative in partnership with private laboratories.

    SARS-CoV-2 Genomic Surveillance

    The current sequencing strategy

    The National Reference Laboratory for Acute Respiratory Infections at LNS continues to improve the representativeness of the pool of sequenced specimens to reach real-time epidemiology, by implementing the following weekly sequencing activities:

    • Sequencing specimens from all hospitalized positive cases
    • Sequencing specimens from all positive cases from Airport testing program
    • Sequencing specimens from all outbreaks and identified clusters
    • Systematic sequencing of specimens from reinfections and post-vaccination-infections
    • Population sequencing of specimens from representative regions and age groups, to follow the evolution of the different variants in the Luxembourg population.

    The representative sequencing sample was based on the minimum number of specimens required to extrapolate prevalence of VOC variants with error rate of 5%. The representative sample was estimated based on the number of positive cases in Luxembourg in week 21 (354). The minimum sample size required to detect prevalence of B.1.1.7 (76%) reported in week 20 with an error margin of 5% was estimated to be 157 specimens. The calculation was based on a sample size calculation tool that uses the expected prevalence of the variant in the total population. (Population Proportion – Sample Size – Select Statistical Consultants (select-statistics.co.uk). This number represented a coverage of 44,3% which exceeds the minimum coverage recommended by ECDC (10%). The number of non-targeted specimens from Luxembourgish residents sequenced this week was 196. Therefore, our sequencing results this week are representative of the circulating variants in Luxembourg.

    The starting material used for sequencing is respiratory specimens (nasopharyngeal or oropharyngeal swabs) that have already been tested positive by RT PCR.

    In parallel, we will introduced the PCR screening for VOC on 14/06/2021, using the Allplex™ SARS-CoV-2 Variants I Assay which will allow simultaneous detection and differentiation of SARS-CoV-2 and three mutation sites in S gene for identification of SARS-CoV-2 variants to detect the Variants of Concern (VOCs. This will enable a faster investigation time of any outbreak and allow us to identify variants of concerns that do not pass the quality criteria for sequencing.

    The LNS sequencing data sharing strategy includes sharing of the sequencing data with GISAID EpiCov database (www.gisaid.org ) on a periodic basis.

    Sequenced specimens

    Last week the microbial genomics platform at the LNS sequenced 293 specimens, with 212 collected in week 21/2021. The sequencing pool referring to Luxembourgish residents represents 55,4% of new infections reported in Luxembourg in week 21/2021. Among these 212 specimens, 12 specimens were reported to be part of a cluster or outbreak investigation, and 15 specimens were from non-residents (5 specimen overlapping). This leads to 190 specimens, collected in week 21, and being the representative population sequencing sample. In the population representative sample of residents, the frequencies of B.1.1.7, B.1.617.2, B.1.351 and P.1 were 65,3%, 16,3%, 3,2% and 2,1% respectively.

    The population sequencing coverage in week 21/2021 was 55,4% (Figure 2). Based on statistical inference, the frequency of the reported variants in week 21/2021 is representative of the circulating variants in Luxembourg with a margin of error of 5%.

    Circulating lineage detection

    Lineages (variants) have been assigned based on Rambaut et al by means of Phylogenetic Assignment of Named Global Outbeak LINeages (pangolin) software  (v3.0.3, pangoLEARN version 2021-05-27).

    The lineage nomenclature system that we use is the one proposed by Rambaut et al. that focuses on actively circulating virus lineages (https://cov-lineages.org ).

    In week 21/2021, in the population representative sample, after removal of cluster specimens, and excluding specimens collected from non-residents, there were 13 variants, with the main three variants being B.1.1.7 (65,3%, CI 58,5% – 72,1%), followed by B.1.617.2 (16,3%, CI 11% – 21,5%) and P.1.1 / B.1.1 (3,7% each , CI 1% – 6,4%), as shown in Figure 3.

    Variants of Concern tracker (B.1.1.7, B.1.351, P.1, B.1.525, B.1.617.2)

    Among specimens collected within the week 21/2021, 140 cases of the B.1.1.7 variant have been detected, representing 66% of the specimens in the week’s sequencing pool (by comparison, the week 20/2021 pool had shown a frequency of 76,1% of this variant, including additional specimens having been sequenced from previous weeks). The total case count of sequenced variant B.1.1.7 was 6053 by week 21/2021. The earliest collection date for this variant remains 19/DEC/2020 and the latest is 30/05/2021.

    In the collection period of week 21/2021, 6 cases of the South African variant B.1.351 have been detected, representing 2,8% of the specimens in the week’s sequencing pool (by comparison, the week 20/2021 pool had shown 2,5% of this variant, including additional specimens having been sequenced from previous weeks). The total case count of sequenced variant B.1.351 was 1031 by week 21/2021. The earliest collection date for this variant remains 11/JAN/2021 and the latest is 28/MAY/2021.

    In week 21/2021, no new case of B.1.525 has been detected, and 6 new cases of the Brazilian variant P.1. The case count by week 21 for B.1.525 remains 45 (latest sampling date 17/MAY/2021) and for P.1 the case count increases to 111 (latest sampling date 30/MAY/2021)

    In week 21/2021, 31 additional cases of the Delta variant B.1.617.2 have been detected (latest sampling date 30/MAY/2021). The case count by week 21 for B.1.617.1 remains 6, and for B.1.617.2 it raises to 85. Since  May 6th, B.1.617.2 has been escalated by Public Health England from a variant under investigation to a variant of concern (Figure 4).

    Lineage B.1.1.7 is characterized by several spike protein mutations, including N501Y, H69/V70del and P861H. The variant seems to have a considerable epidemiological impact, as it has a higher transmissibility rate.

    Lineage B.1.351 holds numerous spike protein mutations, of which three are located in the receptor binding domain (K417N, E484K and N501Y), and are therefore relevant for antibody binding. As for B.1.1.7, a higher transmissibility rate and viral loads seem to be associated with this variant. Due to the K417N and E484K mutations, an impact on vaccination efficacy and possibility of reinfection is subject to scientific investigation.

    Lineage P.1 (descendent of B.1.1.28), initially found in the Amazon region, has a similar mutation profile as the South African variant, including E484K and N501Y. Concerns are, as for the South African variant, higher transmissibility and a decreased protection by neutralizing antibodies.

    Lineage B.1.525 carries several mutations of biological significance, including E484K, Q677H and F888L. It does not carry N501Y, but a set of deletions similar to the B.1.1.7 variant.

    Lineage B.1.617 is a variant first detected in India and was designated “Under Investigation” on 1st  April 2021 by Public Health England. It contains a number of spike mutations associated with antigenic escape or found in other variants of concern, including L452R, E484Q and P681R. Subtype B.1.617.2 does not carry S:E484Q and seems to be at least as transmissible as B.1.1.7 (increasing confidence). Neutralization studies show reductions in cross-neutralizing activity between B.1.1.7 and B.1.351.

    By week 21/2021, 86,3 % of the variants detected in the sequenced specimen pool are declared as either Variants of Concern (VOC – B.1.1.7, B.1.351, P.1, B.1.617.2) or Variants Under Investigation (VUI – B.1.525, B.1.1.318, B.1.617.1, B.1.1).

    New WHO nomeculature to track VOC

    The World Health Organization (WHO) has recently announced a new nomeculature system for tracking SARS-CoV-2 variants of interest (VOI) and variants of concern (VOC). The system is based on the Greek alphabet.

    According to the new system, B.1.1.7 was the first VOC designated by WHO and it is now called Alpha. The B.1.351, which originated in Brazil, is now called Beta. The two other VOCs are the P.1, the variant first identified in Brazil and now referred to as Gamma, and the B.1.617.2 that originated in India, now called Delta (Figure 5).

    The ReViLux will continue to use the Rambaut et al. (“Pango”) nomenclature system to enable linking between any evolving variants and their ancestor.

    Clinically relevant mutations

    Currently the LNS genomic surveillance program – independently from lineage calling – notes the occurrence of 13 different known SARS-CoV-2 mutations, assumed to have clinical and epidemiological relevance. The list of observed mutations is being updated continually, based on the appearance and prevalence of SARS-CoV-2 variants.

    The following table provides the overall frequencies of these mutations, detected in the lineage-assignable genome sequences, analyzed between 01/SEP/2020 and 30/MAY/2021 (N=12080), as well as the frequencies in week 21/2021.

    References

    Genomic sequencing of SARS-CoV-2. A guide to implementation for maximum impact on public health. WHO, 8 January 2021.

    COVID-19 data portal. 2020 (https://www.covid19dataportal.org/sequences )

    J Hadfield et al. Nextstrain: real-time tracking of pathogen evolution. Bioinformatics 2018;34:4121-4123

    A Rambaut et al. A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nat Microbiol 2020;5:1403-1407

    https://github.com/cov-lineages/pangolin

    For more information on lineages visit: https://cov-lineages.org
    For more information and statistics on Covid-19 infections in Luxembourg visit: https://covid19.public.lu/en.html

  • Semaine 20

    Respiratory Viruses in Luxembourg (ReViLux)

    Weekly report (Period 17/05/-23/05/2021)

    Executive Summary

    The aim of the “Sentinel” national surveillance program is to monitor the circulating respiratory viruses, including SARS-CoV-2 variants, and hence underpin public health actions.

    In week 20/2021, the overall frequency of the SARS-CoV-2 B.1.1.7 variant in all sequenced specimens decreased to 76,5% (CI 72,1% – 80,9%, p<0,05). For the SARS-CoV-2 B.1.351 variant, we found an overall frequency of 2,5% (CI 0,9% – 4,1%, p<0,05) within the sequenced sample, while for P.1, the frequency decreased to 2,2% (CI 0,7% – 3,7%, p<0,05). The frequency for the “indian variant” B.1.617.2 increased to 7,5% (CI 4,8% – 10,2%, p<0,05).

    The representative sample was estimated, based on the number of positive cases in Luxembourg for week 20 (495). The minimum sample size required to detect prevalence of B.1.1.7 (79%) reported in week 19, with an error margin of 5%, was estimated to be 169 specimens. This number corresponds to a coverage of 34,1 %, which exceeds the minimum coverage recommended by ECDC (10%). The sequencing results of week 16 are representative of the circulating variants in Luxembourg with a margin of error of 5%.

    The total number of sequences performed this week was 395, with 358 specimens having been collected in the time frame of week 20/2021. The sequencing coverage this week was 66,3% from all positive cases in Luxembourg (based on sequenced samples collected in the time frame of week 20 and corresponding to Luxembourg residents).

    Clinical Surveillance

    The “Sentinel” surveillance network reported 291 consultations in week 20 (17/MAY/2021 – 23/MAY/2021). There were 3 cases of ILI1, corresponding to 1,0% of the consultations, as shown in Figure 1. The number of consultations for ARI2 was 34, which represents 11,7% of the consultations. This exceeds the epidemiological threshold for the third consecutive week for ILI in Luxembourg, which is 2 cases per week.

    Virological Surveillance

    Covid Consultation Centres have been closed by 16/May/2021. We are currently working on an alternative surveillance solution in partnership with private laboratories.

    SARS-CoV-2 Genomic Surveillance

    The current sequencing strategy

    The National Reference Laboratory for Acute Respiratory Infections at LNS continues to improve the representativeness of the pool of sequenced specimens to reach real-time epidemiology, by implementing the following weekly sequencing activities:

    • Sequencing specimens from all hospitalized positive cases
    • Sequencing specimens from all positive cases from Airport testing program
    • Sequencing specimens from all outbreaks and identified clusters
    • Systematic sequencing of specimens from reinfections and post-vaccination-infections
    • Population sequencing of specimens from representative regions and age groups, to follow the evolution of the different variants in the Luxembourg population.

    The representative sequencing sample was based on the minimum number of specimens required to extrapolate prevalence of VOC variants with error rate of 5%. The representative sample was estimated based on the number of positive cases in Luxembourg in week 20 (495). The minimum sample size required to detect prevalence of B.1.1.7 (79%) reported in week 19 with an error margin of 5% was estimated to be 169 specimens. The calculation was based on a sample size calculation tool that uses the expected prevalence of the variant in the total population. (Population Proportion – Sample Size – Select Statistical Consultants (select-statistics.co.uk). This number represented a coverage of 34,1% which exceeds the minimum coverage recommended by ECDC (10%). The number of non-targeted specimens from Luxembourgish residents sequenced this week was 294. Therefore, our sequencing results this week are representative of the circulating variants in Luxembourg.

    The starting material used for sequencing is respiratory specimens (nasopharyngeal or oropharyngeal swabs) that have already been tested positive by RT PCR.

    In parallel, we continue to evaluate commercial PCR screening, using the same starting material, to detect the Variants of Concern (VOCs), with specific PCR. This will enable a faster investigation time of any outbreak and allow us to screen 100% of positive cases referred to LNS, including those that do not pass the quality criteria for sequencing. Specimens that are not eligible for sequencing can thus be used in a PCR to detect the presence of variants of concern.

    The LNS sequencing data sharing strategy includes sharing of the sequencing data with GISAID EpiCov database (www.gisaid.org ) on a periodic basis.

    Sequenced specimens

    Last week the microbial genomics platform at the LNS sequenced 395 specimens, with 358 collected in week 20/2021. The sequencing pool referring to Luxembourgish residence represents 66,3% of new infections reported in Luxembourg in week 20/2021. Among these 358 specimens, 36 specimens were reported to be part of a cluster or outbreak investigation, and 30 specimens were from non-residents (7 specimens overlapping). This leads to 294 specimens, collected in week 20, and being the representative population sequencing sample. In the population representative sample of residents, the frequencies of B.1.1.7, B.1.617.2, B.1.351 and P.1 were 75,5%, 8,2%, 2,7% and 2,4% respectively.

    The population sequencing coverage in week 20/2021 was 66,3% (Figure 2). Based on statistical inference, the frequency of the reported variants in week 20/2021 is representative of the circulating variants in Luxembourg with a margin of error of 5%.

    Circulating lineage detection

    Lineages (variants) have been assigned based on Rambaut et al by means of Phylogenetic Assignment of Named Global Outbeak LINeages (pangolin) software  (v2.4.2, pangoLEARN version 2021-05-12).

    The lineage nomenclature system that we use is the one proposed by Rambaut et al. that focuses on actively circulating virus lineages (https://cov-lineages.org ).

    In week 20/2021, in the population representative sample, after removal of cluster specimens, and excluding specimens collected from non-residents, there were 15 circulating SARS-CoV-2 variants, with the main three variants being B.1.1.7 (75,5%, CI% 70,6% – 80,4%) followed by B.1.617.2 (8,2%, CI 5,1% – 11,3%) and R.1 (2,7%, CI 0,8% – 4,5%), as shown in Figure 3.

    Variants of Concern tracker (B.1.1.7, B.1.351, P.1, B.1.525, B.1.617.2)

    Among specimens collected within the week 20/2021, 274 cases of the B.1.1.7 variant have been detected, representing 76,5% of the specimens in the week’s sequencing pool (by comparison, the week 19/2021 pool had shown a frequency of 78,9% of this variant, including additional specimens having been sequenced from previous weeks). The total case count of sequenced variant B.1.1.7 was 5904 by week 20/2021. The earliest collection date for this variant remains 19/DEC/2020 and the latest is 23/05/2021.

    In the collection period of week 20/2021, 9 cases of the South African variant B.1.351 have been detected, representing 2,5% of the specimens in the week’s sequencing pool (by comparison, the week 19/2021 pool had shown 5,9% of this variant, including additional specimens having been sequenced from previous weeks). The total case count of sequenced variant B.1.351 was 1025 by week 20/2021. The earliest collection date for this variant remains 11/JAN/2021 and the latest is 22/MAY/2021. In week 20/2021, 6 additional cases of B.1.525 has been detected, and 8 new cases of the Brazilian variant P.1. Thus, the case count by week 20 for B.1.525 is 45 (latest sampling date 17/MAY/2021) and for P.1 the case count is 103 (latest sampling date 22/MAY/2021). In week 20/2021, 27 additional cases of the B.1.617 subtype B.1.617.2 have been detected (latest sampling date 22/MAY/2021). The case count by week 20 for B.1.617.1 remains 6, and for B.1.617.2 it raises to 53. Since  May 6th B.1.617.2 has been escalated by Public Health England from a variant under investigation to a variant of concern (Figure 4).

    Lineage B.1.1.7 is characterized by several spike protein mutations, including N501Y, H69/V70del and P861H. The variant seems to have a considerable epidemiological impact, as it has a higher transmissibility rate.

    Lineage B.1.351 holds numerous spike protein mutations, of which three are located in the receptor binding domain (K417N, E484K and N501Y), and are therefore relevant for antibody binding. As for B.1.1.7, a higher transmissibility rate and viral loads seem to be associated with this variant. Due to the K417N and E484K mutations, an impact on vaccination efficacy and possibility of reinfection is subject to scientific investigation.

    Lineage P.1 (descendent of B.1.1.28), initially found in the Amazon region, has a similar mutation profile as the South African variant, including E484K and N501Y. Concerns are, as for the South African variant, higher transmissibility and a decreased protection by neutralizing antibodies.

    Lineage B.1.525 carries several mutations of biological significance, including E484K, Q677H and F888L. It does not carry N501Y, but a set of deletions similar to the B.1.1.7 variant.

    Lineage B.1.617 is a variant first detected in India and was designated “Under Investigation” on 1st  April 2021 by Public Health England. It contains a number of spike mutations associated with antigenic escape or found in other variants of concern, including L452R, E484Q and P681R. Subtype B.1.617.2 does not carry S:E484Q and seems to be at least as transmissible as B.1.1.7 (with increasing confidence). Neutralization studies show reduction in cross-neutralizing activity between B.1.1.7 and B.1.351.

    By week 20/2021, 92,5 % of the variants detected in the sequenced specimen pool are declared as either Variants of Concern (VOC – B.1.1.7, B.1.351, P.1, B.1.617.2) or Variants Under Investigation (VUI – B.1.525, B.1.1.318, B.1.617.1, B.1.1).

    Clinically relevant mutations

    Currently the LNS genomic surveillance program – independently from lineage calling – notes the occurrence of 13 different known SARS-CoV-2 mutations, assumed to have clinical and epidemiological relevance. The list of observed mutations is being updated continually, based on the appearance and prevalence of SARS-CoV-2 variants.

    The following table provides the overall frequencies of these mutations, detected in the lineage-assignable genome sequences, analyzed between 01/SEP/2020 and 23/MAY/2021 (N=11849), as well as the frequencies in week 20/2021.

    References

    Genomic sequencing of SARS-CoV-2. A guide to implementation for maximum impact on public health. WHO, 8 January 2021.

    COVID-19 data portal. 2020 (https://www.covid19dataportal.org/sequences )

    J Hadfield et al. Nextstrain: real-time tracking of pathogen evolution. Bioinformatics 2018;34:4121-4123

    A Rambaut et al. A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nat Microbiol 2020;5:1403-1407

    https://github.com/cov-lineages/pangolin

    For more information on lineages visit: https://cov-lineages.org
    For more information and statistics on Covid-19 infections in Luxembourg visit: https://covid19.public.lu/en.html

     

     

     

  • Semaine 19

    Respiratory Viruses in Luxembourg (ReViLux)

    Weekly report (Period 10/05/-16/05/2021)

    Executive Summary

    The aim of the “Sentinel” national surveillance program is to monitor the circulating respiratory viruses, including SARS-CoV-2 variants, and hence underpin public health actions.

    In week 19/2021, the overall frequency of the SARS-CoV-2 B.1.1.7 variant in all sequenced specimens remained rather stable on 79% (CI 75,6% – 82,4%, p<0,05). For the SARS-CoV-2 B.1.351 variant, we found an overall frequency of 5,7% (CI 3,7% – 7,6%, p<0,05) within the sequenced sample, while for P.1, the frequency decreased to 3,7% (CI 2,1% – 5,3%, p<0,05). The frequency of the “indian variant” B.1.617.2 increased to 3,9% (CI 2,3% – 5,5%, p<0,05).

    The representative sample was estimated, based on the number of positive cases in Luxembourg for week 19 (759). The minimum sample size required to detect prevalence of B.1.1.7 (82%) reported in week 18, with an error margin of 5%, was estimated to be 175 specimens. This number corresponds to a coverage of 23,1 %, which exceeds the minimum coverage recommended by ECDC (10%). The sequencing results of week 16 are representative of the circulating variants in Luxembourg with a margin of error of 5%.

    The total number of sequences performed this week was 630, with 543 specimens having been collected in the time frame of week 19/2021. The sequencing coverage this week was 67,5% from all positive cases in Luxembourg (based on sequenced samples collected in the time frame of week 19 and corresponding to Luxembourg residents).

    Clinical Surveillance

    The “Sentinel” surveillance network reported 299 consultations in week 19 (10/MAY/2021 – 16/MAY/2021). There were 3 cases of ILI1, corresponding to 1% of the consultations, as shown in Figure 1. The number of consultations for ARI2 was 37, which represents 12% of the consultations.

    Virological Surveillance

    Patients presenting with ILI and ARI at the Covid Consultation Centre (CCC) in Luxembourg were tested using a respiratory virus panel (ADV = Adenovirus, FLU A = Influenza A, FLU B = Influenza B, HRV = Human Rhinovirus, MPV = Human metapneumovirus, PIV = Parainfluenza virus, RSV = Respiratory Syncytial Virus, SARS-CoV-2 = Severe acute respiratory syndrome coronavirus 2).

    The SARS-COV-2 was the most prevalent respiratory virus detected in the “Sentinel” network, with 36 positive cases (33%). The wave of Human Rhinovirus (HRV) continued in week 19/2021, with 9 positive cases in 108 tests (8,3%). Four cases of MPV (3,7%) have been detected and no cases of other respiratory viruses like ADV, PIV or RSV.

    No case  of Influenza A/B was detected. (c.f. Figure 2).

    SARS-CoV-2 Genomic Surveillance

    The current sequencing strategy

    The National Reference Laboratory for Acute Respiratory Infections at LNS continues to improve the representativeness of the pool of sequenced specimens to reach real-time epidemiology, by implementing the following weekly sequencing activities:

    • Sequencing specimens from all hospitalized positive cases
    • Sequencing specimens from all positive cases from Airport testing program
    • Sequencing specimens from all outbreaks and identified clusters
    • Systematic sequencing of specimens from reinfections and post-vaccination-infections
    • Population sequencing of specimens from representative regions and age groups, to follow the evolution of the different variants in the Luxembourg population.

    The representative sequencing sample was based on the minimum number of specimens required to extrapolate prevalence of VOC variants with error rate of 5%. The representative sample was estimated based on the number of positive cases in Luxembourg in week 19 (759). The minimum sample size required to detect prevalence of B.1.1.7 (82%) reported in week 18 with an error margin of 5% was estimated to be 175 specimens. The calculation was based on a sample size calculation tool that uses the expected prevalence of the variant in the total population. (Population Proportion – Sample Size – Select Statistical Consultants (select-statistics.co.uk). This number represented a coverage of 23,1% which exceeds the minimum coverage recommended by ECDC (10%). The number of non-targeted specimens from Luxembourgish residents sequenced this week was 449. Therefore, our sequencing results this week are representative of the circulating variants in Luxembourg.

    The starting material used for sequencing is respiratory specimens (nasopharyngeal or oropharyngeal swabs) that have already been tested positive by RT PCR.

    In parallel, we continue to evaluate commercial PCR screening, using the same starting material, to detect the Variants of Concern (VOCs), with specific PCR. This will enable a faster investigation time of any outbreak and allow us to screen 100% of positive cases referred to LNS, including those that do not pass the quality criteria for sequencing. Specimens that are not eligible for sequencing can thus be used in a PCR to detect the presence of variants of concern.

    The LNS sequencing data sharing strategy includes sharing of the sequencing data with GISAID EpiCov database (www.gisaid.org ) on a periodic basis.

    Sequenced specimens

    Last week the microbial genomics platform at the LNS sequenced 630 specimens, with 543 collected in week 19/2021. The sequencing pool referring to Luxembourgish residence represents 67,5% of new infections reported in Luxembourg in week 19/2021. Among these 543 specimens, 65 specimens were reported to be part of a cluster or outbreak investigation, and 31 specimens were from non-residents (2 specimen overlapping). This leads to 449 specimens, collected in week 19, and being the representative population sequencing sample. In the population representative sample of residents, the frequency of B.1.1.7 and B.1.351 was 81,7% and 6% respectively, while the frequency of P.1 and B.1.617.2 was 3,6% and 2,2% respectively.

    The population sequencing coverage in week 19/2021 was 67,5% (Figure 3). Based on statistical inference, the frequency of the reported variants in week 19/2021 is representative of the circulating variants in Luxembourg with a margin of error of 5%.

    Circulating lineage detection

    Lineages (variants) have been assigned based on Rambaut et al by means of Phylogenetic Assignment of Named Global Outbeak LINeages (pangolin) software  (v2.4.2, pangoLEARN version 2021-05-12).

    The lineage nomenclature system that we use is the one proposed by Rambaut et al. that focuses on actively circulating virus lineages (https://cov-lineages.org ).

    In week 19/2021, in the population representative sample, after removal of cluster specimens, and excluding specimens collected from non-residents, there were 14 circulating SARS-CoV-2 variants, with the main three variants being B.1.1.7 (81,7%, CI 78,1% – 85,3%), B.1.351 (6,0%,CI 3,8% – 8,2%), followed by P.1 (3,6%, CI 1,9% – 5,3%), as shown in Figure 4.

    Variants of Concern tracker (B.1.1.7, B.1.351, P.1, A.23.1, B.1.525, B.1.617.2)

    Among specimens collected within the week 19/2021, 429 cases of the B.1.1.7 variant have been detected, representing 79% of the specimens in the week’s sequencing pool (by comparison, the week 18/2021 pool had shown a frequency of 81,6% of this variant, including additional specimens having been sequenced from previous weeks). The total case count of sequenced variant B.1.1.7 was 5610 by week 19/2021. The earliest collection date for this variant remains 19/DEC/2020 and the latest is 16/05/2021.

    In the collection period of week 19/2021, 31 cases of the South African variant B.1.351 have been detected, representing 5,7% of the specimens in the week’s sequencing pool (by comparison, the week 18/2021 pool had shown 7,0% of this variant, including additional specimens having been sequenced from previous weeks). The total case count of sequenced variant B.1.351 was 1007 by week 19/2021. The earliest collection date for this variant remains 11/JAN/2021 and the latest is 15/MAY/2021.

    In week 19/2021, 13 additional cases of B.1.525 has been detected, and 20 new cases of the Brazilian variant P.1. Thus, the case count by week 19 for B.1.525 is 39 (latest sampling date 14/MAY/2021) and for P.1 the case count is 93 (latest sampling date 16/MAY/2021).

    In week 19/2021, 21 additional cases of the B.1.617 subtype B.1.617.2 have been detected (latest sampling date 16/MAY/2021). The case count by week 19 for B.1.617.1 remains 6, and for B.1.617.2 it raises to 26. Since  May 6th B.1.617.2 has been escalated by Public Health England from a variant under investigation to a variant of concern.

    By now, no case of A.23.1 has been detected in Luxembourg (Figure 5).

    Lineage B.1.1.7 is characterized by several spike protein mutations, including N501Y, H69/V70del and P861H. The variant seems to have a considerable epidemiological impact, as it has a higher transmissibility rate.

    Lineage B.1.351 holds numerous spike protein mutations, of which three are located in the receptor binding domain (K417N, E484K and N501Y), and are therefore relevant for antibody binding. As for B.1.1.7, a higher transmissibility rate and viral loads seem to be associated with this variant. Due to the K417N and E484K mutations, an impact on vaccination efficacy and possibility of reinfection is subject to scientific investigation.

    Lineage P.1 (descendent of B.1.1.28), initially found in the Amazon region, has a similar mutation profile as the South African variant, including E484K and N501Y. Concerns are, as for the South African variant, higher transmissibility and a decreased protection by neutralizing antibodies.

    Lineage B.1.525 carries several mutations of biological significance, including E484K, Q677H and F888L. It does not carry N501Y, but a set of deletions similar to the B.1.1.7 variant.

    Lineage B.1.617 is a variant first detected in India and was designated “Under Investigation” on 1st  April 2021 by Public Health England. It contains a number of spike mutations associated with antigenic escape or found in other variants of concern, including L452R, E484Q and P681R. Subtype B.1.617.2 does not carry S:E484Q and seems to be at least as transmissible as B.1.1.7 (with moderate confidence).

    Figure 5  Evolution of variants in Sequencing pool of all specimens including targeted sequencing (cluster/contact tracing/ non residents) since first detection of B.1.1.7 in Luxembourg

    By week 19/2021, 95,6 % of the variants detected in the sequenced specimen pool are declared as either Variants of Concern (VOC – B.1.1.7, B.1.351, P.1, B.1.617.2) or Variants Under Investigation (VUI – B.1.525, B.1.1.318, B.1.617.1).

    Clinically relevant mutations

    Currently the LNS genomic surveillance program – independently from lineage calling – notes the occurrence of 13 different known SARS-CoV-2 mutations, assumed to have clinical and epidemiological relevance. The list of observed mutations is being updated continually, based on the appearance and prevalence of SARS-CoV-2 variants.

    The following table provides the overall frequencies of these mutations, detected in the lineage-assignable genome sequences, analyzed between 01/SEP/2020 and 16/MAY/2021 (N=11447), as well as the frequencies in week 19/2021.

    References

    Genomic sequencing of SARS-CoV-2. A guide to implementation for maximum impact on public health. WHO, 8 January 2021.

    COVID-19 data portal. 2020 (https://www.covid19dataportal.org/sequences )

    J Hadfield et al. Nextstrain: real-time tracking of pathogen evolution. Bioinformatics 2018;34:4121-4123

    A Rambaut et al. A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nat Microbiol 2020;5:1403-1407

    https://github.com/cov-lineages/pangolin

    For more information on lineages visit: https://cov-lineages.org
    For more information and statistics on Covid-19 infections in Luxembourg visit: https://covid19.public.lu/en.html

     

  • Semaine 18

    Respiratory Viruses in Luxembourg (ReViLux)

    Weekly report (Period 03/05/-09/05/2021)

    Executive Summary

    The aim of the “Sentinel” national surveillance program is to monitor the circulating respiratory viruses, including SARS-CoV-2 variants, and hence underpin public health actions.

    In week 18/2021, the overall frequency of the SARS-CoV-2 B.1.1.7 variant in all sequenced specimens remained stable on 81,1% (CI 77,6% – 84,6%, p<0,05). For the SARS-CoV-2 B.1.351 variant, we found an overall frequency of 6,8% (CI 4,5% – 9%, p<0,05) within the sequenced sample, while for P.1, the frequency increased to 4,6% (CI 2,7% – 6,5%, p<0,05).

    The representative sample was estimated, based on the number of positive cases in Luxembourg for week 18 (936). The minimum sample size required to detect prevalence of B.1.1.7 (81%) reported in week 17, with an error margin of 5%, was estimated to be 189 specimens. This number corresponds to a coverage of 20,2 %, which exceeds the minimum coverage recommended by ECDC (10%). The sequencing results of week 16 are representative of the circulating variants in Luxembourg with a margin of error of 5%.

    The total number of sequences performed this week was 500, with 482 specimens (deduplicated) having been collected in the time frame of week 18/2021. The sequencing coverage this week was 47,2% from all positive cases in Luxembourg.

    Clinical Surveillance

    The “Sentinel” surveillance network reported 346 consultations in week 18 (03/MAY/2021 – 09/MAY/2021). There were 2 cases of ILI1, corresponding to 0,6% of the consultations, as shown in Figure 1. The number of consultations for ARI2 was 47, which represents 13,6% of the consultations.

    Virological Surveillance

    Patients presenting with ILI and ARI at the Covid Consultation Centre (CCC) in Luxembourg were tested using a respiratory virus panel (ADV = Adenovirus, FLU A = Influenza A, FLU B = Influenza B, HRV = Human Rhinovirus, MPV = Human metapneumovirus, PIV = Parainfluenza virus, RSV = Respiratory Syncytial Virus, SARS-CoV-2 = Severe acute respiratory syndrome coronavirus 2).

    The SARS-COV-2 was the most prevalent respiratory virus detected in the “Sentinel” network, with 33 positive cases (28,7%). The wave of Human Rhinovirus (HRV) continued in week 18/2021, with 10 positive cases in 115 tests (8,7%). Sporadic cases of other respiratory viruses continued to appear, such as 2 cases of PIV (1,7%) and MPV (each 1,7%) and 1 case of RSV (0,9%). No case  of Influenza A/B was detected. (c.f. Figure 2).

    In Luxembourg, we have tested 115 samples from the Sentinel surveillance network, as compared to 555 specimens tested in Europe, in the week 18/2021. None of these 555 specimens tested positive for Influenza type A/B virus. Overall, surveillance was very efficient over the course of the 2020-2021 season and although there was a small decrease in the number of samples tested as compared with previous seasons, there was a remarkable decrease (>99% decrease) in the number of influenza infections detected, with numbers detected on a weekly basis being similar to those reported during interseasonal periods. (Source: FluNews Europe).

    SARS-CoV-2 Genomic Surveillance

    The current sequencing strategy

    The National Reference Laboratory for Acute Respiratory Infections at LNS continues to improve the representativeness of the pool of sequenced specimens to reach real-time epidemiology, by implementing the following weekly sequencing activities:

    • Sequencing specimens from all hospitalized positive cases
    • Sequencing specimens from all positive cases from Airport testing program
    • Sequencing specimens from all outbreaks and identified clusters
    • Systematic sequencing of specimens from reinfections and post-vaccination-infections
    • Population sequencing of specimens from representative regions and age groups, to follow the evolution of the different variants in the Luxembourg population.

    The representative sequencing sample was based on the minimum number of specimens required to extrapolate prevalence of VOC variants with error rate of 5%. The representative sample was estimated based on the number of positive cases in Luxembourg in week 18 (936). The minimum sample size required to detect prevalence of B.1.1.7 (81%) reported in week 17 with an error margin of 5% was estimated to be 189 specimens. The calculation was based on a sample size calculation tool that uses the expected prevalence of the variant in the total population. (Population Proportion – Sample Size – Select Statistical Consultants (select-statistics.co.uk). This number represented a coverage of 20,2% which exceeds the minimum coverage recommended by ECDC (10%). The number of non-targeted specimens from Luxembourgish residents sequenced this week was 397. Therefore, our sequencing results this week are representative of the circulating variants in Luxembourg.

    The starting material used for sequencing is respiratory specimens (nasopharyngeal or oropharyngeal swabs) that have already been tested positive by RT PCR.

    In parallel, we continue to evaluate commercial PCR screening, using the same starting material, to detect the Variants of Concern (VOCs), with specific PCR. This will enable a faster investigation time of any outbreak and allow us to screen 100% of positive cases referred to LNS, including those that do not pass the quality criteria for sequencing. Specimens that are not eligible for sequencing can thus be used in a PCR to detect the presence of variants of concern.

    The LNS sequencing data sharing strategy includes sharing of the sequencing data with GISAID EpiCov database (www.gisaid.org ) on a periodic basis.

    Sequenced specimens

    Last week the microbial genomics platform at the LNS sequenced 500 specimens, with 482 collected in week 18/2021. The sequencing pool represents 47,2% of new infections reported in Luxembourg in week 18/2021. Among these 482 specimens, 50 specimens were reported to be part of a cluster or outbreak investigation, and 40 specimens were from non-residents (5 specimen overlapping). This leads to 397 specimens, collected in week 18, and being the representative population sequencing sample. In the population representative sample of residents, the frequency of B.1.1.7 and B.1.351 was 83,4% and 5,8% respectively, while the frequency of P.1 was 3,8%.

    The population sequencing coverage in week 18/2021 was 47,2% (Figure 3). Based on statistical inference, the frequency of the reported variants in week 18/2021 is representative of the circulating variants in Luxembourg with a margin of error of 5%.

    Circulating lineage detection

    Lineages (variants) have been assigned based on Rambaut et al by means of Phylogenetic Assignment of Named Global Outbeak LINeages (pangolin) software  (v2.4.2, pangoLEARN version 2021-05-12).

    The lineage nomenclature system that we use is the one proposed by Rambaut et al. that focuses on actively circulating virus lineages (https://cov-lineages.org ).

    In week 18/2021, in the population representative sample, after removal of cluster specimens, and excluding specimens collected from non-residents, there were 13 circulating SARS-CoV-2 variants, with the main three variants being B.1.1.7 (83,4%, CI 79,7% – 87,1%), B.1.351 (5,8%, CI 3,5% – 8,1%), followed by P.1 (3,8%, CI 1,9% – 5,7%), as shown in Figure 4.

    Variants of Concern tracker (B.1.1.7, B.1.351, P.1, A.23.1, B.1.525, B.1.617.2)

    Among specimens collected within the week 18/2021, 391 cases of the B.1.1.7 variant have been detected, representing 81,1% of the specimens in the week’s sequencing pool (by comparison, the week 17/2021 pool had shown a frequency of 80,6% of this variant, including additional specimens having been sequenced from previous weeks). The total case count of sequenced variant B.1.1.7 was 4098 by week 18/2021. The earliest collection date for this variant remains 19/DEC/2020 and the latest is 09/05/2021.

    In the collection period of week 18/2021, 33 cases of the South African variant B.1.351 have been detected, representing 6,8% of the specimens in the week’s sequencing pool (by comparison, the week 17/2021 pool had shown 10,8% of this variant, including additional specimens having been sequenced from previous weeks). The total case count of sequenced variant B.1.351 was 967 by week 18/2021. The earliest collection date for this variant remains 11/JAN/2021 and the latest is 09/MAY/2021.

    In week 18/2021, 1 additional case of B.1.525 has been detected, and 22 new cases of the Brazilian variant P.1. Thus, the case count by week 18 for B.1.525 is 26 (latest sampling date 07/MAY/2021) and for P.1 the case count is 72 (latest sampling date 08/MAY/2021).

    In week 18/2021, 4 additional case of the B.1.617 subtype B.1.617.2 have been detected (latest sampling date 07/MA/2021). The case count by week 18 for B.1.617.1 remains 6, and for B.1.617.2 it raises to 5. Since  May 6th B.1.617.2 has been escalated by Public Health Engand from a variant under investigation to a variant of concern.

    By now, no case of A.23.1 has been detected in Luxembourg (Figure 5).

    Lineage B.1.1.7 is characterized by several spike protein mutations, including N501Y, H69/V70del and P861H. The variant seems to have a considerable epidemiological impact, as it has a higher transmissibility rate.

    Lineage B.1.351 holds numerous spike protein mutations, of which three are located in the receptor binding domain (K417N, E484K and N501Y), and are therefore relevant for antibody binding. As for B.1.1.7, a higher transmissibility rate and viral loads seem to be associated with this variant. Due to the K417N and E484K mutations, an impact on vaccination efficacy and possibility of reinfection is subject to scientific investigation.

    Lineage P.1 (descendent of B.1.1.28), initially found in the Amazon region, has a similar mutation profile as the South African variant, including E484K and N501Y. Concerns are, as for the South African variant, higher transmissibility and a decreased protection by neutralizing antibodies.

    Lineage B.1.525 carries several mutations of biological significance, including E484K, Q677H and F888L. It does not carry N501Y, but a set of deletions similar to the B.1.1.7 variant.

    Lineage B.1.617 is a variant first detected in India and was designated “Under Investigation” on 1st  April 2021 by Public Health England. It contains a number of spike mutations associated with antigenic escape or found in other variants of concern, including L452R, E484Q and P681R. Subtype B.1.617.2 does not carry S:E484Q and seems to be at least as transmissible as B.1.1.7 (with moderate confidence).

    By week 18/2021, 96,5 % of the variants detected in the sequenced specimen pool are declared as either Variants of Concern (VOC – B.1.1.7, B.1.351, P.1, B.1.617.2) or Variants Under Investigation (VUI – B.1.525, B.1.1.318, B.1.617.1).

    Clinically relevant mutations

    Currently the LNS genomic surveillance program – independently from lineage calling – notes the occurrence of 13 different known SARS-CoV-2 mutations, assumed to have clinical and epidemiological relevance. The list of observed mutations is being updated continually, based on the appearance and prevalence of SARS-CoV-2 variants.

    The following table provides the overall frequencies of these mutations, detected in the lineage-assignable genome sequences, analyzed between 01/SEP/2020 and 09/MAY/2021 (N=10831), as well as the frequencies in week 18/2021.

    References

    Genomic sequencing of SARS-CoV-2. A guide to implementation for maximum impact on public health. WHO, 8 January 2021.

    COVID-19 data portal. 2020 (https://www.covid19dataportal.org/sequences )

    J Hadfield et al. Nextstrain: real-time tracking of pathogen evolution. Bioinformatics 2018;34:4121-4123

    A Rambaut et al. A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nat Microbiol 2020;5:1403-1407

    https://github.com/cov-lineages/pangolin

    For more information on lineages visit: https://cov-lineages.org
    For more information and statistics on Covid-19 infections in Luxembourg visit: https://covid19.public.lu/en.html

  • Semaine 17

    Respiratory Viruses in Luxembourg (ReViLux)

    Weekly report (Period 26/04/-02/05/2021)

    Executive Summary

    The aim of the “Sentinel” national surveillance program is to monitor the circulating respiratory viruses, including SARS-CoV-2 variants, and hence underpin public health actions.

    In week 17/2021, the overall frequency of the SARS-CoV-2 B.1.1.7 variant in all sequenced specimens decreased to 80,8% (CI 77,6% – 84%, p<0,05). For the SARS-CoV-2 B.1.351 variant, we found an overall frequency of 10,7% (CI 8,2% – 13,2%, p<0,05) within the sequenced sample, while for P.1, the frequency was 2,6% (CI 1,3% – 3,9%, p<0,05).

    The representative sample was estimated, based on the number of positive cases in Luxembourg for week 17 (1117). The minimum sample size required to detect prevalence of B.1.1.7 (85%) reported in week 16, with an error margin of 5%, was estimated to be 167 specimens. This number corresponds to a coverage of 14,9 %, which exceeds the minimum coverage recommended by ECDC (10%). The sequencing results of week 16 are representative of the circulating variants in Luxembourg with a margin of error of 5%.

    The total number of sequences performed this week was 678, with 588 specimens (deduplicated) having been collected in the time frame of week 17/2021. The sequencing coverage this week was 52,6% from all positive cases in Luxembourg.

    Clinical Surveillance

    The “Sentinel” surveillance network reported 324 consultations in week 17 (26/APR/2021 – 02/MAY/2021). There were 4 cases of ILI1, corresponding to 1,2% of the consultations, as shown in Figure 1. The number of consultations for ARI2 was 23, which represents 7,1% of the consultations.

    Virological Surveillance

    Patients presenting with ILI and ARI at the Covid Consultation Centre (CCC) in Luxembourg were tested using a respiratory virus panel (ADV = Adenovirus, FLU A = Influenza A, FLU B = Influenza B, HRV = Human Rhinovirus, MPV = Human metapneumovirus, PIV = Parainfluenza virus, RSV = Respiratory Syncytial Virus, SARS-CoV-2 = Severe acute respiratory syndrome coronavirus 2).

    The SARS-COV-2 was the most prevalent respiratory virus detected in the “Sentinel” network, with 37 positive cases (28,9%). The wave of Human Rhinovirus (HRV) continued in week 17/2021, with 9 positive cases in 128 tests (7%). Sporadic cases of other respiratory viruses continued to appear, such as 2 cases of PIV and RSV (each 1,5%) and 1 case of ADV. No case  of Influenza A/B was detected. (c.f. Figure 2).

    In Luxembourg, we have tested 128 samples from the Sentinel surveillance network, as compared to 822 specimens tested in Europe, in the week 17/2021. None of these 822 specimens tested positive for Influenza type A/B virus (Source: FluNews Europe).

    SARS-CoV-2 Genomic Surveillance

    The current sequencing strategy

    The National Reference Laboratory for Acute Respiratory Infections at LNS continues to improve the representativeness of the pool of sequenced specimens to reach real-time epidemiology, by implementing the following weekly sequencing activities:

    • Sequencing specimens from all hospitalized positive cases
    • Sequencing specimens from all positive cases from Airport testing program
    • Sequencing specimens from all outbreaks and identified clusters
    • Systematic sequencing of specimens from reinfections and post-vaccination-infections
    • Population sequencing of specimens from representative regions and age groups, to follow the evolution of the different variants in the Luxembourg population.

    The representative sequencing sample was based on the minimum number of specimens required to extrapolate prevalence of VOC variants with error rate of 5%. The representative sample was estimated based on the number of positive cases in Luxembourg in week 17 (1117). The minimum sample size required to detect prevalence of B.1.1.7 (85%) reported in week 16 with an error margin of 5% was estimated to be 167 specimens. The calculation was based on a sample size calculation tool that uses the expected prevalence of the variant in the total population. (Population Proportion – Sample Size – Select Statistical Consultants (select-statistics.co.uk). This number represented a coverage of 14,9% which exceeds the minimum coverage recommended by ECDC (10%). The number of non-targeted specimens from Luxembourgish residents sequenced this week was 498. Therefore, our sequencing results this week are representative of the circulating variants in Luxembourg.

    The starting material used for sequencing is respiratory specimens (nasopharyngeal or oropharyngeal swabs) that have already been tested positive by RT PCR.

    In parallel, we continue to evaluate commercial PCR screening, using the same starting material, to detect the Variants of Concern (VOCs), with specific PCR. This will enable a faster investigation time of any outbreak and allow us to screen 100% of positive cases referred to LNS, including those that do not pass the quality criteria for sequencing. Specimens that are not eligible for sequencing can thus be used in a PCR to detect the presence of variants of concern.

    The LNS sequencing data sharing strategy includes sharing of the sequencing data with GISAID EpiCov database (www.gisaid.org ) on a periodic basis.

    Sequenced specimens

    Last week the microbial genomics platform at the LNS sequenced 678 specimens, with 588 collected in week 17/2021. This represents 52,6% of the new infections reported in Luxembourg in week 17/2021. Among these 588 specimens, 60 specimens were reported to be part of a cluster or outbreak investigation, and 40 specimens were from non-residents (10 specimen overlapping). This leads to 498 specimens, collected in week 17, and being the representative population sequencing sample. In the population representative sample of residents, the frequency of B.1.1.7 and B.1.351 was 82,1% and 10,2% respectively, while the frequency of P.1 was 2,2%.

    The population sequencing coverage in week 17/2021 was 52,6% (Figure 3). Based on statistical inference, the frequency of the reported variants in week 17/2021 is representative of the circulating variants in Luxembourg with a margin of error of 5%.

    Circulating lineage detection

    Lineages (variants) have been assigned based on Rambaut et al by means of Phylogenetic Assignment of Named Global Outbeak LINeages (pangolin) software  (v2.4.2, pangoLEARN version 2021-04-28).

    The lineage nomenclature system that we use is the one proposed by Rambaut et al. that focuses on actively circulating virus lineages (https://cov-lineages.org ).

    In week 17/2021, in the population representative sample, after removal of cluster specimens, and excluding specimens collected from non-residents, there were 13 circulating SARS-CoV-2 variants, with the main three variants being B.1.1.7 (82,1%, CI 78,7% – 85,5%), B.1.351 (10,2%, CI 7,5% – 12,9%), followed by P.1 (2,2%, CI 0,9% – 3,5%), as shown in Figure 4.

    Variants of Concern tracker (B.1.1.7, B.1.351, P.1, A.23.1, B.1.525, B.1.617.2)

    Among specimens collected within the week 17/2021, 475 cases of the B.1.1.7 variant have been detected, representing 80,8% of the specimens in the week’s sequencing pool (by comparison, the week 16/2021 pool had shown a frequency of 85,4% of this variant, including additional specimens having been sequenced from previous weeks). The total case count of sequenced variant B.1.1.7 was 4704 by week 17/2021. The earliest collection date for this variant remains 19/DEC/2020 and the latest is 02/05/2021.

    In the collection period of week 17/2021, 63 cases of the South African variant B.1.351 have been detected, representing 10,7% of the specimens in the week’s sequencing pool (by comparison, the week 16/2021 pool had shown 9,9% of this variant, including additional specimens having been sequenced from previous weeks). The total case count of sequenced variant B.1.351 was 933 by week 17/2021. The earliest collection date for this variant remains 11/JAN/2021 and the latest is 02/MAY/2021.

    In week 17/2021, 10 additional cases of B.1.525 have been detected, and 15 new cases of the Brazilian variant P.1. Thus, the case count by week 17 for B.1.525 is 25 (latest sampling date 30/APR/2021) and for P.1 the case count is 49 (latest sampling date 30/APR/2021).

    In week 17/2021, 1 additional case of the B.1.617 subtype B.1.617.1 has been detected (latest sampling date 26/APR/2021). The case count by week 17 for B.1.617.1 is six, and for B.1.617.2 one. Since  May 6th 2021, B.1.617.2 has been escalated by Public Health Engand from a variant under investigation to a variant of concern.

    By now, no case of A.23.1 has been detected in Luxembourg (Figure 5).

    Lineage B.1.1.7 is characterized by several spike protein mutations, including N501Y, H69/V70del and P861H. The variant seems to have a considerable epidemiological impact, as it has a higher transmissibility rate.

    Lineage B.1.351 holds numerous spike protein mutations, of which three are located in the receptor binding domain (K417N, E484K and N501Y), and are therefore relevant for antibody binding. As for B.1.1.7, a higher transmissibility rate and viral loads seem to be associated with this variant. Due to the K417N and E484K mutations, an impact on vaccination efficacy and possibility of reinfection is subject to scientific investigation.

    Lineage P.1 (descendent of B.1.1.28), initially found in the Amazon region, has a similar mutation profile as the South African variant, including E484K and N501Y. Concerns are, as for the South African variant, higher transmissibility and a decreased protection by neutralizing antibodies.

    Lineage B.1.525 carries several mutations of biological significance, including E484K, Q677H and F888L. It does not carry N501Y, but a set of deletions similar to the B.1.1.7 variant.

    Lineage B.1.617 is a variant first detected in India and was designated “Under Investigation” on 1st  April 2021 by Public Health England. It contains a number of spike mutations associated with antigenic escape or found in other variants of concern, including L452R, E484Q and P681R. Subtype B.1.617.2 does not carry S:E484Q and seems to be at least as transmissible as B.1.1.7 (with moderate confidence).

    By week 17/2021, 97,5 % of detected variants in Luxembourg are declared as either Variants of Concern (VOC – B.1.1.7, B.1.351, P.1, B.1.617.2) or Variants Under Investigation (VUI – B.1.525, B.1.1.318, B.1.617.1).

    Clinically relevant mutations

    Currently the LNS genomic surveillance program – independently from lineage calling – notes the occurrence of 13 different known SARS-CoV-2 mutations, assumed to have clinical and epidemiological relevance. The list of observed mutations is being updated continually, based on the appearance and prevalence of SARS-CoV-2 variants.

    The following table provides the overall frequencies of these mutations, detected in the lineage-assignable genome sequences, analyzed between 01/SEP/2020 and 02/MAY/2021 (N=10333), as well as the frequencies in week 17/2021.

    References

    Genomic sequencing of SARS-CoV-2. A guide to implementation for maximum impact on public health. WHO, 8 January 2021.

    COVID-19 data portal. 2020 (https://www.covid19dataportal.org/sequences )

    J Hadfield et al. Nextstrain: real-time tracking of pathogen evolution. Bioinformatics 2018;34:4121-4123

    A Rambaut et al. A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nat Microbiol 2020;5:1403-1407

    https://github.com/cov-lineages/pangolin

    For more information on lineages visit: https://cov-lineages.org
    For more information and statistics on Covid-19 infections in Luxembourg visit: https://covid19.public.lu/en.html

  • Semaine 16

    Respiratory Viruses in Luxembourg (ReViLux)

    Weekly report (Period 19/04/-25/04/2021)

    Executive Summary

    The aim of the “Sentinel” national surveillance program is to monitor the circulating respiratory viruses, including SARS-CoV-2 variants, and hence underpin public health actions.

    In week 16/2021, the overall frequency of the SARS-CoV-2 B.1.1.7 variant in all sequenced specimens remained stable at 85,2% (CI 82,6% – 87,8%, p<0,05). For the SARS-CoV-2 B.1.351 variant, we found an overall frequency of 9,9% (CI 7,7% – 12,1%, p<0,05) within the sequenced sample, while for P.1, the frequency was 1,4% (CI 0,5% – 2,3%, p<0,05).

    The representative sample was estimated, based on the number of positive cases in Luxembourg for week 16 (1226). The minimum sample size required to detect prevalence of B.1.1.7 (85%) reported in week 14, with an error margin of 5%, was estimated to be 170 specimens. This number corresponds to a coverage of 13,8 %, which exceeds the minimum coverage recommended by ECDC (10%). The sequencing results of week 16 are representative of the circulating variants in Luxembourg with a margin of error of 5%.

    The total number of sequences performed this week was 714, with 695 specimens having been collected in the time frame of week 16/2021. The sequencing coverage this week was 56,7% from all positive cases in Luxembourg, hence representative.

    Clinical Surveillance

    The “Sentinel” surveillance network reported 140 consultations in week 16 (19/APR/2021 – 25/APR/2021). There was no case of ILI1, as shown in Figure 1. The number of consultations for ARI2 was 11, which represents 7,9% of the consultations.

    Virological Surveillance

    Patients presenting with ILI and ARI at the Covid Consultation Centre (CCC) in Luxembourg were tested using a respiratory virus panel (ADV = Adenovirus, FLU A = Influenza A, FLU B = Influenza B, HRV = Human Rhinovirus, MPV = Human metapneumovirus, PIV = Parainfluenza virus, RSV = Respiratory Syncytial Virus, SARS-CoV-2 = Severe acute respiratory syndrome coronavirus 2).

    The SARS-COV-2 was the most prevalent respiratory virus detected in the “Sentinel” network, with 80 positive cases (37,9%). The wave of Human Rhinovirus (HRV) continued in week 16/2021, with 17 positive cases in 211 tests (8%). Sporadic cases of other respiratory viruses continued to appear, such as 2 cases of PIV (0,9%) and 3 cases of ADV. No case  of Influenza A/B was detected. (c.f. Figure 2).

    In Luxembourg, we have tested 211 samples from the Sentinel surveillance network, as compared to 996 specimens tested in Europe, in the week 16/2021. None  of these 996 specimens tested positive for Influenza type A/B virus. Influenza activity remained at interseasonal levels (Source: FluNews Europe).

    SARS-CoV-2 Genomic Surveillance

    The current sequencing strategy

    The National Reference Laboratory for Acute Respiratory Infections at LNS continues to improve the representativeness of the pool of sequenced specimens to reach real-time epidemiology, by implementing the following weekly sequencing activities:

    • Sequencing specimens from all hospitalized positive cases
    • Sequencing specimens from all positive cases from Airport testing program
    • Sequencing specimens from all outbreaks and identified clusters
    • Systematic sequencing of specimens from reinfections and post-vaccination-infections
    • Population sequencing of specimens from representative regions and age groups, to follow the evolution of the different variants in the Luxembourg population.

    The representative sequencing sample was based on the minimum number of specimens required to extrapolate prevalence of VOC variants with error rate of 5%. The representative sample was estimated based on the number of positive cases in Luxembourg in week 16 (1226). The minimum sample size required to detect prevalence of B.1.1.7 (85%) with an error margin of 5% was estimated to be 170 specimens. The calculation was based on a sample size calculation tool that uses the expected prevalence of the variant in the total population. (Population Proportion – Sample Size – Select Statistical Consultants (select-statistics.co.uk). This number represented a coverage of 13,8% which exceeds the minimum coverage recommended by ECDC (10%). The number of non-targeted specimens from Luxembourgish residents sequenced this week was 605. Therefore, our sequencing results this week are representative of the circulating variants in Luxembourg.

    The starting material used for sequencing is respiratory specimens (nasopharyngeal or oropharyngeal swabs) that have already been tested positive by RT PCR.

    In parallel, we are evaluating commercial PCR screening, using the same starting material, to detect the Variants of Concern (VOCs), with specific PCR. This will enable a faster investigation time of any outbreak and allow us to screen 100% of positive cases referred to LNS, including those that do not pass the quality criteria for sequencing. Specimens that are not eligible for sequencing can thus be used in a PCR to detect the presence of variants of concern.

    The LNS sequencing data sharing strategy includes sharing of the sequencing data with GISAID EpiCov database (www.gisaid.org ) on a monthly basis.

    Sequenced specimens

    Last week the microbial genomics platform at the LNS sequenced 714 specimens, with 695 collected in week 16/2021. This represents 56,7% of the new infections reported in Luxembourg in week 16/2021. Among these 650 specimens, 52 specimens were reported to be part of a cluster or outbreak investigation, and 44 specimens were from non-residents (6 specimen overlapping). This leads to 605 specimens, collected in week 16, and being the representative population sequencing sample. In the population representative sample of residents, the frequency of B.1.1.7 and B.1.351 was 85,3% and 10,4% respectively, while the frequency of P.1 was 1,2%.

    The population sequencing coverage in week 16/2021 was 56,7% (Figure 3). Based on statistical inference, the frequency of the reported variants in week 16/2021 is representative of the circulating variants in Luxembourg with a margin of error of 5%.

    Circulating lineage detection

    Lineages (variants) have been assigned based on Rambaut et al by means of Phylogenetic Assignment of Named Global Outbeak LINeages (pangolin) software  (v2.3.8, pangoLEARN version 2021-04-21).

    The lineage nomenclature system that we use is the one proposed by Rambaut et al. that focuses on actively circulating virus lineages (https://cov-lineages.org ).

    In week 16/2021, in the population representative sample, after removal of cluster specimens, and excluding specimens collected from non-residents, there were 14 circulating SARS-CoV-2 variants, with the main three variants being B.1.1.7 (85,3%, CI 82,5% – 88,1%), B.1.351 (10,4%, CI 8% – 12,8%), followed by P.1 (1,2%, CI 0,3% – 2,1%), as shown in Figure 4.

    Variants of Concern tracker (B.1.1.7, B.1.351, P.1, A.23.1 and B.1.525)

    Among specimens collected within the week 16/2021, 592 cases of the B.1.1.7 variant have been detected, representing 85,2% of the specimens in the week’s sequencing pool (by comparison, the week 15/2021 pool had shown a frequency of 85,8% of this variant, including additional specimens having been sequenced from previous weeks). The total case count of sequenced variant B.1.1.7 was 4229 by week 16/2021. The earliest collection date for this variant remains 19/DEC/2020 and the latest is 15/APR/2021.

    In the collection period of week 16/2021, 69 cases of the South African variant B.1.351 have been detected, representing 9,9% of the specimens in the week’s sequencing pool (by comparison, the week 15/2021 pool had shown 8,7% of this variant, including additional specimens having been sequenced from previous weeks). The total case count of sequenced variant B.1.351 was 870 by week 16/2021. The earliest collection date for this variant remains 11/JAN/2021 and the latest is 25/APR/2021.

    In week 16/2021, 7 additional cases of B.1.525 have been detected, and 10 new cases of the Brazilian variant P.1. Thus, the case count by week 16 for B.1.525 is 15 (latest sampling date 23/APR/2021) and for P.1 the case count is 34 (latest sampling date 23/APR/2021).

    In week 16/2021, 3 cases of the so called “double mutant” or “indian variant” B.1.617, subtype B.1.617.1, have been detected in Luxembourg. By now, no case of A.23.1 has been detected in Luxembourg (Figure 5).

    Lineage B.1.1.7 is characterized by several spike protein mutations, including N501Y, H69/V70del and P861H. The variant seems to have a considerable epidemiological impact, as it has a higher transmissibility rate.

    Lineage B.1.351 holds numerous spike protein mutations, of which three are located in the receptor binding domain (K417N, E484K and N501Y), and are therefore relevant for antibody binding. As for B.1.1.7, a higher transmissibility rate and viral loads seem to be associated with this variant. Due to the K417N and E484K mutations, an impact on vaccination efficacy and possibility of reinfection is subject to scientific investigation.

    Lineage P.1 (descendent of B.1.1.28), initially found in the Amazon region, has a similar mutation profile as the South African variant, including E484K and N501Y. Concerns are, as for the South African variant, higher transmissibility and a decreased protection by neutralizing antibodies.

    Lineage B.1.525 carries several mutations of biological significance, including E484K, Q677H and F888L. It does not carry N501Y, but a set of deletions similar to the B.1.1.7 variant.

    Lineage B.1.617 is a variant first detected in India and was designated “Under Investigation” on 1 April 2021 by Public Health England. It contains a number of spike mutations associated with antigenic escape or found in other variants of concern, including L452R, E484Q and P681R.

    By week 16/2021, 98,5 % of detected variants in Luxembourg are declared as either Variants of Concern (VOC – B.1.1.7, B.1.351, P.1) or Variants Under Investigation (VUI – B.1.525, B.1.1.318, B.1.617).

    Clinically relevant mutations

    Currently the LNS genomic surveillance program – independently from lineage calling – notes the occurrence of 13 different known SARS-CoV-2 mutations, assumed to have clinical and epidemiological relevance. The list of observed mutations is being updated continually, based on the appearance and prevalence of SARS-CoV-2 variants.

    The following table provides the overall frequencies of these mutations, detected in the lineage-assignable genome sequences, analyzed between 01/SEP/2020 and 25/APR/2021 (N=9653), as well as the frequencies in week 16/2021.

    References

    Genomic sequencing of SARS-CoV-2. A guide to implementation for maximum impact on public health. WHO, 8 January 2021.

    COVID-19 data portal. 2020 (https://www.covid19dataportal.org/sequences )

    J Hadfield et al. Nextstrain: real-time tracking of pathogen evolution. Bioinformatics 2018;34:4121-4123

    A Rambaut et al. A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nat Microbiol 2020;5:1403-1407

    https://github.com/cov-lineages/pangolin

    For more information on lineages visit: https://cov-lineages.org
    For more information and statistics on Covid-19 infections in Luxembourg visit: https://covid19.public.lu/en.html

  • Semaine 15

    Respiratory Viruses in Luxembourg (ReViLux)

    Weekly report (Period 12/04/-18/04/2021)

    Executive Summary

    The aim of the “Sentinel” national surveillance program is to monitor the circulating respiratory viruses, including SARS-CoV-2 variants, and hence underpin public health actions.

    In week 15/2021, the overall frequency of the SARS-CoV-2 B.1.1.7 variant in all sequenced specimens increased to 85,8% (CI 83,1% – 88,5%, p<0,05). For the SARS-CoV-2 B.1.351 variant, we found an overall frequency of 8,8% (CI 6,6% – 11%, p<0,05) within the sequenced sample, while for P.1, the frequency was 0,77% (CI 0,1% – 1,5%, p<0,05).

    The representative sample was estimated, based on the number of positive cases in Luxembourg for week 15 (1261). The minimum sample size required to detect prevalence of B.1.1.7 (81%) reported in week 14, with an error margin of 5%, was estimated to be 200 specimens. This number corresponds to a coverage of 15,8 %, which exceeds the minimum coverage recommended by ECDC (10%). The sequencing results of week 15 are representative of the circulating variants in Luxembourg with a margin of error of 5%.

    The total number of sequences performed this week was 687, with 650 specimens having been collected in the time frame of week 15/2021. The sequencing coverage this week was 51,6% from all positive cases in Luxembourg.

    Clinical Surveillance

    The “Sentinel” surveillance network reported 146 consultations in week 15 (12/APR/2021 – 18/APR/2021). There was no case of ILI1, as shown in Figure 1. The number of consultations for ARI2 was 14, which represents 9,6% of consultations.

    Virological Surveillance

    Patients presenting with ILI and ARI at the Covid Consultation Centre (CCC) in Luxembourg were tested using a respiratory virus panel (ADV = Adenovirus, FLU A = Influenza A, FLU B = Influenza B, HRV = Human Rhinovirus, MPV = Human metapneumovirus, PIV = Parainfluenza virus, RSV = Respiratory Syncytial Virus, SARS-CoV-2 = Severe acute respiratory syndrome coronavirus 2).

    The SARS-COV-2 was the most prevalent respiratory virus detected in the “Sentinel” network, with 66 positive cases (29,7%). The wave of Human Rhinovirus (HRV) continued in week 15/2021, with 14 positive cases in 222 tests (6,3%). Sporadic cases of other respiratory viruses continued to appear, such as 5 cases of PIV (2,3%), 2 cases of MPV and 1 case of ADV. No case  of Influenza A/B was detected. (c.f. Figure 2).

    In Luxembourg, we have tested 222 samples from the Sentinel surveillance network, as compared to 1271 specimens tested in Europe, in the week 15/2021. Four of these 1271 specimens tested positive for Influenza type A virus. Influenza activity remained at interseasonal levels.(Source: FluNews Europe).

    SARS-CoV-2 Genomic Surveillance

    The current sequencing strategy

    The National Reference Laboratory for Acute Respiratory Infections at LNS continues to improve the representativeness of the pool of sequenced specimens to reach real-time epidemiology, by implementing the following weekly sequencing activities:

    • Sequencing specimens from all hospitalized positive cases
    • Sequencing specimens from all positive cases from Airport testing program
    • Sequencing specimens from all outbreaks and identified clusters
    • Systematic sequencing of specimens from reinfections and post-vaccination-infections
    • Population sequencing of specimens from representative regions and age groups, to follow the evolution of the different variants in the Luxembourg population.

    The representative sequencing sample was based on the minimum number of specimens required to extrapolate prevalence of VOC variants with error rate of 5%. The representative sample was estimated based on the number of positive cases in Luxembourg in week 15 (1261). The minimum sample size required to detect prevalence of B.1.1.7 (81%) with an error margin of 5% was estimated to be 200 specimens. The calculation was based on a sample size calculation tool that uses the expected prevalence of the variant in the total population. (Population Proportion – Sample Size – Select Statistical Consultants (select-statistics.co.uk). This number represented a coverage of 15,8% which exceeds the minimum coverage recommended by ECDC (10%). The number of non-targeted specimens from Luxembourgish residents sequenced this week was 561. Therefore, our sequencing results this week are representative of the circulating variants in Luxembourg.

    The starting material used for sequencing is respiratory specimens (nasopharyngeal or oropharyngeal swabs) that have already been tested positive by RT PCR.

    In parallel, we are evaluating commercial PCR screening, using the same starting material, to detect the Variants of Concern (VOCs), with specific PCR. This will enable a faster investigation time of any outbreak and allow us to screen 100% of positive cases referred to LNS, including those that do not pass the quality criteria for sequencing. Specimens that are not eligible for sequencing can thus be used in a PCR to detect the presence of variants of concern.

    The LNS sequencing data sharing strategy includes sharing of the sequencing data with GISAID EpiCov database (www.gisaid.org ) on a periodic basis.

    Sequenced specimens

    Last week the microbial genomics platform at the LNS sequenced 687 specimens, with 650 collected in week 15/2021. This represents 51,6% of the new infections reported in Luxembourg in week 15/2021. Among these 650 specimens, 46 specimens were reported to be part of a cluster or outbreak investigation, and 43 specimens were from non-residents (10 specimen overlapping). This leads to 561 specimens, collected in week 15, and being the representative population sequencing sample. In the population representative sample of residents, the frequency of B.1.1.7 and B.1.135 was 86,3% and 8,9% respectively, while the frequency pf P.1 was 0,5%.

    The population sequencing coverage in week 15/2021 was 51,6% (Figure 3). Based on statistical inference, the frequency of the reported variants in week 15/2021 is representative of the circulating variants in Luxembourg with a margin of error of 5%.

    Circulating lineage detection

    Lineages (variants) have been assigned based on Rambaut et al by means of Phylogenetic Assignment of Named Global Outbeak LINeages (pangolin) software  (v2.3.8, pangoLEARN version 2021-04-14).

    The lineage nomenclature system that we use is the one proposed by Rambaut et al. that focuses on actively circulating virus lineages (https://cov-lineages.org ).

    In week 15/2021, in the population representative sample, after removal of cluster samples, and excluding specimens collected from non-residents, there were 15 circulating SARS-CoV-2 variants, with the main three variants being  B.1.1.7 (86,3%, CI 83,4% – 89,1%), B.1.351 (8,9%, CI 6,5% – 11,3%), followed by B.1 (0,5%, CI 0% – 1,1%), as shown in Figure 4.

    Variants of Concern tracker (B.1.1.7, B.1.351, P.1, A.23.1 and B.1.525)

    Among specimens collected within the week 15/2021, 558 cases of the B.1.1.7 variant have been detected, representing 85,8% of the specimens in the week’s sequencing pool (by comparison, the week 14/2021 pool had shown a frequency of 81,5% of this variant, including additional specimens having been sequenced from previous weeks). The total case count of sequenced variant B.1.1.7 was 3626 by week 15/2021. The earliest collection date for this variant remains 19/DEC/2020 and the latest is 18/APR/2021.

    In the collection period of week 15/2021, 57 cases of the South African variant B.1.351 have been detected, representing 8,8% of the specimens in the week’s sequencing pool (by comparison, the week 14/2021 pool had shown 14% of this variant, including additional specimens having been sequenced from previous weeks). The total case count of sequenced variant B.1.351 was 799 by week 15/2021. The earliest collection date for this variant remains 11/JAN/2021 and the latest is 18/APR/2021.

    In week 15/2021, three additional cases of B.1.525 have been detected, and 5 new cases of the Brazilian variant P.1. Thus, the case count by week 15 for B.1.525 is 8 (latest sampling date 13/APR/2021) and for P.1 the case count is 24 (latest sampling date 17/APR/2021).

    By now, no case of A.23.1 has been detected in Luxembourg.

    In week 15/2021, 3 cases of the so called “double mutant” or “indian variant” B.1.617 have been detected in Luxembourg. All detected cases are linked to travelling (Figure 5).

    Lineage B.1.1.7 is characterized by several spike protein mutations, including N501Y, H69/V70del and P861H. The variant seems to have a considerable epidemiological impact, as it has a higher transmissibility rate.

    Lineage B.1.351 holds numerous spike protein mutations, of which three are located in the receptor binding domain (K417N, E484K and N501Y), and are therefore relevant for antibody binding. As for B.1.1.7, a higher transmissibility rate and viral loads seem to be associated with this variant. Due to the K417N and E484K mutations, an impact on vaccination efficacy and possibility of reinfection is subject to scientific investigation.

    Lineage P.1 (descendent of B.1.1.28), initially found in the Amazon region, has a similar mutation profile as the South African variant, including E484K and N501Y. Concerns are, as for the South African variant, higher transmissibility and a decreased protection by neutralizing antibodies.

    Lineage B.1.525 carries several mutations of biological significance, including E484K, Q677H and F888L. It does not carry N501Y, but a set of deletions similar to the B.1.1.7 variant.

    Lineage B.1.617 is a variant first detected in India and was designated “Under Investigation” on 1 April 2021 by Public Health England. It contains a number of spike mutations associated with antigenic escape or found in other variants of concern, including L452R, E484Q and P681R.

    By week 15/2021, 96,6 % of detected variants in Luxembourg are declared as either Variants of Concern (VOC – B.1.1.7, B.1.351, P.1) or Variants Under Investigation (VUI – B.1.525, B.1.1.318, B.1.617).

    Clinically relevant mutations

    Currently the LNS genomic surveillance program – independently from lineage calling – notes the occurrence of 13 different known SARS-CoV-2 mutations, assumed to have clinical and epidemiological relevance. The list of observed mutations is being updated continually, based on the appearance and prevalence of SARS-CoV-2 variants.

    The following table provides the overall frequencies of these mutations, detected in the lineage-assignable genome sequences, analyzed between 01/SEP/2020 and 18/APR/2021 (N=8938), as well as the frequencies in week 15/2021.

    References

    Genomic sequencing of SARS-CoV-2. A guide to implementation for maximum impact on public health. WHO, 8 January 2021.

    COVID-19 data portal. 2020 (https://www.covid19dataportal.org/sequences )

    J Hadfield et al. Nextstrain: real-time tracking of pathogen evolution. Bioinformatics 2018;34:4121-4123

    A Rambaut et al. A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nat Microbiol 2020;5:1403-1407

    https://github.com/cov-lineages/pangolin

    For more information on lineages visit: https://cov-lineages.org
    For more information and statistics on Covid-19 infections in Luxembourg visit: https://covid19.public.lu/en.html

  • Semaine 14

    Respiratory Viruses in Luxembourg (ReViLux)

    Weekly report (Period 05/04/-11/04/2021)

    Executive Summary

    The aim of the “Sentinel” national surveillance program is to monitor the circulating respiratory viruses, including SARS-CoV-2 variants, and hence underpin public health actions.

    In week 14/2021, the overall frequency of the SARS-CoV-2 B.1.1.7 variant in all samples sequenced increased to 81,4% (CI 78,4% – 84,4%, p<0,05). For the SARS-CoV-2 B.1.351 variant, we found an overall frequency of 14,2% (CI 11,5% – 16,9%, p<0,05) within the sequenced samples and for P.1, 1,25% (CI 0,4% – 2,1%, p<0,05).

    The representative sample was estimated, based on the number of positive cases in Luxembourg for week 14 (1265). The minimum sample size required to detect prevalence of B.1.1.7 (75%) reported in week 13, with an error margin of 5%, was estimated to be 235 specimens. This number corresponds to a coverage of 18,6 %, which exceeds the minimum coverage recommended by ECDC (10%). The sequencing results of week 14 are representative of the circulating variants in Luxembourg with a margin of error of 5%.

    The total number of sequences performed this week was 661, with 641 specimens having been collected in the time frame of week 14/2021. The sequencing coverage this week was 50,7% from all positive cases in Luxembourg.

    Clinical Surveillance

    The “Sentinel” surveillance network reported 102 consultations in week 14 (05/APR/2021 – 11/APR/2021). There was no case of ILI1, as shown in Figure 1. The number of consultations for ARI2 was 15, which represents 15% of consultations.

    Virological Surveillance

    Patients presenting with ILI and ARI at the Covid Consultation Centre (CCC) in Luxembourg were tested using a respiratory virus panel (ADV = Adenovirus, FLU A = Influenza A, FLU B = Influenza B, HRV = Human Rhinovirus, MPV = Human metapneumovirus, PIV = Parainfluenza virus, RSV = Respiratory Syncytial Virus, SARS-CoV-2 = Severe acute respiratory syndrome coronavirus 2).

    The SARS-COV-2 was the most prevalent respiratory virus detected in the “Sentinel” network, with 92 positive cases (32%). The wave of Human Rhinovirus (HRV) continued in week 14/2021, with 13 positive cases in 289 tests (4,4%). Sporadic cases of other respiratory viruses continued to appear, such as 8 cases of PIV (2,8%), 4 cases of MPV and 1 case of RSV. No case  of Influenza A/B was detected. (c.f. Figure 2).

    In Luxembourg, we have tested 289 samples from the Sentinel surveillance network, as compared to 948 specimens tested in Europe, in the week 14/2021. Two of these 948 specimens tested positive for Influenza type A virus. Influenza activity remained at interseasonal levels.(Source: FluNews Europe).

    SARS-CoV-2 Genomic Surveillance

    The current sequencing strategy

    The National Reference Laboratory for Acute Respiratory Infections at LNS continues to improve the representativeness of the pool of sequenced specimens to reach real-time epidemiology, by implementing the following weekly sequencing activities:

    • Sequencing specimens from all hospitalized positive cases
    • Sequencing specimens from all positive cases from Airport testing program
    • Sequencing specimens from all outbreaks and identified clusters
    • Systematic sequencing of specimens from reinfections and post-vaccination-infections
    • Population sequencing of specimens from representative regions and age groups, to follow the evolution of the different variants in the Luxembourg population.

    The representative sequencing sample was based on the minimum number of specimens required to extrapolate prevalence of VOC variants with error rate of 5%. The representative sample was estimated based on the number of positive cases in Luxembourg for week 14 (1265). The minimum sample size required to detect prevalence of B.1.1.7 (75%) with an error margin of 5% was estimated to be 235 specimens. The calculation was based on a sample size calculation tool that uses the expected prevalence of the variant in the total population. (Population Proportion – Sample Size – Select Statistical Consultants (select-statistics.co.uk). This number represented a coverage of 18,6% which exceeds the minimum coverage recommended by ECDC (10%). The number of non-targeted specimens of Luxembourgish residents sequenced this week was 565. Therefore, our sequencing results this week are representative of the circulating variants in Luxembourg.

    The starting material used for sequencing is respiratory specimens (nasopharyngeal or oropharyngeal swabs) that have already been tested positive by RT PCR.

    The LNS sequencing data sharing strategy includes sharing of the sequencing data with GISAID EpiCov database (www.gisaid.org ) on a periodic basis.

    Sequenced specimens

    Last week the microbial genomics platform at the LNS sequenced 661 specimens, with 641 collected in week 14/2021. This represents 50,7% of the new infections reported in Luxembourg in week 14/2021. Among the 641 specimens, 28 specimens were reported to be part of a cluster or outbreak investigation, and 48 specimens were from non-residents. This leads to 565 specimens, collected in week 14, and being the representative population sequencing sample. In the population representative sample of residents, the frequency of B.1.1.7 and B.1.135 was 81,4% and 14,2% respectively.

    The population sequencing coverage in week 14/2021 was 50,7% (Figure 3). Based on statistical inference, the frequency of the reported variants in week 14/2021 is representative of the circulating variants in Luxembourg with a margin of error of 5%.

    Circulating lineage detection

    Lineages (variants) have been assigned based on Rambaut et al by means of Phylogenetic Assignment of Named Global Outbeak LINeages (pangolin) software  (v2.3.6, pangoLEARN version 2021-03-29).

    The lineage nomenclature system that we use is the one proposed by Rambaut et al. that focuses on actively circulating virus lineages (https://cov-lineages.org ).

    In week 14/2021, in the population representative sample, after removal of cluster samples, and excluding specimens collected from non-residents, there were 13 circulating SARS-CoV-2 variants, with the main three variants being B.1.1.7 (81,4%, CI 78,4% – 84,4%) followed by B.1.351 (14,2%, CI 11,5% – 16,9%) and P.1 (1,25% , CI 0,4% – 2,1%), as shown in Figure 4.

    Variants of Concern tracker (B.1.1.7, B.1.351, P.1, A.23.1 and B.1.525)

    Among specimens collected within the week 14/2021, 522 cases of the B.1.1.7 variant have been detected, representing 81,4% of the specimens in the week’s sequencing pool (by comparison, the week 13/2021 pool had shown a frequency of 75,5% of this variant, including additional specimens having been sequenced from previous weeks). The total case count of sequenced variant B.1.1.7 was 3028 by week 14/2021. The earliest collection date for this variant remains 19/DEC/2020 and the latest is 11/APR/2021.

    In the collection period of week 14/2021, 91 cases of the South African variant B.1.351 have been detected, representing 14,2% of the specimens in the week’s sequencing pool (by comparison, the week 13/2021 pool had shown 17,7% of this variant, including additional specimens having been sequenced from previous weeks). The total case count of sequenced variant B.1.351 was 734 by week 14/2021. The earliest collection date for this variant remains 11/JAN/2021 and the latest is 11/APR/2021.

    In week 14/2021 two additional cases of B.1.525 and 8 new cases of the Brazilian variant P.1 have been detected. Thus, the case count by week 14 for B.1.525 is 5 (latest sampling date 07/APR/2021) and for P.1, 17 cases (latest sampling date 10/APR/2021).

    By now, no case of A.23.1 has been detected in Luxembourg (Figure 5).

    Lineage B.1.1.7 is characterized by several spike protein mutations, including N501Y, H69/V70del and P861H. The variant seems to have a considerable epidemiological impact, as it has a higher transmissibility rate.

    Lineage B.1.351 holds numerous spike protein mutations, of which three are located in the receptor binding domain (K417N, E484K and N501Y), and are therefore relevant for antibody binding. As for B.1.1.7, a higher transmissibility rate and viral loads seem to be associated with this variant. Due to the K417N and E484K mutations, an impact on vaccination efficacy and possibility of reinfection is subject to scientific investigation.

    Lineage P.1 (descendent of B.1.1.28), initially found in the Amazon region, has a similar mutation profile as the South African variant, including E484K and N501Y. Concerns are, as for the South African variant, higher transmissibility and a decreased protection by neutralizing antibodies.

    Lineage B.1.525 carries several mutations of biological significance, including E484K, Q677H and F888L. It does not carry N501Y, but a set of deletions similar to the B.1.1.7 variant.

    Clinically relevant mutations

    Currently the LNS genomic surveillance program – independently from lineage calling – notes the occurrence of 13 different known SARS-CoV-2 mutations, assumed to have clinical and epidemiological relevance. The list of observed mutations is being updated continually, based on the appearance and prevalence of SARS-CoV-2 variants.

    The following table provides the overall frequencies of these mutations, detected in the lineage-assignable genome sequences, analyzed between 01/SEP/2020 and 11/APR/2021 (N=8251), as well as the frequencies in week 14/2021.

    References

    Genomic sequencing of SARS-CoV-2. A guide to implementation for maximum impact on public health. WHO, 8 January 2021.

    COVID-19 data portal. 2020 (https://www.covid19dataportal.org/sequences )

    J Hadfield et al. Nextstrain: real-time tracking of pathogen evolution. Bioinformatics 2018;34:4121-4123

    A Rambaut et al. A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nat Microbiol 2020;5:1403-1407

    https://github.com/cov-lineages/pangolin

    For more information on lineages visit: https://cov-lineages.org
    For more information and statistics on Covid-19 infections in Luxembourg visit: https://covid19.public.lu/en.html

     

  • Semaine 13

    Respiratory Viruses in Luxembourg (ReViLux)

    Weekly report (Period 29/03/-04/04/2021)

    Executive Summary

    The aim of the “Sentinel” national surveillance program is to monitor the circulating respiratory viruses, including SARS-CoV-2 variants, and hence underpin public health actions.

    In week 13/2021, the overall frequency of the SARS-CoV-2 B.1.1.7 variant in all samples sequenced increased to 75,5% (CI 71,6% – 79,4%, p<0,05). For the SARS-CoV-2 B.1.351 variant, we found an overall frequency of 17,9% (CI 14,4% – 21,3%, p<0,05) within the sequenced samples.

    The representative sample was estimated, based on the number of positive cases in Luxembourg for week 13 (1544). The minimum sample size required to detect prevalence of B.1.1.7 (74%) reported in week 12, with an error margin of 5%, was estimated to be 249 specimens. This number corresponds to a coverage of 16,1 %, which exceeds the minimum coverage recommended by ECDC (10%). The sequencing results of week 13 are representative of the circulating variants in Luxembourg with a margin of error of 5%.

    The total number of sequences performed this week was 529, with 474 specimens having been collected in the time frame of week 13/2021. The sequencing coverage this week was 30,7% from all positive cases in Luxembourg.

    Clinical Surveillance

    The “Sentinel” surveillance network reported 178 consultations in week 13 (29/MAR/2021 – 04/APR/2021). There was no case of ILI1, as shown in Figure 1. The number of consultations for ARI2 was 35, which represents 20% of consultations.

    Virological Surveillance

    Patients presenting with ILI and ARI at the Covid Consultation Centre (CCC) in Luxembourg were tested using a respiratory virus panel (ADV = Adenovirus, FLU A = Influenza A, FLU B = Influenza B, HRV = Human Rhinovirus, MPV = Human metapneumovirus, PIV = Parainfluenza virus, RSV = Respiratory Syncytial Virus, SARS-CoV-2 = Severe acute respiratory syndrome coronavirus 2).

    The SAR-COV-2 was the most prevalent respiratory virus detected in the “Sentinel” network, with 46 positive cases (22%). The wave of Human Rhinovirus (HRV) continued in week 13/2021, with 21 positive cases in 208 tests (10,1%). Sporadic cases of other respiratory viruses continued to appear, such as 6 cases of PIV in 208 tests (2,8%), 2 cases of MPV and 1 case of ADV. One case  of Influenza B was detected and no case of Influenza A (Figure 2).

    In Luxembourg, we have tested 208 samples from the Sentinel surveillance network, as compared to 1019 specimens tested in Europe, in the week 13/2021. One of these 1189 specimens tested positive for Influenza type B virus. The influenza epidemic in the European Region has usually reached its peak and starts to decline by this time of the year but, despite widespread and regular testing for influenza, reported influenza activity still remains at a very low level, likely due to the impact of the various public health and social measures, implemented to reduce transmission of SARS-CoV-2 (Source: FluNews Europe).

    Virological Surveillance

    Patients presenting with ILI and ARI at the Covid Consultation Centre (CCC) in Luxembourg were tested using a respiratory virus panel (ADV = Adenovirus, FLU A = Influenza A, FLU B = Influenza B, HRV = Human Rhinovirus, MPV = Human metapneumovirus, PIV = Parainfluenza virus, RSV = Respiratory Syncytial Virus, SARS-CoV-2 = Severe acute respiratory syndrome coronavirus 2).

    The SAR-COV-2 was the most prevalent respiratory virus detected in the “Sentinel” network, with 46 positive cases (22%). The wave of Human Rhinovirus (HRV) continued in week 13/2021, with 21 positive cases in 208 tests (10,1%). Sporadic cases of other respiratory viruses continued to appear, such as 6 cases of PIV in 208 tests (2,8%), 2 cases of MPV and 1 case of ADV. One case  of Influenza B was detected and no case of Influenza A (Figure 2).

    In Luxembourg, we have tested 208 samples from the Sentinel surveillance network, as compared to 1019 specimens tested in Europe, in the week 13/2021. One of these 1189 specimens tested positive for Influenza type B virus. The influenza epidemic in the European Region has usually reached its peak and starts to decline by this time of the year but, despite widespread and regular testing for influenza, reported influenza activity still remains at a very low level, likely due to the impact of the various public health and social measures, implemented to reduce transmission of SARS-CoV-2 (Source: FluNews Europe).

    SARS-CoV-2 Genomic Surveillance

    The current sequencing strategy

    The National Reference Laboratory for Acute Respiratory Infections at LNS continues to improve the representativeness of the pool of sequenced specimens to reach real-time epidemiology, by implementing the following weekly sequencing activities:

    • Sequencing specimens from all hospitalized positive cases
    • Sequencing specimens from all positive cases from Airport testing program
    • Sequencing specimens from all outbreaks and identified clusters
    • Systematic sequencing of specimens from reinfections and post-vaccination-infections
    • Population sequencing of specimens from representative regions and age groups, to follow the evolution of the different variants in the Luxembourg population.

    The representative sequencing sample was based on the minimum number of specimens required to extrapolate prevalence of VOC variants with error rate of 5%. The representative sample was estimated based on the number of positive cases in Luxembourg for week 13 (1544). The minimum sample size required to detect prevalence of B.1.1.7 (74%) with an error margin of 5% was estimated to be 249 specimens. The calculation was based on a sample size calculation tool that uses the expected prevalence of the variant in the total population. (Population Proportion – Sample Size – Select Statistical Consultants (select-statistics.co.uk). This number represented a coverage of 16,1% which exceeds the minimum coverage recommended by ECDC (10%). The number of non-targeted specimens of Luxembourgish residents sequenced this week was 382. Therefore, our sequencing results this week are representative of the circulating variants in Luxembourg.

    The starting material used for sequencing is respiratory specimens (nasopharyngeal or oropharyngeal swabs) that have already been tested positive by RT PCR.

    The LNS sequencing data sharing strategy includes sharing of the sequencing data with GISAID EpiCov database (www.gisaid.org ) on a periodic basis.

    Sequenced specimens

    Last week the microbial genomics platform at the LNS sequenced 529 specimens, with 474 collected in week 13/2021. This represents 30,7% of the new infections reported in Luxembourg in week 13/2021. Among the 474 specimens, 58 specimens were reported to be part of a cluster or outbreak investigation, and 37 specimens were from non-residents (3 specimens belong to both groups). This leads to 382 specimens, collected in week 13, and being the representative population sequencing sample. In the population representative sample of residents, the frequency of B.1.1.7 and B.1.135 was 74,1% and 19,4% respectively.

    The population sequencing coverage in week 13/2021 was 30,7% (Figure 3). Based on statistical inference, the frequency of the reported variants in week 13/2021 is representative of the circulating variants in Luxembourg with a margin of error of 5%.

    Circulating lineage detection

    Lineages (variants) have been assigned based on Rambaut et al by means of Phylogenetic Assignment of Named Global Outbeak LINeages (pangolin) software  (v2.3.6, pangoLEARN version 2021-03-29).

    The lineage nomenclature system that we use is the one proposed by Rambaut et al. that focuses on actively circulating virus lineages (https://cov-lineages.org ).

    In week 13/2021, in the population representative sample, after removal of cluster samples, and excluding specimens collected from non-residents, there were 13 variants, with the main three variants being B.1.1.7 (74,1%, CI 69,7% – 78,5%), B.1.351 (19,4%, CI 15,4% – 23,4%), followed by P.1 / B.1 (1% each, CI 0% – 2%) as shown in Figure 4.

    Variants of Concern tracker (B.1.1.7, B.1.351, P.1, A.23.1 and B.1.525)

    Among specimens collected within the week 13/2021, 358 cases of the B.1.1.7 variant have been detected, representing 75,5% of the specimens in the week’s sequencing pool (by comparison, the week 12/2021 pool had shown a frequency of 74,1% of this variant, including additional specimens having been sequenced from previous weeks). The total case count of sequenced variant B.1.1.7 was 2496 by week 13/2021. The earliest collection date for this variant remains 19/DEC/2020 and the latest is 04/APR/2021.

    In the collection period of week 13/2021, 85 cases of the South African variant B.1.351 have been detected, representing 17,9% of the specimens in the week’s sequencing pool (by comparison, the week 12/2021 pool had shown 18,2% of this variant, including additional specimens having been sequenced from previous weeks). The total case count of sequenced variant B.1.351 was 643 by week 13/2021. The earliest collection date for this variant remains 11/JAN/2021 and the latest is 04/APR/2021.

    In week 13/2021 one additional case of B.1.525 has been detected and 6 new cases of the Brazilian variant P.1. Thus, the case count by week 13 for B.1.525 is 3 (latest sampling date 31/MAR/2021) and for P.1 nine (latest sampling date 03/APR/2021).

    By now, no case of A.23.1 has been detected in Luxembourg (Figure 5).

    Lineage B.1.1.7 is characterized by several spike protein mutations, including N501Y, H69/V70del and P861H. The variant seems to have a considerable epidemiological impact, as it has a higher transmissibility rate.

    Lineage B.1.351 holds numerous spike protein mutations, of which three are located in the receptor binding domain (K417N, E484K and N501Y), and are therefore relevant for antibody binding. As for B.1.1.7, a higher transmissibility rate and viral loads seem to be associated with this variant. Due to the K417N and E484K mutations, an impact on vaccination efficacy and possibility of reinfection is subject to scientific investigation.

    Lineage P.1 (descendent of B.1.1.28), initially found in the Amazon region, has a similar mutation profile as the South African variant, including E484K and N501Y. Concerns are, as for the South African variant, higher transmissibility and a decreased protection by neutralizing antibodies.

    Lineage B.1.525 carries several mutations of biological significance, including E484K, Q677H and F888L. It does not carry N501Y, but a set of deletions similar to the B.1.1.7 variant.

    Clinically relevant mutations

    Currently the LNS genomic surveillance program – independently from lineage calling – notes the occurrence of 13 different known SARS-CoV-2 mutations, assumed to have clinical and epidemiological relevance. The list of observed mutations is being updated continually, based on the appearance and prevalence of SARS-CoV-2 variants.

    The following table provides the overall frequencies of these mutations, detected in the lineage-assignable genome sequences, analyzed between 01/SEP/2020 and 04/APR/2021 (N=7583), as well as the frequencies in week 13/2021.

    References

    Genomic sequencing of SARS-CoV-2. A guide to implementation for maximum impact on public health. WHO, 8 January 2021.

    COVID-19 data portal. 2020 (https://www.covid19dataportal.org/sequences )

    J Hadfield et al. Nextstrain: real-time tracking of pathogen evolution. Bioinformatics 2018;34:4121-4123

    A Rambaut et al. A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nat Microbiol 2020;5:1403-1407

    https://github.com/cov-lineages/pangolin

    Y Guangchuang et al. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods in Ecology and Evolution 2017;8:28-36

    For more information on lineages visit: https://cov-lineages.org
    For more information and statistics on Covid-19 infections in Luxembourg visit: https://covid19.public.lu/en.html

  • Semaine 12

    Respiratory Viruses in Luxembourg (ReViLux)

    Weekly report (Period 22-28/03/2021)

    Executive Summary

    The aim of the “Sentinel” national surveillance program is to monitor the circulating respiratory viruses, including SARS-CoV-2 variants, and hence underpin public health actions.

    In week 12/2021, the overall frequency of the SARS-CoV-2 B.1.1.7 variant in all samples sequenced increased to 73,5% (CI 69,8% – 77,2%, p<0,05). For the SARS-CoV-2 B.1.351 variant, we found an overall frequency of 18,4% (CI 15,2% – 21,6%, p<0,05) within the sequenced samples.

    The representative sample was estimated, based on the number of positive cases in Luxembourg for week 12 (1690). The minimum sample size required to detect prevalence of B.1.1.7 (68%) reported in week 11, with an error margin of 5%, was estimated to be 280 specimens. This number corresponds to a coverage of 16,5 %, which exceeds the minimum coverage recommended by ECDC (10%). The sequencing results of week 12 are representative of the circulating variants in Luxembourg with a margin of error of 5%.

    The total number of sequences performed this week was 689, with 548 specimens having been collected in the time frame of week 12/2021. The sequencing coverage this week was 32,4% from all positive cases in Luxembourg.

    Clinical Surveillance

    The “Sentinel” surveillance network reported 178 consultations in week 12 (22/MAR/2021 – 28/MAR/2021). There was no case of ILI1, as shown in Figure 1. The percentage of consultations for ARI2 was 19.6%.

    1. ILI: – Influenza-Like Illness: Acute respiratory symptoms <10 days, Fever 38C, systematic symptoms (myalgia, malaise, …)
    2. ARI: – Acute Respiratory Infection: Acute respiratory symptoms (bronchitis, pharyngitis, rhinitis, pneumonia…) with or without fever.

    Virological Surveillance

    Patients presenting with ILI and ARI at the Covid Consultation Centre (CCC) in Luxembourg were tested using a respiratory virus panel (ADV = Adenovirus, FLU A = Influenza A, FLU B = Influenza B, HRV = Human Rhinovirus, MPV = Human metapneumovirus, PIV = Parainfluenza virus, RSV = Respiratory Syncytial Virus, SARS-CoV-2 = Severe acute respiratory syndrome coronavirus 2).

    The SAR-COV-2 was the most prevalent respiratory virus detected in the “Sentinel” network, with 69 positive cases (28%). The wave of Human Rhinovirus (HRV) continued in week 12/2021, with 37 positive cases in 243 tests (15,2%). Sporadic cases of other respiratory viruses continued to appear, such as 6 cases of PIV in 243 tests (2,4%). No cases of Influenza A/B were detected, indicating absence of circulation of Influenza viruses in Luxembourg, as shown in Figure 2.

    In Luxembourg, we have tested 243 samples from the Sentinel surveillance network, as compared to 1189 specimens tested in Europe, in the week 12/2021. None of these 1189 specimens tested positive for type A Influenza virus. The influenza epidemic in the European Region has usually reached its peak by this point of the year but, despite widespread and regular testing for influenza, reported influenza activity still remains at a very low level, likely due to the impact of the various public health and social measures, implemented to reduce transmission of SARS-CoV-2 (Source: FluNews Europe).

    SARS-CoV-2 Genomic Surveillance

    The current sequencing strategy

    The National Reference Laboratory for Acute Respiratory Infections at LNS continues to improve the representativeness of the pool of sequenced specimens to reach real-time epidemiology, by implementing the following weekly sequencing activities:

    • Sequencing specimens from all hospitalized positive cases
    • Sequencing specimens from all positive cases from Airport testing program
    • Sequencing specimens from all outbreaks and identified clusters
    • Systematic sequencing of specimens from reinfections and post-vaccination-infections
    • Population sequencing of specimens from representative regions and age groups, to follow the evolution of the different variants in the Luxembourg population.

    The representative sequencing sample was based on the minimum number of specimens required to extrapolate prevalence of VOC variants with error rate of 5%. The representative sample was estimated based on the number of positive cases in Luxembourg for week 12 (1690). The minimum sample size required to detect prevalence of B.1.1.7 (68%) with an error margin of 5% was estimated to be 280 specimens. The calculation was based on a sample size calculation tool that uses the expected prevalence of the variant in the total population. (Population Proportion – Sample Size – Select Statistical Consultants (select-statistics.co.uk). This number represented a coverage of 16,5% which exceeds the minimum coverage recommended by ECDC (10%). The number of non-targeted specimens of Luxembourgish residents sequenced this week was 498. Therefore, our sequencing results this week are representative of the circulating variants in Luxembourg.

    The starting material used for sequencing is respiratory specimens (nasopharyngeal or oropharyngeal swabs) that have already been tested positive by RT PCR.

    The LNS sequencing data sharing strategy includes sharing of the sequencing data with GISAID EpiCov database (www.gisaid.org ) on a periodic basis.

    Sequenced specimens

    Last week the microbial genomics platform at the LNS sequenced 548 specimens having been collected in week 12/2021. This represents 32,4% of the new infections reported in Luxembourg in week 12/2021. Among the 548 specimens, 29 specimens were reported to be part of a cluster or outbreak investigation, and 21 specimens were from non-residents. This leads to 498 specimens, collected in week 12, and being the representative population sequencing sample. In the population representative sample of residents, the frequency of B.1.1.7 and B.1.135 was 74,1% and 18,1% respectively.

    The population sequencing coverage in week 12/2021 was 32,4% (Figure 3). Based on statistical inference, the frequency of the reported variants in week 12/2021 is representative of the circulating variants in Luxembourg with a margin of error of 5%.

    Circulating lineage detection

    Lineages (variants) have been assigned based on Rambaut et al by means of Phylogenetic Assignment of Named Global Outbeak LINeages (pangolin) software  (v2.3.6, pangoLEARN version 2021-03-29).

    The lineage nomenclature system that we use is the one proposed by Rambaut et al. that focuses on actively circulating virus lineages (https://cov-lineages.org ).

    In week 12/2021, in the population representative sample, after removal of cluster samples, and excluding specimens collected from non-residents, there were 13 variants, with the main three variants being B.1.1.7 (74,1%, CI 70,2% – 77,9%), B.1.351 (18,1%, CI 14,7% – 21,5%), followed by B.1 (1,6%, CI 0,5% – 2,7%), as shown in Figure 4.

    Variants of Concern tracker (B.1.1.7, B.1.351, P.1, A.23.1 and B.1.525)

    Among specimens collected within the week 12/2021, 403 cases of the B.1.1.7 variant have been detected, representing 73,5% of the specimens in the week’s sequencing pool (by comparison, the week 11/2021 pool had shown a frequency of 67,8% of this variant, including additional specimens having been sequenced from previous weeks). The total case count of sequenced variant B.1.1.7 was 2115 by week 12/2021. The earliest collection date for this variant remains 19/DEC/2020 and the latest is 28/MAR/2021.

    In the collection period of week 12/2021, 101 cases of the South African variant B.1.351 have been detected, representing 18,4% of the specimens in the week’s sequencing pool (by comparison, the week 11/2021 pool had shown 22,9% of this variant, including additional specimens having been sequenced from previous weeks). The total case count of sequenced variant B.1.351 was 554 by week 12/2021. The earliest collection date for this variant remains 11/JAN/2021 and the latest is 28/MAR/2021.

    In week 12/2021 one additional case has been detected for B.1.525, but not any of the other variants of concern (P.1, A.23.1) (Figure 5).

    Lineage B.1.1.7 is characterized by several spike protein mutations, including N501Y, H69/V70del and P861H. The variant seems to have a considerable epidemiological impact, as it has a higher transmissibility rate.

    Lineage B.1.351 holds numerous spike protein mutations, of which three are located in the receptor binding domain (K417N, E484K and N501Y), and are therefore relevant for antibody binding. As for B.1.1.7, a higher transmissibility rate and viral loads seem to be associated with this variant. Due to the K417N and E484K mutations, an impact on vaccination efficacy and possibility of reinfection is subject to scientific investigation.

    Lineage P.1 (descendent of B.1.1.28), initially found in the Amazon region, has a similar mutation profile as the South African variant, including E484K and N501Y. Concerns are, as for the South African variant, higher transmissibility and a decreased protection by neutralizing antibodies.

    Lineage B.1.525 carries several mutations of biological significance, including E484K, Q677H and F888L. It does not carry N501Y, but a set of deletions similar to the B.1.1.7 variant.

    Clinically relevant mutations

    Currently the LNS genomic surveillance program – independently from lineage calling – notes the occurrence of 13 different known SARS-CoV-2 mutations, assumed to have clinical and epidemiological relevance. The list of observed mutations is being updated continually, based on the appearance and prevalence of SARS-CoV-2 variants.

    The following table provides the overall frequencies of these mutations, detected in the lineage-assignable genome sequences, analyzed between 01/SEP/2020 and 22/MAR/2021 (N=7040), as well as the frequencies in week 12/2021.

    References

    Genomic sequencing of SARS-CoV-2. A guide to implementation for maximum impact on public health. WHO, 8 January 2021.

    COVID-19 data portal. 2020 (https://www.covid19dataportal.org/sequences )

    J Hadfield et al. Nextstrain: real-time tracking of pathogen evolution. Bioinformatics 2018;34:4121-4123

    A Rambaut et al. A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nat Microbiol 2020;5:1403-1407

    https://github.com/cov-lineages/pangolin

    Y Guangchuang et al. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods in Ecology and Evolution 2017;8:28-36

    For more information on lineages visit: https://cov-lineages.org
    For more information and statistics on Covid-19 infections in Luxembourg visit: https://covid19.public.lu/en.html

  • Semaine 11

    Respiratory Viruses in Luxembourg (ReViLux)

    Weekly report (Period 15-21/03/2021)

    Executive Summary

    The aim of the “Sentinel” national surveillance program is to monitor the circulating respiratory viruses, including SARS-CoV-2 variants, and hence underpin public health actions.
    In week 11/2021, the overall frequency of the SARS-CoV-2 B.1.1.7 variant in all samples sequenced increased 68,1% (CI 64,2% – 72%, p<0,05). For the SARS-CoV-2 B.1.351 variant, we found an overall frequency of 23% (CI 19.4% - 26,5%, p<0,05) within the sequenced samples. The representative sample was estimated, based on the number of positive cases in Luxembourg for week 11 (1570). The minimum sample size required to detect prevalence of B.1.1.7 (68%) reported in week 11, with an error margin of 5%, was estimated to be 276 specimens. This number corresponds to a coverage of 17,6%, which exceeds the minimum coverage recommended by ECDC (10%). The sequencing results of week 11 are representative of the circulating variants in Luxembourg with a margin of error of 5%. The total number of sequences performed this week was 540, with all specimens having been collected in the time frame of week 11/2021. The sequencing coverage this week was 34,4% from all positive cases in Luxembourg.

    Clinical Surveillance

    The “Sentinel” surveillance network reported 263 consultations in week 11 (15/MAR/2021 – 21/MAR/2021). There was 5 cases of ILI1, as shown in Figure 1, corresponding to 1,9% of consultations. The percentage of consultations for ARI2 was 17,9%.

    1. ILI: – Influenza-Like Illness: Acute respiratory symptoms <10 days, Fever 38C, systematic symptoms (myalgia, malaise, …)
    2. ARI: – Acute Respiratory Infection: Acute respiratory symptoms (bronchitis, pharyngitis, rhinitis, pneumonia…) with or without fever.

    Virological Surveillance

    Patients presenting with ILI and ARI at the Covid Consultation Centre (CCC) in Luxembourg were tested using a respiratory virus panel (ADV = Adenovirus, FLU A = Influenza A, FLU B = Influenza B, HRV = Human Rhinovirus, MPV = Human metapneumovirus, PIV = Parainfluenza virus, RSV = Respiratory Syncytial Virus, SARS-CoV-2 = Severe acute respiratory syndrome coronavirus 2).

    The SAR-COV-2 was the most prevalent respiratory virus detected in the “Sentinel” network, with 64 positive cases (22%). The wave of Human Rhinovirus (HRV) continued in week 11/2021, with 34 positive cases in 291 tests (11,7%). Sporadic cases of other respiratory viruses continued to appear as one case of PIV was identified in week 11 (0,3%) and two cases of Adenovirus (ADV), corresponding to 0,7% of all tests. No cases of Influenza A/B were detected, indicating absence of circulation of Influenza viruses in Luxembourg, as shown in Figure 2.

    In Luxembourg, we have tested 291samples from the Sentinel surveillance network, as compared to 1256 specimens tested in Europe, in the week 11/2021. One of these 1256 specimens tested positive for type A Influenza virus. The influenza epidemic in the European Region has usually reached its peak by this point of the year but, despite widespread and regular testing for influenza, reported influenza activity still remains at a very low level, likely due to the impact of the various public health and social measures, implemented to reduce transmission of SARS-CoV-2 (Source: FluNews Europe).

    SARS-CoV-2 Genomic Surveillance

    The current sequencing strategy

    The National Reference Laboratory for Acute Respiratory Infections at LNS continues to improve the representativeness of the pool of sequenced specimens to reach real-time epidemiology, by implementing the following weekly sequencing activities:

    1. Sequencing specimens from all hospitalized positive cases
    2. Sequencing specimens from all positive cases from Airport testing program
    3. Sequencing specimens from all outbreaks and identified clusters
    4. Systematic sequencing of specimens from reinfections and post-vaccination-infections
    5. Population sequencing of specimens from representative regions and age groups, to follow the evolution of the different variants in the Luxembourg population.

    The representative sequencing sample was based on the minimum number of specimens required to extrapolate prevalence of VOC variants with error rate of 5%. The representative sample was estimated based on the number of positive cases in Luxembourg for week 11 (1570). The minimum sample size required to detect prevalence of B.1.1.7 (68%) with an error margin of 5% was estimated to be 276 specimens. The calculation was based on a sample size calculation tool that uses the expected prevalence of the variant in the total population. (Population Proportion – Sample Size – Select Statistical Consultants (select-statistics.co.uk). This number represented a coverage of 17,6% which exceeds the minimum coverage recommended by ECDC (10%). The number of non-targeted specimens sequenced this week was 515. Therefore, our sequencing results this week are representative of the circulating variants in Luxembourg with a margin of error of 5%.

    The starting material used for sequencing is respiratory specimens (nasopharyngeal or oropharyngeal swabs) that have already been tested positive by RT PCR.

    The LNS sequencing data sharing strategy includes sharing of the sequencing data with GISAID EpiCov database (www.gsaid.org ) on a periodic basis.

    Sequenced specimens

    Last week the microbial genomics platform at the LNS sequenced 540 specimens. All of these were collected in week 11/2021. This represents 32,8% of the new infections reported in Luxembourg in week 11/2021. Among the 540 specimens, 25 specimens were reported to be part of a cluster or outbreak investigation, and 41 specimens were from non-residents. This leads to 474 specimens, collected in week 11, and being the representative population sequencing sample. In the population representative sample of residents, the frequency of B.1.1.7 and B.1.135 was 68.3% and 22.5% respectively.

    The population sequencing coverage in week 11/2021 was 34,4% (Figure 3). Based on statistical inference, the frequency of the reported variants in week 11/2021 is representative of the circulating variants in Luxembourg with a margin of error of 5%.

    Circulating lineage detection

    Lineages (variants) have been assigned based on Rambaut et al by means of Phylogenetic Assignment of Named Global Outbeak LINeages (pangolin) software (v2.3, pangoLEARN version 2021-02-21).

    In week 11/2021, in the population representative sample, after removal of the 25 cluster samples, and excluding specimens collected from non-residents, there were 13 variants, with the main three variants being B.1.1.7 (68,3%, CI 64,1% – 72,5%), B.1.351 (22.5%, CI 18,7% – 26,3%), followed by B.1.1.29 (2.1%, CI 0,8% – 3,4%), as shown in Figure 4.

    Variants of concern tracker (B.1.1.7, B.1.351, P.1, A.23.1 and B.1.525)

    Among specimens collected within the week 11/2021, 368 cases of the B.1.1.7 variant have been detected, representing 68,1% of the specimens in the week’s sequencing pool (by comparison, the week 10/2021 pool had shown a frequency of 63,5% of this variant). The total case count of sequenced variant B.1.1.7 was 1623 by week 11/2021. The earliest collection date for this variant remains 19/DEC/2020 and the latest is 21/MAR/2021.

    In the collection period of week 11/2021, 124 cases of the South African variant B.1.351 have been detected, representing 23% of the specimens in the week’s sequencing pool (by comparison, the week 10/2021 pool had shown 20,4% of this variant). The total case count of sequenced variant B.1.351 was 423 by week 10/2021. The earliest collection date for this variant remains 11/JAN/2021 and the latest is 21/MAR/2021.

    In week 11/2021 no additional cases have been dected for any of the other variants of concern (P.1, B.1.525 or A.23.1) (Figure 5).

    Lineage B.1.1.7 is characterized by several spike protein mutations, including N501Y, H69/V70del and P861H. The variant seems to have a considerable epidemiological impact, as it has a higher transmissibility rate.

    Lineage B.1.351 holds numerous spike protein mutations, of which three are located in the receptor binding domain (K417N, E484K and N501Y), and are therefore relevant for antibody binding. As for B.1.1.7, a higher transmissibility rate and viral loads seem to be associated with this variant. Due to the K417N and E484K mutations, an impact on vaccination efficacy and possibility of reinfection is subject to scientific investigation.

    Lineage P.1 (descendent of B.1.1.28), initially found in the Amazon region, has a similar mutation profile as the South African variant, including E484K and N501Y. Concerns are, as for the South African variant, higher transmissibility and a decreased protection by neutralizing antibodies.

    Lineage B.1.525 carries several mutations of biological significance, including E484K, Q677H and F888L. It does not carry N501Y, but a set of deletions similar to the B.1.1.7 variant.

    Of note, additional specimens are in the pipeline for sequencing, so that numbers may change with increasing representativeness of circulating variants and proportions.

    Clinically relevant mutations

    Currently the LNS genomic surveillance program – independently from lineage calling – notes the occurrence of 13 different known SARS-CoV-2 mutations, assumed to have clinical and epidemiological relevance. The list of observed mutations is being updated continually, based on the appearance and prevalence of SARS-CoV-2 variants.

    The following table provides the overall frequencies of these mutations, detected in the lineage-assignable genome sequences, analyzed between 01/SEP/2020 and 21/MAR/2021 (N=6345), as well as the frequencies in week 11/2021.

    References

    Genomic sequencing of SARS-CoV-2. A guide to implementation for maximum impact on public health. WHO, 8 January 2021.
    COVID-19 data portal. 2020 (https://www.covid19dataportal.org/sequences )

    J Hadfield et al. Nextstrain: real-time tracking of pathogen evolution. Bioinformatics 2018;34:4121-4123

    A Rambaut et al. A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nat Microbiol 2020;5:1403-1407
    https://github.com/cov-lineages/pangolin

    Y Guangchuang et al. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods in Ecology and Evolution 2017;8:28-36

    For more information on lineages visit: https://cov-lineages.org

    For more information and statistics on Covid-19 infections in Luxembourg visit: https://covid19.public.lu/en.html

  • Semaine 10

    Respiratory Viruses in Luxembourg (ReViLux)

    Weekly report (Period 08-14/03/2021)

    Executive Summary

    The aim of the “Sentinel” national surveillance program is to monitor the circulating respiratory viruses, including SARS-CoV-2 variants, and hence underpin public health actions.
    In week 10/2021, the overall frequency of the SARS-CoV-2 B.1.1.7 variant in all samples sequenced remained stable at 63,5% (CI 57,6% – 69,3%, p<0,05). For the SARS-CoV-2 B.1.351 variant, we found an overall frequency of 20,4% (CI 15.5% – 25,3%, p<0,05) within the sequenced samples.

    The representative sample was estimated, based on the number of positive cases in Luxembourg for week 10 (1249). The minimum sample size required to detect prevalence of B.1.1.7 (63%) reported in week 9, with an error margin of 5%, was estimated to be 279 specimens. This number corresponds to a coverage of 22,34%, which exceeds the minimum coverage recommended by ECDC (10%). Our sequencing results this week are representative of the circulating variants in Luxembourg with a margin of error of 6%.
    The total number of sequences performed this week was 260, with all specimens having been collected in the time frame of week 10/2021. The sequencing coverage this week was 20,8% from all positive cases in Luxembourg.

    Clinical Surveillance

    The “Sentinel” surveillance network reported 146 consultations in week 10 (08/MAR/2021 – 14/MAR/2021). There was no case of ILI1, as shown in Figure 1. The percentage of consultations for ARI2 was 16,4%.

    1. ILI: – Influenza-Like Illness: Acute respiratory symptoms <10 days, Fever 38C, systematic symptoms (myalgia, malaise, …)
    2. ARI: – Acute Respiratory Infection: Acute respiratory symptoms (bronchitis, pharyngitis, rhinitis, pneumonia…) with or without fever.

    Virological Surveillance

    Patients presenting with ILI and ARI at the Covid Consultation Centre (CCC) in Luxembourg were tested using a respiratory virus panel (ADV = Adenovirus, FLU A = Influenza A, FLU B = Influenza B, HRV = Human Rhinovirus, MPV = Human metapneumovirus, PIV = Parainfluenza virus, RSV = Respiratory Syncytial Virus, SARS-CoV-2 = Severe acute respiratory syndrome coronavirus 2).

    The SAR-COV-2 was the most prevalent respiratory virus detected in the “Sentinel” network, with 62 positive cases (24,9%). The wave of Human Rhinovirus (HRV) continued in week 10/2021, with 19 positive cases in 249 tests (7,6%). Three cases of PIV were identified in week 10 (1,2%). No cases of Influenza A/B were detected, indicating absence of circulation of Influenza viruses in Luxembourg, as shown in Figure 2.

    In Luxembourg, we have tested 249 samples from the Sentinel surveillance network, as compared to 1110 samples tested in Europe, in the week 10/2021. None of these 1110 specimens tested for Influenza viruses were positive. The influenza epidemic in the European Region has usually reached its peak by this point of the year but, despite widespread and regular testing for influenza, reported influenza activity still remains at a very low level, likely due to the impact of the various public health and social measures, implemented to reduce transmission of SARS-CoV-2 (Source: FluNews Europe).

    SARS-CoV-2 Genomic Surveillance

    The current sequencing strategy

    The National Reference Laboratory for Acute Respiratory Infections at LNS continues to improve the representativeness of the pool of sequenced specimens to reach real-time epidemiology, by implementing the following weekly sequencing activities:

    1. Sequencing specimens from all hospitalized positive cases
    2. Sequencing specimens from all positive cases from Airport testing program
    3. Sequencing specimens from all outbreaks and identified clusters
    4. Systematic sequencing of specimens from reinfections and post-vaccination-infections
    5. Population sequencing of specimens from representative regions and age groups, to follow the evolution of the different variants in the Luxembourg population.

    The representative sequencing sample was based on the minimum number of specimens required to extrapolate prevalence of VOC variants with error rate of 5%. The representative sample was estimated based on the number of positive cases in Luxembourg for week 10 (1249). The minimum sample size required to detect prevalence of B.1.1.7 (63%) with an error margin of 5% was estimated to be 279 specimens. The calculation was based on a sample size calculation tool that uses the expected prevalence of the variant in the total population. (Population Proportion – Sample Size – Select Statistical Consultants (select-statistics.co.uk). This number represented a coverage of 22.3% which exceeds the minimum coverage recommended by ECDC (10%). The number of non-targeted specimens sequenced this week was 232, which is slightly lower that the above estimated sample size. Therefore, our sequencing results this week are representative of the circulating variants in Luxembourg with a margin of error of 6%.

    For the purposes of the weekly genomic surveillance, and for this week’s representative population sample, we removed all cluster samples (28) from our sequencing pool. The remaining sample was considered as this week’s representative population sample (N=232, corresponding to 18,7% of the new infections).

    The starting material used for sequencing is respiratory specimens (nasopharyngeal or oropharyngeal swabs) that have already been tested positive by RT PCR.

    The LNS sequencing data sharing strategy includes sharing of the sequencing data with GISAID EpiCov database (www.gsaid.org ) on a periodic basis.

    Sequenced specimens

    Last week the microbial genomics platform at the LNS sequenced 260 specimens. All of these were collected in week 10/2021. This represents 20,8% of the new infections reported in Luxembourg in week 10/2021. Among the 260 specimens, 28 specimens were reported to be part of a cluster or outbreak investigation, and 23 specimens were from non-residents.
    The population sequencing coverage in week 10/2021 was 20,34% (Figure 3). Based on statistical inference, the frequency of the reported variants in Week 10/2021 is representative of the circulating variants in Luxembourg with a margin of error of 6%.

    Circulating lineage detection

    Lineages (variants) have been assigned based on Rambaut et al by means of Phylogenetic Assignment of Named Global Outbeak LINeages (pangolin) software (v2.3, pangoLEARN version 2021-02-21).
    The lineage nomenclature system that we use is the one proposed by Rambaut et al. that focuses on actively circulating virus lineages (https://cov-lineages.org ).
    In the sampling period of week 10/2021, in the population representative sample, after removal of the 28 cluster samples, and excluding specimens collected from non-residents, there were 8 variants, with the main three variants being B.1.1.7 (66,2%, CI 59,8% – 72,6%), B.1.351 (20%, CI 14,6% – 25,4%), followed by B.1.1.29 (6%, CI 2,8% – 9,2%), as shown in Figure 4.

    Variants of concern tracker (B.1.1.7, B.1.351, P.1, A.23.1 and B.1.525)

    Among specimens collected within the week 10/2021, 165 cases of the B.1.1.7 variant have been detected, representing 63,5% of the specimens in the week’s sequencing pool (by comparison, the week 9/2021 pool had shown the same frequency of 63,5% of this variant). The total case count of sequenced variant B.1.1.7 was 1255 by week 10/2021. The earliest collection date for this variant remains 19/DEC/2020 and the latest is 14/MAR/2021.
    In the collection period of week 10/2021, 53 cases of the South African variant B.1.351 have been detected, representing 20,4% of the specimens in the week’s sequencing pool (by comparison, the week 9/2021 pool had shown 18,7% of this variant). The total case count of sequenced variant B.1.351 was 299 by week 10/2021. The earliest collection date for this variant remains 11/JAN/2021 and the latest is 14/MAR/2021.
    In week 10/2021 no additional cases have been dected for any of the other variants of concern (P.1, B.1.525 or A.23.1) (Figure 5).
    Lineage B.1.1.7 is characterized by several spike protein mutations, including N501Y, H69/V70del and P861H. The variant seems to have a considerable epidemiological impact, as it has a higher transmissibility rate.
    Lineage B.1.351 holds numerous spike protein mutations, of which three are located in the receptor binding domain (K417N, E484K and N501Y), and are therefore relevant for antibody binding. As for B.1.1.7, a higher transmissibility rate and viral loads seem to be associated with this variant. Due to the K417N and E484K mutations, an impact on vaccination efficacy and possibility of reinfection is subject to scientific investigation.
    Lineage P.1 (descendent of B.1.1.28), initially found in the Amazon region, has a similar mutation profile as the South African variant, including E484K and N501Y. Concerns are, as for the South African variant, higher transmissibility and a decreased protection by neutralizing antibodies.
    Lineage B.1.525 carries several mutations of biological significance, including E484K, Q677H and F888L. It does not carry N501Y, but a set of deletions similar to the B.1.1.7 variant.

    Of note, additional specimens are in the pipeline for sequencing, so that numbers may change with increasing representativeness of circulating variants and proportions.

    Clinically relevant mutations

    Currently the LNS genomic surveillance program – independently from lineage calling – notes the occurrence of 13 different known SARS-CoV-2 mutations, assumed to have clinical and epidemiological relevance. The list of observed mutations is being updated continually, based on the appearance and prevalence of SARS-CoV-2 variants.
    The following table provides the overall frequencies of these mutations, detected in the lineage-assignable genome sequences, analyzed between 01/SEP/2020 and 14/MAR/2021 (N=5802), as well as the frequencies in week 10/2021.

    References

    Genomic sequencing of SARS-CoV-2. A guide to implementation for maximum impact on public health. WHO, 8 January 2021.
    COVID-19 data portal. 2020 (https://www.covid19dataportal.org/sequences )
    J Hadfield et al. Nextstrain: real-time tracking of pathogen evolution. Bioinformatics 2018;34:4121-4123
    A Rambaut et al. A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nat Microbiol 2020;5:1403-1407
    https://github.com/cov-lineages/pangolin
    Y Guangchuang et al. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods in Ecology and Evolution 2017;8:28-36
    For more information on lineages visit: https://cov-lineages.org
    For more information and statistics on Covid-19 infections in Luxembourg visit: https://covid19.public.lu/en.html

  • Semaine 9

    Respiratory Viruses in Luxembourg (ReViLux)

    Weekly report (Period 01-07/03/2021)

    Executive Summary

    The aim of the “Sentinel” national surveillance program is to monitor the circulating respiratory viruses, including SARS-CoV-2 variants, and hence underpin public health actions.

    In week 9/2021, the overall frequency of the SARS-CoV-2 B.1.1.7 variant in all specimens sequenced remained stable at 62,8% (CI 58,1% – 67,5%, p<0,05). For the SARS-CoV-2 B.1.351 variant, we found an overall frequency of 18,5% (CI 14,7% – 22,2%, p<0,05) within the sequenced specimens.

    The representative sample was estimated, based on the number of positive cases in Luxembourg for week 9 (1191). The minimum sample size required to detect prevalence of B.1.1.7 (63%) reported in week 8 with an error margin of 5% was estimated to be 276 specimens. This number corresponds to a coverage of 23.1% which exceeds the minimum coverage recommended by ECDC (10%). Hence our sequencing results this week are representative of the circulating variants in Luxembourg.

    The total number of sequences performed this week was 475, with 411 specimens collected in the time frame of week 9/2021. The sequencing coverage this week was 34% of all positive cases in Luxembourg.

    Scope

    At present, the scope of the ReViLux report is to provide (i) surveillance and descriptive epidemiology data, including data on molecular phylogenies (identification of importation events, changes in outbreak size over time), and (ii) phylogenetic interpretation of regional virus spread and circulation in Luxembourg, and cluster investigation. The scope of the ReViLux report is not to attempt phylogeographical reconstructions in Luxembourg, as a whole.

    Clinical Surveillance

    The “Sentinel” surveillance network reported 294 consultations in week 9 (01/MAR/2021 – 07/MAR/2021). There was no case of ILI1, as shown in Figure 1. The percentage of consultations for ARI2 was 7,8%.

    1. ILI: – Influenza-Like Illness: Acute respiratory symptoms <10 days, Fever 38C, systematic symptoms (myalgia, malaise, …)
    2. ARI: – Acute Respiratory Infection: Acute respiratory symptoms (bronchitis, pharyngitis, rhinitis, pneumonia…) with or without fever.

    Virological Surveillance

    Patients presenting with ILI and ARI at the Covid Consultation Centre (CCC) in Luxembourg were tested using a respiratory virus panel (ADV = Adenovirus, FLU A = Influenza A, FLU B = Influenza B, HRV = Human Rhinovirus, MPV = Human metapneumovirus, PIV = Parainfluenza virus, RSV = Respiratory Syncytial Virus, SARS-CoV-2 = Severe acute respiratory syndrome coronavirus 2).

    The SAR-COV-2 was the most prevalent respiratory virus detected in the “Sentinel” network, with 33 positive cases (19%). The wave of Human Rhinovirus (HRV) continued in week 9/2021, with 16 positive cases in 174 tests (9%). Sporadic cases of other respiratory viruses were identified in week 9, including 2 cases of PIV (1%), 2 cases of ADV (1%) and 1 case of MPV (0,5%). No cases of Influenza A/B were detected, indicating absence of circulation of Influenza viruses in Luxembourg, as shown in Figure 2.

    In Luxembourg, we have tested 174 specimens from the Sentinel surveillance network, as compared to 1026 specimens tested in Europe, in the week 09/2021. Three of these 1026 specimens, tested for influenza viruses, were positive. The influenza epidemic in the European Region has usually reached its peak by this point of the year but, despite widespread and regular testing for influenza, reported influenza activity still remains at a very low level, likely due to the impact of the various public health and social measures, implemented to reduce transmission of SARS-CoV-2 (Source: FluNews Europe).

    SARS-CoV-2 Genomic Surveillance

    The current sequencing strategy

    The National Reference Laboratory for Acute Respiratory Infections at LNS continues to improve the representativeness of the pool of sequenced specimens to reach real-time epidemiology, by implementing the following weekly sequencing activities:

    • Sequencing specimens from all hospitalized positive cases
    • Sequencing specimens from all positive cases from Airport testing program
    • Sequencing specimens from all outbreaks and identified clusters
    • Systematic sequencing of specimens from reinfections and post-vaccination-infections
    • Population sequencing of specimens from representative regions and age groups, to follow the evolution of the different variants in the Luxembourg population.

    The representative sequencing sample was based on the minimum number of specimens required to extrapolate prevalence of VOC variants with error rate of 5%. The representative sample was estimated based on the number of positive cases in Luxembourg for week 9 (1191). The minimum sample size required to detect prevalence of B.1.1.7 (63%) with an error margin of 5% was estimated to be 276 specimens. The calculation was based on a sample size calculation tool that uses the expected prevalence of the variant in the total population. (Population Proportion – Sample Size – Select Statistical Consultants (select-statistics.co.uk). This number represented a coverage of 23.1% which exceeds the minimum coverage recommended by ECDC (10%). Hence our sequencing results this week are representative of the circulating variants in Luxembourg.

    This week, the Health Inspection provided a set of 300 randomly selected cases. Between this list and our sequencing pool, there was an overlap of 91 specimens. This set of 91 specimens represents an alternative representative sample for the purposes of the weekly genomic surveillance. We will call this sample “randomized sample”.

    The starting material used for sequencing is respiratory specimens (nasopharyngeal or oropharyngeal swabs) that have already been tested positive by RT PCR.

    The LNS sequencing data sharing strategy includes sharing of the sequencing data with GISAID EpiCov database (www.gsaid.org ) on a periodic basis.

    Sequenced specimens

    Last week the microbial genomics platform at the LNS sequenced 475 specimens. Out of these, 411 specimens were collected in week 9/2021. This represents 34% of the new infections reported in Luxembourg in week 9/2021. Among the 475 specimens, 70 specimens were reported to be part of a cluster or outbreak investigation.

    The population sequencing coverage in week 9/2021 was 34% (Figure 3). Based on statistical inference, the frequency of the reported variants in Week 9/2021 is representative of the circulating variants in Luxembourg.

    Circulating lineage detection

    Lineages (variants) have been assigned based on Rambaut et al by means of Phylogenetic Assignment of Named Global Outbeak LINeages (pangolin) software  (v2.3, pangoLEARN version 2021-02-21).

    The lineage nomenclature system that we use is the one proposed by Rambaut et al. that focuses on actively circulating virus lineages (https://cov-lineages.org ).

    In the sampling period of week 9/2021, 20 circulating SARS-CoV-2 variants were detected within our sequencing pool, as shown in Figure 4a. The most prevalent lineage was B.1.1.7 (62,8%, CI 58,1% – 67,5%), followed by B.1.351 (18.5%, CI 14,7% – 22,2%) and B.1.1.29 (9%, CI 6,2% – 11,8%).

    The “randomized sample” of 91 specimens included 10 variants, again with the main three variants being B.1.1.7 (58,2%, CI 48,1% – 68,3%), B.1.351 (19,8%, CI 11,6% – 28%), followed by B.1.1.29 (12,1, CI 5,9% – 19,5%), as shown in Figure 4b.

    Variants of concern tracker (B.1.1.7, B.1.351, P.1, A.23.1 and B.1.525)

    Among specimens collected within the week 9/2021, 258 cases of the B.1.1.7 variant have been detected, representing 62,7% of the specimens in the week’s sequencing pool (by comparison, the week 8/2021 pool, which also included specimens from previous weeks’ collections, had shown 63,7% of this variant). The total case count of sequenced variant B.1.1.7 was 1090 by week 9/2021. The earliest collection date for this variant remains 19/DEC/2020 and the latest is 07/MAR/2021.

    In the collection period of week 9/2021, 76 cases of the South African variant B.1.351 have been detected, representing 18,5% of the specimens in the week’s sequencing pool (by comparison, the week 8/2021 pool, which also included specimens from previous weeks’ collections, had shown 17,2% of this variant). The total case count of sequenced variant B.1.351 was 246 by week 9/2021. The earliest collection date for this variant remains 11/JAN/2021 and the latest is 07/MAR/2021.

    In week 9/2021, an additional case of the Brazilian variant P.1 was detected, therefore the total case count of variant P.1 was 3 by week 9/2021 (latest collection date 05/MAR/2021).

    No additional cases have been detected for lineage B.1.525, and by now no specimen in Luxembourg corresponded to the A.23.1 variant (Figure 5).

    Lineage B.1.1.7 is characterized by several spike protein mutations, including N501Y, H69/V70del and P861H. The variant seems to have a considerable epidemiological impact, as it has a higher transmissibility rate.

    Lineage B.1.351 holds numerous spike protein mutations, of which three are located in the receptor binding domain (K417N, E484K and N501Y), and are therefore relevant for antibody binding. As for B.1.1.7, a higher transmissibility rate and viral loads seem to be associated with this variant. Due to the K417N and E484K mutations, an impact on vaccination efficacy and possibility of reinfection is subject to scientific investigation.

    Lineage P.1 (descendent of B.1.1.28), initially found in the Amazon region, has a similar mutation profile as the South African variant, including E484K and N501Y. Concerns are, as for the South African variant, higher transmissibility and a decreased protection by neutralizing antibodies.

    Lineage B.1.525 carries several mutations of biological significance, including E484K, Q677H and F888L. It does not carry N501Y, but a set of deletions similar to the B.1.1.7 variant.

    Of note, additional specimens are in the pipeline for sequencing, so that numbers may change with increasing representativeness of circulating variants and proportions.

    Clinically relevant mutations

    Currently the LNS genomic surveillance program – independently from lineage calling – notes the occurrence of 13 different known SARS-CoV-2 mutations, assumed to have clinical and epidemiological relevance. The list of observed mutations is being updated continually, based on the appearance and prevalence of SARS-CoV-2 variants.

    The following table provides the overall frequencies of these mutations, detected in the lineage-assignable genome sequences, analyzed between 01/SEP/2020 and 07/MAR/2021 (N=5542), as well as the frequencies in week 9/2021.

    Conclusion

    The ReViLux data are communicated as support to the understanding of respiratory virus transmission dynamics, including introduction of new variants, to the evaluation of the impact of response measures, to the contact tracing and the investigation of clusters.

    References

    Genomic sequencing of SARS-CoV-2. A guide to implementation for maximum impact on public health. WHO, 8 January 2021.

    COVID-19 data portal. 2020 (https://www.covid19dataportal.org/sequences)

    J Hadfield et al. Nextstrain: real-time tracking of pathogen evolution. Bioinformatics 2018;34:4121-4123

    A Rambaut et al. A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nat Microbiol 2020;5:1403-1407

    https://github.com/cov-lineages/pangolin

    Y Guangchuang et al. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods in Ecology and Evolution 2017;8:28-36

    For more information on lineages visit: https://cov-lineages.org
    For more information and statistics on Covid-19 infections in Luxembourg visit: https://covid19.public.lu/en.html

  • Semaine 8

    Respiratory Viruses in Luxembourg (ReViLux)

    Weekly report (Period 22-28/02/2021)

    Executive Summary

    The aim of the “Sentinel” national surveillance program is to monitor the circulating respiratory viruses, including SARS-CoV-2 variants, and hence underpin public health actions.

    In Week 8/2021, the overall frequency of the SARS-CoV-2 B.1.1.7 variant, in all sequenced samples, increased to 64.4% (CI 59,4% – 69,4%, p<0,05). For the SARS-CoV-2 B.1.351 variant, we found an overall frequency of 16.4% (CI 12,5% – 20,3%, p<0,05).

    The representative sample size was estimated, based on the number of positive cases in Luxembourg for week 8 (1315). The minimum sample size required to detect prevalence of B.1.1.7 (56%) with an error margin of 5% was estimated to be 295 specimens. This number corresponds to a coverage of 22.4%, which exceeds the minimum coverage recommended by ECDC (10%). Hence our sequencing results this week are representative of the circulating variants in Luxembourg.

    The total number of sequences performed this week was 570, with 354 samples collected in the time frame of week 8/2021. The sequencing coverage this week was 27% of all positive cases in Luxembourg.

    Scope

    At present, the scope of the ReViLux report is to provide (i) surveillance and descriptive epidemiology data, including data on molecular phylogenies (identification of importation events, changes in outbreak size over time), and (ii) phylogenetic interpretation of regional virus spread and circulation in Luxembourg, and cluster investigation. The scope of the ReViLux report is not to attempt phylogeographical reconstructions in Luxembourg, as a whole.

    Clinical Surveillance

    The “Sentinel” surveillance network reported 210 consultations  in week 8 (22/FEB/2021 – 28/FEB/2021). There was one case of ILI1, representing 0.47% of the consultations (epidemiological threshold is 2 new cases per week), as shown in Figure 1. The percentage of consultations for ARI2 was 7,6%.

    1. ILI: – Influenza-Like Illness: Acute respiratory symptoms <10 days, Fever 38C, systematic symptoms (myalgia, malaise, …)
    2. ARI: – Acute Respiratory Infection: Acute respiratory symptoms (bronchitis, pharyngitis, rhinitis, pneumonia…) with or without fever.

    Virological Surveillance

    Patients presenting with ILI and ARI at the Covid Consultation Centre (CCC) in Luxembourg were tested using a respiratory virus panel (ADV = Adenovirus, FLU A = Influenza A, FLU B = Influenza B, HRV = Human Rhinovirus, MPV = Human metapneumovirus, PIV = Parainfluenza virus, RSV = Respiratory Syncytial Virus, SARS-CoV-2 = Severe acute respiratory syndrome coronavirus 2). The SAR-COV-2 was the most prevalent respiratopry virus detected in the “Sentinel” network, with 39 positive cases (25%). The wave of Human Rhinovirus (HRV) continued in week 8/2021, with 19 positive cases in 156 tests (12.2%). Three cases of PIV were identified in week 8. No cases of Influenza A/B were detected, indicating absence of circulation of influenza viruses in Luxembourg, as shown in Figure 2.

    In Luxembourg, we have tested 156 samples from the “Sentinel” surveillance network, as compared to 1045 samples tested in Europe, in the week 08/2021. Three of these 1045 specimens tested for influenza viruses were positive. The influenza epidemic in the European Region has usually reached its peak by this point of the year but, despite widespread and regular testing for influenza, reported influenza activity still remains at a very low level, likely due to the impact of the various public health and social measures, implemented to reduce transmission of SARS-CoV-2 (Source: FluNews Europe).

    SARS-CoV-2 Genomic Surveillance

    The current sequencing strategy

    The National Reference Laboratory for Acute Respiratory Infections at LNS continues to improve the representativeness of the pool of sequenced specimens to reach real-time epidemiology, by implementing the following weekly sequencing activities:

    • Sequencing specimens from all hospitalized positive cases
    • Sequencing specimens from all positive cases from Airport testing program
    • Sequencing specimens from all outbreaks and identified clusters
    • Systematic sequencing of specimens from reinfections and post-vaccination-infections
    • Population representative sequencing of specimens to follow the evolution of the different variants in the Luxembourg population.

    The representative sequencing sample size calculation was based on the minimum number of specimens required to extrapolate prevalence of VOC variants with error rate of 5%. The representative sample size was estimated based on the number of positive cases in Luxembourg for week 8 (1315). The minimum sample size required to detect prevalence of B.1.1.7 (56%) with an error margin of 5% was estimated to be 295 specimens. The calculation was based on a sample size calculation tool that uses the expected prevalence of the variant in the population of interest. (Population Proportion – Sample Size – Select Statistical Consultants (select-statistics.co.uk). This number represented a coverage of 22.4% which exceeds the minimum coverage recommended by ECDC (10%). Hence our sequencing results this week are representative of the circulating variants in Luxembourg.

    The starting material used for sequencing is respiratory specimens (nasopharyngeal or oropharyngeal swabs) that have already been tested positive by RT PCR.

    The LNS sequencing data sharing strategy includes sharing of the sequencing data with GSAID EpiCov database (www.gsaid.org ) on a periodic basis.

    Sequenced specimens

    Last week the microbial genomics platform at the LNS sequenced 570 specimens. Out of these, 354 specimens were collected in week 8/2021. This represents 27% of the new infections reported in Luxembourg in week 8/2021. Among the 354 specimens, no specimens were reported to be part of a cluster investigation.

    The population sequencing coverage in week 8/2021 was 27%. Based on statistical inference, the frequency of the reported variants in Week 8/2021 is representative of the circulating variants in Luxembourg.

    In the weekly population sequencing pool from representative regions, 17 specimens were collected from non-residents. This leads to 337 specimens, collected in Week 8, and being the representative population sequencing sample.

    Circulating lineage detection

    Lineages (variants) have been assigned based on Rambaut et al by means of Phylogenetic Assignment of Named Global Outbeak LINeages (pangolin) software  (v2.3.3, pangoLEARN version 2021-02-21).

    The lineage nomenclature system that we use is the one proposed by Rambaut et al. that focuses on actively circulating virus lineages (https://cov-lineages.org ).

    In the sampling period of week 8/2021, 17 circulating SARS-CoV-2 variants were detected within our representative sequencing pool, as shown in Figure 3. The most prevalent lineage was B.1.1.7 (65.5%, CI 60,4% – 70,6%), followed by B.1.351 (16%, CI 12,1% – 19,9%) and B.1.1.29 (6%, CI 3,4% – 8,4%).

    Variants of Concern tracker (B.1.1.7, B.1.351, P.1, A.23.1 and B.1.525)

    Among specimens collected within the week 8/2021, 221 cases of the B.1.1.7 variant have been detected, representing 65.5% of the specimens in the week’s representative sample (by comparison, the week 7/2021 had shown 53.7% of this variant). The total case count of sequenced variant B.1.1.7 was 813 by week 8/2021. The earliest collection date for this variant remains 19/DEC/2020 and the latest is 28/FEB/2021.

    In the collection period of week 8/2021, 54 cases of the South African variant B.1.351 have been detected, representing 16% of the specimens in the week’s sequencing pool (by comparison, the week 7/2021 had shown 14.8% of this variant). The total case count of sequenced variant B.1.351 was 159 by week 8/2021. The earliest collection date for this variant remains 11/JAN/2021 and the latest is 28/FEB/2021.

    In week 8/2021, one case of the Brazilian variant P.1 was detected, therefore the total case count of variant P.1 was 2 by week 8/2021 (collection date 02/FEB/2021 and 26/FEB/2021).

    The pangolin group, which provides a global report on novel coronavirus haplotypes, published two additional variants of concern, assigned as A.23.1 and B.1.525. Both variants have already been reported by neighboring countries (Belgium, France). Retrospectively, one case of the B.1.525 variant has been detected for the week 7/2021 (sampling date 20/FEB/2021).

    Lineage B.1.1.7 is characterized by several spike protein mutations, including N501Y, H69/V70del and P861H. The variant seems to have a considerable epidemiological impact, as it has a higher transmissibility rate.

    Lineage B.1.351 holds numerous spike protein mutations, of which three are located in the receptor binding domain (K417N, E484K and N501Y), and are therefore relevant for antibody binding. As for B.1.1.7, a higher transmissibility rate and viral loads seem to be associated with this variant. Due to the K417N and E484K mutations, an impact on vaccination efficacy and possibility of reinfection is subject to scientific investigation.

    Lineage P.1 (descendent of B.1.1.28), initially found in the Amazon region, has a similar mutation profile as the South African variant, including E484K and N501Y. Concerns are, as for the South African variant, higher transmissibility and a decreased protection by neutralizing antibodies.

    Lineage B.1.525 carries several mutations of biological significance, including E484K, Q677H and F888L. It does not carry N501Y, but a set of deletions similar to the B.1.1.7 variant.

    Of note, additional specimens are in the pipeline for sequencing, so that numbers may change with increasing representativeness of circulating variants and proportions.

    Clinically relevant mutations

    Currently the LNS genomic surveillance program – independently from lineage calling – notes the occurrence of 13 different known SARS-CoV-2 mutations, assumed to have clinical and epidemiological relevance. The list of observed mutations is being updated continually, based on the appearance and prevalence of SARS-CoV-2 variants.

    The following table provides the overall frequencies of these mutations, detected in the lineage-assignable genome sequences, analyzed between 01/SEP/2020 and 28/FEB/2021 (N=5098), as well as the mutation frequencies in week 8/2021.

    Conclusion

    The ReViLux data are communicated as support to the understanding of respiratory virus transmission dynamics, including introduction of new variants, to the evaluation of the impact of response measures, to the contact tracing and the investigation of clusters.

    References

    Genomic sequencing of SARS-CoV-2. A guide to implementation for maximum impact on public health. WHO, 8 January 2021.

    COVID-19 data portal. 2020 (https://www.covid19dataportal.org/sequences )

    J Hadfield et al. Nextstrain: real-time tracking of pathogen evolution. Bioinformatics 2018;34:4121-4123

    A Rambaut et al. A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nat Microbiol 2020;5:1403-1407

    https://github.com/cov-lineages/pangolin

    Y Guangchuang et al. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods in Ecology and Evolution 2017;8:28-36

    For more information on lineages visit: https://cov-lineages.org
    For more information and statistics on Covid-19 infections in Luxembourg visit: https://covid19.public.lu/en.html

  • Semaine 7

    Respiratory Viruses in Luxembourg (ReViLux)

    Weekly report (Period 15-22/02/2021)

    Executive Summary

    The aim of the “Sentinel” national surveillance program is to monitor the circulating respiratory viruses, including SARS-CoV-2 variants, and hence underpin public health actions.

    In Week 7/2021, the overall frequency of the SARS-CoV-2 B.1.1.7 variant in all samples sequenced remained stable at 53%. After excluding specimens obtained via target sequencing, the prevalence of the B.1.1.7 variant, in the non-targeted sequencing sample, was 56% and comparable to last week’s prevalence. For the SARS-CoV-2 B.1.351 variant, we found an overall frequency of 22.7% within the sequenced samples. However, as 8 cases were from non-residents, the corrected frequency in all sequenced samples was 15.9%.

    The total number of sequences performed this week was 272, with only 97 samples sequenced for the time frame of week 7/2021. The sequencing coverage dropped this week to 7,77% from all positive cases in Luxembourg, while the newly sequenced specimens had improved the sequencing coverage in week 5/2021 (39.6%) and week 6/2021 (22.2%). Therefore, this week’s sequencing coverage cannot be considered as representative of the general population.

    Scope

    At present, the scope of the ReViLux report is to provide (i) surveillance and descriptive epidemiology data, including data on molecular phylogenies (identification of importation events, changes in outbreak size over time), and (ii) phylogenetic interpretation of regional virus spread and circulation in Luxembourg, and cluster investigation. The scope of the ReViLux report is not to attempt phylogeographical reconstructions in Luxembourg, as a whole.

    Clinical Surveillance

    The “Sentinel” surveillance network is composed of 37 general practicioners and paediatricians around Luxembourg (General Practice and Paediatrics). The “Sentinel” surveillance network reported 133 consultations in week 7 (15/2/2021 – 22/2/2021). There were no cases of ILI1, representing 0% of consultations (epidemiological threshold is 2 new cases per week), as shown in Figure 1. The percentage of consultations for ARI2 was 12%.

    Figure 1 Percentage of patients with ILI over the epidemiological surveillance weeks

    1. ILI: – Influenza-Like Illness: Acute respiratory symptoms <10 days, Fever 38C, systematic symptoms (myalgia, malaise, …)
    2. ARI: – Acute Respiratory Infection: Acute respiratory symptoms (bronchitis, pharyngitis, rhinitis, pneumonia…) with or without fever.

    Virological Surveillance

    Patients presenting with ILI and ARI at the Covid Consultation Centre (CCC) in Luxembourg were tested using a respiratory virus panel (ADV = Adenovirus, FLU A = Influenza A, FLU B = Influenza B, HRV = Human Rhinovirus, MPV = Human metapneumovirus, PIV = Parainfluenza virus, RSV = Respiratory Syncytial Virus, SARS-CoV-2 = Severe acute respiratory syndrome coronavirus 2). The SAR-COV-2 was the most prevalent respiratopry virus detected in the “Sentinel” network, with 48 positive cases (25.3%). The wave of Human Rhinovirus (HRV), circulating currently in Luxembourg, continued in week 7/2021, with 30 positive cases in 183 tests (15.8%). No cases of Influenza A/B were detected, indicating absence of circulation of Influenza viruses in Luxembourg, as shown in Figure 2.

    In Luxembourg, we have tested 190 samples from the Sentinel surveillance network, as compared to 996 samples tested in Europe, in the week 07/2021. Two of these 996 specimens tested for influenza viruses were positive. The influenza epidemic in the European Region has usually reached its peak by this point of the year but, despite widespread and regular testing for influenza, reported influenza activity still remains at a very low level, likely due to the impact of the various public health and social measures, implemented to reduce transmission of SARS-CoV-2 (Source: FluNews Europe).

    SARS-CoV-2 Genomic Surveillance

    The current sequencing strategy

    The National Reference Laboratory for Acute Respiratory Infections at LNS strives to achieve representativeness of the pool of sequenced specimens to reach real-time epidemiology, by implementing the following weekly sequencing activities:

    • Sequencing specimens from all hospitalized positive cases
    • Sequencing specimens from all positive cases from Airport testing program
    • Sequencing specimens from all outbreaks and identified clusters
    • Systematic sequencing of specimens from reinfections and post-vaccination-infections
    • Population sequencing of specimens from representative regions and age groups, to follow the evolution of the different variants in the Luxembourg population.

    A representative sequencing sample calculation was based on the minimum number of specimens required to extrapolate prevalence of VOC variants with error rate of 5%. Based on the total number of positive specimens during the period 01-21/FEB/2021 (3443) , and their geographic distribution across Luxembourg, we concluded on the minimum number of specimens per each canton, as shown in Figure 3. An average sequencage coverage of 11% is the minimum coverage to allow extrapolation of frequencies of variants with confidence.

    The starting material used for sequencing is respiratory specimens (nasopharyngeal or oropharyngeal swabs) that have already been tested positive by RT PCR.

    The LNS sequencing data sharing strategy includes sharing of the sequencing data with GSAID EpiCov database (www.gsaid.org ) on a periodic basis.

    Sequenced specimens

    Last week the microbial genomics platform at the LNS sequenced 272 specimens. Out of these, 97 specimens were collected in week 7/2021. This represents 7.77% of new infections reported in Luxembourg in week 7/2021. Among the 97 specimens, 16% (15 samples) corresponded to targeted specimens (contact tracing with 14 specimens and cluster investigation with 1 specimen).

    The population sequencing coverage in week 7/2021 was 6,57%. This is below the estimated coverage of 11% being the minimum requirement for a representative population sequencing sample. Based on statistical inference, the frequency of the reported variants in Week 7/2021 is not representative of the circulating variants in Luxembourg.

    Circulating lineage detection

    Lineages (variants) have been assigned based on Rambaut et al by means of Phylogenetic Assignment of Named Global Outbeak LINeages (pangolin) software  (v2.3, pangoLEARN version 2021-02-18).

    The lineage nomenclature system that we use is the one proposed by Rambaut et al. that focuses on actively circulating virus lineages (https://cov-lineages.org ).

    In the sampling period of week 7/2021, 11 circulating SARS-CoV-2 variants were detected within our sequencing pool, as shown in Figure 3. The most prevalent lineage was B.1.1.7 (52.6%), followed by B.1.351 (22.7%) and B.1.160 (12.4%). However, the number of local cases of B.1.351 variant was corrected to be 14 only, with 6 cases originating from France and 2 cases from Belgium.

    Variants of Concern tracker (B.1.1.7, B.1.351, P.1, A.23.1 and B.1.525)

    Among specimens collected within the week 7/2021, 51 cases of the B.1.1.7 variant have been detected, representing 52,6% of the specimens in the week’s sequencing pool (by comparison, the week 6/2021 pool, which also included specimens from previous weeks’ collections, had shown 54,1% of this variant). The total case count of sequenced variant B.1.1.7 was 543 by week 7/2021. The earliest collection date for this variant remains 19/DEC/2020 and the latest is 19/FEB/2021.

    In the collection period of week 7/2021, 22 cases of the South African variant B.1.351 have been detected, representing 22,7% of the specimens in the week’s sequencing pool (by comparison, the week 6/2021 pool, which also included specimens from previous weeks’ collections, had shown 10,7% of this variant). The total case count of sequenced variant B.1.351 was 83 by week 7/2021. The earliest collection date for this variant remains 11/JAN/2021 and the latest is 19/FEB/2021.

    In week 7/2021, no cases of the Brazilian variant P.1 were detected, therefore the total case count of variant P.1 was 1 by week 7/2021 (collection date 02/FEB/2021). Last week, the pangolin group, which provides a global report on novel coronavirus haplotypes, published two additional variants of concern, assigned as A.23.1 and B.1.525. Both variants have already been reported by neighboring countries (Belgium, France). However, none of these variants has been detected in Luxembourg.

    Lineage B.1.1.7 is characterized by several spike protein mutations, including N501Y, H69/V70del and P861H. The variant seems to have a considerable epidemiological impact, as it has a higher transmissibility rate.

    Lineage B.1.351 holds numerous spike protein mutations, of which three are located in the receptor binding domain (K417N, E484K and N501Y), and are therefore relevant for antibody binding. As for B.1.1.7, a higher transmissibility rate and viral loads seem to be associated with this variant. Due to the K417N and E484K mutations, an impact on vaccination efficacy and possibility of reinfection is subject to scientific investigation.

    Lineage P.1 (descendent of B.1.1.28), initially found in the Amazon region, has a similar mutation profile as the South African variant, including E484K and N501Y. Concerns are, as for the South African variant, higher transmissibility and a decreased protection by neutralizing antibodies.

    Of note, additional specimens are in the pipeline for sequencing, so that numbers may change with increasing representativeness of circulating variants and proportions.

    Phylogenetic analysis

    Phylogenetic analysis is done by means of Nextstrain (https://nextstrain.org/sars-cov-2/) and is based on genetic distances including a timeline on the x-axis. The phylogenetic tree is rooted against the first sequence obtained in Luxembourg (29/FEB/2020), which is considered as our “outgroup”. Sequences obtained before 01/NOV/2020 are shown as grey dots. Sequences obtained within the last 2 weeks, are represented in colour and by greater dot diameter. In the context of increasing numbers of sequences, a random subsampling of 300 sequences over the whole sequencing period, starting 01/SEP/2020, was performed.

    The phylogenetic tree shows four visually well separated clusters. These clusters correspond to the lineages B.1.160, B.1.177, B.1.1.7 and B.1.221. Due to random selection of sequences and the intentional insertion of variants of concern, the cluster representation is mostly qualitative and does not necessarily correlate with relative prevalence of the respective variants (Figure 5).

    Lineage B.1.1.7 (represented by light brownish dots) forms a well distinguishable cluster, due to the high number of accumulated mutations. B.1.1.7 subtrees might indicate different subgroups, possibly related to different routes of infection.

    Clinically relevant mutations

    Currently the LNS genomic surveillance program – independently from lineage calling – notes the occurrence of 13 different known SARS-CoV-2 mutations, assumed to have clinical and epidemiological relevance. The list of observed mutations is being updated continually, based on the appearance and prevalence of SARS-CoV-2 variants.

    The following table provides the overall frequencies of these mutations, detected in the lineage-assignable genome sequences, analyzed between 01/SEP/2020 and 19/FEB/2021 (N=4665), as well as the frequencies in week 7/2021.

    Conclusion

    The ReViLux data are communicated as support to the understanding of respiratory virus transmission dynamics, including introduction of new variants, to the evaluation of the impact of response measures, to the contact tracing and the investigation of clusters.

     

    References

    Genomic sequencing of SARS-CoV-2. A guide to implementation for maximum impact on public health. WHO, 8 January 2021.

    COVID-19 data portal. 2020 (https://www.covid19dataportal.org/sequences )

    J Hadfield et al. Nextstrain: real-time tracking of pathogen evolution. Bioinformatics 2018;34:4121-4123

    A Rambaut et al. A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nat Microbiol 2020;5:1403-1407

    https://github.com/cov-lineages/pangolin

    Y Guangchuang et al. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods in Ecology and Evolution 2017;8:28-36

    For more information on lineages visit: https://cov-lineages.org
    For more information and statistics on Covid-19 infections in Luxembourg visit: https://covid19.public.lu/en.html

  • Semaine 6

    Respiratory Viruses in Luxembourg (ReViLux)

    Weekly report (Period 08-14/02/2021)

    Executive Summary

    The aim of the “Sentinel” national surveillance program is to monitor the circulating respiratory viruses, including SARS-CoV-2 variants, and hence underpin public health actions. ECDC and WHO have recently recommended that national sequencing programs should cover a minimum of 10% of all SARS-CoV-2 positive specimens, or 500 specimens, whichever is less.

    In week 5/2021, the SARS-CoV-2 sequencing coverage had reached 27% of all identified positive cases, yielding a representative population sequencing sample. Luxembourg reported the second highest sequencing coverage in EU, surpassed only by Denmark. In week 6/2021, this coverage was 19.5%.

    In week 6/2021, the overall prevalence of the SARS-CoV-2 B.1.1.7 variant in the sequencing sample was 53%. After correction for the bias linked to sequencing of targeted, instead of random specimens, the prevalence of the B.1.1.7 variant, in the representative population sequencing sample, was 57%. A circumscript outbreak of 17 cases of the B.1.351 variant, appeared in the hospital environment.

     

     

    Scope

    At present, the scope of the ReViLux report is to provide (i) surveillance and descriptive epidemiology data, including data on molecular phylogenies (identification of importation events, changes in outbreak size over time), and (ii) phylogenetic interpretation of regional virus spread and circulation in Luxembourg, and cluster investigation. The scope of the ReViLux report is not to attempt phylogeographical reconstructions in Luxembourg, as a whole.

    Clinical Surveillance

    The “Sentinel” surveillance network is composed of 37 general practicioners and paediatricians around Luxembourg (General Practice and Paediatrics). This week we had 145 consultations reported by 9 of these general paractitioners and pediatricians (24% of the network size).

    During week 6 (8/2/2021 – 14/2/2021), there were 2 cases of ILI1 representing 1.37% of consultations (epidemiological threshold is 2 new cases per week), as shown in Figure 1. The percentage of consultations for ARI2 was 14%.

    Figure 1 Percentage of patients with ILI over the epidemiological weeks

    1. ILI: – Influenza-Like Illness: Acute respiratory symptoms <10 days, Fever 38C, systematic symptoms (myalgia, malaise, …)
    2. ARI: – Acute Respiratory Infection: Acute respiratory symptoms (bronchitis, pharyngitis, rhinitis, pneumonia…) with or without fever.
    
    

    Virological Surveillance

    Patients presenting with ILI and ARI at the Covid Consultation Centre (CCC) in Luxembourg were tested using a respiratory virus panel (ADV = Adenovirus, FLU A = Influenza A, FLU B = Influenza B, HRV = Human Rhinovirus, MPV = Human metapneumovirus, PIV = Parainfluenza virus, RSV = Respiratory Syncytial Virus, SARS-CoV-2 = Severe acute respiratory syndrome coronavirus 2). The SAR-COV-2 was the most prevalent respiratopry virus detected in the “Sentinel” network, with 38 positive cases (20.8%). The wave of Human Rhinovirus (HRV), circulating currently in Luxembourg, continued in week 6/2021, with 36 positive cases in 183 tests (19.7%). Only three positive cases of Parainfluenza viruses were detected. No cases of Influenza A/B were detected, indicating absence of circulation of Influenza viruses in Luxembourg as shown in Figure 2.

    In Luxembourg, we have tested 183 samples from the Sentinel surveillance network, as compared to 1268 samples tested in Europe, in the week 06/2021. None of these 1268 specimens tested for influenza viruses were positive. The influenza epidemic in the European Region has usually reached its peak by this point of the year but, despite widespread and regular testing for influenza, reported influenza activity still remains at a very low level, likely due to the impact of the various public health and social measures, implemented to reduce transmission of SARS-CoV-2 (Source: FluNews Europe).

     

     

    SARS-CoV-2 Genomic Surveillance

    The current sequencing strategy

    The National Reference Laboratory for Acute Respiratory Infections at LNS continues to improve the representativeness of the pool of sequenced specimens to reach real-time epidemiology, by implementing the following weekly sequencing activities:

    1. Sequencing specimens from all hospitalized positive cases
    2. Sequencing specimens from all positive cases from Airport testing program
    3. Sequencing specimens from all outbreaks and identified clusters
    4. Systematic sequencing of specimens from reinfections and post-vaccination-infections
    5. Population sequencing of specimens from representative regions and age groups, to follow the evolution of the different variants in the Luxembourg population.

    The starting material used for sequencing is respiratory specimens (nasopharyngeal or oropharyngeal swabs) that have already been tested positive by RT PCR.

    Sequenced specimens

    Last week the microbial genomics platform at the LNS has sequenced 390 specimens. Out of these, 214 specimens were collected in week 6/2021. This represents 19.5% of new infections reported in Luxembourg in week 6/2021. Among the 214 specimens, 38% (82 samples) corresponded to targeted specimens (contact tracing with 46 specimens and cluster investigation with 36 specimens).

    After filtering out specimens referred for sequencing in a targeted way, the population sequencing coverage in week 6/2021 was 12%. This exceeds the ECDC recommendation of 10% being the minimum requirement for a representative population sequencing sample.

    Circulating lineage detection

    Lineages (variants) have been assigned based on Rambaut et al by means of Phylogenetic Assignment of Named Global Outbeak LINeages (pangolin) software  (v2.3, pangoLEARN version 2021-02-18).

    The lineage nomenclature system that we use is the one proposed by Rambaut et al. that focuses on actively circulating virus lineages (https://cov-lineages.org).

    In the sampling period of week 6/2021, in the population representative sample (132 specimens), 13 variants were detected, with the main three variants being B.1.1.7 (57.6%), B.1.160 (13.6%), followed by B.1.221 (7.6%), as shown in Figure 3.

     

     

    Variants of Concern (B.1.1.7, B.1.351, P.1, A.23.1 and B.1.525)

    Among specimens collected within the week 6/2021, 114 cases of the B.1.1.7 variant have been detected, representing 53,5% of the specimens in the week’s sequencing pool (by comparison, the week 5/2021 pool, which also included specimens from previous weeks’ collections, had shown 54,2% of this variant). The total case count of sequenced variant B.1.1.7 was 403 by week 6/2021. The earliest collection date for this variant remains 19/DEC/2020 and the latest is 14/FEB/2021.

    In the collection period of week 6/2021, 24 cases of the South African variant B.1.351 have been detected. The total case count of sequenced variant B.1.351 was 52 by week 6/2021. The earliest collection date for this variant remains 11/JAN/2021 and the latest is 14/FEB/2021.

    In week 6/2021, no additional cases of the Brazilian variant P.1 were detected, therefore the total case count of variant P.1 was 1 by week 6/2021 (collection date 02/FEB/2021). Last week, the pangolin group, which provides a global report on novel coronavirus haplotypes, published two additional variants of concern, assigned as A.23.1 and B.1.525. Both variants have already been reported by neighboring countries (Belgium, France). However, none of these variants has been detected in Luxembourg (Figure 4).

    Lineage B.1.1.7 is characterized by several spike protein mutations, including N501Y, H69/V70del and P861H. The variant seems to have a considerable epidemiological impact, as it has a higher transmissibility rate.

    Lineage B.1.351 holds numerous spike protein mutations, of which three are located in the receptor binding domain (K417N, E484K and N501Y), and are therefore relevant for antibody binding. As for B.1.1.7, a higher transmissibility rate and viral loads seem to be associated with this variant. Due to the K417N and E484K mutations, an impact on vaccination efficacy and possibility of reinfection is subject to scientific investigation.

    Lineage P.1 (descendent of B.1.1.28), initially found in the Amazon region, has a similar mutation profile as the South African variant, including E484K and N501Y. Concerns are, as for the South African variant, higher transmissibility and a decreased protection by neutralizing antibodies.

    Of note, additional specimens are in the pipeline for sequencing, so that numbers may change with increasing representativeness of circulating variants and proportions.

     

    Phylogenetic analysis

    Phylogenetic analysis is done by means of Nextstrain (https://nextstrain.org/sars-cov-2/) and is based on genetic distances including a timeline on the x-axis. The phylogenetic tree is rooted against the first sequence obtained in Luxembourg (29/FEB/2020), which is considered as our “outgroup”. Sequences obtained before 01/NOV/2020 are shown as grey dots. Sequences obtained within the last 2 weeks, are represented in colour and by greater dot diameter. In the context of increasing numbers of sequences, a random subsampling of 300 sequences over the whole sequencing period, starting 01/SEP/2020, was performed.

    The phylogenetic tree shows four visually well separated clusters. These clusters correspond to the lineages B.1.160, B.1.177, B.1.1.7 and B.1.221. Due to random selection of sequences and the intentional insertion of variants of concern, the cluster representation is mostly qualitative and does not necessarily correlate with relative prevalence of the respective variants (Figure 5).

    Lineage B.1.1.7 (represented by light brownish dots) forms a well distinguishable cluster, due to the high number of accumulated mutations. B.1.1.7 subtrees might indicate different subgroups, possibly related to different routes of infection.

    Clinically relevant mutations

    Currently the LNS genomic surveillance program – independently from lineage calling – notes the occurrence of 13 different known SARS-CoV-2 mutations, assumed to have clinical and epidemiological relevance. The list of observed mutations is being updated continually, based on the appearance and prevalence of SARS-CoV-2 variants.

    The following table provides the overall frequencies of these mutations, detected in the lineage-assignable genome sequences, analyzed between 01/SEP/2020 and 14/FEB/2021 (N=4392), as well as the frequencies in week 6/2021.

     

    Conclusion

    The ReViLux data are communicated as support to the understanding of respiratory virus transmission dynamics, including introduction of new variants, to the evaluation of the impact of response measures, to the contact tracing and the investigation of clusters.

    The SARS-CoV-2 sequencing program at the LNS continues to expand, both with higher coverage and with retrospective epidemiological metadata annotations.

    References

    Genomic sequencing of SARS-CoV-2. A guide to implementation for maximum impact on public health. WHO, 8 January 2021.

    COVID-19 data portal. 2020 (https://www.covid19dataportal.org/sequences )

    J Hadfield et al. Nextstrain: real-time tracking of pathogen evolution. Bioinformatics 2018;34:4121-4123

    A Rambaut et al. A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nat Microbiol 2020;5:1403-1407

    https://github.com/cov-lineages/pangolin

    Y Guangchuang et al. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods in Ecology and Evolution 2017;8:28-36

    For more information on lineages visit: https://cov-lineages.org
    For more information and statistics on Covid-19 infections in Luxembourg visit: https://covid19.public.lu/en.html

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