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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, en partenariat avec les laboratoires privés. Ce rapport hebdomadaire est publié par le département de microbiologie du LNS dans le cadre de ses missions de surveillance, de vigilance 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

Le LNS traite les données recueillies pour l’envoi de documentations liés à ses activités. Pour en savoir plus sur la gestion des données personnelles et pour exercer vos droits, vous pouvez vous reporter à la politique de protection des données sur le site internet du LNS à l’adresse suivante : https://lns.lu/donnees-personnelles/ et plus particulièrement dans la rubrique « Dans le cadre des opérations de communication du LNS et de son site internet». Si vous souhaitez ne plus recevoir ces communications, vous pouvez vous désabonner à la newsletter. Pour cela, veuillez envoyer un mail à revilux@lns.etat.lu.


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  • Semaine 01

    Respiratory Viruses in Luxembourg (ReViLux)

    Weekly report (3 – 9 January 2022)

    Executive Summary

    The Sentinel Surveillance Network identified 15 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 LNS analysed 665 specimens from residents in Luxembourg in week 01/2022 (from 10 680 total cases in the Grand Duchy of Luxembourg; 6.2%). This reaches the ECDC recommendations to detect emerging variants at 2.5% prevalence (minimum sample size of 568). Including PCR screening results, 1546 national specimens were analysed globally (14.5%).

    The Omicron variant was assigned to 89.6% of national cases collected during week 01/2022, remaining the dominant one.

    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).

    The current influenza season started in week 40/2021. 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. The number of ILI cases identified in the week of study was 15 (out of 347 consultations); therefore, the percentage of ILI (4.32%) exceeds the threshold for the epidemic season (2.59%), according to the ECDC.

    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.

    Due to the emergence of the new Omicron variant of concern, as well as the high incidence rates in the European context, targeted PCR  tests are carried systematically in order to detect potential Omicron cases within 24h from reception of the specimen. The PCR kits used target the following spike mutations: 69/70del, K417N, N501Y. The potential cases identified this way are then prioritised for confirmation by sequencing.

    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 (v3.1.17, pangoLEARN 2021-12-06). 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).

    Screening and sequenced specimens

    In week 01/2022, 10 680 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 568 specimens (5.3%).

    Last week, 3912 specimens were received. Of these, 1120 specimens (including 992 national specimens) were screened by targeted PCR for the Omicron variant, in order to enable an earlier detection of potential Omicron cases (see results in the following section). In parallel, the microbial genomics unit at the LNS sequenced 738 specimens, including 665 specimens having been collected from residents. The weekly sequencing coverage remains at 6.2% (665 out of 10 680 cases registered in Luxembourg; see coverage trend in Figure 2). Overall, 1546 national specimens were analysed either by sequencing or screening (14.5%).

    Omicron screening results

    As shown in Figure 3, of the 1120 specimens from week 01/2022 which were screened by targeted PCR, 984 were identified as potential Omicron cases (87.9%).

    Circulating lineage detection

    The distribution of successfully assigned lineages within the national selection is shown in Figure 4. Regarding Delta AY sublineages, only a selection is displayed, 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 Omicron variant remains the dominant one (89.6%) within national specimens. All Omicron cases were assigned to the lineage BA.1 (the most common worldwide). Within the Delta variant, the lineage AY.43 remained the most frequent one.

    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 42 mutations to the spike protein frequently associated to VOCs. Additionally to the 509 national specimens successfully assigned to the Omicron variant in the week of study, 15 sequences with insufficient quality to be assigned to any lineage were found to carry characteristic mutations of this variant.

    References

    Centers for Disease Control and Prevention. SARS-CoV-2 Variant Classifications and Definitions. Retrieved 17 January 2022, from https://www.cdc.gov/coronavirus/2019-ncov/variants/variant-info.html

    COVID-19 Data Portal – accelerating scientific research through data. (2021). Retrieved 17 January 2022, 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 17 January 2022, 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 17 January 2022, 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 17 January 2022, from: https://www.pango.network/new-ay-lineages/

    Pango Network. New AY lineages. Retrieved 17 January 2022, 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

    According to the WHO