bg image

Semaine 48

Respiratory Viruses in Luxembourg (ReViLux)

Weekly report (29 Nov – 05 Dec 2021)

Executive Summary

The Sentinel Surveillance Network identified 27 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 812 specimens from residents in Luxembourg in week 48/2021 (from 2699 total cases in the Grand Duchy of Luxembourg, 30,1%). This does not reach the new ECDC recommendations to detect emerging variants at 1% prevalence (minimum sample size of 927). Including complementary screening results by PCR, 1158 national specimens were analysed globally.

All specimens sequenced in week 48 were assigned to the Delta variant. The first Omicron case has been detected among specimens from week 49. The most frequent lineages are AY.43 (34,8%), AY.4 (11,8%) and AY.98.1 (8,4%). A similar distribution was observed for target groups (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.


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. The number of ILI cases identified in week 47 was 27 (out of 528s consultations); therefore, the percentage of ILI (5,11%) exceeds 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.

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 expanding its sequencing capacity and reactivity. Additionally, targeted PCR  tests are carried systematically in order to detect potential Omicron cases within 24h from reception of the specimen. These potential cases 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 (v3.1.16, pangoLEARN 2021-11-25). 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 48, 2699 new cases were registered in Luxembourg. Given the epidemiological situation after the emergence of the new Omicron variant, achieving a 1% incidence detection capacity is preferrable than the usual 2.5%, according to the ECDC. For that, the recommended sample size is estimated in 973 specimens (36.1%).

Last week, the microbial genomics unit at the LNS analysed 906 specimens from week 48, with 812 specimens having been collected in week 48 from residents. As this sample did not reach the ECDC-recommended sample size, another 346 specimens from residents were tested by targeted PCR for the Omicron variant (overall, 42,9% coverage of the 2699 total cases registered in Luxembourg; see coverage trend in Figure 2).

Circulating lineage detection

The distribution of successfully assigned lineages within the representative sample is shown in Figure 3. 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 lineage AY.43 continues to be the most frequent one (34,8%), followed by AY.4 (11,8%), while the remaining lineages show frequencies lower than 10%. No Omicron cases were assigned in week 48, but the first case has been sequenced in a national specimen collected in week 49.

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. Accordingly to the distribution lineages, most of the mutations found during the last 2 weeks are linked to Delta cases. No specimen displayed a mutation pattern suspicious of Omicron variant.


Centers for Disease Control and Prevention. SARS-CoV-2 Variant Classifications and Definitions. Retrieved 13 December 2021, from

COVID-19 Data Portal – accelerating scientific research through data. (2021). Retrieved 13 December 2021, from

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 December 2021, from

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 December 2021, from

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 December 2021, from:

Pango Network. New AY lineages. Retrieved 13 December 2021, from:

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


Appendix 1: SARS-CoV-2 variants of concern

According to the ECDC


  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:
  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:
  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:
  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:
  11. Public Health England. SARS-CoV-2 variants of concern and variants under investigation in England Technical briefing 16 2021 [Available from:

According to the WHO