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Semaine 50

Respiratory Viruses in Luxembourg (ReViLux)

Weekly report (13 – 19 December 2021)

Executive Summary

The Sentinel Surveillance Network identified 7 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 LNS analysed 798 specimens from residents in Luxembourg in week 50/2021 (from 2727 total cases in the Grand Duchy of Luxembourg, 29,3%). This does not reach the new ECDC recommendations to detect emerging variants at 1% prevalence (minimum sample size of 927). Including both sequencing and screening results by PCR, 1188 national specimens were analysed globally (43,6%).

The Omicron variant was assigned to 50 national cases collected during week 50, and the Delta variant remains the dominant one. The most frequent lineages are AY.43 (26,6%), AY.4 (9,4%) and AY.98.1 (8,4%). A similar distribution was observed for target groups (hospital specimens and post-vaccination breakthrough cases), although a preliminary analysis shows higher transmission of Omicron than previous variants, among fully vaccinated individuals.


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-CO-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 the week of study was 7 (out of 493 consultations); therefore, the percentage of ILI (1,42%) falls bellow 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. The PCR kits 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). 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.

Screening and sequenced specimens

In week 50, 2727 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 preferable than the usual 2.5%, according to the ECDC. For that, the recommended sample size is estimated to be 977 specimens (35.8%).

Last week, 2986 specimens were received. Of these, 1155 specimens (including 1054 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 912 specimens, including 798 specimens having been collected from residents; hence, the weekly sequencing coverage remains at 29.3% (798 out of 2727 cases registered in Luxembourg; see coverage trend in Figure 2). Although this does not reach the recommended sample size in the current epidemiological situation, overall, 1188 national specimens were analysed either by sequencing or screening (43,6%).

Omicron screening results

As shown in Figure 3, of the 1155 specimens from week 50 which were screened by targeted PCR, 60 were identified as potential Omicron cases (5,2%) and were prioritised for confirmatory sequencing.

Circulating lineage detection

The distribution of successfully assigned lineages within the national selection sample is shown in Figure 4. Regarding Delta AY sublineages, only a selection is displayed, 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 (26,6%), although its proportion has been decreasing for four weeks in a row. It is followed by AY.4 (9,4%), AY.98.1 (8,4%) and Omicron (BA.1, 7,1%). Nevertheless, these results must be interpreted with caution: potential Omicron cases detected by PCR screening are prioritised for sequencing, and this prioritization might lead to an overestimation of the actual presence of this variant.

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 50 national specimens successfully assigned to the Omicron variant in week 50, 3 more sequences with insufficient quality to be assigned to any specific lineage were found to carry characteristic mutations of the this variant.


Centers for Disease Control and Prevention. SARS-CoV-2 Variant Classifications and Definitions. Retrieved 27 December 2021, from

COVID-19 Data Portal – accelerating scientific research through data. (2021). Retrieved 27 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 27 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 27 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 27 December 2021, from:

Pango Network. New AY lineages. Retrieved 27 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


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  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. 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.
  4. Pearson CA. Estimates of severity and transmissibility of novel South Africa SARS-CoV-2 variant 501Y.V2 [Available from:]
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  6. 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.
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  12. Public Health England. SARS-CoV-2 variants of concern and variants under investigation in England Technical briefing 16 2021 [Available from:]
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