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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).


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 ( 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 ( 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.


Centers for Disease Control and Prevention. SARS-CoV-2 Variant Classifications and Definitions. Retrieved 24 August 2021, from

COVID-19 Data Portal – accelerating scientific research through data. (2021). Retrieved 23 August 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

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

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:

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


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).