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.
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.
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.
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.
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.
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.
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.
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
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).
