The aim of the “Sentinel” national surveillance program is to monitor the circulating respiratory viruses, including SARS-CoV-2 variants, and hence underpin public health actions.
In week 11/2021, the overall frequency of the SARS-CoV-2 B.1.1.7 variant in all samples sequenced increased 68,1% (CI 64,2% – 72%, p<0,05). For the SARS-CoV-2 B.1.351 variant, we found an overall frequency of 23% (CI 19.4% - 26,5%, p<0,05) within the sequenced samples.
The representative sample was estimated, based on the number of positive cases in Luxembourg for week 11 (1570). The minimum sample size required to detect prevalence of B.1.1.7 (68%) reported in week 11, with an error margin of 5%, was estimated to be 276 specimens. This number corresponds to a coverage of 17,6%, which exceeds the minimum coverage recommended by ECDC (10%). The sequencing results of week 11 are representative of the circulating variants in Luxembourg with a margin of error of 5%.
The total number of sequences performed this week was 540, with all specimens having been collected in the time frame of week 11/2021. The sequencing coverage this week was 34,4% from all positive cases in Luxembourg.
The “Sentinel” surveillance network reported 263 consultations in week 11 (15/MAR/2021 – 21/MAR/2021). There was 5 cases of ILI1, as shown in Figure 1, corresponding to 1,9% of consultations. The percentage of consultations for ARI2 was 17,9%.
Patients presenting with ILI and ARI at the Covid Consultation Centre (CCC) in Luxembourg were tested using a respiratory virus panel (ADV = Adenovirus, FLU A = Influenza A, FLU B = Influenza B, HRV = Human Rhinovirus, MPV = Human metapneumovirus, PIV = Parainfluenza virus, RSV = Respiratory Syncytial Virus, SARS-CoV-2 = Severe acute respiratory syndrome coronavirus 2).
The SAR-COV-2 was the most prevalent respiratory virus detected in the “Sentinel” network, with 64 positive cases (22%). The wave of Human Rhinovirus (HRV) continued in week 11/2021, with 34 positive cases in 291 tests (11,7%). Sporadic cases of other respiratory viruses continued to appear as one case of PIV was identified in week 11 (0,3%) and two cases of Adenovirus (ADV), corresponding to 0,7% of all tests. No cases of Influenza A/B were detected, indicating absence of circulation of Influenza viruses in Luxembourg, as shown in Figure 2.
In Luxembourg, we have tested 291samples from the Sentinel surveillance network, as compared to 1256 specimens tested in Europe, in the week 11/2021. One of these 1256 specimens tested positive for type A Influenza virus. The influenza epidemic in the European Region has usually reached its peak by this point of the year but, despite widespread and regular testing for influenza, reported influenza activity still remains at a very low level, likely due to the impact of the various public health and social measures, implemented to reduce transmission of SARS-CoV-2 (Source: FluNews Europe).
The National Reference Laboratory for Acute Respiratory Infections at LNS continues to improve the representativeness of the pool of sequenced specimens to reach real-time epidemiology, by implementing the following weekly sequencing activities:
The representative sequencing sample was based on the minimum number of specimens required to extrapolate prevalence of VOC variants with error rate of 5%. The representative sample was estimated based on the number of positive cases in Luxembourg for week 11 (1570). The minimum sample size required to detect prevalence of B.1.1.7 (68%) with an error margin of 5% was estimated to be 276 specimens. The calculation was based on a sample size calculation tool that uses the expected prevalence of the variant in the total population. (Population Proportion – Sample Size – Select Statistical Consultants (select-statistics.co.uk). This number represented a coverage of 17,6% which exceeds the minimum coverage recommended by ECDC (10%). The number of non-targeted specimens sequenced this week was 515. Therefore, our sequencing results this week are representative of the circulating variants in Luxembourg with a margin of error of 5%.
The starting material used for sequencing is respiratory specimens (nasopharyngeal or oropharyngeal swabs) that have already been tested positive by RT PCR.
The LNS sequencing data sharing strategy includes sharing of the sequencing data with GISAID EpiCov database (www.gsaid.org ) on a periodic basis.
Last week the microbial genomics platform at the LNS sequenced 540 specimens. All of these were collected in week 11/2021. This represents 32,8% of the new infections reported in Luxembourg in week 11/2021. Among the 540 specimens, 25 specimens were reported to be part of a cluster or outbreak investigation, and 41 specimens were from non-residents. This leads to 474 specimens, collected in week 11, and being the representative population sequencing sample. In the population representative sample of residents, the frequency of B.1.1.7 and B.1.135 was 68.3% and 22.5% respectively.
The population sequencing coverage in week 11/2021 was 34,4% (Figure 3). Based on statistical inference, the frequency of the reported variants in week 11/2021 is representative of the circulating variants in Luxembourg with a margin of error of 5%.
Lineages (variants) have been assigned based on Rambaut et al by means of Phylogenetic Assignment of Named Global Outbeak LINeages (pangolin) software (v2.3, pangoLEARN version 2021-02-21).
In week 11/2021, in the population representative sample, after removal of the 25 cluster samples, and excluding specimens collected from non-residents, there were 13 variants, with the main three variants being B.1.1.7 (68,3%, CI 64,1% – 72,5%), B.1.351 (22.5%, CI 18,7% – 26,3%), followed by B.1.1.29 (2.1%, CI 0,8% – 3,4%), as shown in Figure 4.
Among specimens collected within the week 11/2021, 368 cases of the B.1.1.7 variant have been detected, representing 68,1% of the specimens in the week’s sequencing pool (by comparison, the week 10/2021 pool had shown a frequency of 63,5% of this variant). The total case count of sequenced variant B.1.1.7 was 1623 by week 11/2021. The earliest collection date for this variant remains 19/DEC/2020 and the latest is 21/MAR/2021.
In the collection period of week 11/2021, 124 cases of the South African variant B.1.351 have been detected, representing 23% of the specimens in the week’s sequencing pool (by comparison, the week 10/2021 pool had shown 20,4% of this variant). The total case count of sequenced variant B.1.351 was 423 by week 10/2021. The earliest collection date for this variant remains 11/JAN/2021 and the latest is 21/MAR/2021.
In week 11/2021 no additional cases have been dected for any of the other variants of concern (P.1, B.1.525 or A.23.1) (Figure 5).
Lineage B.1.1.7 is characterized by several spike protein mutations, including N501Y, H69/V70del and P861H. The variant seems to have a considerable epidemiological impact, as it has a higher transmissibility rate.
Lineage B.1.351 holds numerous spike protein mutations, of which three are located in the receptor binding domain (K417N, E484K and N501Y), and are therefore relevant for antibody binding. As for B.1.1.7, a higher transmissibility rate and viral loads seem to be associated with this variant. Due to the K417N and E484K mutations, an impact on vaccination efficacy and possibility of reinfection is subject to scientific investigation.
Lineage P.1 (descendent of B.1.1.28), initially found in the Amazon region, has a similar mutation profile as the South African variant, including E484K and N501Y. Concerns are, as for the South African variant, higher transmissibility and a decreased protection by neutralizing antibodies.
Lineage B.1.525 carries several mutations of biological significance, including E484K, Q677H and F888L. It does not carry N501Y, but a set of deletions similar to the B.1.1.7 variant.
Of note, additional specimens are in the pipeline for sequencing, so that numbers may change with increasing representativeness of circulating variants and proportions.
Currently the LNS genomic surveillance program – independently from lineage calling – notes the occurrence of 13 different known SARS-CoV-2 mutations, assumed to have clinical and epidemiological relevance. The list of observed mutations is being updated continually, based on the appearance and prevalence of SARS-CoV-2 variants.
The following table provides the overall frequencies of these mutations, detected in the lineage-assignable genome sequences, analyzed between 01/SEP/2020 and 21/MAR/2021 (N=6345), as well as the frequencies in week 11/2021.
Genomic sequencing of SARS-CoV-2. A guide to implementation for maximum impact on public health. WHO, 8 January 2021.
COVID-19 data portal. 2020 (https://www.covid19dataportal.org/sequences )
J Hadfield et al. Nextstrain: real-time tracking of pathogen evolution. Bioinformatics 2018;34:4121-4123
A Rambaut et al. A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nat Microbiol 2020;5:1403-1407
https://github.com/cov-lineages/pangolin
Y Guangchuang et al. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods in Ecology and Evolution 2017;8:28-36
For more information on lineages visit: https://cov-lineages.org
For more information and statistics on Covid-19 infections in Luxembourg visit: https://covid19.public.lu/en.html