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 23/2021, the overall frequency of the SARS-CoV-2 B.1.1.7 variant in all sequenced specimens slightly increased to 50,5% (CI 40,8% – 60,2%, p<0,05). One case of SARS-CoV-2 B.1.351 (1%, CI 0% – 2,9%, p<0,05) and 4 cases of P.1 variant (3,9%, CI 0% – 7,6%, p<0,05) were detected, while the frequency of the variant B.1.617.2 increased slightly to 36% (CI 26,7% – 45,3%, p<0,05).
The representative sample size was estimated, based on the number of positive cases in Luxembourg for week 23 (189). The minimum sample size required to detect prevalence of B.1.1.7 (47%) reported in week 22, with an error margin of 5%, was estimated to be 127 specimens. This number corresponds to a coverage of 67,2 %, which exceeds the minimum coverage recommended by ECDC (10%). The sequencing results of week 23 are not representative of the circulating variants in Luxembourg with an error margin of 5%.
The total number of sequences performed this week was 283, with 103 specimens having been collected in the time frame of week 23/2021. The sequencing coverage – based on sequenced samples collected in week 23 and corresponding to Luxembourg residents and to non-targeted collections – was 36% of all positive cases in Luxembourg.
The “Sentinel” surveillance network reported 375 consultations in week 23 (07/JUNE/2021 – 13/JUNE/2021). There were 4 cases of ILI1, corresponding to 1,1% of the consultations, as shown in Figure 1. The number of consultations for ARI2 was 35, which represents 9,3% of the consultations.
Covid Consultation Centres have been closed since 16/May/2021. We are currently working on an alternative in partnership with private laboratories.
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 in week 23 (189). The minimum sample size required to detect prevalence of B.1.1.7 (47%) reported in week 22 with an error margin of 5% was estimated to be 127 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 67,2% which exceeds the minimum coverage recommended by ECDC (10%). The number of non-targeted specimens from Luxembourgish residents sequenced this week was 68. Therefore, our sequencing results this week are not representative of the circulating variants in Luxembourg.
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.gisaid.org ) on a periodic basis.
Last week the microbial genomics platform at the LNS sequenced 283 specimens, with 103 collected in week 23/2021. The sequencing pool referring to Luxembourgish residents represents 52,4% of new infections reported in Luxembourg in week 23/2021. Among these 103 specimens, 34 specimens were reported to be part of a cluster or outbreak investigation, and 5 specimens were from non-residents (4 specimen overlapping). This leads to 68 specimens, collected in week 23, and not being a representative population sequencing sample. In the population sample of residents, the frequency of B.1.1.7 was 58,8%, while the frequency for B.1.617.2 was 30,9%. Two cases have been detected for the P1 and 1 case for the B.1.351 variant, representing 2,9% and 1,5% respectively.
The population sequencing coverage in week 23/2021 was 36% (Figure 2). Based on statistical inference, the frequency of the reported variants in week 23/2021 is not 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 (v3.0.3, pangoLEARN version 2021-05-27).
The lineage nomenclature system that we use is the one proposed by Rambaut et al. that focuses on actively circulating virus lineages (https://cov-lineages.org ).
In week 23/2021, in the population sample, after removal of cluster samples, and excluding specimens collected from non-residents, there were 7 circulating SARS-CoV-2 variants, with the main three variants being B.1.1.7 (58,8%, CI 47,1% – 70,5%), B.1.617.2 (30,9%, CI 19,9% – 41,9%) and P.1 (2,9%, CI 0% – 6,9%), as shown in Figure 3.
Among specimens collected within the week 23/2021, 52 cases of the B.1.1.7 variant have been detected, representing 50,5% of the specimens in the week’s sequencing pool (by comparison, the week 22/2021 pool had shown a frequency of 47,4% of this variant, including additional specimens having been sequenced from previous weeks). The total case count of sequenced variant B.1.1.7 was 6460 by week 23/2021.
In the collection period of week 23/2021, 1 case of the South African variant B.1.351 has been detected, representing 1% (by comparison, the week 22/2021 pool had shown 0% of this variant). The total case count of sequenced variant B.1.351 was 1079 by week 23/2021.
Four new cases of the P.1 variant have been detected in week 23/2021, corresponding to 3,9%, while the previous week no case had been detected. The total case count of sequenced variant P.1 was 122 by week 23/2021.
In week 23/2021, no new case of B.1.525 has been detected. The case count by week 23 for B.1.525 is 46.
In week 23/2021, 36 additional cases of the Delta variant B.1.617.2 have been detected (latest sampling date 11/JUNE/2021). The case count by week 23 for B.1.617.1 increases by retrospective sequencing to 8, and for B.1.617.2 it raises to 186. Since May 6th B.1.617.2 has been escalated by Public Health England from a variant under investigation to a variant of concern (Figure 4).
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.
Lineage B.1.617 is a variant first detected in India and was designated “Under Investigation” on 1st April 2021 by Public Health England. It contains a number of spike mutations associated with antigenic escape or found in other variants of concern, including L452R, E484Q and P681R. Subtype B.1.617.2 does not carry S:E484Q and seems to more transmissible as B.1.1.7 (increasing confidence). Neutralization studies show reductions in cross-neutralizing activity between B.1.1.7 and B.1.351.
By week 23/2021, 89,3 % of the variants detected in the sequenced specimen pool are declared as either Variants of Concern, including the B.1.1.7, the B.1.617.2 (increasing trend) and P.1 variant.
The ReViLux will continue to use the (Pango) system to allow easier visualisation of links between any evolving variants and their ancestor (Figure 5).
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 13/JUNE/2021 (N=12723), as well as the frequencies in week 23/2021.
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