Respiratory Viruses
SENTINELLE Newsletter
ReViLux Bulletin hebdomadaire
12 January 2021
Semaine: 1
Résultats cliniques de la sentinelle
La surveillance SENTINELLE des infections respiratoires aiguës est une collaboration entre le Laboratoire national de santé (LNS), la Direction de la Santé et un réseau de médecins-généralistes et de pédiatres répartis à travers tout le Luxembourg. Ce rapport hebdomadaire est publié par le départment de microbiologie du LNS dans le cadre de ses missions de surveillance, de vigilance et d’alerte dans les domaines de la santé publique, l'analyse des données rapportant l’activité clinique dans la Sentinelle et des données virologiques à l’appui.
Au cours de la semaine 1 (04/01/2021 - 10/01/2021), l'activité grippale reste faible.
Le taux de consultations avec ILI1 est de 0% (seuil épidémiologique à 3%).
Le taux de consultations avec ARI2 est de 14%.
- ILI: - Influenza-Like Illness: Signes respiratoires aigus <10 jours, Fièvre 38∘C, Signes systémiques (myalgie, malaise, maux de tête, …)
- ARI: - Infection Respiratoire Aiguë: Signes respiratoires aigus (bronchite, pharyngite, rhinite, pneumonie…) avec ou sans fièvre
| Number of Patients | Percentage | |
|---|---|---|
| ARI (acute respiratory infections) | 34 | 14% |
| ILI (influenza-like illness) | 1 | 0% |
| Consultations | 243 |
Respiratory viruses circulating in Luxembourg
| results | |
|---|---|
| Cumulative number of tests performed | 114 |
| Cumulative number of positive samples | 38 |
| Positivity rate | 33% |
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). We noticed a high positivity rate of SARS-CoV-2 with 33 positive cases in 114 tests (29%). Moreover, there is a wave of Human Rhinovirus (HRV) circulating currently in Luxembourg.
SARS-CoV-2 Sequencing
Sequenced Samples
The microbial genomics platform of the microbiology department sequenced 3779 SARS-CoV-2 positive samples since 29/02/2020, wherein 3305 have been added to the sequencing pool since 01/09/2020. From those, the data analysis of 2347 positive samples provides high quality consensus sequences with 90 % reference sequence3 coverage at a minimum sequencing depth of 20.
From this week on, we will report only on samples being taken since 01/09/2020
- RefSeq ID NC_045512.2, Wuhan-1
Circulating Lineages
Lineages have been assigned based on Rambaut et al by means of pangolin (v2.1.6, pangoLEARN version 2021-01-06), allowing for a geographical classification of circulating viral genomes.
The most recent sequencing pool is represented by 311 high quality genomes, being sequenced between the 5th and 10th of January. It comprises positive SARS-CoV-2 samples being taken between the 30th of November and 3rd of January.
For the sampling time frame 28th December until 3rd of January 10 circulating SARS-CoV-2 variants have been detected in 127 samples, confirming the observations made in previous weeks with three main circulating strains, being lineages B.1.160 (31%), B.1.177 (38%) and B.1.221 (13%). Singular cases have been observed for lineages B.1.1, B.1.1.70, B.1.1.177.19 and B.1.367 (European lineages) and small fractions of B.1 (9%;large European cluster) and A.2.4 (2%; Panama lineage).
Lineage B.1.160 represents an EU/EEA and UK multi-country cluster which involves Belgium, France, Germany, Switzerland and the United Kingdom. It is characterized by a spike protein mutation S: S477N, occurring in combination with N: M234I, A376T, ORF1a: M3087I, ORF1b: A176S and most also with ORF1b: V767L K1141R, E1184D.
Lineage B.1.177, the so called “Spain to Europe lineage” is as well prevalent in many other European countries. It is characterized by the spike protein mutation A222V and A220V in the nucleoprotein.
Lineage B.1.221 is annotated as a Dutch and Belgian variant, but is also very common in Denmark and UK.
Internationally reported variants
Three new cases of the UK variant B.1.1.7 have been detected, taking the total number of samples in Luxembourg carrying this variant to six. The samples have been collected on December 30th/31st and January 3rd respectively. While one case was identified by contract tracing, two have been sampled by routine SARS-CoV-2 testing on prescription. The UK lineage represents 3.14% of circulating strains in week 53 (5 cases, 3 newly plus 2 cases being detected within the previous week)
Lineage B.1.1.7 is characterized by several spike protein mutations, which seem to have a considerable epidemiological impact, as this variant has a higher transmissibility (more efficient and rapid).
Neither cases of the South African variant B.1.351 nor the Japanese variant B.1.1.248 have been detected.
Phylogenetic Analysis
Phylogenetic analysis has been done by means of nextstrain4 and is based on genetic distance including a timeline on the x-axis. The tree is rooted versus the first sequence obtained in Luxembourg (29/02/2020). Sequences obtained before 01/11/2020 are in grey and those obtained within the last 2 weeks (20th December - 3rd January) are represented in color and by greater diameter. Due to the increasing number of sequences represented, we performed a random subsampling of 300 sequences over the complete sequencing time frame since 01/09/2020, adding on top the sequences related to B.1.1.7.
The tree shows three well separated clusters. As in previous weeks, the biggest clusters are formed by the lineages B.1.177, B.1.160 and B.1.221.
The B.1.1.7 lineage is genetical distance wise well separated from the remaining sequences, mirroring the relatively high amount of accumulated mutations in this lineage. It can be found at the bottom of the tree represented by a mini cluster of overlapping pinkish dots.
- Nextstrain applied an additional filter on genome length > 27000, 305 sequences shown
Clinically relevant mutations
Currently genomic surveillance is observing the occurence of 13 different known SARS-Cov-2 mutations, which are assumed to have a clinical or epidemiological relevance. The pool of observed mutations is updated continously, depending on the development of SARS-CoV-2 variants and their prevalence.
Due to the increasing incidence of B.1.1.7 variant in European countries like the UK, Denmark and Ireland, the characterizing mutations N501Y, H69/V70del, Y144del and P681H have been integrated in weekly reporting. Additionally, the mutation E848K has been added, which is in combination with N501Y characteristic for the South African and Japanese variant.
The following table provides the overall frequency of these mutations between September 1st and 3rd of January within high quality genomes (N=2348).
| Mutation | Gene | Genomic position in reference | Frequency overall | Frequency recent 14days | Characteristics | Reference |
|---|---|---|---|---|---|---|
| D614G | S gene | 23402 | 100.0% | 100.0% | Higher infectivity, higher case fatality rate, higher transmission; replaced original Wuhan strain, became globally dominant form of the virus | Eaaswarkhanth, al Madhoun, and Al-Mulla 2020, Becerra-Flores and Cardozo 2020, Hu et al. 2020, Plante et al. 2020 |
| E848K | S gene | 23012 | 0.0% | 0.0% | 501Y.V2 / possible impact on antibody neutralization activity (escape mutation), improved ACE2 binding affinity | Greaney et al, 2020 |
| G204R | N gene | 28883 | 7.0% | 5.0% | Fitness advantage for the virus | Leary et al. 2020 |
| H69/V70del | S gene | 21765-21770 | 2.0% | 2.0% | possible impact on antibody neutralization activity and reinfection; included in "mink" mutation | Kemp et al 2020, Kemp et al 2020 |
| K417N | S gene | 22813 | 0.0% | 0.0% | 501Y.V2 / possible impact on antibody binding affinity (escape mutation) | Kemp et al 2020 |
| L37F | Nsp6 | 11081 | 7.0% | 7.0% | Favored viral infection, higher severity | Aiewsakun et al. 2020 |
| N439K | S gene | 26143 | 3.0% | 5.0% | Improved ACE2 binding affinity | Zhou et al, 2020 |
| N501Y | S gene | 23063 | 0.0% | 2.0% | 501Y.V1/V2; Improved ACE2 binding affinity/higher transmissibility | Filip Fratev 2020 COVID-19 Genomics Consortium UK, 2020 |
| P323L | ORF1ab (RdRP gene, nsp12) | 14407 | 99.0% | 98.0% | Higher severity | Biswas and Mudi 2020 |
| P681H | S gene | 23604 | 3.0% | 11.0% | immediately adjacent to the furin cleavage site, a known location of biological significance | COVID-19 Genomics Consortium UK, 2020 |
| Q57H | ORF3a | 25561 | 43.0% | 42.0% | Higher severity | Biswas and Mudi 2020 |
| R203K | N gene | 28880 | 7.0% | 5.0% | Fitness advantage for the virus | Leary et al. 2020 |
| Y144del | S gene | 21991-21993 | 1.0% | 4.0% | possible impact on antibody binding affinity | Dawood et al 2020 |
Clinically relevant mutations frequencies over time
The D614G and P323L mutations have been and are continuously present in a vast majority of sequences. They mainly occur together. The frequencies for mutations related to the UK variant (N501Y, H69/V70del, Y144del, P681H) are not considerably increasing by now, but need close surveillance in the upcoming weeks. Same applies to E848K (South African and Japanese variant), which has by now not been detected in Luxembourg.
Additional Information
For more information on lineages visit: https://cov-lineages.org
For more information on protein structures and a global phylogeny visit: https://genome.lux-covid19.lu/
For more information and statistics on Covid-19 infections in Luxembourg visit: https://covid19.public.lu/en.html
References
Rambaut, A., Holmes, E.C., O’Toole, Á. et al. A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nat Microbiol 5, 1403–1407 (2020). https://doi.org/10.1038/s41564-020-0770-5
Pangolin (pangolin assigns lineages to query sequences as described in Rambaut et al 2020); Áine O’Toole, JT McCrone, Emily Scher; github.com/cov-lineages/pangolin
Hadfield et al., Nextstrain: real-time tracking of pathogen evolution, Bioinformatics (2018)
Guangchuang Yu, David Smith, Huachen Zhu, Yi Guan, Tommy Tsan-Yuk Lam. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods in Ecology and Evolution 8(1) 28-36 (2017). https://doi.org/10.1111/2041-210X.12628