Respiratory Viruses
SENTINELLE Newsletter
ReViLux Bulletin hebdomadaire
25 January 2021
Semaine: 3
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 3 (18/01/2021 - 24/01/2021), 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 10%.
- 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) | 22 | 10.4% |
| ILI (influenza-like illness) | 1 | 0.5% |
| Consultations | 211 |
Respiratory viruses circulating in Luxembourg
| results | |
|---|---|
| Cumulative number of tests performed | 131 |
| Cumulative number of positive samples | 31 |
| Positivity rate | 24% |
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 decrease in the positivity rate of SARS-CoV-2 with 20 positive cases in 131 tests (15%). Moreover, the Human Rhinovirus (HRV) continues to circulate in Luxembourg.
SARS-CoV-2 Sequencing
Sequenced Samples
For data presentation purposes we use a window of 5 months so the plotted data are starting on 01/09/2020. From this week on we switch to real-time epidemiology. The delay in reporting is represented by the technical process for sequencing samples upon reception to our premises which ranges 5-7 days. However, we will report also first results for week 3/2021.
Starting next week, the newsletter will be issued on Wednesdays, instead of Tuesdays.
The microbial genomics platform of the microbiology department has generated since March 2020 2998 high quality SARS-CoV-2 consensus sequences with 90 % reference sequence coverage at a minimum sequencing depth of 20, wherein 306 sequences have been added last week. These 306 sequences cover a sampling time frame of 11th November until 20th of January. The relatively old sampling time is related to catch-up sequencing to screen for possible early introductions of the B.1.1.7 variant to Luxembourg.
- RefSeq ID NC_045512.2, Wuhan-1
Circulating Lineages
Lineages have been assigned based on Rambaut et al by means of pangolin (v2.1.8, pangoLEARN version 2021-01-22), allowing for a geographical classification of circulating viral genomes.
For the sampling time frame week 2/2021 (11th-17th January) 12 circulating SARS-CoV-2 variants have been detected within 84 high quality genomes.
In comparison to last week the composition of main circulating strains has changed. As in previous weeks the most prevalent lineage is B.1.160 (38%) followed by B.1.177 (16%) both representing big European clusters. On position three we observe a switch from B.1.221 (9%) to B.1.1.7 (17%, details see below).
Regardless of variants of concern (c.f. below), we detected a small fraction for B.1.474 (5%) and B.1.1.10 as well as singular cases for B.1, B.1.1.1, B.1.177.18, all representing lineages commonly prevalent in Europe.
Variants of Concern (B.1.1.7, B.1.351, P.1)
Referring to week 2/2021 14 new cases of B.1.1.7 have been detected, representing 16.7% of circulating strains (week 1/2020 9.3%, additional samples have been added, reaching 10% coverage of new infections by sequencing). Including genomes with less, but sufficient quality for lineage call, the proportion of B.1.1.7 lowers to 15.4% for week 2/2021 (1 additional case in lower quality sequences). Due to catch-up sequencing of elderly samples, additional cases have been detected retrospectively as well as 4 cases referring to week 3/2021.
Accordingly, by now, the number of detected B.1.1.7 cases is set to 36. The earliest sampling date remains 19/12/2020 and the latest is 19/01/2021.
For the sampling time frame of week 2/2021 the first 2 cases of the South African variant B.1.351 have been detected. One additional case has been found referring to week 3/2021, taking the case count to 3, sampled between 11th and 18th of January.
No cases have been detected for the Japanese/Brazilian variant P.1 in Luxembourg by now. Though, we detected 2 cases of the Brazilian lineage B.1.1.28, which is closely related to P.1, being described as its predecessor. The two cases detected in Luxembourg (sampled 12th and 17th of January) carry the spike protein mutation E484K, but lack N501Y and K417N.
Lineage B.1.1.7 is characterized by several spike protein mutations including S:N501Y, deletion S:H69/V70 and S:P861H. The variant seems to have a considerable epidemiological impact, as it has a higher transmissibility (more efficient and rapid).
Lineage B.1.351 holds numerous spike protein mutations, wherein three are located in the receptor binding domain (K417N, E484K and N501Y), which is relevant for antibody binding. As for B.1.1.7, a higher transmissibility and viral load is in discussion. Due to K417N and E484K an impact on vaccination and possible reinfection is subject of scientific investigation.
Lineage P.1 (descendent of B.1.1.28) initially been 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.
It is to note, that additional samples are in preparation for sequencing, so that numbers might change with increasing representativeness of circulating strains and proportions.
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 from most recent sampling date (20th January) are represented in colour 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, B.1.351 and B.1.1.28.
The tree shows four visually well separated clusters. These clusters are represented by the lineages B.1.160, B.1.177, B.1.1.7 and B.1.221. Due to random selection of sequences and the explicit insertion of variants of interest, the size of clusters might be misleading and does not necessarily correlate with the prevalence of the respective variant.
Lineage B.1.1.7 (represented by green dots) forms a very well distinguished cluster, due to its high amount of accumulated mutations. B.1.1.7 subtrees might direct to different subgroups, possibly related to different sources of infection.
The cases for B.1.351 (light brownish dots, close to the bottom of the tree) and B.1.1.28 (overlapping violet dots, underneath the B.1.1.7 cluster) are as well separating well from common circulating strains.
- Nextstrain applied an additional filter on genome length > 27000, 330 sequences shown
Clinically relevant mutations
Currently genomic surveillance is - independently from lineage call - observing the occurence of 13 different known SARS-Cov-2 mutations, being assumend 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 the variant B.1.1.7, the characterizing mutations N501Y, H69/V70del, Y144del and P681H are integrated in weekly reporting. Additionally, the mutation E484K is under observation, which is in combination with N501Y and K417N characteristic for the South African and Japanese/Brazilian variant.
The following table provides the overall frequency of these mutations in high quality genomes between 01/09/2020 and the last sequenced sampling date 20th January 2021 (N=2998), as well as a close-up of the last 14 days.
| Mutation | Gene | Genomic position in reference | Frequency overall | Frequency recent 14days | Characteristics | Reference |
|---|---|---|---|---|---|---|
| D614G | S gene | 23402 | 100.00% | 100.00% | 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 |
| E484K | S gene | 23012 | 0.00% | 3.00% | 501Y.V2 / possible impact on antibody neutralization activity (escape mutation), improved ACE2 binding affinity | Greaney et al, 2020 |
| G204R | N gene | 28883 | 7.00% | 17.00% | Fitness advantage for the virus | Leary et al. 2020 |
| H69/V70del | S gene | 21765-21770 | 3.00% | 13.00% | possible impact on antibody neutralization activity and reinfection; included in "mink" mutation | Kemp et al 2020, Kemp et al 2020 |
| K417N | S gene | 22813 | 0.00% | 2.00% | 501Y.V2 / possible impact on antibody binding affinity (escape mutation) | Kemp et al 2020 |
| L37F | Nsp6 | 11081 | 8.00% | 7.00% | Favored viral infection, higher severity | Aiewsakun et al. 2020 |
| N439K | S gene | 26143 | 3.00% | 0.00% | Improved ACE2 binding affinity | Zhou et al, 2020 |
| N501Y | S gene | 23063 | 1.00% | 15.00% | 501Y.V1/V2; Improved ACE2 binding affinity/higher transmissibility | Filip Fratev 2020 COVID-19 Genomics Consortium UK, 2020 |
| P323L | ORF1ab (RdRP gene, nsp12) | 14407 | 99.00% | 99.00% | Higher severity | Biswas and Mudi 2020 |
| P681H | S gene | 23604 | 5.00% | 19.00% | immediately adjacent to the furin cleavage site, a known location of biological significance | COVID-19 Genomics Consortium UK, 2020 |
| Q57H | ORF3a | 25561 | 45.00% | 54.00% | Higher severity | Biswas and Mudi 2020 |
| R203K | N gene | 28880 | 7.00% | 17.00% | Fitness advantage for the virus | Leary et al. 2020 |
| Y144del | S gene | 21991-21993 | 2.00% | 14.00% | 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.
In comparison to the previous week the frequency within the last 14 days increased for S:N501Y from 4% to 15%, for S:H69/V70 deletion from 5% to 13%, for S:P681H from 12% to 19% and for S:Y144del from 5% to 14%. Due to its detection in all over 5 samples, the E484K shows an initial frequency of 3% within the last 14 days.
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