Respiratory Viruses
SENTINELLE Newsletter
ReViLux Bulletin hebdomadaire
09 novembre 2020
Semaine: 44
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 44 (2020-10-26 - 2020-11-01), l’activité grippale reste modérée.
Le taux de consultations avec ILI1 est de 2.1% (seuil épidémiologique à 2.57%).
Le taux de consultations avec ARI2 est de 21.8%.
- 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
| Nombre de Patients | Pourcentage | |
|---|---|---|
| ARI (acute respiratory infections) | 63 | 21.8% |
| ILI (influenza-like illness) | 6 | 2.1% |
| Consultations | 289 |
SARS-CoV-2 Sequencing
Sequenced Samples
The microbial genomics platform of the microbiology department sequenced 725 SARS-CoV-2 positive samples since 2020-02-29, wherein 125 have been added since 01/10/2020. The data analysis of 472 samples (92/472 since October 1st) provides high quality consensus sequences with 90 % reference sequence3 coverage at a minimum sequencing depth of 20.
- RefSeq ID NC_045512.2, Wuhan-1
Circulating Lineages
Lineages have been assigned based on Rambaut et al by means of pangolin, allowing for a geographical classification of circulating viral genomes.
Between June and August the majority of circulating lineages was the so called Luxembourg/ UK/ Portugal lineage (B.1.1.15). In week 43 the two major circulating lineages are B.1.160 (former B.1.36) and B.1.78 (Netherlands), no sequence has been assigned to B.1.1.15.
The number of sequences assigned to lineage B.1.160 is increasing since end of August. This lineage represents an EU/EEA and UK multi-country cluster which involves Belgium, France, Germany 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. A second variant of the B.1 lineage, characterized by spike protein mutation A222V is circulating in Luxembourg as well being part of a mostly European cluster, involving Belgium, France, Germany, Hong-Kong, Ireland, Italy, Latvia, The Netherlands, Norway, Spain, Switzerland, The United Kingdom. The origin is likely Spain.
The 10 most frequent lineages are highlighted in different colors, other lineages are shown in grey (“other”).
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 01/09/2020 are in grey, Sequences obtained after are coloured according to their lineage, dots of sequences from week 43 are represented by greater diameter.
The tree shows six separated clusters. Wherein two, mainly comprising European lineages (B.1.1, B.1.1.1), are very close with regard to their genetic distance. The other four show a considerable genetic distance. The biggest cluster is formed by the B.1.160 lineage, referring to the S: S477N cluster, another one represents the B.1 cluster (c.f. above) and a third cluster is shaped by the B.1.78 lineage (Netherlands).
- Nextstrain applied an additional filter on genome length > 27000, 420 sequences shown
Clinically relevant mutations
By literature review 8 highly frequent point mutations with possible clinical impact have been selected being continuously monitored by whole genome sequencing of SARS-CoV-2 full genomes. The following table provides the overall frequency of these mutations between 29/02/2020 and today within high quality genomes (N=472).
| Mutation | Gene | Genomic position in reference | Frequency overall | Frequency last 30 days | Characteristics | Reference |
|---|---|---|---|---|---|---|
| D614G | S gene | 23402 | 97% | 100% | Higher infectivity, higher case fatality rate, higher transmission | (Eaaswarkhanth, al Madhoun, and Al-Mulla 2020) (Becerra-Flores and Cardozo 2020) ( Hu et al. 2020) |
| G204R | N gene | 28883 | 29% | 20% | Fitness advantage for the virus | (Leary et al. 2020) |
| G251V | ORF3a | 26143 | 1% | 0% | Higher immune evasion, viral spread, and pathogenesis | (Issa et al. 2020) |
| L37F | Nsp6 | 11081 | 9% | 12% | Favored viral infection, higher severity | (Aiewsakun et al. 2020) |
| L84S | ORF8 | 28143 | 1% | 0% | Mild severity | (Biswas and Mudi 2020) |
| P323L | ORF1ab (RdRP gene, nsp12) | 14407 | 95% | 99% | Higher severity | (Biswas and Mudi 2020) |
| Q57H | ORF3a | 25561 | 27% | 42% | Higher severity | (Biswas and Mudi 2020) |
| R203K | N gene | 28880 | 29% | 22% | Fitness advantage for the virus | (Leary 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. The mutations R203K and G204R have their highest frequencies between June and August, following the lineage distributions in which they occurring in combination with D614G and P323L (Luxembourg/BeNeLux lineages). Their presence is reducing along with the increasing prevalence of B.1.60 and and B.1.78. After its relatively high occurrence in March/April and low frequency between June and August Q75H shows increasing frequencies since September (occurs in B.1.160 in combination with D614G and P323L). The prevalence of G251V, L37F and L84S is continuously low.
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/
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). doi:10.1111/2041-210X.12628