Respiratory Viruses
SENTINELLE Newsletter
ReViLux Bulletin hebdomadaire
08 December 2020
Semaine: 49
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 49 (30/11/2020 - 06/12/2020), l'activité grippale reste modérée.
Le taux de consultations avec ILI1 est de 1% (seuil épidémiologique à 3%).
Le taux de consultations avec ARI2 est de 16%.
- 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) | 43 | 16% |
| ILI (influenza-like illness) | 3 | 1% |
| Consultations | 275 |
Respiratory viruses circulating in Luxembourg
| results | |
|---|---|
| Cumulative number of tests performed | 271 |
| Cumulative number of positive samples | 153 |
| Positivity rate | 56% |
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 119 positive cases in 271 tests (44%). 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 2077 SARS-CoV-2 positive samples since 29/02/2020, wherein 1335 have been added to the sequencing pool since 01/10/2020. The data analysis of 1295 samples including 1048 positive samples, sequenced since 01/10/2020, 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.
Most recent sequencing data referring to week 45 confirm observations made since beginning of September. The main circulating strains are lineages B.1.160 (36%), B.1.177 (25%) and B.1.78 (29%; Netherlands).
Lineage B.1.160 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.
Lineage B.1.177 (cluster 20A.EU1, Hodcroft 2020) appeared in early summer 2020 and has its origin presumably in Spain. It spread to multiple European countries and its frequency rose to 40-70% in Switzerland, Ireland and the United Kingdom in September. It is as well prevalent in other Luxembourg neighboring countries like Netherlands and France. It has the mutations A222V in the spike protein and A220V in the nucleoprotein
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 46 if available, are represented by greater diameter.
The tree shows five well separated clusters, wherein three are large and very well distinguishable and two are rather small and genetically more close to each other. The biggest cluster is formed by the B.1.160 lineage, referring to the S: S477N cluster, another one represents the B.1.177 cluster (c.f. above) and a third cluster is shaped by the B.1.78 lineage (Netherlands). The two remaining clusters, mainly comprising European lineages (B.1.1 (Europe incl. Portugal as most common country), B.1.1.1 (UK/Europe)), but also some other individual lineages, like B.1.98 (UK/US/Australia) are very close with regard to their genetic distance to each other, but quite different from the main strains.
- Nextstrain applied an additional filter on genome length > 27000, 1229 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 recent 14days | Characteristics | Reference |
|---|---|---|---|---|---|---|
| D614G | S gene | 23402 | 99.0% | 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, Plante et al. 2020) |
| G204R | N gene | 28883 | 15.0% | 0% | Fitness advantage for the virus | (Leary et al. 2020) |
| G251V | ORF3a | 26143 | 0.0% | 0% | Higher immune evasion, viral spread, and pathogenesis | (Issa et al. 2020) |
| L37F | Nsp6 | 11081 | 7.0% | 0% | Favored viral infection, higher severity | (Aiewsakun et al. 2020) |
| L84S | ORF8 | 28143 | 0.0% | 0% | Mild severity | (Biswas and Mudi 2020) |
| P323L | ORF1ab (RdRP gene, nsp12) | 14407 | 98.0% | 100% | Higher severity | (Biswas and Mudi 2020) |
| Q57H | ORF3a | 25561 | 35.0% | 17% | Higher severity | (Biswas and Mudi 2020) |
| R203K | N gene | 28880 | 15.0% | 0% | 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/
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