Analysis of SARS-CoV-2 variants from 24,181 patients exemplifies the role of globalisation and zoonosis in pandemics
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Abstract
After the end of the first epidemic episode of SARS-CoV-2 infections, as cases began to rise again during the summer of 2020, we at IHU Méditerranée Infection in Marseille, France, intensified the genomic surveillance of SARS-CoV-2, and described the first viral variants. In this study, we compared the incidence curves of SARS-CoV-2-associated deaths in different countries and reported the classification of SARS-CoV-2 variants detected in our institute, as well as the kinetics and sources of the infections. We used mortality collected from a COVID-19 data repository for 221 countries. Viral variants were defined based on ≥5 hallmark mutations shared by ≥30 genomes. SARS-CoV-2 genotype was determined for 24,181 patients using next-generation genome and gene sequencing (in 47% and 11% of cases, respectively) or variant-specific qPCR (in 42% of cases). Sixteen variants were identified by analysing viral genomes from 9,788 SARS-CoV-2-diagnosed patients. Our data show that since the first SARS-CoV-2 epidemic episode in Marseille, importation through travel from abroad was documented for seven of the new variants. In addition, for the B.1.160 variant of Pangolin classification (a.k.a. Marseille-4), we suspect transmission from mink farms. In conclusion, we observed that the successive epidemic peaks of SARS-CoV-2 infections are not linked to rebounds of viral genotypes that are already present but to newly-introduced variants. We thus suggest that border control is the best mean of combating this type of introduction, and that intensive control of mink farms is also necessary to prevent the emergence of new variants generated in this animal reservoir.
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SciScore for 10.1101/2021.09.10.21262922: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Software and Algorithms Sentences Resources The data mining process was done using ‘R’(https://www.r-project.org/) with the packages ‘vegan’, ‘forecast’, ‘dynamictreecut’ and ‘rnaturalearth’. https://www.r-project.org/suggested: (R Project for Statistical Computing, RRID:SCR_001905)SARS-CoV-2 genome sequences were obtained by next-generation sequencing with various procedures since February 2020 until August 2021: (i) with the Illumina technology using the Nextera XT paired end strategy on MiSeq instruments (Illumina Inc., San Diego, CA, USA), as previously described (3); (ii) with the Illumina COVIDSeq protocol on a NovaSeq 6000 … SciScore for 10.1101/2021.09.10.21262922: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Software and Algorithms Sentences Resources The data mining process was done using ‘R’(https://www.r-project.org/) with the packages ‘vegan’, ‘forecast’, ‘dynamictreecut’ and ‘rnaturalearth’. https://www.r-project.org/suggested: (R Project for Statistical Computing, RRID:SCR_001905)SARS-CoV-2 genome sequences were obtained by next-generation sequencing with various procedures since February 2020 until August 2021: (i) with the Illumina technology using the Nextera XT paired end strategy on MiSeq instruments (Illumina Inc., San Diego, CA, USA), as previously described (3); (ii) with the Illumina COVIDSeq protocol on a NovaSeq 6000 instrument (Illumina Inc.) since April 2021; or (iii) with Oxford Nanopore technology (ONT) on MinION or GridION instruments (Oxford Nanopore Technologies Ltd., Oxford, UK), as previously described (3) MinIONsuggested: (MinION, RRID:SCR_017985)Genome sequence analyses: Genome consensus sequences were generated by mapping on the SARS-CoV-2 genome GenBank accession no. NC_045512.2 (Wuhan-Hu-1 isolate) with the CLC Genomics workbench v.7 (with the following thresholds: 0.8 for coverage and 0.9 for similarity) (https://digitalinsights.qiagen.com/), as previously described (3), or the Minimap2 software (44). Genomesuggested: (JGI Genome Portal, RRID:SCR_002383)SAMtools was used for soft clipping of Artic primers (https://artic.network/), and to remove PCR duplicates (46) SAMtoolssuggested: (SAMTOOLS, RRID:SCR_002105)Pairwise nucleotide distances between SARS-CoV-2 genomes were computed using the MEGA7 software v10.2.5 (https://www.megasoftware.net/). MEGA7suggested: NoneSARS-CoV-2 classification and naming system: Phylogeny reconstructions based on the SARS-CoV-2 genomes obtained in our laboratory were performed using the nextstrain/ncov tool (https://github.com/nextstrain/ncov) then visualised with Auspice (https://docs.nextstrain.org/projects/auspice/en/stable/) or FigTree v1.4.4 (http://tree.bio.ed.ac.uk/software/figtree/); the limitation of sampling per date of collection of respiratory specimens was desactivated. FigTreesuggested: (FigTree, RRID:SCR_008515)Statistical analyses: Statistical tests were carried out using R 4.0.2 (https://cran.r-project.org/) and GraphPad software v5.01 (https://www.graphpad.com/). https://cran.r-project.org/suggested: (CRAN, RRID:SCR_003005)GraphPadsuggested: (GraphPad Prism, RRID:SCR_002798)Results from OddPub: Thank you for sharing your code and data.
Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
- No protocol registration statement was detected.
Results from scite Reference Check: We found no unreliable references.
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