The emergence, spread and vanishing of a French SARS‐CoV‐2 variant exemplifies the fate of RNA virus epidemics and obeys the Mistigri rule
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Abstract
The nature and dynamics of mutations associated with the emergence, spread, and vanishing of SARS‐CoV‐2 variants causing successive waves are complex. We determined the kinetics of the most common French variant (“Marseille‐4”) for 10 months since its onset in July 2020. Here, we analyzed and classified into subvariants and lineages 7453 genomes obtained by next‐generation sequencing. We identified two subvariants, Marseille‐4A, which contains 22 different lineages of at least 50 genomes, and Marseille‐4B. Their average lifetime was 4.1 ± 1.4 months, during which 4.1 ± 2.6 mutations accumulated. Growth rate was 0.079 ± 0.045, varying from 0.010 to 0.173. Most of the lineages exhibited a bell‐shaped distribution. Several beneficial mutations at unpredicted sites initiated a new outbreak, while the accumulation of other mutations resulted in more viral heterogenicity, increased diversity and vanishing of the lineages. Marseille‐4B emerged when the other Marseille‐4 lineages vanished. Its ORF8 gene was knocked out by a stop codon, as reported in SARS‐CoV‐2 of mink and in the Alpha variant. This subvariant was associated with increased hospitalization and death rates, suggesting that ORF8 is a nonvirulence gene. We speculate that the observed heterogenicity of a lineage may predict the end of the outbreak.
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SciScore for 10.1101/2022.01.04.22268715: (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 Statistical processes were performed using R software version 4.0.2 (https://cran.r-project.org/). https://cran.r-project.org/suggested: (CRAN, RRID:SCR_003005)Samtools (https://www.htslib.org/) was used for soft clipping of Artic primers (https://artic.network/) and to remove sequence duplicates5. Samtoolssuggested: (SAMTOOLS, RRID:SCR_002105)Mutation detection was performed using the Nextclade tool (https://clades.nextstrain.org/) and freebayes (https://github.com/freebayes/freebayes)6 using a mapping quality score of 20 and results filtered by the Python script based on major … SciScore for 10.1101/2022.01.04.22268715: (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 Statistical processes were performed using R software version 4.0.2 (https://cran.r-project.org/). https://cran.r-project.org/suggested: (CRAN, RRID:SCR_003005)Samtools (https://www.htslib.org/) was used for soft clipping of Artic primers (https://artic.network/) and to remove sequence duplicates5. Samtoolssuggested: (SAMTOOLS, RRID:SCR_002105)Mutation detection was performed using the Nextclade tool (https://clades.nextstrain.org/) and freebayes (https://github.com/freebayes/freebayes)6 using a mapping quality score of 20 and results filtered by the Python script based on major nucleotide frequencies ≥ 70% and nucleotide depths ≥ 10 (when sequence reads were generated on the NovaSeq Illumina instrument (Illumina Inc.)) or ≥ 5 (when sequence reads were generated on the MiSeq Illumina instrument). Pythonsuggested: (IPython, RRID:SCR_001658)SARS-CoV-2 genotyping was performed using a second in-house script written in Python language (https://www.python.org/) by comparing mutation patterns with those of our database of SARS-CoV-2 variants. https://www.python.org/suggested: (CVXOPT - Python Software for Convex Optimization, RRID:SCR_002918)Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
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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