Meta-Analysis and Structural Dynamics of the Emergence of Genetic Variants of SARS-CoV-2

  1. Nicolas Castonguay
  2. Wandong Zhang
  3. Marc-André Langlois

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Abstract

Errors are regularly made when SARS-CoV-2 replicates its RNA genome. The viral polymerase complex is error-prone with imperfect proofreading abilities. These errors or mutations often lead to deleterious or neutral effects on the virus. However, sometimes these mutations have a positive effect and create genetic variants of the virus with different features including increased transmissibility, pathogenicity, and immune escape capabilities. When mutations work collaboratively to create a new virus feature, this is called epistasis.

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  1. Version published to 10.3389/fmicb.2021.676314
  2. ScreenIT

    SciScore for 10.1101/2021.03.06.21252994: (What is this?)

    Please note, not all rigor criteria are appropriate for all manuscripts.

    Table 1: Rigor

    Institutional Review Board Statementnot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    MUSCLE alignment tool on UGene, and SnapGene was used to determine the nucleotide mutations and codon changes of the non-synonymous and synonymous mutations by sequence alignments with NCBI SARS-CoV-2 reference genome (NC_045512).
    MUSCLE
    suggested: (MUSCLE, RRID:SCR_011812)
    SnapGene
    suggested: (SnapGene, RRID:SCR_015052)
    Graphs of mutations and variants were performed on RStudio with timelines, and genomes illustrations were produced in Biorender.
    RStudio
    suggested: (RStudio, RRID:SCR_000432)
    Figures and rendering were prepared with PyMOL.
    PyMOL
    suggested: (PyMOL, RRID:SCR_000305)

    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.

    About SciScore

    SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

  3. Version published to 10.1101/2021.03.06.21252994 on medRxiv