Analysis of SARS-CoV-2 synonymous codon usage evolution throughout the COVID-19 pandemic

  1. Ezequiel G. Mogro
  2. Daniela Bottero
  3. Mauricio J. Lozano

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Abstract

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  1. Version published to 10.1016/j.virol.2022.01.011
  2. ScreenIT

    SciScore for 10.1101/2021.12.17.472912: (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
    SentencesResources
    CD-HIT server [61] (http://weizhonglab.ucsd.edu/cdhit-web-server/) was used to remove identical sequences, a total of 2725 sequences remained.
    CD-HIT
    suggested: (CD-HIT, RRID:SCR_007105)
    The transcripts for all the human genes were downloaded from Gencode release 38
    Gencode
    suggested: (GENCODE, RRID:SCR_014966)
    Phylogenetic analysis: To construct a phylogenetic tree, a Multiple Sequence Alignment (MSA) of the complete genomes of reference beta-coronavirus (Beta-CoVs) and SARS-CoV-2 was obtained using MAFFT [63] (https://mafft.cbr-c.jp/alignment/software/closelyrelatedviralgenomes.html; MAFFT v7).
    MAFFT
    suggested: (MAFFT, RRID:SCR_011811)
    For the second alignment, containing all 2725 SARS-CoV-2 sequences, a maximum likelihood phylogenetic tree was constructed with Fasttree [65] (v2.1.10, at Galaxy Australia) using the GTR model with four gamma rate categories.
    Fasttree
    suggested: (FastTree, RRID:SCR_015501)
    First, codon counts, synonymous codon usage frequencies, and average codon usage frequencies for each set of genes were calculated using either Gary Olsen codon usage scripts (https://www.life.illinois.edu/gary/programs/codon_usage.html), or the coRdon R package [66].
    coRdon
    suggested: None

    Results from OddPub: Thank you for sharing your code.

    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.

    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 10.1101/2021.12.17.472912 on bioRxiv