Variation in synonymous nucleotide composition among genomes of sarbecoviruses and consequences for the origin of COVID-19

  1. Alexandre Hassanin

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  1. Version published to 10.1016/j.gene.2022.146641
  2. ScreenIT

    SciScore for 10.1101/2021.08.26.457807: (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
    Genomic alignment of Sarbecovirus sequences: Full genomes of Sarbecovirus available in May 2021 in GenBank (https://www.ncbi.nlm.nih.gov/) and GISAID (https://www.epicov.org/) databases were donwloaded in Fasta format.
    https://www.ncbi.nlm.nih.gov/
    suggested: (GENSAT at NCBI - Gene Expression Nervous System Atlas, RRID:SCR_003923)
    The protein coding sequences (cds) of the 54 genomes were aligned in Geneious Prime® 2020.0.3 with MAFFT version 7.450 (Katoh and Standley 2013) using default parameters.
    Geneious
    suggested: (Geneious, RRID:SCR_010519)
    MAFFT
    suggested: (MAFFT, RRID:SCR_011811)
    Then, the alignment was corrected manually on AliView 1.26 (Larsson 2014) based on translated and untranslated nucleotide sequences using the three following criteria: (i) the number of indels was minimized because they are rarer events than amino-acid or nucleotide substitutions; (ii) changes between similar amino-acids were preferred; and (iii) transitions were privileged over transversions because they are more frequent.
    AliView
    suggested: (AliView, RRID:SCR_002780)
    Phylogeny of sarbecoviruses: All phylogenetic analyses were carried out using the maximum likelihood (ML) method under RAxML version 8.2.10 (Stamatakis 2014) with 25 rate categories, different GTRCAT models for the three codon-positions, and 1000 bootstrap replicates.
    RAxML
    suggested: (RAxML, RRID:SCR_006086)
    The 1000 bootstrap RAxML trees were then executed in PAUP 4* version 4b10 (Swofford 2003) to construct a 70% majority-rule consensus tree.
    PAUP
    suggested: (PAUP, RRID:SCR_014931)
    The four variables measured were then summarised by a principal component analysis (PCA) using the FactoMineR package (Lê et al. 2008) in R version 3.6.1 (from http://www.R-project.org/).
    FactoMineR
    suggested: (FactoMineR, RRID:SCR_014602)

    Results from OddPub: Thank you for sharing your 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.

    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 10.1101/2021.08.26.457807v1 on bioRxiv