Different selection dynamics of S and RdRp between SARS-CoV-2 genomes with and without the dominant mutations

  1. Necla Koçhan
  2. Doğa Eskier
  3. Aslı Suner
  4. Gökhan Karakülah
  5. Yavuz Oktay

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  1. Version published to 10.1016/j.meegid.2021.104796
  2. ScreenIT

    SciScore for 10.1101/2021.01.03.20237602: (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
    To ensure alignment accuracy, all nonstandard unverified nucleotide masking was changed to N due to the specifications of the alignment software, using the Linux sed command, and the isolates were aligned against the SARS-CoV-2 reference genome (NCBI Reference Sequence NC_045512.2, available at https://www.ncbi.nlm.nih.gov/nuccore/NC_045512.2) using the MAFFT (v7.450) alignment software (Katoh et al., 2002), using the parameters outlined in the software manual for aligning closely related viral genomes (available at https://mafft.cbrc.jp/alignment/software/closelyrelatedviralgenomes.html).
    MAFFT
    suggested: (MAFFT, RRID:SCR_011811)
    The FASTA files were converted into PHYLIP files for downstream analyses using the msa_view utility of the PHAST software package (last updated 2 July 2019), with the parameters “-i FASTA -o PHYLIP input.file > output.file” (Hubisz, Pollard & Siepel, 2011).
    PHAST
    suggested: (PHAST, RRID:SCR_003204)
    Evolutionary rate assessment: The rate of accumulation of synonymous mutations per synonymous site (dS), the rate of accumulation of non-synonymous mutations per non-synonymous site (dN) and their ratio (dN/dS), which is also known as w or Ka /KS were calculated using PAML package (version 4.9j, available at http://abacus.gene.ucl.ac.uk/software/paml.html) (Yang, 2007), with the parameters “runmode=-2, Codonfreq=2” in codeml.ctl (pairwise sequence comparison).
    PAML
    suggested: (PAML, RRID:SCR_014932)

    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.

    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 10.1101/2021.01.03.20237602v1 on medRxiv