Phylogenomics and Phylodynamics of SARS-CoV-2 Genomes Retrieved From India

  1. Sameera Farah
  2. Ashwin Atkulwar
  3. Manas Ranjan Praharaj
  4. Raja Khan
  5. Ravikumar Gandham
  6. Mumtaz Baig

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Abstract

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  1. Version published to 10.2217/fvl-2020-0243
  2. ScreenIT

    SciScore for 10.1101/2020.06.23.20138222: (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
    These genomes were aligned using Clustal Omega23 and number of haplotypes was determined using DnaSP v624.
    DnaSP
    suggested: (DnaSP, RRID:SCR_003067)
    Estimation of effective reproductive number and phylodynamics: Birth-death serial model (BDSIR) as implemented in the BEAST2 package was used to estimate the effective reproduction number of SARS-CoV-2 in India26, 27.
    BEAST2
    suggested: (BEAST2, RRID:SCR_017307)
    The effective sample sizes and 95% highest posterior density intervals for the parameters like basic reproduction number, BecomeUinfectiousRate, growth rate and the demographic reconstruction of growth rates with exponential growth priors were inspected using Tracer v1.7.0.
    Tracer
    suggested: (Tracer, RRID:SCR_019121)
    The time-scaled Maximum Clade Credibility (MCC) tree based on MCMC analysis of the 138 SARS-CoV-2 genomes was visualized in FigTree v1.4.4 tree viewer.
    FigTree
    suggested: (FigTree, RRID:SCR_008515)
    Population dynamics of SARS-CoV-2: Bayesian Skyline Plot (BSP) method as implemented in BEAST v2.2.0 was used to estimate the effective population size (Ne) for these 138 Indian isolates.
    BEAST
    suggested: (BEAST, RRID:SCR_010228)

    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 10.1101/2020.06.23.20138222v1 on medRxiv