Variant analysis of SARS-CoV-2 genomes in the Middle East

  1. Khalid Mubarak Bindayna
  2. Shane Crinion

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  1. Version published to 10.1016/j.micpath.2021.104741
  2. ScreenIT

    SciScore for 10.1101/2020.10.09.332692: (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
    10 samples was selected as the optimum number to cover all possible countries and remain within alignment file limit of size 4 Mb (maximum size for Clustal Omega tool).
    Clustal Omega tool
    suggested: None
    The Clustal Omega online tool was used to perform the alignment (found at: https://www.ebi.ac.uk/Tools/msa/clustalo/).
    Clustal Omega
    suggested: (Clustal Omega, RRID:SCR_001591)
    SnpEff also predicts the effect of the variants.
    SnpEff
    suggested: (SnpEff, RRID:SCR_005191)
    To create the SnpEff database, we downloaded data from NCBI for Wuhan reference NC_045512.2 and uploaded to Galaxy.
    Galaxy
    suggested: (Galaxy, RRID:SCR_006281)
    The dplyr v0.8.4 package was used to summarise and align the data13.
    dplyr
    suggested: (dplyr, RRID:SCR_016708)
    The ggplot2 package was used to align the identified variants and visualise the types of mutations that re-occur14.
    ggplot2
    suggested: (ggplot2, RRID:SCR_014601)
    We first select the file generated using BEAST and outputted the tree file.
    BEAST
    suggested: (BEAST, RRID:SCR_010228)
    Then the output NEXUS file was imported to FigTree program to display.
    FigTree
    suggested: (FigTree, RRID:SCR_008515)

    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 10.1101/2020.10.09.332692v1 on bioRxiv
  4. ScreenIT

    SciScore for 10.1101/2020.06.18.156810: (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
    Sample filing: We performed multiple sequence alignments (MSA) using EMBOSS Clustal Omega8 and observed for conserved and consensus sequences to study the evolutionary relationship between the genomes.
    EMBOSS
    suggested: (EMBOSS, RRID:SCR_008493)
    SNPeff, a genetic variant annotation program in the Galaxy server, was used to identify the protein level changes caused by SNPs11.
    SNPeff
    suggested: (SnpEff, RRID:SCR_005191)
    Galaxy
    suggested: (Galaxy, RRID:SCR_006281)
    The genome database for both SARS-CoV-2 NC_045512.2 and SARS NC_004718 were built and compared using SNPeff, and Genbank7.
    SARS-CoV-2
    suggested: (Active Motif Cat# 91351, RRID:AB_2847848)
    (BEAST) v1.10.4, is used to perform Bayesian analysis of molecular sequences using MCMC14.
    BEAST
    suggested: (BEAST, RRID:SCR_010228)
    The unrooted tree obtained from the models and the phylogenetic tree generated by Clustal Omega is used to predict the associations between samples.
    Clustal Omega
    suggested: (Clustal Omega, RRID:SCR_001591)

    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.

  5. Version published to 10.1101/2020.06.18.156810v1 on bioRxiv