1. Adriana Heguy

    Review 2: "A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa"

    This preprint explores the genetic changes of SARS-CoV-2 in Africa by offering an in-depth epidemiological analysis of virus introduction, circulation, and evolution over a year. Reviewers agree that the claims are reliable and supported by the data.

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  2. M Hossain

    Review 1: "A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa"

    This preprint explores the genetic changes of SARS-CoV-2 in Africa by offering an in-depth epidemiological analysis of virus introduction, circulation, and evolution over a year. Reviewers agree that the claims are reliable and supported by the data.

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  3. Strength of evidence

    Reviewers: M Hossain (University of Dhaka) | 📘📘📘📘📘
    Adriana Heguy (NYU Langone Medical Center) | 📘📘📘📘📘

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  4. SciScore for 10.1101/2021.05.12.21257080: (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
    Phylogenetic reconstruction: The African sequences were aligned against the reference panel using MAFFT v7.471 (23).
    MAFFT
    suggested: (MAFFT, RRID:SCR_011811)
    Prior to phylogeographic reconstruction each cluster/lineage was assessed for molecular clock signal in TempEst v1.5.3 (30) following the removal of potential outliers that may violate the molecular clock assumption.
    TempEst
    suggested: (TempEst, RRID:SCR_017304)
    Markov Chain Monte Carlo (MCMC) analyses were set up in BEAST v1.10.4 in duplicate for 100 million interactions and sampling every 10,000 steps in the chain.
    BEAST
    suggested: (BEAST, RRID:SCR_010228)
    Convergence for each run was assessed in Tracer v1.7.1 (ESS for all relevant model parameters >200).
    Tracer
    suggested: (Tracer, RRID:SCR_019121)
    Country level maps of each variable were created using ArcGIS® by ESRI version 10.5 (http://www.esri.com).
    ArcGIS®
    suggested: (ArcGIS for Desktop Basic, RRID:SCR_011081)

    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.
    • Thank you for including a protocol registration statement.

    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.

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