Genetic diversity and genomic epidemiology of SARS-CoV-2 in Morocco

  1. Bouabid Badaoui
  2. Khalid Sadki
  3. Chouhra Talbi
  4. Driss Salah
  5. Lina Tazi

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Abstract

No abstract available

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  1. Version published to 10.1016/j.bsheal.2021.01.003
  2. Version published to 10.1101/2020.06.23.165902v2 on bioRxiv
  3. ScreenIT

    SciScore for 10.1101/2020.06.23.165902: (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
    For comparative analyze of SARS-Cov-2 genome sequences we have used the following protocol: i) Collection of SARS-CoV-2 Sequences and the corresponding metadata from the GISAID database. ii) Filtering the SARS-CoV-2 Sequences to exclude inaccurate sequences based on missing bases and sequence length and to set a fixed number of samples per group according to their similarities.
    GISAID
    suggested: (GISAID, RRID:SCR_018279)
    In this stage, 20 sequences from the 22 corresponding to the Moroccan patients remained for the subsequent analyses. iii) Performing a multi sequence alignment via MAFFT. vi) Inferring a phylogenetic tree from the multi-sequence alignment, getting a time-resolved tree via TreeTime and inferring ancestral traits sequences v) Identifying the mutations.
    MAFFT
    suggested: (MAFFT, RRID:SCR_011811)

    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: We detected the following sentences addressing limitations in the study:
    This genomic survey of SARS-CoV-2 in Morocco has at least two limitations. First, the sampling size is relatively weak which might hinder a compelling interpretation of the epidemiological situation in the country. Second, all the samples analyzed, except one, were obtained from public health laboratories and thus may not be representative of the general population.

    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.
    • No funding statement was detected.
    • 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.

  4. Version published to 10.1101/2020.06.23.165902v1 on bioRxiv