Investigating the possible origin and transmission routes of SARS-CoV-2 genomes and variants of concern in Bangladesh

  1. Abdullah Al Nahid
  2. Ajit Ghosh

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Abstract

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  1. Version published to 10.1016/j.meegid.2021.105057
  2. Version published to 10.1101/2021.05.24.444482v3 on bioRxiv
  3. Version published to 10.1101/2021.05.24.444482v2 on bioRxiv
  4. ScreenIT

    SciScore for 10.1101/2021.05.24.444482: (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
    2.2 Exploratory Data Analysis: The metadata of G1 subset samples was analyzed with Python version 3.8.527 to investigate the Nextstrain clade distribution among divisions, as well as the gender and age-group distribution in Bangladeshi samples.
    Python
    suggested: (IPython, RRID:SCR_001658)
    G1 samples with no division data were labeled NA (Not Available), and the missing gender and age-group data were discarded before plotting with ggplot2 version 3.3.328 and tidyverse version 1.3.029 packages of R programming language version 3.6.330.
    ggplot2
    suggested: (ggplot2, RRID:SCR_014601)
    2.3 Phylogenetic Analysis: Quality filtered sequences of G2 subset were aligned to the reference SARS-CoV-2 sequence (NC_045512.2)31 using MAFFT version 7.47532.
    MAFFT
    suggested: (MAFFT, RRID:SCR_011811)
    A total of 1,966 subsampled genomes were used to construct a maximum-likelihood phylogenetic tree with IQ-TREE version 2.0.333, and further refined by TreeTime version 0.8.134.
    IQ-TREE
    suggested: (IQ-TREE, RRID:SCR_017254)

    Results from OddPub: Thank you for sharing your code and data.

    Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
    Findings from this study should be taken into consideration within the context of a few caveats. During the subsampling process, a fixed number of samples were selected for the final grouping, hence may not be included all foreign samples that are possibly close to the focal samples. Besides, samples for the variant phylogenies may be biased towards the country of initial emergence of the variants. Despite these limitations, the findings regarding the origin of these variants are very alarming and should be brought to the notice of policymakers and public health authorities right away to prevent further escalation of viral transmission on a community level in Bangladesh.

    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.

    Results from scite Reference Check: We found no unreliable references.

    About SciScore

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  5. Version published to 10.1101/2021.05.24.444482v1 on bioRxiv