Genomic analysis of SARS-CoV-2 variants of concern identified from the ChAdOx1 nCoV-19 immunized patients from Southwest part of Bangladesh

  1. Hassan M. Al-Emran
  2. Md. Shazid Hasan
  3. Md. Ali Ahasan Setu
  4. M. Shaminur Rahman
  5. ASM Rubayet Ul Alam
  6. Shovon Lal Sarkar
  7. Md. Tanvir Islam
  8. Mir Raihanul Islam
  9. Mohammad Mahfuzur Rahman
  10. Ovinu Kibria Islam
  11. Iqbal Kabir Jahid
  12. M. Anwar Hossain

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Abstract

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  1. Version published to 10.1016/j.jiph.2021.12.002
  2. ScreenIT

    SciScore for 10.1101/2021.08.09.21261778: (What is this?)

    Please note, not all rigor criteria are appropriate for all manuscripts.

    Table 1: Rigor

    EthicsConsent: Verbal consent was taken from all participants after reading the purpose and objectives.
    Field Sample Permit: The Genome Centre, Jashore University of Science and Technology, Jashore, Bangladesh is conducting COVID-19 diagnosis and covering four districts (Jashore, Magura, Narail and Jhenaidha) as a part of the national surveillance system approved by DGHS [7].
    Sex as a biological variablenot detected.
    RandomizationIn this study, we included day-wise random number generated 135 cases (out of 834), of which, only 108 were available for telephone interview with a prior verbal consent.
    Blindingnot detected.
    Power Analysisnot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    The amplicons, confirmed in 1% (w/v) agarose, were sequenced using the BigDye® Terminator v3.1 Cycle Sequencing Kit (Applied Biosystem, ThemoFisher Scientific, Inc., USA).
    ThemoFisher Scientific
    suggested: None
    SARS-CoV-2 Genome consensus generation: Short read of Binary Alignment Map files were converted to Fastq file by using SAMtools v1.12 [11] and the quality checked by using FastQC 0.11.9 [12].
    SAMtools
    suggested: (SAMTOOLS, RRID:SCR_002105)
    FastQC
    suggested: (FastQC, RRID:SCR_014583)
    Trimmomatic v0.39 [13] was used to trimmed low quality read (phred score less than 20) and consensus were generated by using Burrows-Wheeler Aligner (BWA v0.7.17) [14], SAMtools v1.12 [11] and BEDTools v2.30.0 [15] by aligning a reference genome (hCoV-19/Wuhan/WIV04 (GenBank accession no. MN996528.1).
    Trimmomatic
    suggested: (Trimmomatic, RRID:SCR_011848)
    BWA
    suggested: (BWA, RRID:SCR_010910)
    BEDTools
    suggested: (BEDTools, RRID:SCR_006646)
    Nextstrain uses MAFFT [18] as an alignment tools, IQ-TREE [19] and TreeTime [20] to reconstruct tree and Auspice web server (https://auspice.us/) to visualize the tree.
    MAFFT
    suggested: (MAFFT, RRID:SCR_011811)
    IQ-TREE
    suggested: (IQ-TREE, RRID:SCR_017254)
    Mutations and clades have assigned from CoVserver mutation app (https://www.gisaid.org/epiflu-applications/covsurver-mutations-app/) of Global initiative on sharing all influenza data (GISAID) where hCoV-19/Wuhan/WIV04 (GenBank accession no. MN996528.1) was used as a reference genome.
    CoVserver
    suggested: None
    Heatmap with nonsynonymous mutations was generated by using an R package Pheatmap [21] and violin plot of between synonymous and nonsynonymous mutations was generated by using ggplot2 [22].
    Pheatmap
    suggested: (pheatmap, RRID:SCR_016418)
    ggplot2
    suggested: (ggplot2, RRID:SCR_014601)

    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.

    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.

  3. Version published to 10.1101/2021.08.09.21261778v1 on medRxiv