Genome Analysis of SARS-CoV-2 Isolate from Bangladesh

  1. Saam Hasan
  2. Salim Khan
  3. Giasuddin Ahsan
  4. Muhammad Maqsud Hossain

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Abstract

Recently the first genome sequence for a Severe acute respiratory syndrome coronavirus 2 or SARS-CoV-2 isolate from Bangladesh became available. The sequencing was carried out by the Child Health Research Foundation and provided the first insight into the genetic details of the viral strain responsible for the SARS-CoV-2 infections in Bangladesh. Here we carried out a comparative study were we explored the phylogenetic relationship between the Bangladeshi isolate with other isolates from different parts of the world. Afterwards we identified single nucleotide variants in the Bangladeshi isolate, using the Wuhan virus reference sequence. We found a total of 9 variants in the Bangladeshi isolate using 2 separate tools. Barring 2, the rest of these variants were also observed in other isolates from different countries. Most of the variants occurred in the ORF1ab gen. Another noteworthy finding was a sequence of three consecutive variants in the N protein gene that were observed in other isolates as well. Lastly the phylogenetic analysis revealed a close relationship between the Bangladeshi isolate and those from Taiwan, Kazakhstan, Greece, California, Spain, Israel, and Sri Lanka.

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  1. ScreenIT

    SciScore for 10.1101/2020.05.13.094441: (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
    An initial BLAST [7] run was also carried with the Bangladeshi isolate genome (EPI_ISL_437912) and the top nine hits were automatically chosen to be included in this analysis.
    BLAST
    suggested: (BLASTX, RRID:SCR_001653)
    Supplementary table 2 shows the BLAST alignment summary for all these isolates, including the Bangladeshi one, with the SARS-CoV-2 RefSeq.
    SARS-CoV-2
    suggested: (Active Motif Cat# 91351, RRID:AB_2847848)
    RefSeq
    suggested: (RefSeq, RRID:SCR_003496)
    The generated alignment file from the MAFFT alignment was then used to create the phylogenetic tree for all these viral isolates.
    MAFFT
    suggested: (MAFFT, RRID:SCR_011811)
    This was done using the MEGA tool for phylogenetic analysis [10].
    MEGA
    suggested: (Mega BLAST, RRID:SCR_011920)
    For identifying SNPs, we used a combination of the MismatchTable function from Biostrings and the BasebyBase tool from the Viral Bioinformatics Research Centre [11].
    Biostrings
    suggested: (Biostrings, RRID:SCR_016949)

    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.
    • No funding statement was detected.
    • No protocol registration statement was detected.

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  2. Version published to 10.1101/2020.05.13.094441v2 on bioRxiv
  3. Version published to 10.1101/2020.05.13.094441v1 on bioRxiv