In silico comparative genomics of SARS-CoV-2 to determine the source and diversity of the pathogen in Bangladesh

  1. Tushar Ahmed Shishir
  2. Iftekhar Bin Naser
  3. Shah M. Faruque

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Abstract

The COVID19 pandemic caused by SARS-CoV-2 virus has severely affected most countries of the world including Bangladesh. We conducted comparative analysis of publicly available whole-genome sequences of 64 SARS-CoV-2 isolates in Bangladesh and 371 isolates from another 27 countries to predict possible transmission routes of COVID19 to Bangladesh and genomic variations among the viruses. Phylogenetic analysis indicated that the pathogen was imported in Bangladesh from multiple countries. The viruses found in the southern district of Chattogram were closely related to strains from Saudi Arabia whereas those in Dhaka were similar to that of United Kingdom and France. The 64 SARS-CoV-2 sequences from Bangladesh belonged to three clusters. Compared to the ancestral SARS-CoV-2 sequence reported from China, the isolates in Bangladesh had a total of 180 mutations in the coding region of the genome, and 110 of these were missense. Among these, 99 missense mutations (90%) were predicted to destabilize protein structures. Remarkably, a mutation that leads to an I300F change in the nsp2 protein and a mutation leading to D614G change in the spike protein were prevalent in SARS-CoV-2 genomic sequences, and might have influenced the epidemiological properties of the virus in Bangladesh.

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  1. Version published to 10.1371/journal.pone.0245584
  2. ScreenIT

    SciScore for 10.1101/2020.07.20.212563: (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
    Selected sequences were annotated by Viral Annotation Pipeline and iDentification (VAPiD) tool (14), and multiple sequence alignment was carried out using Mafft algorithm (15).
    Mafft
    suggested: (MAFFT, RRID:SCR_011811)
    Maximum likelihood phylogenetic tree was constructed with IQ-TREE (16), the generated tree was reconstructed based on time-calibration by TreeTime (17), and visualized on iTOL server (18).
    IQ-TREE
    suggested: (IQ-TREE, RRID:SCR_017254)
    For analysis of mutations, sequence were mapped with minimap2 (19), and variants were detected using SAMtools (20) and snp-sites (21).
    SAMtools
    suggested: (SAMTOOLS, RRID:SCR_002105)
    The direction of selection in sequences from Bangladesh was calculated by the SLAC algorithm (27) in the Datamonkey server (28).
    Datamonkey
    suggested: (DataMonkey, RRID:SCR_010278)

    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.

    About SciScore

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  3. Version published to 10.1101/2020.07.20.212563 on bioRxiv