Emergence of multiple variants of SARS-CoV-2 with signature structural changes

  1. Debaleena Bhowmik
  2. Sourav Pal
  3. Abhishake Lahiri
  4. Arindam Talukdar
  5. Sandip Paul

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Abstract

This study explores the divergence pattern of SARS-CoV-2 using whole genome sequences of the isolates from various COVID-19 affected countries. The phylogenomic analysis indicates the presence of at least four distinct groups of the SARS-CoV-2 genomes. The emergent groups have been found to be associated with signature structural changes in specific proteins. Also, this study reveals the differential levels of divergence patterns for the protein coding regions. Moreover, we have predicted the impact of structural changes on a couple of important viral proteins via structural modelling techniques. This study further advocates for more viral genetic studies with associated clinical outcomes and hosts’ response for better understanding of SARS-CoV-2 pathogenesis enabling better mitigation of this pandemic situation.

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  1. ScreenIT

    SciScore for 10.1101/2020.04.26.062471: (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
    Phylogenetic reconstruction and average nucleotide identity calculation: The genome alignment was performed using MUSCLE aligner in default mode present in the UGENE v34 (Edgar RC., 2004; Okonechnikov et al., 2012).
    MUSCLE
    suggested: (MUSCLE, RRID:SCR_011812)
    Evolutionary analysis was performed using PhyML integrated in Seaview 5.0.2 (Guindon et al., 2005; Gouy et al., 2010).
    PhyML
    suggested: (PhyML, RRID:SCR_014629)
    Seaview
    suggested: (SeaView, RRID:SCR_015059)
    Further, the tree was visualized and edited with FigTree 1.4.4 (Rambaut., 2012).
    FigTree
    suggested: (FigTree, RRID:SCR_008515)
    We used the standalone version of NCBI BLAST with an in-house developed perl script to fetch all the genes from each of the 109 genomes.
    BLAST
    suggested: (BLASTX, RRID:SCR_001653)
    Using DnaSP (Rozas et al., 2017), we calculated nucleotide diversity, synonymous and non-synonymous substitution rates for each gene.
    DnaSP
    suggested: (DnaSP, RRID:SCR_003067)
    Further, the TimeZone software was employed for phylogenetic analysis of each gene and detection of structural mutations in them (Chattopadhyay et al. 2013).
    TimeZone
    suggested: (TimeZone, RRID:SCR_018564)
    Comparison of sequential alignment between Wuhan isolated spike sequences with 33 sequences of Indian origin was performed by Multiple Sequence Alignment (MSA) tool using Clustal Omega.
    Clustal Omega
    suggested: (Clustal Omega, RRID:SCR_001591)
    The mutation on the identified protein residues was analyzed on Pymol with a pre-existing suitable rotamer library.
    Pymol
    suggested: (PyMOL, RRID:SCR_000305)

    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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  2. Version published to 10.1101/2020.04.26.062471v2 on bioRxiv
  3. Version published to 10.1101/2020.04.26.062471v1 on bioRxiv