Population genetic analysis of Indian SARS-CoV-2 isolates reveals a unique phylogenetic cluster

  1. Dhruv Das
  2. V.S.S.N.R Akkipeddi

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Abstract

The SARS-CoV-2 pandemic originated from Wuhan, China in December 2019 raised an alarming situation all over the globe. Sequencing of this novel virus provides an opportunity to evaluate the genetic polymorphism present in the viral population. Herein, we analysed 173 sequences isolated from Indian patients and performed SNP linkage, clustering and phylogenetic analysis to understand the local genetic diversity. We found that the SNP linkages that lead to the identification of some global clades, do not hold true for the local clade classification. In addition to the unique cluster, established by another Indian study, we identified a new cluster (I-20D) that encompasses 28% of the analysed sequences. This cluster is defined by two linked variations – C22444T and C28854T. A detailed study of such polymorphisms can be useful for drug and vaccine development.

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    SciScore for 10.1101/2020.07.19.197129: (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
    Multiple Sequence Alignment (MSA) of initial set sequences was performed using MUSCLE algorithm in MEGA14.
    MUSCLE
    suggested: (MUSCLE, RRID:SCR_011812)
    TASSEL version 5.2.6116 was used to generate linkage plot between the selected SNPs using HapMap file.
    TASSEL
    suggested: (TASSEL, RRID:SCR_012837)
    HapMap
    suggested: None
    Correlation analysis between mutations, sequences and geographical locations was performed using ClustVis17 tool.
    ClustVis17
    suggested: None
    Functional Characterization of amino acid change: The N-gene variant, C194T, was evaluated for the functional characterization using the Protein Variant Effect Analyser (PROVEAN) and PolyPhen-2.
    PROVEAN
    suggested: (PROVEAN, RRID:SCR_002182)
    PolyPhen-2
    suggested: None
    Default parameters has been used for calculating the Polyphen-2 score.
    score
    suggested: (SCORE, RRID:SCR_014165)

    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 10.1101/2020.07.19.197129 on bioRxiv