Phylo-geo-network and haplogroup analysis of 611 novel coronavirus (SARS-CoV-2) genomes from India

  1. Rezwanuzzaman Laskar
  2. Safdar Ali

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Abstract

The novel coronavirus (SARS-CoV-2) from Wuhan China discovered in December 2019 has since developed into a global epidemic. Presently, we constructed and analyzed the phylo-geo-network of SARS-CoV-2 genomes from across India to understand the viral evolution in the country. A total of 611 full-length genomes from different states of India were extracted from the EpiCov repository of GISAID initiative on 6 June, 2020. Their alignment with the reference sequence (Wuhan, NCBI accession number NC_045512.2 ) uncovered 270 parsimony informative sites. Furthermore, 339 genomes were divided into 51 haplogroups. The network revealed the core haplogroup as that of reference sequence NC_045512.2 (Haplogroup A1) with 157 identical sequences present across 16 states. Remaining haplogroups had <10 identical sequences across a maximum of three states. Some states with fewer samples had more haplogroups. Forty-one haplogroups were localized exclusively to any one state. The two most common lineages are B6 and B1 (Pangolin) whereas clade A2a (Covidex) appears to be the most predominant in India. Because the pandemic is still emerging, the observations need to be monitored.

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  1. Version published to 10.26508/lsa.202000925
  2. ScreenIT

    SciScore for 10.1101/2020.09.03.281774: (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
    Sequence Alignment: The congregations are aligned with the FFT-NS-fragment method using rapid calculation of full-length MSA of closely related viral genomes, a light-weight algorithm of MAFFT v7 web-server (https://mafft.cbrc.jp/alignment/software/closelyrelatedviralgenomes.html) (Katoh et al., 2018) and keeping alignment size exactly throughout the reference sequence.
    MAFFT
    suggested: (MAFFT, RRID:SCR_011811)
    The nucleotide transformation sites of the alignment were further studied using MEGA X (Kumar et al., 2018) Phylogenetic Network Analysis: Aligned sequences were used to generated parsimony based TCS networks (Clement et al., 2002) implemented in Population Analysis with Reticulate Trees (PopART v1.7) software (Leigh and Bryant, 2015) where over 5 percent sites contain undefined states and will be masked.
    MEGA
    suggested: (Mega BLAST, RRID:SCR_011920)

    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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  3. Version published to 10.1101/2020.09.03.281774v2 on bioRxiv
  4. Version published to 10.1101/2020.09.03.281774v1 on bioRxiv