Diversity of SARS-CoV-2 genome among various strains identified in Lucknow, Uttar Pradesh

  1. Biswajit Sahoo
  2. Pramod Kumar Maurya
  3. Ratnesh Kumar Tripathi
  4. Jyotsana Agarwal
  5. Swasti Tiwari

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Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has emerged as a significant challenge worldwide. Rapid genome sequencing of SARS-CoV-2 is going on across the globe to detect mutations and genomic modifications in SARS-CoV-2. In this study, we have sequenced twenty-three SARS-CoV-2 positive samples collected during the first pandemic from the state of Uttar Pradesh, India. We observed a range of already reported mutations (2-22), including; D614G, L452R, Q613H, Q677H, T1027I in the S gene; S194L in the N gene; Q57H, L106F, T175I in the ORF3. Few unreported mutations such as P309S in the ORF1ab gene; T379I in the N gene; and L52F, V77I in the ORF3a gene were also detected. Phylogenetic genome analysis showed similarity with other SARS-CoV-2 viruses reported from Uttar Pradesh. The observed mutations may be associated with SARS-CoV-2 virus pathogenicity or disease severity.

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  1. Version published to 10.1101/2021.10.05.463185v3 on bioRxiv
  2. ScreenIT

    SciScore for 10.1101/2021.10.05.463185: (What is this?)

    Please note, not all rigor criteria are appropriate for all manuscripts.

    Table 1: Rigor

    EthicsIRB: This study protocol was approved by Institutional Human Ethics Committee SGPGIMS, Lucknow (Ref N. 111 PGI/BE/327/2020)
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    MAFFT was used to align the whole sequences of the 24 genomes to SARS-CoV-2 reference genome (MN908947.3)[17], [18].
    MAFFT
    suggested: (MAFFT, RRID:SCR_011811)
    SnpEff v4.3 was used to identify the SNPs and changes in the amino acid produced by the gene in the genome[19].
    SnpEff
    suggested: (SnpEff, RRID:SCR_005191)

    Results from OddPub: Thank you for sharing your data.

    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.
    • Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
    • No protocol registration statement was detected.

    Results from scite Reference Check: We found no unreliable references.

    About SciScore

    SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

  3. Version published to 10.1101/2021.10.05.463185v2 on bioRxiv
  4. Version published to 10.1101/2021.10.05.463185v1 on bioRxiv