Genotypic and antigenic study of SARS-CoV-2 from an Indian isolate

  1. Ruby Dhar
  2. Akhauri Yash Sinha
  3. Ashikh Seethy
  4. Sri Anusha Matta
  5. Karthikeyan Pethusamy
  6. Trymbak Srivastava
  7. Sunil Singh
  8. Indrani Mukherjee
  9. Sajib Sarkar
  10. Rashmi Minocha
  11. Kakali Purkayastha
  12. Jai Bhagwan Sharma
  13. Suman Paine
  14. Subhradip Karmakar

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Abstract

Coronaviruses (CoVs) are one of the largest groups of positive-sense RNA virus families within the Nidovirales order, which are further classified into four genera: alpha, beta, gamma, and delta. Coronaviruses have an extensive range of natural hosts and are known to be responsible for a broad spectrum of diseases in multiple species. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the ongoing coronavirus disease 2019 (COVID-19) that has unleashed a global threat to public health and the economy. Coronaviruses are extensively present in birds and mammals, with horseshoe bats ( Rhinolophus affinis ), being the reservoir for the ongoing SARS-CoV-2 that seems to have resulted from a zoonotic spillover to the human host, causing respiratory infections, lung injury and Acute Respiratory Distress Syndrome(ARDS). About six coronavirus serotypes are linked with the disease in humans, namely HCoV-229E, HCoV-NL63, HCoV-OC43, HCoV-HKU1, SARS-CoV, SARS-CoV-2, and MERS-CoV. SARS-CoV-2 is the seventh CoV to infect humans. We analyzed the genome sequence of CoV-2 from isolates derived from China as well from India and encountered minute variations in their sequence. A cladogram analysis revealed the predominant strain circulating in India belongs to the A2a clad. We took one such strain (MT012098) and performed a rigorous in-silico genotypic and antigenic analysis to identify its relatedness to other strains. Further, we also performed a detailed prediction for B and T cell epitopes using BepiPred 2.0 server and NetCTL 1.2 server (DTU Bioinformatics), respectively. We hope this information may assist in an effective vaccine designing program against SARS-CoV-2.

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  1. ScreenIT

    SciScore for 10.1101/2020.06.10.140657: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board Statementnot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.
    Cell Line Authenticationnot detected.

    Table 2: Resources

    Experimental Models: Cell Lines
    SentencesResources
    Blast: Blast P of NCBI was used for Structural protein comparisons between reference strain NC_045512 and Indian Strain MT012098 B cell Epitope prediction: For B cell linear epitopes Bepipred version 2 algorithm was used.
    MT012098
    suggested: None
    Software and Algorithms
    SentencesResources
    Complete Genome of SARS CoV-2 strains Reference genome NCBI ID, NC_045512, and Indian genome GenBank ID, MT012098, were taken from NCBI website.
    NCBI
    suggested: (NCBI, RRID:SCR_006472)
    ElliPro (Ellipsoid and Protrusion), is a web-tool that implements a modified version of Thornton’s method(Thorton et al. 1986).
    Protrusion
    suggested: None

    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.
    • No funding statement was detected.
    • No protocol registration statement was detected.

    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.

  2. Version published to 10.1101/2020.06.10.140657v1 on bioRxiv