An immunoinformatics approach to study the epitopes contributed by Nsp13 of SARS-CoV-2

  1. Sushant Kumar
  2. Gajendra Kumar Azad

Reviewed by

Read the full article

Listed in

Log in to save this article

Abstract

The on-going coronavirus disease-19 (COVID-19) pandemic caused by SARS-CoV-2 has infected hundreds of millions of people and killed more than two million people worldwide. Currently, there are no effective drugs available for treating SARS-CoV-2 infections; however, vaccines are now being administered worldwide to control this virus. In this study, we have studied SARS-CoV-2 helicase, Nsp13, which is critical for viral replication. We compared the Nsp13 sequences reported from India with the first reported sequence from Wuhan province, China to identify and characterize the mutations occurring in this protein. To correlate the functional impact of these mutations, we characterised the most prominent B cell and T cell epitopes contributed by Nsp13. Our data revealed twenty-one epitopes, which exhibited high antigenicity, stability and interactions with MHC class-I and class-II molecules. Subsequently, the physiochemical properties of these epitopes were also analysed. Furthermore, several of these Nsp13 epitopes harbour mutations, which were further characterised by secondary structure and per-residue disorderness, stability and dynamicity predictions. Altogether, we report the candidate epitopes of Nsp13 that may help the scientific community to understand the evolution of SARS-CoV-2 variants and their probable implications.

Article activity feed

  1. ScreenIT

    SciScore for 10.1101/2021.04.02.438155: (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
    The Orf1ab sequence reported from Wuhan, China was used as a reference sequence (Protein accession number: YP_009724389) for MSA studies using Clustal Omega tool [17] as described earlier [18].
    Clustal Omega
    suggested: (Clustal Omega, RRID:SCR_001591)
    The DiscoTope 2.0 was used for prediction of Discontinuous B cell epitope using threshold value set at −5.5 and its three dimensional structure were represented by AutoDock software.
    DiscoTope
    suggested: (DiscoTope, RRID:SCR_018530)
    AutoDock
    suggested: (AutoDock, RRID:SCR_012746)
    Antigenicity of all selected epitopes was predicted from Vaxijen 2.0 webserver, whereas allergenicity was predicted by AllergenFP v.1.0. MHC class II molecules: IEDB recommended 2.22 prediction method was used to predict MHC class II epitopes.
    Vaxijen
    suggested: (VaxiJen, RRID:SCR_018514)

    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.
    • 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.

    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 10.1101/2021.04.02.438155v1 on bioRxiv