Immunoinformatic Approach for the identification of T Cell and B Cell Epitopes in the Surface Glycoprotein and Designing a Potent Multiepitope Vaccine Construct Against SARS-CoV-2 including the new UK variant

  1. Gracy Fathima Selvaraj
  2. Kiruba Ramesh
  3. Padmapriya Padmanabhan
  4. Vidya Gopalan
  5. Karthikeyan Govindan
  6. Aswathi Chandran
  7. Sivasubramanian Srinivasan
  8. Kaveri Krishnasamy

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Abstract

The emergence of a novel coronavirus in China in late 2019 has turned into a SARS-CoV-2 pandemic affecting several millions of people worldwide in a short span of time with high fatality. The crisis is further aggravated by the emergence and evolution of new variant SARS-CoV-2 strains in UK during December, 2020 followed by their transmission to other countries. A major concern is that prophylaxis and therapeutics are not available yet to control and prevent the virus which is spreading at an alarming rate, though several vaccine trials are in the final stage. As vaccines are developed through various strategies, their immunogenic potential may drastically vary and thus pose several challenges in offering both arms of immunity such as humoral and cell-mediated immune responses against the virus. In this study, we adopted an immunoinformatics-aided identification of B cell and T cell epitopes in the Spike protein, which is a surface glycoprotein of SARS-CoV-2, for developing a new Multiepitope vaccine construct (MEVC). MEVC has 575 amino acids and comprises adjuvants and various cytotoxic T-lymphocyte (CTL), helper T-lymphocyte (HTL), and B-cell epitopes that possess the highest affinity for the respective HLA alleles, assembled and joined by linkers. The computational data suggest that the MEVC is non-toxic, non-allergenic and thermostable with the capability to elicit both humoral and cell-mediated immune responses. The population coverage of various countries affected by COVID-19 with respect to the selected B and T cell epitopes in MEVC was also investigated. Subsequently, the biological activity of MEVC was assessed by bioinformatic tools using the interaction between the vaccine candidate and the innate immune system receptors TLR3 and TLR4. The epitopes of the construct were analyzed with that of the strains belonging to various clades including the new variant UK strain having multiple unique mutations in S protein. Due to the advantageous features, the MEVC can be tested in vitro for more practical validation and the study offers immense scope for developing a potential vaccine candidate against SARS-CoV-2 in view of the public health emergency associated with COVID-19 disease caused by SARS-CoV-2.

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  1. ScreenIT

    SciScore for 10.1101/2021.03.15.435391: (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
    For the current study, 31 sequences of full-length genome sequences of SARS-CoV-2 including 2 sequences of UK variant strains were downloaded from GISAID database and the nucleotide sequences of spike protein were selected and translated by the tool Translate (https://www.expasy.org/) and were subjected to multiple sequence alignment by MEGA 10 (www.megasoftware.net).
    MEGA
    suggested: (Mega BLAST, RRID:SCR_011920)
    The epitopes were docked corresponding to MHC I and II allele protein structures by PatchDock (http://bioinfo3d.cs.tau.ac.il/PatchDock/) (Schneidman-Duhovny, 2005) server.
    PatchDock
    suggested: (PatchDock, RRID:SCR_017589)
    The predicted epitopes were checked for their antigenicity using VaxiJen server, allergenicity by AllerTop, conservancy by IEDB tool and toxicity by ToxinPred server.
    VaxiJen
    suggested: (VaxiJen, RRID:SCR_018514)
    ElliPro server predicts conformational and linear B cell epitopes using Thornton’s method and by MODELLER program or BLAST search of PDB predict and visualize antibody epitopes (Ponomarenko et al., 2007, 2008). 2.12.
    MODELLER
    suggested: (MODELLER, RRID:SCR_008395)
    BLAST
    suggested: (BLASTX, RRID:SCR_001653)
    Mutation analyses of CTL, HTL and B cell epitopes across various SARS-CoV-2 isolates: To analyze the mutations across various SARS-CoV-2 isolates, about 3156 sequences of spike protein from India as well as other countries representing all clades were downloaded from GISAID and subjected to multiple sequence alignment using BioEdit 7.2 and analyzed for amino acid mutations with respect to the 36 selected CTL, HTL and B cell epitopes.
    BioEdit
    suggested: (BioEdit, RRID:SCR_007361)
    The physiochemical characteristics of the vaccine were determined using the ProtParam tool of the ExPASy database server (http://web.expasy.org/protparam/). 2.15.
    ProtParam
    suggested: (ProtParam Tool, RRID:SCR_018087)
    ExPASy
    suggested: None
    Structure prediction, validation and docking with the receptor: The secondary structure of the subunit vaccine construct was predicted using PSIPred 4.0 Protein Sequence Analysis Workbench (http:// bioinf.cs.ucl.ac.uk/psipred/), while the tertiary structure was predicted by GalaxyWeb server (http://galaxy.seoklab.org/tbm), which is based on the TBM method (Shin et al., 2014).
    PSIPred
    suggested: (PSIPRED, RRID:SCR_010246)
    GalaxyWeb
    suggested: (GalaxyWEB, RRID:SCR_018558)
    The best-modeled structure was refined using the Galaxy Refine server at (http://galaxy.seoklab.org/cgi-bin/submit.cgi?-type=REFINE) (Heo et al., 2013) by molecular dynamics simulation.
    Galaxy
    suggested: (Galaxy, RRID:SCR_006281)

    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: We detected the following sentences addressing limitations in the study:
    Inclusion of more potential epitopes from other proteins in the MEVC may suffer the limitation of complexity of the construct besides the challenges associated with the synthesis. A recent study focused on the single protein (spike protein) to generate multiple epitopes such as 13 for MHC I and 3 for MHC II epitopes (Bhattacharya et al., 2020); but, this study has the limitation of not considering the B cell epitopes. Another recent study reported the design of subunit vaccines against SARS-CoV-2 that used only CTL epitopes without considering the significance of B-cell or HTL epitopes (Seema, 2020). Some studies have used other proteins of the virus and restrict the analyses to one of these three epitopes (Joshi et al., 2020). The present study has an advantage in providing a potential MEVC as it contains all three types of epitopes such as CTL, HTL and B cell epitopes. This in silico study is an attempt to describe the potential immunogenic target over the structural proteins and to propose a novel MVEC, for providing new rays of hope in the initial phase of vaccine development and subsequent experimental validation to confer protection against SARS-CoV-2 infection.

    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 10.1101/2021.03.15.435391 on bioRxiv