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Immunodominant conserved moieties on spike protein of SARS-CoV-2 renders virulence factor for the design of epitope-based peptide vaccines

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Abstract

The outbreak of novel SARS-CoV-2 virion has wreaked havoc with a high prevalence of respiratory illness and high transmission due to a vague understanding of the viral antigenicity, augmenting the dire challenge to public health globally. This viral member necessitates the expansion of diagnostic and therapeutic tools to track its transmission and confront it through vaccine development. Therefore, prophylactic strategies are mandatory. Virulent spike proteins can be the most desirable candidate for the computational design of vaccines targeting SARS-CoV-2, followed by the meteoric development of immune epitopes. Spike protein was characterized using existing bioinformatics tools with a unique roadmap related to the immunological profile of SARS-CoV-2 to predict immunogenic virulence epitopes based on antigenicity, allergenicity, toxicity, immunogenicity, and population coverage. Applying in silico approaches, a set of twenty-four B lymphocyte-based epitopes and forty-six T lymphocyte-based epitopes were selected. The predicted epitopes were evaluated for their intrinsic properties. The physico-chemical characterization of epitopes qualifies them for further in vitro and in vivo analysis and pre-requisite vaccine development. This study presents a set of screened epitopes that bind to HLA-specific allelic proteins and can be employed for designing a peptide vaccine construct against SARS-CoV-2 that will confer vaccine-induced protective immunity due to its structural stability.

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Acknowledgements

Author acknowledges Priyank Shukla’s contribution towards verifying and guiding through initial data analysis.

Funding

We acknowledge NIT Rourkela for supporting this research on COVID-19.

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Authors and Affiliations

  1. Immunology and Molecular Medicine Laboratory, Department of Life Science, National Institute of Technology Rourkela, Rourkela, Odisha, 769008, India

    Subhashree Mohapatra & Bismita Nayak

  2. RNA Biology Laboratory, Department of Life Science, National Institute of Technology Rourkela, Rourkela, Odisha, 769008, India

    Santosh Kumar

  3. Molecular Signalling and Drug Discovery Laboratory, Department of Biochemistry, Central University of Punjab, Bathinda, Punjab, 151401, India

    Shashank Kumar & Atul Kumar Singh

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Contributions

SM has contributed towards literature survey, formal analysis, data curation and wrote the whole manuscript. SK has contributed to data analysis. SK and AKS helped in molecular docking study. BN has supervised and validated the entire manuscript and helped in editing the manuscript.

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Correspondence to Bismita Nayak.

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Mohapatra, S., Kumar, S., Kumar, S. et al. Immunodominant conserved moieties on spike protein of SARS-CoV-2 renders virulence factor for the design of epitope-based peptide vaccines. VirusDis. 34, 456–482 (2023). https://doi.org/10.1007/s13337-023-00852-9

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