Bioinformatics prediction of B and T cell epitopes within the spike and nucleocapsid proteins of SARS-CoV2

Theodor Bilharz Research Institute

Bibliographic Information

Authors: Dawood R.M.; El-Meguid M.A.; Salum G.M.; El-Wakeel K.; Shemis M.; El Awady M.K.

Journal: Journal of Infection and Public Health

Publisher: Elsevier Ltd

Publication Date: February 2021

Volume / Issue: Volume 14 / Issue 2

Pages: 169–178

ISSN: 18760341

DOI: 10.1016/j.jiph.2020.12.006

Scopus: View on Scopus

PubMed: 33486372

Document Type: Article

Access: All Open Access; Gold Open Access; Green Open Access

Authors and Affiliations

Dawood R.M., Department of Microbial Biotechnology, Genetic Engineering Division, National Research Centre, 33 EL Bohouth Street, Dokki, 12622, Giza, Egypt; El-Meguid M.A., Department of Microbial Biotechnology, Genetic Engineering Division, National Research Centre, 33 EL Bohouth Street, Dokki, 12622, Giza, Egypt; Salum G.M., Department of Microbial Biotechnology, Genetic Engineering Division, National Research Centre, 33 EL Bohouth Street, Dokki, 12622, Giza, Egypt; El-Wakeel K., Biological Anthropology Department, Medical Research Division, National Research Centre, Dokki, Giza, Egypt; Shemis M., Department of Biochemistry and Molecular biology, Theodor Bilharz Research Institute, Egypt; El Awady M.K., Department of Microbial Biotechnology, Genetic Engineering Division, National Research Centre, 33 EL Bohouth Street, Dokki, 12622, Giza, Egypt

Abstract

Background: The striking difference in severity of SARS CoV2 infection among global population is partly attributed to viral factors. With the spike (S) and nucleocapsid (N) are the most immunogenic subunits, genetic diversity and antigenicity of S and N are key players in virulence and in vaccine development. Aim: This paper aims at identifying immunogenic targets for better vaccine development and/or immunotherapy of COVID 19 pandemic. Methods: 18 complete genomes of SARS CoV2 (n = 14), SARS CoV (n = 2) and MERS CoV (n = 2) were examined. Bioinformatics of viral genetics and protein folding allowed functional tuning of NH2 Terminal Domain (NTD) of S protein and development of epitope maps for B and T cell responses. Conclusion: A deletion of amino acid residues Y144 and G107 were discovered in NTD of S protein derived from Indian and French isolates resulting in altered pocket structure exclusively located in NTD and reduced affinity of NTD binding to endogenous nAbs and disrupted NTD mediated cell entry. We therefore, proposed a set of B and T cell epitopes based on Immune Epitope Database, homologous epitopes for nAbs in convalescent plasma post SARS CoV infection and functional domains of S (NTD, Receptor Binding domain and the unique polybasic Furin cleavage site at S1/S2 junction). Nevertheless, laboratory data are required to develop vaccine and immunotherapeutics. © 2020 The Authors

Keywords

Furin cleavage site; Genetic distance; NH2 Terminal Domain; Phylogenetic tree; SARS CoV2; Antibodies, Neutralizing; Antibodies, Viral; Computational Biology; Coronavirus Nucleocapsid Proteins; Epitopes, B-Lymphocyte; Epitopes, T-Lymphocyte; Humans; Phosphoproteins; RNA, Viral; SARS-CoV-2; Spike Glycoprotein, Coronavirus; amino acid; B lymphocyte antigen; convalescent plasma; coronavirus nucleocapsid protein; coronavirus spike glycoprotein; dipeptidyl peptidase IV; epitope; furin; neutralizing antibody; T lymphocyte antigen; nucleocapsid phosphoprotein, SARS-CoV-2; phosphoprotein; spike protein, SARS-CoV-2; virus antibody; virus RNA; amino acid sequence; amino terminal sequence; Article; B lymphocyte; bioinformatics; cellular immunity; clinical article; controlled study; coronavirus disease 2019; epitope mapping; France; gene deletion; human; human cell; immunogenicity; Indian; ligand binding; Middle East respiratory syndrome coronavirus; nonhuman; nucleotide sequence; pandemic; priority journal; protein cleavage; protein folding; protein function; protein structure; severe acute respiratory syndrome; Severe acute respiratory syndrome coronavirus 2; T lymphocyte; viral genetics; virus entry; virus genome; virus isolation; virus virulence; biology; genetics; immunology

Citation Information

Scopus Citations: 17

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