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Research article - Peer-reviewed, 2021

Identification of Unique Peptides for SARS-CoV-2 Diagnostics and Vaccine Development by an In Silico Proteomics Approach

Kesarwani, Veerbhan; Gupta, Rupal; Vetukuri, Ramesh Raju; Kushwaha, Sandeep Kumar; Gandhi, Sonu

Abstract

Ongoing evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus strains is posing new COVID-19 diagnosis and treatment challenges. To help efforts to meet these challenges we examined data acquired from proteomic analyses of human SARS-CoV-2-infected cell lines and samples from COVID-19 patients. Initially, 129 unique peptides were identified, which were rigorously evaluated for repeats, disorders, polymorphisms, antigenicity, immunogenicity, toxicity, allergens, sequence similarity to human proteins, and contributions from other potential cross-reacting pathogenic species or the human saliva microbiome. We also screened SARS-CoV-2-infected NBHE and A549 cell lines for presence of antigenic peptides, and identified paratope peptides from crystal structures of SARS-CoV-2 antigen-antibody complexes. We then selected four antigen peptides for docking with known viral unbound T-cell receptor (TCR), class I and II peptide major histocompatibility complex (pMHC), and identified paratope sequences. We also tested the paratope binding affinity of SARS-CoV T- and B-cell peptides that had been previously experimentally validated. The resultant antigenic peptides have high potential for generating SARS-CoV-2-specific antibodies, and the paratope peptides can be directly used to develop a COVID-19 diagnostics assay. The presented genomics and proteomics-based in-silico approaches have apparent utility for identifying new diagnostic peptides that could be used to fight SARS-CoV-2.

Keywords

SARS-CoV-2; COVID-19 vaccines; diagnostic peptides; docking; paratopes; TCR; MHC

Published in

Frontiers in Immunology
2021, volume: 12, article number: 725240

Authors' information

Kesarwani, Veerbhan
National Institute of Animal Biotechnology (NIAB)
Gupta, Rupal
National Institute of Animal Biotechnology (NIAB)
Vetukuri, Ramesh (Ramesh, Vetukuri)
Swedish University of Agricultural Sciences, Department of Plant Breeding
Kushwaha, Sandeep Kumar
National Institute of Animal Biotechnology (NIAB)
Gandhi, Sonu
National Institute of Animal Biotechnology (NIAB)

Sustainable Development Goals

SDG3 Good health and wellbeing

UKÄ Subject classification

Immunology in the medical area

Publication Identifiers

DOI: https://doi.org/10.3389/fimmu.2021.725240

URI (permanent link to this page)

https://res.slu.se/id/publ/113620