Genome-wide analysis of Indian SARS-CoV-2 genomes to identify T-cell and B-cell epitopes from conserved regions based on immunogenicity and antigenicity

Abstract

SARS-CoV-2 has a high transmission rate and shows frequent mutations, thus making vaccine development an arduous task. However, researchers around the globe are working hard to find a solution e.g. synthetic vaccine. Here, we have performed genome-wide analysis of 566 Indian SARS-CoV-2 genomes to extract the potential conserved regions for identifying peptide based synthetic vaccines, viz. epitopes with high immunogenicity and antigenicity. In this regard, different multiple sequence alignment techniques are used to align the SARS-CoV-2 genomes separately. Subsequently, consensus conserved regions are identified after finding the conserved regions from each aligned result of alignment techniques. Further, the consensus conserved regions are refined considering that their lengths are greater than or equal to 60nt and their corresponding proteins are devoid of any stop codons. Subsequently, their specificity as query coverage are verified using Nucleotide BLAST. Finally, with these consensus conserved regions, T-cell and B-cell epitopes are identified based on their immunogenic and antigenic scores which are then used to rank the conserved regions. As a result, we have ranked 23 consensus conserved regions that are associated with different proteins. This ranking also resulted in 34 MHC-I and 37 MHC-II restricted T-cell epitopes with 16 and 19 unique HLA alleles and 29 B-cell epitopes. After ranking, the consensus conserved region from NSP3 gene is obtained that is highly immunogenic and antigenic. In order to judge the relevance of the identified epitopes, the physico-chemical properties and binding conformation of the MHC-I and MHC-II restricted T-cell epitopes are shown with respect to HLA alleles.

Keywords: B-cell epitopes; Conserved regions; Peptide based vaccine; Physico-chemical properties; SARS-CoV-2; T-cell epitopes.

Fig. 1

Pipeline of the Workflow.

Fig. 2

125 Consensus Conserved Regions (CCnRs) from the four alignment techniques.

Fig. 3

Graphical representation of B-cell epitopes for TLVSDIDITFLKKDAP and LHPDSATLVSDIDITF with the threshold marked by red line.

Fig. 4

MHC-I, MHC-II restricted T-cell and B-cell epitopes underlined in the protein sequences of top 5 CCnRs for (a) NSP3 (b) 3CL-Proteinase (c) NSP10 (d) NSP3 and (e) NSP4.

Fig. 5

Structural analysis for the highly immunogenic MHC-I restricted T-cell epitope “FLKKDAPYI” for NSP3 coded protein (a) 2D pose representation between the epitope and HLA allele showing the different non-covalent bonds (b) Docking structure of MHC-I restricted T-cell epitope (c) The surface interaction between the allele and epitopes showing the fitting sites in binding grooves (d) Ramachandran plot of the epitope allele structure showing lower energy sites of the residues in different frame (e) Z-score plot and (f) all residue energy.

Fig. 6

Structural analysis for the highly antigenic MHC-I restricted T-cell epitope “TAVVIPTKK” for NSP3 coded protein (a) 2D pose representation between the epitope and HLA allele showing the different non-covalent bonds (b) Docking structure of MHC-I restricted T-cell epitope (c) The surface interaction between the allele and epitopes showing the fitting sites in binding grooves (d) Ramachandran plot of the epitope allele structure showing lower energy sites of the residues in different frame (e) Z-score plot and (f) all residue energy.

Fig. 7

Structural analysis for the highly immunogenic MHC-II restricted T-cell epitope “ITFLKKDAPYIVGDV” for NSP3 coded protein (a) 2D pose representation between the epitope and HLA allele showing the different non-covalent bonds (b) Docking structure of MHC-II restricted T-cell epitope (c) The surface interaction between the allele and epitopes showing the fitting sites in binding grooves (d) Ramachandran plot of the epitope allele structure showing lower energy sites of the residues in different frame (e) Z-score plot and (f) all residue energy.

Fig. 8

Structural analysis for the highly antigenic MHC-II restricted T-cell epitope “IDITFLKKDAPYIVG” for NSP3 coded protein (a) 2D pose representation between the epitope and HLA allele showing the different non-covalent bonds (b) Docking structure of MHC-II restricted T-cell epitope (c) The surface interaction between the allele and epitopes showing the fitting sites in binding grooves (d) Ramachandran plot of the epitope allele structure showing lower energy sites of the residues in different frame (e) Z-score plot and (f) all residue energy.