Immunogenicity and antigenicity based T-cell and B-cell epitopes identification from conserved regions of 10664 SARS-CoV-2 genomes

Abstract

The surge of SARS-CoV-2 has created a wave of pandemic around the globe due to its high transmission rate. To contain this virus, researchers are working around the clock for a solution in the form of vaccine. Due to the impact of this pandemic, the economy and healthcare have immensely suffered around the globe. Thus, an efficient vaccine design is the need of the hour. Moreover, to have a generalised vaccine for heterogeneous human population, the virus genomes from different countries should be considered. Thus, in this work, we have performed genome-wide analysis of 10,664 SARS-CoV-2 genomes of 73 countries around the globe in order to identify the potential conserved regions for the development of peptide based synthetic vaccine viz. epitopes with high immunogenic and antigenic scores. In this regard, multiple sequence alignment technique viz. Clustal Omega is used to align the 10,664 SARS-CoV-2 virus genomes. Thereafter, entropy is computed for each genomic coordinate of the aligned genomes. The entropy values are then used to find the conserved regions. These conserved regions are refined based on the criteria that their lengths should be greater than or equal to 60 nt and their corresponding protein sequences are without any stop codons. Furthermore, Nucleotide BLAST is used to verify the specificity of the conserved regions. As a result, we have obtained 17 conserved regions that belong to NSP3, NSP4, NSP6, NSP8, RdRp, Helicase, endoRNAse, 2'-O-RMT, Spike glycoprotein, ORF3a protein, Membrane glycoprotein and Nucleocapsid protein. Finally, these conserved regions are used to identify the T-cell and B-cell epitopes with their corresponding immunogenic and antigenic scores. Based on these scores, the most immunogenic and antigenic epitopes are then selected for each of these 17 conserved regions. Hence, we have obtained 30 MHC-I and 24 MHC-II restricted T-cell epitopes with 14 and 13 unique HLA alleles and 21 B-cell epitopes for the 17 conserved regions. Moreover, for validating the relevance of these epitopes, the binding conformation of the MHC-I and MHC-II restricted T-cell epitopes are shown with respect to HLA alleles. Also, the physico-chemical properties of the epitopes are reported along with Ramchandran plots and Z-Scores and the population coverage is shown as well. Overall, the analysis shows that the identified epitopes can be considered as potential candidates for vaccine design.

Keywords: B-cell epitopes; Conserved regions; Epitopes; SARS-CoV-2; Synthetic vaccine; T-cell epitopes.

Fig. 1

Pipeline of the workflow.

Fig. 2

Graphical representation of B-cell epitopes for 17 CnRs belonging to (a) NSP3 (b) NSP4 (c) NSP6 (d) NSP8 (e) RdRp (f) RdRp (g) Helicase (h) Helicase (i) Helicase (j) endoRNAse (k) 2’-O-RMT (l) Spike glycoprotein (m) Spike glycoprotein (n) ORF3a protein (o) Membrane glycoprotein (p) Membrane glycoprotein and (q) Nucleocapsid protein.

Fig. 3

MHC-I, MHC-II restricted T-cell and B-cell epitopes underlined in the protein sequences of 17 CnRs for (a) NSP3 (b) NSP4 (c) NSP6 (d) NSP8 (e) RdRp (f) RdRp (g) Helicase (h) Helicase (i) Helicase (j) endoRNAse (k) 2’-O-RMT (l) Spike glycoprotein (m) Spike glycoprotein (n) ORF3a protein (o) Membrane glycoprotein (p) Membrane glycoprotein and (q) Nucleocapsid protein.

Fig. 4

Modelling of MHC-I, MHC-II restricted T-cell and B-cell epitopes for 17 CnRs belonging to (a) NSP3 (b) NSP4 (c) NSP6 (d) NSP8 (e) RdRp (f) Helicase (g) endoRNAse (h) 2’-O-RMT (i) Spike glycoprotein (j) ORF3a protein (k) Membrane glycoprotein (l) Nucleocapsid protein.

Fig. 4

Modelling of MHC-I, MHC-II restricted T-cell and B-cell epitopes for 17 CnRs belonging to (a) NSP3 (b) NSP4 (c) NSP6 (d) NSP8 (e) RdRp (f) Helicase (g) endoRNAse (h) 2’-O-RMT (i) Spike glycoprotein (j) ORF3a protein (k) Membrane glycoprotein (l) Nucleocapsid protein.

Fig. 4

Modelling of MHC-I, MHC-II restricted T-cell and B-cell epitopes for 17 CnRs belonging to (a) NSP3 (b) NSP4 (c) NSP6 (d) NSP8 (e) RdRp (f) Helicase (g) endoRNAse (h) 2’-O-RMT (i) Spike glycoprotein (j) ORF3a protein (k) Membrane glycoprotein (l) Nucleocapsid protein.

Fig. 4

Modelling of MHC-I, MHC-II restricted T-cell and B-cell epitopes for 17 CnRs belonging to (a) NSP3 (b) NSP4 (c) NSP6 (d) NSP8 (e) RdRp (f) Helicase (g) endoRNAse (h) 2’-O-RMT (i) Spike glycoprotein (j) ORF3a protein (k) Membrane glycoprotein (l) Nucleocapsid protein.

Fig. 5

Structural analysis for the most immunogenic MHC-I restricted T-cell epitope “DTDFVNEFY” in 17 CnRs (a) Docking structure of MHC-I restricted T-cell epitope (b) 2D pose representation between the epitope and HLA allele showing the different non-covalent bonds (c) 3D structure of the epitope (d) Chemical structure of the epitope (e) Ramachandran plot of the epitope allele structure showing lower energy sites of the residues in different frames and (f) Z-Score plot.

Fig. 6

Structural analysis for the most antigenic MHC-I restricted T-cell epitope “IPARARVECFF” in 17 CnRs (a) Docking structure of MHC-I restricted T-cell epitope (b) 2D pose representation between the epitope and HLA allele showing the different non-covalent bonds (c) 3D structure of the epitope (d) Chemical structure of the epitope (e) Ramachandran plot of the epitope allele structure showing lower energy sites of the residues in different frames and (f) Z-Score plot.

Fig. 7

Structural analysis for the most immunogenic MHC-II restricted T-cell epitope “VGNICYTPSKLIEYT” in 17 CnRs (a) Docking structure of MHC-II restricted T-cell epitope (b) 2D pose representation between the epitope and HLA allele showing the different non-covalent bonds (c) 3D structure of the epitope (d) Chemical structure of the epitope (e) Ramachandran plot of the epitope allele structure showing lower energy sites of the residues in different frames and (f) Z-Score plot.

Fig. 8

Structural analysis for the most immunogenic MHC-II restricted T-cell epitope “NYVFTGYRVTKNSKV” in 17 CnRs (a) Docking structure of MHC-II restricted T-cell epitope (b) 2D pose representation between the epitope and HLA allele showing the different non-covalent bonds (c) 3D structure of the epitope (d) Chemical structure of the epitope (e) Ramachandran plot of the epitope allele structure showing lower energy sites of the residues in different frames and (f) Z-Score plot.

Fig. 9

Structural analysis for the most immunogenic MHC-II restricted T-cell epitope “IWDYKRDAPAHISTI” in 17 CnRs (a) Docking structure of MHC-II restricted T-cell epitope (b) 2D pose representation between the epitope and HLA allele showing the different non-covalent bonds (c) 3D structure of the epitope (d) Chemical structure of the epitope (e) Ramachandran plot of the epitope allele structure showing lower energy sites of the residues in different frames and (f) Z-Score plot.

Fig. 10

Structural analysis for the most immunogenic MHC-II restricted T-cell epitope “LHSYFTSDYYQLYST” in 17 CnRs (a) Docking structure of MHC-II restricted T-cell epitope (b) 2D pose representation between the epitope and HLA allele showing the different non-covalent bonds (c) 3D structure of the epitope (d) Chemical structure of the epitope (e) Ramachandran plot of the epitope allele structure showing lower energy sites of the residues in different frames and (f) Z-Score plot.

Fig. 11

Structural analysis for the most antigenic MHC-II restricted T-cell epitope “TEILPVSMTKTSVDC” in 17 CnRs (a) Docking structure of MHC-II restricted T-cell epitope (b) 2D pose representation between the epitope and HLA allele showing the different non-covalent bonds (c) 3D structure of the epitope (d) Chemical structure of the epitope (e) Ramachandran plot of the epitope allele structure showing lower energy sites of the residues in different frames and (f) Z-Score plot.

Fig. 12

Structural analysis for the most antigenic MHC-II restricted T-cell epitope “WNLVIGFLFLTWICL” in 17 CnRs (a) Docking structure of MHC-II restricted T-cell epitope (b) 2D pose representation between the epitope and HLA allele showing the different non-covalent bonds (c) 3D structure of the epitope (d) Chemical structure of the epitope (e) Ramachandran plot of the epitope allele structure showing lower energy sites of the residues in different frames and (f) Z-Score plot.