Immunoinformatic based analytics on T-cell epitope from spike protein of SARS-CoV-2 concerning Indian population.

Abstract

The whole world is drastically affected by the current pandemic due to severe virus, SARS-CoV-2 and scientists are rigorously looking for the efficient vaccine against it that become an emergent issue. Reverse vaccinology approach may provide us with significant therapeutic leads in this direction and further determination of T-cell / B-cell response to antigen. In the present study, we conducted population coverage analysis referring to the diverse Indian population. By using tools from Immune epitope database (IEDB), HLA- distribution analysis was performed to find the most promiscuous T-cell epitope out of In silico determined epitope of Spike protein from SARS-CoV-2. Selection of these epitopes have been conducted based on their binding affinity with the maximum number of HLA alleles belong to the highest population coverage rate values for the chosen geographical area in India. 404 cleavage sites within the 1288 amino acids sequence of spike glycoprotein were determined by NetChop proteasomal cleavage prediction suggesting that this protein has adequate sites in the protein sequence for cleaving into appropriate epitopes. For population coverage analysis, 221 selected epitopes are considered that shows the projected population coverage as 83.08% with 19.29 average hit (average number of epitope hits/HLA combinations recognized by the population) and 5.91 pc90 (minimum number of epitope hits/HLA combinations recognized by 90% of the population). 54 epitopes are found with the highest coverage among the Indian population and highly conserved within the given spike RBD domain sequence. Docking analysis of each epitope with their respective allele suggests that the epitope NSFTRGVYY represents highest binding affinity with docking score -7.6 kcal/mol with its allele HLA-C*07:01 among all the epitopes. Since the Covid-19 cases are still in progress and seem to remain like this until we find an effective vaccine, moreover in countries like India, vast diversity in the population may present a hindrance to particular vaccine efficiency. Outcomes from this study could be critical to design vaccine against SARS-CoV-2 for a different set of the population within the country.