Scouting the Receptor Binding Domain of COVID-19: A Comprehensive Immunoinformatics Inquisition

The December of 2019 witnessed emergence of worldwide outbreak by a novel strain of coronavirus termed COVID-19 with sequence similarity of overall 96.2% with BatCoV RaTG13 (coronavirus isolated from bat) and 94% sequence identity with Severe Acute respiratory syndrome Virus (SARS-CoV) that resulted in outbreak in 2002-2003. There is no therapeutic or preventive strategy like vaccine developed so far to overcome infection.The receptor binding domain (RBD) of COVID-19 for any potential vaccine epitopes were explored. The structure of RBD of COVID-19, BatCoV RaTG13 and bACE2 were chalked through homology modeling followed by molecular docking and structural validation. A comprehensive immunoinformatics approach mapped conserved peptide sequence on COVID-19 RBD for their B-, Helper T- & Cytotoxic T-cell epitope profile. The recognized epitopes were further studied and validated for their docking interaction with MHC-I and MHC-II alleles. Through immune-informatics approaches the study identified conserved B- and T-cell epitopes in RBD. The B-cell epitopes lying within the receptor binding motif, LFRKSN and SYGFQPT l were found to be highly antigenic. Among T-cell epitopes, the epitope CVADYSVLY and FTNVYADSF were antigenic and exhibited affinity for maximum number of MHC-I alleles. The T cell epitopes YRLFRKSNL, VYAWNRKRI displayed affinity for maximum number of MHC-II alleles. The docking analysis of the epitopes with MHC proteins revealed strong interactions of T-cell epitopes with MHC-I and MHC-II alleles. The overlapping epitope among B- and T-cells was YRLFRKSNL. The deployment of these epitopes in potential vaccine against COVID-19 may help in sweeping the COVID-19 infectious spread.