Scrutinizing the SARS-CoV-2 protein information for the designing an effective vaccine encompassing both the T-cell and B-cell epitopes

Neha Jain; Uma Shankar; Prativa Majee; Amit Kumar

The Fasta sequences of all these proteins were retrieved from NCBI and used for epitope screening ( Table 1 ). All the sequences were analyzed for their antigenic nature by using VaxiJen server which is based upon auto cross covariance (ACC) transformation. VaxiJen classifies the proteins into antigens and non-antigens solely based on the physiochemical properties and is sequence alignment independent. The ACC score threshold for the virus model is kept 0.4 that increases the prediction accuracy. All the SARS-CoV-2 proteins except NSP16 (2'-O-ribose methyltransferase) resulted in the ACC score higher than 0.4 depicting the antigenic nature of the viral proteome (Table 1 ). All the antigenic proteins were further screened for the presence of HTL, CTL and B-cell epitopes by using various tools and databases ( Figure 1 ). HTLs act as the central mediators of immune response and coordinates with B lymphocytes, T C cells and macrophages via signaling through interleukins and cytokines synthesis. HTLs recognize the epitopes presented on MHCII biding cleft. Herein, NetMHCPanII server was utilized for predicting 15 mer HTL epitopes having high binding affinity to the selected 20 MHC II alleles. Only the strong binders for the respective HLA alleles were selected with a percentile rank of ≤1. The selected epitopes were further analyzed using another MHC II prediction tool available at IEDB server and filtered on the basis of percentile rank. The resultant epitopes were checked for their antigenicity, allergenicity and toxicity. Finally, the best HLA-epitope pairs with the highest antigenicity and were non-allergen and non-toxic were used for multi-epitope vaccine construct. On analysis, we received, 2 best HLA-epitope pairs each for Helicase and RdRp. Three best HLA-epitope pairs were obtained for non-structural protein 2 (NSP2) and Spike glycoprotein (S) and one pair each for membrane glycoprotein (M), ORF3a and ORF8 proteins. In summary, non-toxic, non-allergenic epitopes with high binding affinity and antigenicity were obtained for 15 MHC class II alleles and their respective epitopes were used for multi-epitope vaccine construct. Best binding epitopes for the remaining 5 MHC II alleles were either nonantigenic, or were allergens and thus were excluded (Supplementary Table S1 ).