Understanding the B and T cells epitopes of spike protein of severe respiratory syndrome coronavirus-2: A computational way to predict the immunogens

Yoya Vashi; Vipin Jagrit; Sachin Kumar

Using the same module, B-cell discontinuous epitopes were predicted, which gave 16 133 epitope regions that contained regions from 18 of our selected peptides highlighted in red 134 (Table 3) . Six peptides (peptide numbers 3, 5, 14, 19, 23, and 24 in Table 1 ) were not predicted 135 as discontinuous B-cell epitopes. To further confirm, we used ABCpred server to detect B-cell 136 epitopes, with default threshold of 0.51. It identified various epitopes with different length and 137 scores; out of those, the regions which contained our selected peptides are highlighted in red 138 (Table 4) . A high score represents a good binding affinity with epitopes, and most of our 139 peptides scored more than 0.7 and were predicted as linear B-cell epitopes. 140 We used the IEDB server to determine the binding affinity for human leucocyte antigen 141 7 epitope(s) with high binding affinity with HLA-A and HLA-B alleles, except one. Similarly, 149 the list of binding affinities for MHC-II T-cell epitopes are given in Table 6 . Regions from our 150 selected peptides are highlighted in red. The results revealed that around half of our selected 151 peptides are potential T-cell epitope(s) with high binding affinity with HLA-DRB and HLA-152 DP/DQ alleles.