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

CTLs eliminate foreign particles thereby helping in pathogen clearance and are required for maintaining the cellular integrity. MHC class I molecules represent the epitopes to the CTLs which after activation perform cytotoxic activities. Here, we used NetMHCpan v.4 for the mining of CTL epitopes that have high binding affinity with the 14 class I molecules. The strong binders obtained from NetMHCpan server were then analyzed for their immunogenicity by using class I Immunogenicity tool. Depending upon the amino acid composition, properties and their position in the epitope, class I immunogenicity tool predicts the immunogenicity of a MHC class Iepitope complex. Higher the score depicts higher immunogenicity and vice-versa. Here, all the epitopes with positive score were taken and analyzed for antigenicity, allergenicity and toxicity. Finally, the epitopes with highest antigenicity, non-allergen and non-toxic were selected for the vaccine construction. Upon The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.03.26.009209 doi: bioRxiv preprint analysis, 3 HLA-epitope pairs were obtained for ORF3a protein, 2 pairs for membrane protein, nucleo-capsid protein, and spike glycoprotein each while one HLA-epitope pair each for NSP2, NSP4, Envelope protein, and ORF8 (Supplementary Table S2 ). Overlapping sequences were merged into one or both MHC class I and class II binding epitopes Apart from cellular mediated immunity, the humoral immune response mediates pathogen clearance in the antibody dependent manner. Hence the proteome of SARC-CoV-2 was further scanned for linear B-cell epitopes by using ABCPred server. For higher selectivity and sensitivity, the threshold of ABCPred was kept 0.9. The predicted epitopes were checked for their antigenicity, allergenicity and toxicity and the best epitopes were taken for further consideration. On the basis of above criteria, we received one B-cell epitope each for Nucleocapsid, Guanine-N7 methyltransferase (ExoN), ORF3a, ORF7a, and Surface glycoprotein (Supplementary Table S3 ). The locations of the selected epitopes in the respective protein structures are represented by Figure 2 . Overall, the antigenic 13 HTL and 12 CTL epitopes having highest affinity for the respective HLA alleles and 5 B-cell epitopes that are non-allergenic, non-toxic and can generate a potential immune response were selected for incorporation into the multi-epitope vaccine construct.