Bio-Computational Prediction of Novel Epitopes on VP2 Protein of Infectious Bursal Disease Virus

Abstract

Aim: Recently, many viral Immunogenic peptides or epitopes have been used as potential vaccine and also immuno-diagnostic candidates. In this study, we predicted different epitopic peptides on VP2 protein of infectious bursal disease virus (IBDV) using bioinformatics tools, which can be potential vaccine as well as diagnostic candidate for IBD, in future. Study Design:  In the present study, B-cell epitopes (linear or continuous, and conformational) and T-cell epitopes were predicted on VP2 protein. Place and Duration of Study: Bihar Animal Sciences University, Patna, and Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, India between June and December 2023. Methodology: For the prediction of linear B-cell epitopes, Bepipred Linear Epitope Prediction 2.0, SVMTriP, and BCPred tools were used, while Ellipro was used for conformational B-cell epitopes prediction. In the absence of immune-bioinformatics tool is available to predict poultry MHC-peptide binding, only those human MHC-I/II alleles having greater than 70% identities those of poultry MHC-I/II alleles were selected. NetMHCcons 1.1 and NetMHCIIpan - 4.0 tools were used to predict strong binding affinity of peptides  with MHC-I and MHC-II, respectively. Results: As per analysis by four different tools, the peptide ‘SYDLGYVRLGDPIPAIGLDPKMV ATCDSSDRPRVYTITAADDYQFSSQYQPGGV164-217’ (EpitopeL) was predicted as the most prominent linear B-cell epitope. Two peptides, i.e. ANLNSPLKIAG (EpitopeC 1) and SSQYQPGGRTSVHGLGLTTGTDKSGGQAGDQMS (EpitopeC 2) were predicted as potent conformational B-cell epitopes. During T-cell epitopes prediction, human HLA*B 40:06, HLA*B 41:03 and HLA*B 41:04 alleles chosen as homologues of poultry MHC class I alleles while DRB1:1310, DRB1:1366, DRB1:1445, and DRB1:1482 chosen as homologues of poultry MHC class II alleles. A 9-mer GELVFQTSV236-244 peptide was predicted as MHC-I strong binder ability while, two 15-mer peptides, i.e. YTKLILSERDRLGIK389-403 and QMLLTAQNLPASYNY76-90 were predicted as MHC-II strong binder ability. Conclusion: Using bio-computational analysis, one linear and two conformational B-cell epitopes were predicted on VP2 protein of IBDV. During T-cell epitopes prediction one 9-mer peptide and two 15-mer peptides were predicted as MHC-I and MHC-II strong binding peptides, respectively. After assessing protective immune responses through in vitro and in vivo studies, these predicted peptides could be potential candidates for developing subunit vaccines.