In silico analysis of VP1 gene for prediction of peptide vaccine against three serotypes (O, A & Asia1) of Foot & Mouth Disease Virus circulating in Bangladesh

Foot and mouth disease (FMD) is a severe, highly contagious, and economically devastating viral disease affecting domestic cloven-hoofed animals. Etiological agent of this life threatening disease is positive sense RNA virus named Foot and Mouth Disease Virus (FMDV).Currently three serotypes O, A and Asia1 are circulating in Bangladesh. This virus lacks the proofreading activity of the viral replicase. As a result, the viral genome becomes subjected highly to genetic diversity. For this reason, FMDV can escape the protective immunity induced by conventional vaccine, which also may induce allergic responses. Besides, the stability and longevity of conventional vaccines are affected due to frequent antigenic drift of the virus. Therefore, the study focused on designing safer and alternative peptide vaccines. The computational analysis of the sequence data, from Gene Bank and study isolates, was performed to detect desirable T and B cell epitopes located in the VP1 of all serotypes circulating in the country. From amino acid alignment of Gene Bank sequences, the motif DLXXLA was found conserved for all the three serotypes. The linear B-cell epitopes were detected in amino acid sequence position 39-43 for serotype O, position 49-65 for serotype A and position 1-9 for serotype Asia1 through computational analysis using IEDB and BCPREDS webserver. IEDB MHC-1 binding prediction tool has predicted T-cell epitopes interacting with different type of MHC class 1 Bola alleles. TSFNYGAIK (for BoLA-N:01201 allele) , ASFNFGAIK (for BoLA-N:01301 allele) and QMMNFDLLK (for BoLA-N:05501 and BoLA-N:00301 allele) were predicted as T-cell epitope for serotype O, A & Asia1 respectively using IEDB resources as their percentile rank is lower than 1.00. The 3D structure of VP1 protein has showed all the predicted epitopes. However, these predicted B-cell and T-cell epitopes were expected for efficient induction of either humoral and cell mediated immunity.