The use of bovine MHC class I allele-specific peptide motifs and proteolytic cleavage specificities for the prediction of potential cytotoxic T lymphocyte epitopes of bovine viral diarrhea virus.

Cell mediated immunity (CMI) is crucial for the defense against viruses. Cytotoxic T lymphocytes (CTLs) play a major role in CMI. They recognize endogenous antigenic peptides presented by antigen presenting cells in association with the major histocompatibility complex (MHC) class I molecules. The elucidation of the sequence of CTL epitopes of viruses should help in designing better vaccines. In this study, we have identified candidate epitopes restricted by five bovine MHC class I molecules that are potentially available for presentation to CTLs. The candidate peptide epitopes were identified by using the computer programs available as a part of the Genetics Computer Group package and applying the information on allele-specific peptide motifs and intracellular enzymatic cleavage patterns to the bovine viral diarrhea virus polyprotein. Several candidate peptides were found for each of the bovine lymphocyte antigens (BoLA)-A11, -A20, -HD1, and -HD6 whereas no peptide was found for BoLA-HD7. Based on this finding, the probable contribution of genomic segments of BVDV to the CTL response and strategies for recombinant vaccines are discussed.