Some years ago, researchers at EpiVax developed a tool to map and predict T cell epitopes in pigs. Similarly to EpiMatrix, this tool was based on the pocket profile method. The team developed a class II prediction matrix for a specific swine allele. Using a similar approach, we overcome a lack of T cell epitope data to construct swine epitope predictors by systematically leveraging available human information. Applying the pocket profile method, we use sequence and structural similarities in the binding pockets of human and swine major histocompatibility complex proteins to infer Swine Leukocyte Antigen (SLA) peptide binding preferences. We have developed and validated in silico, predictions tool for for three SLA class I alleles (SLA-1*0401, 2*0401 and 3*0401) and one class II allele (SLA-DRB1*0201). We have recently expanded the set of alleles to include commonly expressed class I and II swine alleles. We are using PigMatrix to screen swine viruses such as influenza, porcine reproductive and respiratory syndrome and porcine epidemic diarrhea, for T cell epitopes. Recently, we have identified and validated T cell epitopes cross-conserved in prevalent swine influenza viruses.
We are also working on developing a tool that compares predicted T cell epitope content to better define the degree of conservation between vaccines strains and circulating strains. In addition to pig prediction tools, fish tools are being developed and tested in collaboration with a private company. The current projects involve Andres Gutierrez Nuñez, an PhD student in Dr. De Groot’s laboratory, Dr. Lenny Moise and Ryan Tassone of iCubed, Frances Terry and Bill Martin of EpiVax, Crystal Loving of the USDA.