Producers need better vaccines for controlling disease and spread associated with PRRSv infection. This has been an extremely different task because the face of PRRSv is constantly changing making an escape from the host immune system, which is coupled with the ability to suppress the pig immune response. Until we have a better understanding of how the pig immune system “sees” PRRSv and thus, identify components of many different viral strains into a single vaccine the battle will continue. Our work used an objective classification scheme characterizing PRRSv’s based on what the host sees, or T cell epitopes. This information alone will be extremely valuable because it gives producers a better system for making informed choices about which commercial vaccine to select in order to provide maximal protection to the strain actually infecting the farm. For example, our computational results indicate that contemporary isolates are quite distant than three commercially available vaccines regardless of comparison method (full genome versus epitope content) but that using EpiCC comparison, one vaccine may be better than another. Our work to validate epitope predictions was limited given the ability of PRRSv to impact host immune responses, thus future work will need to consider another vaccination/disease system for validation. We performed a vaccine/challenge study using chimeric viruses or an attenuated strain of more contemporary isolate, but protection was minimal against a mildly virulent isolate of PRRSv174. Collectively, the approach can help with vaccine selection, but our work highlights that focus needs to shift away from using PRRSv vaccinated or infected pigs to identify T cell correlates of protection.