The overall goal of this project was to implement the innovative iVAX suite of immunoinformatics vaccine design tools that have been extensively validated in pre-clinical studies of human vaccines, modify their core elements (matrices) for swine, and apply them to the design of a swine vaccine for Influenza A Virus (IAV). Vaccine design using the new PigMatrices and iVAX toolkit, offers significant advantages over other approaches to developing vaccines for pathogens affecting the pork industry because (i) the tools can be used to accelerate vaccine design for new pathogens; (ii) the tools can be used to improve existing vaccines; and (iii) the tools can be used to predict the efficacy of existing vaccines against new circulating strains. For example, validation of these tools will make it possible to accelerate the development of vaccines and diagnostics for new and emerging infections such as PEDv and ASF.

In the context of the current grant, we used the PigMatrices and iVAX toolkit to identify highly conserved genome components (T cell epitopes) of circulating IAV strains that should drive cross-protective immune responses to IAV. The concept driving this vaccine is that it would reduce the need to produce a new vaccine for each emerging IAV strain. First, the iVAX toolkit was adapted for swine influenza vaccine design. We developed six new swine SLA prediction matrices, four more the number of matrices originally proposed in the grant. Second, we selected 48 highly cross-conserved (“universal”) IAV T cell epitopes, and integrated them into a vaccine that was used to validate the predictions and vaccinate pigs in a head-to-head comparison with an existing influenza vaccine. Third, we performed a challenge study that was carried out in collaboration with Crystal Loving of the USDA. All of the pigs received a standard intranasal flu challenge. The results were surprisingly good. The first test of this prototype showed immunogenicity, but lack of protection in terms of viral load. A repeat study will need to be performed, with epitopes representing additional SLA allele predictions, which can be expected to will improve the efficacy of the vaccine. Overall, the program was remarkably successful, considering we went from “zero to sixty”; we validated our predictions and developed our first prototype PigMatrix-epitope based vaccine and performed a challenge study within the timeframe of the grant. Further development of the PigMatrix tool for iVAX is likely to yield a means of accelerating and improving vaccines for the pork industry.

These results provide a very exciting proof-of-concept that using the new PigMatrices with the iVAX toolkit, we can design vaccines that stimulate responses specific to the predicted epitopes in swine. In addition to designing new, and possibly more effective vaccines for PEDv, PRRSv, ASF and IAV, the tools could be used to identify components that will boost immune responses to any whole antigen vaccine. In addition, predicted immunogenic epitopes can be integrated into low immunogenic antigens to improve their protective response. We are eager to pursue additional tests of the potential of these tools for accelerating vaccine design.

We also developed a new tool for predicting vaccine efficacy. Using these tools we have also developed a new method for classifying vaccines that we hope to validate and then commercialize. We developed a “vaccine classification tool” called Epitope Content Comparison (EpiCC) tool. EpiCC compares the epitope content across strains and would allow pork producers to determine whether a given vaccine would work for emerging strains of influenza or PRRSv. We plan to test this tool, beginning by comparing existing viral strains to vaccines, so as to determine if we can accurately predict vaccine efficacy.