Influenza Prime-Boost Vaccination, Diversity, And Evolution In Pigs

Abstract

Swine influenza is an important disease that affects pigs of all ages and impacts swine productivity and public health. Vaccination is the primary measure employed to control the disease, and it is widely implemented in pigs in the United States. However, controlling influenza infections is hard due to the high genetic and antigenic diversity of the influenza A virus (IAV). The continuous evolution and population dynamics of IAVs facilitates its circulation in endemically infected herds. The overall goal of this dissertation was to explore the application of multiple prime-boost vaccination protocols to prevent influenza infections in pigs, and characterize the immune response, the within-host evolution of IAV, and the emergence of novel reassortant influenza viruses in vaccinated pigs compared to unvaccinated pigs. We evaluated different prime-boost vaccination protocols in pigs co-challenged with H1 and H3 influenza subtypes using a seeder pig infection model under experimental conditions. We characterized the immune response, the within-host evolution, and the emergence of novel reassortant influenza viruses in the upper and lower respiratory tracts of pigs with different vaccination statuses. We found that the heterologous prime-boost vaccination protocols provided broader protection against multiple subtype IAVs in pigs. Pigs that received the heterologous prime-boost vaccination protocols showed more favorable disease outcomes than their comparison groups in reducing the number of IAV infected pigs, virus shedding, and inducing humoral immunity. We found that vaccination decreased the risk of influenza reassortment but not genetic variation as measured in the lungs of pigs co-infected with H1 and H3 subtypes. The results of IAV within-host diversity from the swine nasal cavities also showed that vaccination had a limited effect on the evolutionary selection processes across the entire IAV genome, possibly due to the short longevity of IAV infection in individual pigs. However, vaccination may have shifted the selection patterns of IAV variants at specific amino acid sites during the infection process. Besides, a large proportion of IAV variants generated in the pigs became lost during transmission events among immune pigs of the same room. In addition, we observed that multiple subtype IAVs could infect pigs consecutively and concomitantly, which facilitated virus reassortment and altered variant selection by flipping the interaction of the suite of mutations (epistasis), finally changing the overall diversity of virus populations in pigs. The studies in this dissertation revealed a tangled relationship between IAV vaccination, diversity, and evolution in pigs. The knowledge generated from this thesis will help design more effective IAV surveillance and control programs in pigs worldwide and prevent infections between pigs and people.