Influenza A virus (IAV) can persist in populations for prolonged periods of time. The objectives of this study were to estimate the diversity of IAV in an infected growing pig population, and to determine the extent of pig re-infection with resident viruses. This study is important in order to understand why IAV persist in swine populations. One hundred thirty two pigs were selected at weaning and tested to determine their weekly flu status, and monthly to evaluate seroconversion. Pigs that tested positive for the presence of virus were selected and samples were submitted for whole genome sequencing using next generation sequencing techniques. Sequencing was conducted directly from nasal swabs to capture the breath of genetic diversity.

Our results indicated that IAV spread rapidly after weaning and that all pigs became infected despite the presence of immunity at weaning. Interestingly there were three genetically distinct viruses identified in the population that caused two distinct IAV epidemics. The first and second epidemic peaks were dominated by H1 and H3 viruses respectively. However both subtypes were identified co-circulating during both epidemic peaks. This is interesting since it shows that multiple IAV strains and subtypes can co-circulate within a population at different levels. We also showed that a significant percentage of pigs became re-infected with IAV and most often this re-infection was with a different IAV subtype. However, there were some pigs that became re-infected with the same subtype but a different strain, and other pigs that became re-infected with the same strain.

Our results provide the first basic understanding on influenza virus diversity and transmission in pigs after weaning in a commercial herd. We identified conditions for IAV persistence and reassortment after weaning. This information is relevant in order to understand why influenza persists in populations and what risk endemically infected populations represent in the generation of new viruses. Our results should assist in the development of better vaccines and strategies to control and reduce the impact of IAV in pigs.