Influenza A virus diversity and evolutionary dynamics during natural swine infections
This project involved sampling an influenza A outbreak in pigs during a week-long county fair to characterize viral diversity and evolution in this important reservoir host. Nasal wipes were collected on a daily basis from all pigs present at the fair, yielding up to 421 samples per day. Subtyping of PCR-positive samples revealed the co-circulation of H1N1 and H3N2 subtype IAVs. PCR-positive samples with high viral loads were deep-sequenced, yielding 506 sequenced samples from a total of 253 pigs. Positive samples were sequenced twice, from separate RNA extractions.