Naturally occurring influenza reassortment in pigs facilitates the emergence of intrahost virus subpopulations with distinct genotypes and replicative fitness

Pigs play a crucial role in driving influenza A virus (IAV) diversification and evolution by reassorting the viruses originating from different hosts. Despite IAV reassortment and diversity being well documented in pig populations at different scales (e.g., farm, region, country), limited field research has explored the extent of reassortment happening at the single pig level and how that contributes to the overall genetic and biological variation observed in populations. We provide initial information on levels of reassortment happening at the single pig level in naturally infected pigs, and that particular pigs can shed a plethora of distinct genotypes, with certain genotypes having distinct replicative fitness on swine and human respiratory tracts, which preserves the potential for IAV long-term evolution and facilitates the emergence of zoonotic/pandemic-capable reassortants.