Influenza A virus reassortment and genetic variation in lower respiratory tracts of vaccinated and unvaccinated pigs.

Influenza A virus (IAV) is well known for its fast-changing genetic and antigenic characteristics which benefit from its genetic evolution mechanisms - antigenic drift and antigenic shift. The low proofreading ability of the influenza RNA polymerase and the segmented genome, which contributes to gene exchange during virus replication, significantly contributes to influenza virus genetic diversity. The high diversity and fast mutation rate of IAV-S presents a huge challenge for disease control by vaccination. IAV evolves rapidly to escape host immunity and transmit under immune pressure conditions. The impact of immune pressure on influenza diversity has been documented in previous studies based on the nasal swabs by characterizing the significant intra- and inter-host evolutionary dynamics of the influenza virus within multiple vaccinated animal models. However, studies that explore the extent of genetic variation and reassortment of IAV in lower respiratory tracts of pigs vaccinated by multiple prime-boost vaccination protocols are lacking. Here we assess and quantify the within-host mutational spectra of influenza viruses by performing the deep sequencing directly on 28 BALF samples collected from infected pigs vaccinated with different protocols after the simultaneous H1N1 and H3N2 viruses challenge, and out of them, 13 samples were successfully performed the plaque purifications. We totally isolated 202 plaques for whole-genome sequencing to evaluate the emergence of new reassortant viruses in pigs co-infected with two influenza viruses of different subtypes and lineages.