Swine influenza viruses (SIV) produce a highly contagious and worldwide distributed
disease that can cause important economic losses to the pig industry. Currently, this virus is endemic
in farms and, although used limitedly, trivalent vaccine application is the most extended strategy
to control SIV. The presence of pre-existing immunity against SIV may modulate the evolutionary
dynamic of this virus. To better understand these dynamics, the viral variants generated in vaccinated
and nonvaccinated H3N2 challenged pigs after recovery from a natural A(H1N1) pdm09 infection
were determined and analyzed. In total, seventeen whole SIV genomes were determined, 6 from
vaccinated, and 10 from nonvaccinated animals and their inoculum, by NGS. Herein, 214 de novo
substitutions were found along all SIV segments, 44 of them being nonsynonymous ones with an
allele frequency greater than 5%. Nonsynonymous substitutions were not found in NP; meanwhile,
many of these were allocated in PB2, PB1, and NS1 proteins. Regarding HA and NA proteins, higher
nucleotide diversity, proportionally more nonsynonymous substitutions with an allele frequency
greater than 5%, and different domain allocations of mutants, were observed in vaccinated animals,
indicating different evolutionary dynamics. This study highlights the rapid adaptability of SIV in
different environments.info:eu-repo/semantics/publishedVersio
