Evolution of Swine Influenza Virus H3N2 in Vaccinated and Nonvaccinated Pigs After Previous Natural H1N1 Infection

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 highly prevalent 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 vac-cinated and nonvaccinated, H3N2 challenged pigs after recovering from a natural A(H1N1) pdm09 infection, were determined, and analysed. In total, seventeen whole SIV genome were de-termined, 6 from vaccinated, 10 from nonvaccinated animals and the inoculum, by NGS. Herein, 214 de novo substitutions were found along all SIV segments. In this study, the impact that the 44 nonsynonymous substitutions found, which exceed the 5% of allele frequency, may have on virus fitness is hypothesized according to previous literature . Nonsynonymous substitutions were not found on NP, meanwhile, much of these were allocated in PB2, PB1 and NS1 proteins. Regarding HA and NA proteins, higher nucleotide diversity, proportionally more nonsynonymous substitutions, 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