PRJNA763061
Identification and characterization of swine influenza virus H1N1 variants generated in vaccinated and non-vaccinated, challenged pigs
Influenza viruses represent a continuous threat to both animal and human health. The 2009 pan-demic H1N1 A influenza highlighted the importance of swine host in adaptation of influenza viruses to human. Nowadays, one of the most extended strategy used to control Swine influenza viruses (SIVs) is the trivalent vaccine application, which formulation contains the most fre-quently circulating SIV subtypes H1N1, H1N2 and H3N2. These vaccines do not provide full protection against the virus, potentially favoring viral evolutionary dynamics. To better under-stand the main mechanisms that shape viral evolution, here, the SIV intra-host diversity was an-alyzed in samples collected from both, vaccinated and non-vaccinated animals challenged with H1N1 influenza A virus. Twenty-eight whole SIV genomes were obtained by next generation sequencing and differences in nucleotide variants between groups were established. Substitu-tions were allocated along all influenza genetic segments, while the most relevant non-synonymous substitutions were allocated in the NS1 protein on samples collected from vaccinated animals, suggesting that SIV is continuously evolving despite vaccine application. Moreover, new viral variants were found in both vaccinated and non-vaccinated pigs, showing relevant substitutions in the HA, NA and NP proteins, which may increase viral fitness under field conditions