Genetic analysis of influenza A viruses of swine from commercial farms in Serbia

Swine influenza presents a very important health and economic issue in pig productions worldwide. Viruses that cause the disease are genetically very diverse but usually belong to the H1N1, H1N2 and H3N2 subtype of influenza A viruses. In this study, we sequenced and analyzed the full genome of viruses detected in swine from seven commercial farms. Through the analysis of the complete sequences of internal gene cassette together with previously characterized HA and NA genes we found three different genotypes amongst five completely sequenced viruses. Two viruses possessed a completely H1avN1 genotype (40%) and belonged to the H1avN1 lineage, which is prevalent in European swine populations. The other three viruses have arisen through the reassortment of the genes of H1avN1 and H1N1pdm09 lineages. In one sample we detected coinfection with viruses of H3N2 subtype with genes of H1avN1, H1N1pdm09 and A/swine/Gent/1/1984-like H3N2 lineages that presents a potential environment for the generation of a triple reassortant virus. The presence of the H1N1pdm09 origin M gene in this sample implies the potential risk of the introduction of these viruses into the human population. Phylogenetic analysis of internal gene cassette revealed slower evolution within genes of H1N1pdm09 lineage than those of H1avN1 lineage.