Circulation of multiple genotypes of H1N2 viruses in a swine farm in Italy over a two-month period

•Two distinct H1N2 genotypes were detected in a swine farm over a two month period in North Italy.•Genotype F and a novel one were detected during this study.•The novel genotype differs from the F genotype by the acquisition of the MP gene from the pandemic H1N1.•Within the novel genotypes reassortment events occurred and 3 distinct variants were detected.•Mutations in the PB1-F2 gene associated with increased virulence and transmission efficiency in mammals were detected. In August 2012 repeated respiratory outbreaks caused by swine influenza A virus (swIAV) were registered for a whole year in a breeding farm in northeast Italy that supplied piglets for fattening. The virus, initially characterized in the farm, was a reassortant Eurasian avian-like H1N1 (H1avN1) genotype, containing a haemagglutinin segment derived from the pandemic H1N1 (A(H1N1)pdm09) lineage. To control infection, a vaccination program using vaccines against the A(H1N1)pdm09, human-like H1N2 (H1huN2), human-like H3N2 (H3N2), and H1avN1 viruses was implemented in sows in November 2013. Vaccine efficacy was assessed by sampling nasal swabs for two months in 35–75 day-old piglets born from vaccinated sows. Complete genome sequencing of eight swIAV-positive nasal swabs collected longitudinally from piglets after the implementation of the vaccination program was conducted to investigate the virus characteristics. Over the two-month period, two different genotypes involving multiple reassortment events were detected. The unexpected circulation of multiple reassortant genotypes in such a short time highlights the complexity of the genetic diversity of swIAV and the need for a better surveillance plan, based on the combination of clinical signs, epidemiological data and whole genome characterization.