Comparative whole genome characterization of swine and human influenza A viruses isolated during surveillance activity in Northern Italy (2010-2014): preliminary results.

Background: Swine influenza A viruses (IAVs) avian-like H1N1 , human-like H1N2 and human like H3N2 subtypes circulate actively in the Italian pig population. Since its appearance in human population, the H1N1 2009 pandemic (H1N1pdm) virus spread in swine population. Preliminary findings of a genomic study (PRC2012002) of IAVs circulating in pigs and humans during passive surveillance of respiratory illness in 2010-2014 in Northern Italy are reported. Methods: Nasal/oropharyngeal swabs from human were analyzed within the InfluNet programme in Lombardia and Emilia Romagna regions. Samples from respiratory outbreaks in pig farms were collected and analyzed by the OIE Reference Laboratory for Swine Influenza in IZSLER. Real-Time PCR positive samples were submitted to virus isolation, HA/NA subtyping was performed. A total of 86 (26%) swine IAVs and 70 (4.5 %) human IAVs were fully sequenced by Illumina NGS (Table). Results: Phylogenetic analysis was performed to assign each gene segment to its origin. We analyzed the combination of viral segments and detected two clusters of H3N2 IAV subtype: H3N2 human strains belonging to the seasonal lineage, and H3N2 pig strains belonging to the swine H3N2 lineage. No evidence of gene introduction/reassortment between the two clusters was detected. Human H1N1 strains belonged to H1N1pdm lineage whereas H1N1 pig strains were mainly (80%) avian-like swine H1N1, sporadically (12%) H1N1pdm or pandemic reassortant strains (8%) were detected. H1N2 strains isolated from pigs were characterized as human like H1N2, moreover gene reassortment events (14%) between this H1N2 strain and H1N1pdm strain were observed. Conclusions In the same area, a zoonotic event due to swine IAV H3N2 was reported in an immunocompromised patient (Piralla et Al. ESCV 2014), this study did not point out gene reassortment events between the human and swine H3N2 IAVs. In this study a low prevalence of pdmH1N1in pig population as opposed to humans was observed. Regarding human population, in spite of the high rate of circulation, the genetic characteristic of the pdmH1N1 seems to be steady. In swine the study highlights the occurrence of gene reassortment among pdmH1N1 and the formerly established H1N2 and H1N1 swine IAVs. This aspect should be monitored since the increasing variety of pdmH1N1-derived AIVs could enhance their adaptation/infectivity in pigs and reach higher level of circulation in this population.