Co-circulation of multiple influenza A variants in swine harboring genes from seasonal human and swine influenza viruses

Abstract

Since the influenza pandemic in 2009, there has been an increased focus on swine influenza A virus (swIAV) surveillance. This paper describes the results of the surveillance of swIAV in Danish swine from 2011 to 2018.In total, 3800 submissions were received with a steady increase in swIAV positive submissions, reaching 56% in 2018. Ten different swIAV subtypes were detected. Full genome sequences were obtained from 129 swIAV positive samples. Altogether, 17 different circulating genotypes were identified including novel reassortants and subtypes harboring human seasonal IAV gene segments. The phylogenetic analysis revealed substantial genetic drift and also evidence of positive selection occurring mainly in antigenic sites of the hemagglutinin protein and confirmed the presence of a swine divergent cluster among the H1pdm09Nx viruses.The results provide essential data for the control of swIAV in pigs and for early detection of novel swIAV strains with zoonotic potential.

Airborne Transmission of Avian Origin H9N2 Influenza A Viruses in Mammals

“…In addition, the 2WF10:6pH1N1 virus was also able to transmit by airborne route, although with delayed replication kinetics, whereas no evidence of airborne transmission with 1WF10:7pH1N1 was observed, suggesting that compatibility and balance between the HA and NA is also important (Figure 2B). It is tempting to speculate that the pH1N1 backbone is more flexible to accept reassortment with diverse surface genes and does provide a replicative advantage in mammals, as has been observed in multiple examples of reassortant H1N1 and H3N2 viruses in swine [127][128][129][130]. Sequencing information showed a S261N mutation in PB1 and V104A in HA in the viruses isolated from respiratory contact animals (Table 1); however, the role of those positions in airborne transmission remains unknown [88].…”