Abstract
Swine play an important role in the ecology of influenza A viruses (IAVs), acting as mixing vessels. Swine (sw) IAVs of H1N1 (including H1N1pdm09), H3N2, and H1N2 subtypes are enzootic in pigs globally, with different geographic distributions. This study investigated the genetic diversity of swIAVs detected during passive surveillance of pig farms in Northern Italy between 2017 and 2020. A total of 672 samples, IAV-positive according to RT-PCR, were subtyped by multiplex RT-PCR. A selection of strains was fully sequenced. High genotypic diversity was detected among the H1N1 and H1N2 strains, while the H3N2 strains showed a stable genetic pattern. The hemagglutinin of the H1Nx swIAVs belonged to HA-1A, HA-1B, and HA-1C lineages. Increasing variability was found in HA-1C strains with the circulation of HA-1C.2, HA-1C.2.1 and HA-1C.2.2 sublineages. Amino acid deletions in the HA-1C receptor binding site were observed and antigenic drift was confirmed. HA-1B strains were mostly represented by the Δ146-147 Italian lineage HA-1B.1.2.2, in combination with the 1990s human-derived NA gene. One antigenic variant cluster in HA-1A strains was identified in 2020. SwIAV circulation in pigs must be monitored continuously since the IAVs’ evolution could generate strains with zoonotic potential.
Highlights
Swine play an important role in the ecology of influenza A viruses (IAVs), acting as mixing vessels
The high incidence of IAV infection in the European swine population and the cocirculation of these different lineages contributed to the generation of reassortant strains with different combinations of swine, avian, and human genes [6]
In northern European countries (Germany, Denmark, Sweden), the H1huN2 was replaced by novel reassortant H1pdm09N2 and H1avN2 strains [14], increasing the genetic and antigenic variability described among the HA-1A and HA-1C lineages, cocirculating with different NA genes [5,6,9,16,17,18]
Summary
Swine influenza viruses are a common cause of respiratory disease in pigs. Given their role as a mixing vessel for viruses of human and avian origin, swine are important for the influenza A viruses’ (IAV) ecology [1]. The high incidence of IAV infection in the European swine population and the cocirculation of these different lineages contributed to the generation of reassortant strains with different combinations of swine, avian, and human (seasonal and pandemic) genes [6] Some of these new strains emerged and replaced the endemic pig swIAV strains; in the UK, the H1N1pdm replaced the H1Nx strains; in Denmark, H1avN2 (H1N2dk) supplanted. In northern European countries (Germany, Denmark, Sweden), the H1huN2 was replaced by novel reassortant H1pdm09N2 and H1avN2 strains [14], increasing the genetic and antigenic variability described among the HA-1A and HA-1C lineages, cocirculating with different NA genes [5,6,9,16,17,18] The emergence of these drifted and swine-adapted strains is evidence of the active circulation of swine influenza viruses among European pig herds. High genotypic diversity was detected among the H1N1 and H1N2 strains, whilst the H3N2 strains showed a stable genetic pattern
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