Abstract
European H1N2 swine influenza viruses (EU H1N2SIVs) arose from multiple reassortment events among human H1N1, human H3N2, and avian influenza viruses. We investigated the evolutionary dynamics of 53 Italian H1N2 strains by comparing them with EU H1N2 SIVs. Hemagglutinin (HA) phylogeny revealed Italian strains fell into four groups: Group A and B (41 strains) had a human H1 similar to EU H1N2SIVs, which probably originated in 1986. However Group B (38 strains) formed a subgroup that had a two-amino acid deletion at positions 146/147 in HA. Group C (11 strains) contained an avian H1 that probably originated in 1996, and Group D (1 strain) had an H1 characteristic of the 2009 pandemic strain. Neuraminidase (NA) phylogeny suggested a series of genomic reassortments had occurred. Group A had an N2 that originated from human H3N2 in the late 1970s. Group B had different human N2 that most likely arose from a reassortment with the more recent human H3N2 virus, which probably occurred in 2000. Group C had an avian-like H1 combined with an N2 gene from one of EU H1N2SIVs, EU H3N2SIVs or Human H3N2. Group D was part of the EU H3N2SIVs clade. Although selection pressure for HA and NA was low, several positively selected sites were identified in both proteins, some of which were antigenic, suggesting selection influenced the evolution of SIV. The data highlight different evolutionary trends between European viruses and currently circulating Italian B strains and show the establishment of reassortant strains involving human viruses in Italian pigs.
Highlights
Influenza A viruses of subtypes H1N1, H3N2 and H1N2 have been reported in pig populations around the world
Group B was characterized by the deletion of two amino acids in the HA protein at positions 146 and 147; Group C included 11 strains that have an avian-like H1 that placed them in the clade of EU H1N1 Swine influenza viruses (SIVs); Group D contained one reassorted H1N2 strain (A/Sw/It/ 116114/10) that was derived from the H1N1 pandemic viruses (H1N1pdm) [32], and which was grouped together with the H1N1pdm strains isolated from pig farms in Italy [33]
Our analyses revealed a clear difference between Italian strains of group A, which were closely related to the EU H1N2 SIVs, and group B, which had a different HA-NA combination
Summary
Influenza A viruses of subtypes H1N1, H3N2 and H1N2 have been reported in pig populations around the world. The epidemiology of European SIV has changed considerably; the prevalent H1N1 viruses in European countries are antigenically distinct from the classical H1N1 strains and apparently stem from the introduction of an avian virus in toto [1]. These avian-like closely related to that of human H1N1 viruses, an NA gene derived from human H3N2 viruses, and internal genes of avian origin [6]. In Italy, the continuous circulation of the H1N1, H1N2, and H3N2 SIV subtypes in pig populations has been reported [3,7,9]. During this time it represented 37% of all isolations, compared to 35% for H1N1 and 28% for H3N2 [10]
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