Abstract
Influenza A viruses (IAVs) are respiratory pathogens associated with an acute respiratory disease that occurs year-round in swine production. It is currently one of the most important pathogens in swine populations, with the potential to infect other host species including humans. Ongoing research indicates that the three major subtypes of IAV—H1N1, H1N2, and H3N2—continue to expand in their genetic and antigenic diversity. In this study, we conducted a comprehensive genomic analysis of 16 IAVs isolated from different clinical outbreaks in Alberta, Manitoba, Ontario, and Saskatchewan in 2014. We also examined the genetic basis for probable antigenic differences among sequenced viruses. On the basis of phylogenetic analysis, all 13 Canadian H3N2 viruses belonged to cluster IV, eight H3N2 viruses were part of the IV-C cluster, and one virus belonged to the IV-B and one to the IV-D cluster. Based on standards used in this study, three H3N2 viruses could not be clearly classified into any currently established group within cluster IV (A to F). Three H1N2 viruses were part of the H1α cluster.
Highlights
Influenza A virus (IAV) infection remains one of the important causes of respiratory disease in swine populations
The second group consisted of five viruses with HA, NA, PB1, and NS genes originating from the triple-reassortant H3N2 (trH3N2) virus, and PA, PB2, NP, and M genes originating from the pandemic A(H1N1)pdm09 virus
The third group consisted of two viruses with HA, NA, PB1, PB2, NP, and NS genes originating from the trH3N2, and PA and M genes originating from the A(H1N1)pdm09 virus
Summary
Influenza A virus (IAV) infection remains one of the important causes of respiratory disease in swine populations. 1918 “Spanish flu” [1], and the causative agent was subsequently characterized as H1N1 [2] This classical-swine H1N1 (cH1N1) remained stable and the predominant subtype for almost 80 years in. (trH3N2) viruses were reported in swine populations [3]. H3N2 and cH1N1 resulted in double-reassortant viruses, while additional reassortment with the avian influenza virus resulted in the trH3N2 virus [3]. These triple-reassortant viruses subsequently further reassorted with cH1N1 viruses, resulting in distinct H1N1 or H1N2 subtype lineages [4].
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