Evolving H3N2 and emerging H1N2 swine influenza viruses in the United States

Background: Reassortant H3N2 influenza viruses have recently become established in swine populations throughout the United States. Viruses of two genotypes (a human and swine virus reassortant and a human, swine, and avian virus reassortant) were isolated from swine during the index disease outbreaks. Methods: To identify the genetic composition of the currently circulating viruses, we sequenced the genes of seven isolates from different infected herds. Results: Six viruses contained the human/swine/avian gene complex, but the complex was associated with three phylogenetically distinct human H3 haemagglutinins (HA). The remaining virus was an H1N2 reassortant containing seven genes similar to those of swine H3N2 viruses and an HA gene derived from a classical-swine H1N1 virus. The non-HA genes of this H1N2 virus were more similar to those of swine H3N2 viruses than to those of the recently reported H1N2 swine virus from Indiana [J. Clin. Microbiol. 38 (2000) 2453]. This finding suggests that each of the H1N2 viruses were derived through independent reassortment events. Conclusions: We conclude that viruses containing the avian-like genes are primarily responsible for the increased prevalence of H3N2 viruses throughout U.S. swine populations. H3N2 viruses have continued to spread and have undergone further reassortment with human and swine viruses resulting in the emergence of viruses with distinct antigenicity and subtype.