Estimating reassortment rates in co-circulating Eurasian swine influenza viruses

Swine have often been considered as a mixing vessel for different influenza strains. In order to assess their role in more detail we undertook a retrospective sequencing study to detect and characterise the reassortants present in European swine and to estimate the rate of reassortment between H1N1, H1N2 and H3N2 subtypes with Eurasian (avian-like) internal protein coding segments. We analysed 69 newly obtained whole genome sequences of subtypes H1N1-H3N2 from swine influenza viruses sampled between 1982- 2008, using Illumina and 454 platforms. Analyses of these genomes, together with previously-published genomes revealed a large monophyletic clade of Eurasian swine lineage polymerase segments containing H1N1, H1N2 and H3N2 subtypes. We subsequently examined reassortments between the hemagglutinin (HA) and neuraminidase (NA) segments and estimated the reassortment rates between lineages using a recently-developed evolutionary analysis method. High rates of reassortment between H1N2 and H1N1-Eurasian swine lineages were detected in European strains, with one reassortment every 2-3 years, on average. This rapid reassortment results from co-circulating lineages in swine, and in consequence we should expect further reassortments between currently circulating swine strains and the recent swine-origin H1N1v pandemic strain.