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 characterize 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 and 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 haemagglutinin and neuraminidase 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 an average of one reassortment every 2-3 years. 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.

Original publication




Journal article


The Journal of general virology

Publication Date





2326 - 2336


Institute of Evolutionary Biology, University of Edinburgh, Kings Buildings, West Mains Road, Edinburgh EH9 3JT, UK. samantha.lycett@ed.ac.uk


Combating Swine Influenza Initiative-COSI Consortium, Animals, Swine, Reassortant Viruses, Influenza A virus, Orthomyxoviridae Infections, Swine Diseases, Neuraminidase, RNA, Viral, Hemagglutinins, Likelihood Functions, Retrospective Studies, Phylogeny, Consensus Sequence, Genotype, Genome, Viral, Molecular Sequence Data, Asia, Europe, Pandemics, Real-Time Polymerase Chain Reaction