Estimating reassortment rates in co-circulating Eurasian swine influenza viruses.

Journal article

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.

Authors: Lycett, S; Baillie, G; Coulter, E; Bhatt, S; Kellam, P

• Publication status: Published
• Journal: Journal of general virology More from this journal
• Volume: 93
• Issue: Pt 11
• Pages: 2326-2336
• Publication date: 2012-11-01
• DOI: 10.1099/vir.0.044503-0
• EISSN: 1465-2099
• ISSN: 0022-1317
• Language: English
• Keywords: Genotype; Phylogeny; Hemagglutinins; Orthomyxoviridae Infections; Real-Time Polymerase Chain Reaction; Combating Swine Influenza Initiative-COSI Consortium; Genome, Viral; Neuraminidase; Retrospective Studies; Asia; Consensus Sequence; Europe; Swine; Swine Diseases; Molecular Sequence Data; Pandemics; Influenza A virus; Likelihood Functions; RNA, Viral; Animals; Reassortant Viruses