title: Estimating reassortment rates in co-circulating Eurasian swine influenza viruses.
abstract: 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.affiliation: Institute of Evolutionary Biology, University of Edinburgh, Kings Buildings, West Mains Road, Edinburgh EH9 3JT, UK.
authors.forename: S J
authors.initials: SJ
authors.lastname: Lycett
authors.affiliation: Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
authors.forename: G
authors.initials: G
authors.lastname: Baillie
authors.affiliation: Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
authors.forename: E
authors.initials: E
authors.lastname: Coulter
authors.affiliation: Department of Zoology, University of Oxford, The Tinbergen Building, South Parks Road, Oxford OX1 3PS, UK.|Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
authors.forename: S
authors.initials: S
authors.lastname: Bhatt
authors.affiliation: Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
authors.forename: P
authors.initials: P
authors.lastname: Kellam
authors.affiliation: Division of Virology, MRC National Institute for Medical Research, Mill Hill, London NW7 1AA, UK.
authors.forename: J W
authors.initials: JW
authors.lastname: McCauley
authors.affiliation: Cambridge Infectious Diseases Consortium, Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK.
authors.forename: J L N
authors.initials: JLN
authors.lastname: Wood
authors.affiliation: Animal Health and Veterinary Laboratories Agency - Weybridge, Addlestone, Surrey, KT15 3NB, UK.
authors.forename: I H
authors.initials: IH
authors.lastname: Brown
authors.affiliation: Department of Zoology, University of Oxford, The Tinbergen Building, South Parks Road, Oxford OX1 3PS, UK.
authors.forename: O G
authors.initials: OG
authors.lastname: Pybus
authors.affiliation: Institute of Evolutionary Biology, University of Edinburgh, Kings Buildings, West Mains Road, Edinburgh EH9 3JT, UK.
authors.forename: A J
authors.initials: AJ
authors.lastname: Leigh Brown
authors.lastname: For The Combating Swine Influenza Initiative Cosi Consortium
mesh_terms: D000818:Animals; D001208:Asia / Q000453:epidemiology; D016384:Consensus Sequence; D005060:Europe / Q000453:epidemiology; D016679:Genome, Viral; D005838:Genotype; D006388:Hemagglutinins / Q000235:genetics; D009980:Influenza A virus / Q000235:genetics* / Q000502:physiology; D016013:Likelihood Functions; D008969:Molecular Sequence Data; D009439:Neuraminidase / Q000235:genetics; D009976:Orthomyxoviridae Infections / Q000453:epidemiology / Q000662:veterinary* / Q000821:virology; D058873:Pandemics / Q000662:veterinary; D010802:Phylogeny; D012367:RNA, Viral / Q000737:chemistry / Q000302:isolation & purification; D060888:Real-Time Polymerase Chain Reaction; D016865:Reassortant Viruses / Q000235:genetics*; D012189:Retrospective Studies; D013552:Swine; D013553:Swine Diseases / Q000453:epidemiology / Q000821:virology*
chemical_list: D006388:Hemagglutinins; D012367:RNA, Viral; D009439:Neuraminidase