title: Phylogeny of Spanish swine influenza viruses isolated from respiratory disease outbreaks and evolution of swine influenza virus within an endemically infected farm.
abstract: In the present study, outbreaks of respiratory disease were investigated for the presence of swine influenza virus (SIV). In 14 cases the circulating SIV strains were isolated, fully sequenced and compared with other known SIVs. The viruses causing the outbreaks belonged to the H1N1 (including human pandemic H1N1), H3N2 and H1N2 subtypes. In 11/14 cases the phylogenetic analyses indicated the occurrence of probable reassortment events. In the second part of the study, the genetic evolution of H1N1 SIV was assessed in a longitudinal study in closed groups of pigs over six months. Sequencing of the 22 isolates indicated co-circulation of two different variants for the same virus, as well as the emergence of SIV reassortants at certain time-points. These results indicate that reassortment events in SIV are common, and point towards the need for a better understanding of the epidemiology of SIV, particularly in endemic farms.
authors.affiliation: Centre de Recerca en Sanitat Animal (CReSA), UAB-IRTA, Campus de la Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain. Electronic address: g.e.martinvalls@gmail.com.
authors.forename: Gerard E
authors.initials: GE
authors.lastname: Martín-Valls
authors.affiliation: Centre de Recerca en Sanitat Animal (CReSA), UAB-IRTA, Campus de la Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain. Electronic address: meritxell.simon@hipra.es.
authors.forename: Meritxell
authors.initials: M
authors.lastname: Simon-Grifé
authors.affiliation: Department of Virology, Erasmus Medical Center, Erasmus University, 3015GE Rotterdam, The Netherlands. Electronic address: s.vanboheemen@erasmusmc.nl.
authors.forename: Sander
authors.initials: S
authors.lastname: van Boheemen
authors.affiliation: Department of Virology, Erasmus Medical Center, Erasmus University, 3015GE Rotterdam, The Netherlands. Electronic address: m.degraaf@erasmusmc.nl.
authors.forename: Miranda
authors.initials: M
authors.lastname: de Graaf
authors.affiliation: Department of Virology, Erasmus Medical Center, Erasmus University, 3015GE Rotterdam, The Netherlands. Electronic address: t.bestebroer@erasmusmc.nl.
authors.forename: Theo M
authors.initials: TM
authors.lastname: Bestebroer
authors.affiliation: Centre de Recerca en Sanitat Animal (CReSA), UAB-IRTA, Campus de la Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain. Electronic address: nuria.busquets@cresa.uab.cat.
authors.forename: Núria
authors.initials: N
authors.lastname: Busquets
authors.affiliation: Centre de Recerca en Sanitat Animal (CReSA), UAB-IRTA, Campus de la Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain; Departament de Sanitat i Anatomia animals, Universitat Autònoma de Barcelona (UAB), 08193 Bellaterra, Barcelona, Spain. Electronic address: marga.martin@uab.cat.
authors.forename: Margarita
authors.initials: M
authors.lastname: Martín
authors.affiliation: Centre de Recerca en Sanitat Animal (CReSA), UAB-IRTA, Campus de la Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain; Departament de Sanitat i Anatomia animals, Universitat Autònoma de Barcelona (UAB), 08193 Bellaterra, Barcelona, Spain. Electronic address: jordi.casal@uab.cat.
authors.forename: Jordi
authors.initials: J
authors.lastname: Casal
authors.affiliation: Department of Virology, Erasmus Medical Center, Erasmus University, 3015GE Rotterdam, The Netherlands. Electronic address: r.fouchier@erasmusmc.nl.
authors.forename: Ron A M
authors.initials: RA
authors.lastname: Fouchier
authors.affiliation: Centre de Recerca en Sanitat Animal (CReSA), UAB-IRTA, Campus de la Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain; Departament de Sanitat i Anatomia animals, Universitat Autònoma de Barcelona (UAB), 08193 Bellaterra, Barcelona, Spain. Electronic address: enric.mateu@uab.cat.
authors.forename: Enric
authors.initials: E
authors.lastname: Mateu
mesh_terms: D000818:Animals; D001483:Base Sequence; D019143:Evolution, Molecular; D053118:Influenza A Virus, H1N1 Subtype / Q000145:classification / Q000235:genetics / Q000302:isolation & purification; D057221:Influenza A Virus, H1N2 Subtype / Q000145:classification / Q000235:genetics / Q000302:isolation & purification; D053122:Influenza A Virus, H3N2 Subtype / Q000145:classification / Q000235:genetics / Q000302:isolation & purification; D009980:Influenza A virus / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D008969:Molecular Sequence Data; D009976:Orthomyxoviridae Infections / Q000662:veterinary* / Q000821:virology; D010802:Phylogeny; D016865:Reassortant Viruses / Q000145:classification / Q000235:genetics / Q000302:isolation & purification; D016415:Sequence Alignment; D012689:Sequence Homology, Nucleic Acid; D013030:Spain; D013552:Swine; D013553:Swine Diseases / Q000821:virology*
keywords: Influenza; Reassortment; SIV emergence; Swine