title: Molecular characterization of H3N2 influenza A viruses isolated from Ontario swine in 2011 and 2012.
abstract: BACKGROUND
  Data about molecular diversity of commonly circulating type A influenza viruses in Ontario swine are scarce. Yet, this information is essential for surveillance of animal and public health, vaccine updates, and for understanding virus evolution and its large-scale spread.
  
  
  METHODS
  The study population consisted of 21 swine herds with clinical problems due to respiratory disease. Nasal swabs from individual pigs were collected and tested by virus isolation in MDCK cells and by rtRT-PCR. All eight segments of 10 H3N2 viruses were sequenced using high-throughput sequencing and molecularly characterized.
  
  
  RESULTS
  Within-herd prevalence ranged between 2 and 100%. Structurally, Ontario H3N2 viruses could be classified into three different groups. Group 1 was the most similar to the original trH3N2 virus from 2005. Group 2 was the most similar to the Ontario turkey H3N2 isolates with PB1 and NS genes originating from trH3N2 virus and M, PB2, PA and NP genes originating from the A(H1N1)pdm09 virus. All Group 3 internal genes were genetically related to A(H1N1)pdm09. Analysis of antigenic sites of HA1 showed that Group 1 had 8 aa changes within 4 antigenic sites, A(1), B(3), C(2) and E(2). The Group 2 viruses had 8 aa changes within 3 antigenic sites A(3), B(3) and C(2), while Group 3 viruses had 4 aa changes within 3 antigenic sites, B(1), D(1) and E(2), when compared to the cluster IV H3N2 virus [A/swine/Ontario/33853/2005/(H3N2)].
  
  
  CONCLUSIONS
  The characterization of the Ontario H3N2 viruses clearly indicates reassortment of gene segments between the North American swine trH3N2 from cluster IV and the A(H1N1)pdm09 virus.
authors.affiliation: Department of Population Medicine, Ontario Veterinary College, University of Guelph, Guelph, Ontario, N1G 2 W1, Canada. hgrgic@uoguelph.ca.|Centre for Public Health and Zoonoses, University of Guelph, Guelph, Canada. hgrgic@uoguelph.ca.
authors.forename: Helena
authors.initials: H
authors.lastname: Grgić
authors.affiliation: Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario, N1G 2 W1, Canada. costam@uoguelph.ca.|Centre for Public Health and Zoonoses, University of Guelph, Guelph, Canada. costam@uoguelph.ca.
authors.forename: Marcio
authors.initials: M
authors.lastname: Costa
authors.affiliation: Department of Population Medicine, Ontario Veterinary College, University of Guelph, Guelph, Ontario, N1G 2 W1, Canada. rfriends@uoguelph.ca.|Centre for Public Health and Zoonoses, University of Guelph, Guelph, Canada. rfriends@uoguelph.ca.
authors.forename: Robert M
authors.initials: RM
authors.lastname: Friendship
authors.affiliation: Animal Health Laboratory, University of Guelph, Guelph, Ontario, N1H 6R8, Canada. scarman@uoguelph.ca.
authors.forename: Susy
authors.initials: S
authors.lastname: Carman
authors.affiliation: Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario, N1G 2 W1, Canada. enagy@ovc.uoguelph.ca.|Centre for Public Health and Zoonoses, University of Guelph, Guelph, Canada. enagy@ovc.uoguelph.ca.
authors.forename: Éva
authors.initials: É
authors.lastname: Nagy
authors.affiliation: South-West Ontario Veterinary Services, Stratford, Ontario, Canada. gwideman@gmail.com.
authors.forename: Greg
authors.initials: G
authors.lastname: Wideman
authors.affiliation: Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario, N1G 2 W1, Canada. jsweese@uoguelph.ca.|Centre for Public Health and Zoonoses, University of Guelph, Guelph, Canada. jsweese@uoguelph.ca.
authors.forename: Scott
authors.initials: S
authors.lastname: Weese
authors.affiliation: Department of Population Medicine, Ontario Veterinary College, University of Guelph, Guelph, Ontario, N1G 2 W1, Canada. zpoljak@uoguelph.ca.|Centre for Public Health and Zoonoses, University of Guelph, Guelph, Canada. zpoljak@uoguelph.ca.
authors.forename: Zvonimir
authors.initials: Z
authors.lastname: Poljak
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D014644:Genetic Variation; D005838:Genotype; D053122:Influenza A Virus, H3N2 Subtype / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D008969:Molecular Sequence Data; D009864:Ontario; D009976:Orthomyxoviridae Infections / Q000662:veterinary* / Q000821:virology; D010802:Phylogeny; D012367:RNA, Viral / Q000235:genetics*; D060888:Real-Time Polymerase Chain Reaction; D016865:Reassortant Viruses / Q000145:classification / Q000235:genetics / Q000302:isolation & purification; D020133:Reverse Transcriptase Polymerase Chain Reaction; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D017385:Sequence Homology; D013552:Swine; D013553:Swine Diseases / Q000821:virology*
chemical_list: D012367:RNA, Viral