title: Characterisation of the epidemic strain of H3N8 equine influenza virus responsible for outbreaks in South America in 2012.
abstract: BACKGROUND
  An extensive outbreak of equine influenza occurred across multiple countries in South America during 2012. The epidemic was first reported in Chile then spread to Brazil, Uruguay and Argentina, where both vaccinated and unvaccinated animals were affected. In Brazil, infections were widespread within 3months of the first reported cases. Affected horses included animals vaccinated with outdated vaccine antigens, but also with the OIE-recommended Florida clade 1 strain South Africa/4/03.
  
  
  METHODS
  Equine influenza virus strains from infected horses were isolated in eggs, then a representative strain was subjected to full genome sequencing using segment-specific primers with M13 tags. Phylogenetic analyses of nucleotide sequences were completed using PhyML. Amino acid sequences of haemagglutinin and neuraminidase were compared against those of vaccine strains and recent isolates from America and Uruguay, substitutions were mapped onto 3D protein structures using PyMol. Antigenic analyses were completed by haemagglutination-inhibition assay using post-infection ferret sera.
  
  
  RESULTS
  Nucleotide sequences of the haemaglutinin (HA) and neuraminidase (NA) genes of Brazilian isolate A/equine/Rio Grande do Sul/2012 were very similar to those of viruses belonging to Florida clade 1 and clustered with contemporary isolates from the USA. Comparison of their amino acid sequences against the OIE-recommended Florida clade 1 vaccine strain A/equine/South Africa/4/03 revealed five amino acid substitutions in HA and seven in NA. Changes in HA included one within antigenic site A and one within the 220-loop of the sialic acid receptor binding site. However, antigenic analysis by haemagglutination inhibition (HI) assay with ferret antisera raised against representatives of European, Kentucky and Florida sublineages failed to indicate any obvious differences in antigenicity.
  
  
  CONCLUSIONS
  An extensive outbreak of equine influenza in South America during 2012 was caused by a virus belonging to Florida clade 1, closely related to strains circulating in the USA in 2011. Despite reports of vaccine breakdown with products containing the recommended strain South Africa/03, no evidence was found of significant antigenic drift. Other factors may have contributed to the rapid spread of this virus, including poor control of horse movement.
authors.affiliation: Universidade Estadual de Londrina, Rodovia Celso Garcia Cid - Pr 445 Km 380, Campus Universitário, Londrina, Paraná, CEP 86057-970, Brazil.
authors.forename: Edsel
authors.initials: E
authors.lastname: Alves Beuttemmüller
authors.affiliation: Animal Health Trust, Lanwades Park, Kentford, Suffolk, CB8 7UU, UK.
authors.forename: Alana
authors.initials: A
authors.lastname: Woodward
authors.affiliation: Animal Health Trust, Lanwades Park, Kentford, Suffolk, CB8 7UU, UK.
authors.forename: Adam
authors.initials: A
authors.lastname: Rash
authors.affiliation: Laboratórios Vencofarma do Brasil, Travessa Dalva de Oliveira, 237, Londrina, Paraná, CEP 86030-370, Brazil.
authors.forename: Luis Eduardo
authors.initials: LE
authors.lastname: Dos Santos Ferraz
authors.affiliation: Universidade Estadual de Londrina, Rodovia Celso Garcia Cid - Pr 445 Km 380, Campus Universitário, Londrina, Paraná, CEP 86057-970, Brazil.
authors.forename: Alice
authors.initials: A
authors.lastname: Fernandes Alfieri
authors.affiliation: Universidade Estadual de Londrina, Rodovia Celso Garcia Cid - Pr 445 Km 380, Campus Universitário, Londrina, Paraná, CEP 86057-970, Brazil.
authors.forename: Amauri Alcindo
authors.initials: AA
authors.lastname: Alfieri
authors.affiliation: Animal Health Trust, Lanwades Park, Kentford, Suffolk, CB8 7UU, UK. debra.elton@aht.org.uk.
authors.forename: Debra
authors.initials: D
authors.lastname: Elton
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D004196:Disease Outbreaks; D062306:Geography, Medical; D019267:Hemagglutinin Glycoproteins, Influenza Virus / Q000737:chemistry / Q000235:genetics; D049674:History, 21st Century; D006734:Horse Diseases / Q000175:diagnosis / Q000453:epidemiology* / Q000266:history / Q000517:prevention & control / Q000821:virology*; D006736:Horses; D053123:Influenza A Virus, H3N8 Subtype / Q000145:classification* / Q000235:genetics / Q000276:immunology / Q000302:isolation & purification; D007252:Influenza Vaccines; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009439:Neuraminidase / Q000737:chemistry / Q000235:genetics; D009976:Orthomyxoviridae Infections / Q000662:veterinary*; D010802:Phylogeny; D011487:Protein Conformation; D012367:RNA, Viral; D016415:Sequence Alignment; D013020:South America / Q000453:epidemiology; D014611:Vaccination; D014764:Viral Proteins / Q000737:chemistry / Q000235:genetics
chemical_list: D019267:Hemagglutinin Glycoproteins, Influenza Virus; D007252:Influenza Vaccines; D012367:RNA, Viral; D014764:Viral Proteins; C487630:NA protein, influenza A virus; D009439:Neuraminidase
keywords: Brazil; Epidemic; Equine influenza; Florida clade 1; Haemagglutinin; Neuraminidase