title: Pyrosequencing as a fast and reliable tool to determine clade affiliation for equine Influenza A virus.
abstract: The objective of our study was to determine the clade affiliation of 116 contemporary equine Influenza A virus (EIV) isolates using pyrosequencing. The EIV isolates originated from horses with clinical signs of equine influenza and laboratory confirmation of EIV by real-time quantitative PCR (qPCR) in nasal secretions. Clade affiliation was performed on the basis of a single nucleotide polymorphism at 2 positions of the hemagglutinin 1 gene. Pyrosequencing was able to clearly classify EIV Florida sublineage prototype A/equine/Ohio/1/2003 and prototype A/equine/Richmond/1/2007 as clade 1 and 2, respectively. Out of the 116 EIV qPCR-positive samples, 113 (97.4%) were classified as belonging to clade 1 Florida sublineage, whereas 3 (2.6%) were classified as clade 2. All clade 1 EIV strains were detected in domestic horses, whereas the 3 clade 2 EIV strains originated from horses recently imported to the United States. Although clade 1 EIV strains are endemic in the United States, international transportation of horses represents a real risk in introducing clade 2 EIV strains into North America.
authors.affiliation: Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, CA.
authors.forename: Pedro N
authors.initials: PN
authors.lastname: Bernardino
authors.affiliation: Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, CA.
authors.forename: Samantha M
authors.initials: SM
authors.lastname: Mapes
authors.affiliation: Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, CA.
authors.forename: Rachel
authors.initials: R
authors.lastname: Corbin
authors.affiliation: Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, CA npusterla@ucdavis.edu.
authors.forename: Nicola
authors.initials: N
authors.lastname: Pusterla
keywords: Clade affiliation; equine influenza virus; horses; pyrosequencing