Pyrosequencing as a fast and reliable tool to determine clade affiliation for equine Influenza A virus

Pedro N. Bernardino, Samantha M. Mapes, Rachel Corbin, Nicola Pusterla

Research output: Contribution to journalArticlepeer-review

8 Scopus citations


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.

Original languageEnglish (US)
Pages (from-to)323-326
Number of pages4
JournalJournal of Veterinary Diagnostic Investigation
Issue number3
StatePublished - 2016


  • Clade affiliation
  • equine influenza virus
  • horses
  • pyrosequencing

ASJC Scopus subject areas

  • veterinary(all)


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