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EQUINE influenza (EI) is caused by type A influenza virus (IVA) belonging to the genus Influenzavirus A of the family Orthomyxoviridae. EI is a severe respiratory disease of horses with high morbidity and low mortality (Mumford and others 1990, Daly and others 2004). It is commonly encountered in most countries except Australia, Iceland and New Zealand (Daly and others 2004, OIE 2011). Until 2007, Australia had always been free of EI virus (EIV), but experienced a severe outbreak in August 2007 following the introduction of virus with imported horses (Kirkland and others 2011, Watson and others 2011). More than 75,000 horses were infected on approximately 10,000 farms in the two eastern states of New South Wales (NSW) and Queensland (Gilkerson 2011, Moloney and others 2011). The disease was brought under control and eradicated within six months following the application of strict movement controls, zoning of areas with differing levels of infection or freedom, implementation of biosecurity measures in affected premises and vaccination of healthy horses in buffer zones surrounding the affected areas (Scott-Orr 2011). For immunisation, a recombinant canarypox virus vector expressing the haemagglutinin gene of two strains of EIV (H3N8) was used (Paillot and others 2006, Perkins and others 2011).
Detection of EIV was routinely undertaken during diagnostic and surveillance operations during the outbreak with a real-time quantitative RT-PCR (qRT-PCR) assay that had originally been developed for the surveillance of type A avian …
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