This review discusses some of the challenges still faced in the control of equine influenza virus H3N8 infection. A widespread outbreak of equine influenza in the United Kingdom during 2003 in vaccinated Thoroughbred racehorses challenged the current dogma on vaccine strain selection. Furthermore, several new developments in the first decade of the 21st century, including transmission to and establishment in dogs, a presumed influenza-associated encephalopathy in horses and an outbreak of equine influenza in Australia, serve as a reminder of the unpredictable nature of influenza viruses. The application of newly available techniques described in this review may further elucidate some of the viral factors that underlie recent events and provide the tools to better evaluate when vaccine strains should be updated.
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