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Confirmation or rule out of equine influenza virus infection can be performed relatively quickly (same day if samples can be delivered to a prepared laboratory in good time) with the specific polymerase chain reaction (PCR) test. Upper respiratory tract sampling should be performed using special long nasopharyngeal swabs taken by a veterinary surgeon, in a satisfactory manner and placed into specific viral transport media. The PCR test determines whether specific EI viral RNA is present in the test sample, consistent with EI virus infection.

Confirmation or rule out of a specific immune response (antibodies) to EI can be made by the testing of blood (serum) samples collected during the early phase (acute sample) of the infection and then from the same horse 10-14 days later, when the animal is recovering (convalescent sample). A 4-fold or greater rise in specific EI antibody level (titre) in the second blood sample compared to the first (seroconversion) confirms an immunological response to EI infection and suggests a diagnosis of EI if the horse has not been recently vaccinated. However, this test relies on taking two blood samples 10-14 days apart and the interpretation of results for horses that have been fully and recently vaccinated may not be easy to interpret.

Therefore, for the most timely confirmation and rule out of the virus at the time that clinical signs are present or when there is any suspicion of upper respiratory infectious disease, the specific nasopharyngeal swab PCR test is required. Nevertheless, serological (antibody) blood testingmayalso be helpful in assessing the development of immunity and recovery and/or risk of transmission, in particular circumstances.