The best ante mortem samples to detect influenza are

Oral fluids contain inhibitors that may affect detection by RT-PCR, and the presence of low amounts of virus may prevent sequencing or virus isolation. Nasal swabs are typically more successful for the sequencing and isolation of influenza virus due to the larger amounts of virus in the sample, but require sample collection from individual swine or a sufficient number of pigs to represent the population during the acute phase of infection.