Development of real-time fluorescent quantitative PCR assay for rapid detection of H3N8 subtype Equine influenza virus

A real-time fluorescent quantitative PCR assay was developed based on primers and TaqMan probes derived from highly conserved regions of the hemagglutinin gene of equine influenza virus subtype(H3N8 EIV).A total number of 135 nasopharyngeal swabs collected from suspected equine influenza in Xinjiang and other provinces were tested by real-time PCR,RT-PCR and viruses isolation.The results showed that the positive detection rates of these methods were 54.07 %,37.78 %,0.89 %,respectively.The detection limit of the real-time PCR assay was 10 copies per reaction.This assay was sensitive,specific and reproducible and had no cross-reaction with other equine respiratory diseases.This real-time PCR assay reported here is suitable for rapid and quantitative detection of H3N8 EIV under clinical conditions and molecular epidemiological investigation.