Rapid detection of influenza A3 virus by TaqMan-based real-time RT-PCR assay

To establish a specific, sensitive method of TaqMan-based real time RT-PCR assay for the rapid detection of influenza A3 virus, the hemagglutinin (HA) gene of influenza virus down-loaded from Genbank was aligned by using the biologic software, and the specific primers and probes were designed in the conserved regions of HA gene. The primers and probes as well as the reaction condition were optimized to improve the sensitivity and specificity of the assay. The throat swab specimens used in this assay were taken from patients with acute respiratory tract infections. It was found that the specificity of this assay was high without any cross-reactions with influenza A1, A5 ,B viruses, SARS virus and other commonly encountered viruses. The sensitivity of this assay was 0.01 TCID_~50 , and the viral RNA could be detected directly from the clinical specimens. It took only 3 hours to complete the whole course of reaction including extraction of viral RNA and the real-time PCR. It concludes that the TaqMan-based real-time RT-PCR assay is a rapid, sensitive and specific method for the detection of influenza A3 virus.