Duplex TaqMan qPCR for Detecting Porcine Epidemic Diarrhea and Transmissible Gastroenteritis Viruses and Epidemic Study in Fujian

  Objective  A TaqMan probe-based duplex real-time PCR for rapid detection of porcine epidemic diarrhea virus (PEDV) and transmissible gastroenteritis virus (TGEV) was developed. A study was conducted using the methodology to analyze the related 2019–2021 epidemic occurred in Fujian.

  Method  Specific primers and probes labeled with FAM and VIC were designed to amplify the N gene of PEDV and the S gene of TGEV, respectively. A reaction system for the assay was established, optimized, and tested for sensitivity, specificity, and repeatability. The assay was used for the viral detection on 297 suspected clinic specimens collected from 2019 to 2021 for an epidemiology study.

  Result   The newly developed duplex qPCR methodology showed a sensitivity of 10 copies·μL⁻¹ on PEDV and TGEV, which was 100 times higher than that of regular PCR. There were no cross reactions with other common viruses. The inter- and intra-assays had variations on Ct values below 1%. On the 297 specimens, the infection rate of PEDV was 88.89%, that of TGEV 1.01%, and that of both PEDV and TGEV 3.37%.

  Conclusion   The established duplex qPCR had high sensitivity, specificity, repeatability, and reproducibility for detecting PEDV and TGEV. The 2019–2021 epidemic involving the viruses appeared to be mostly PEDV with low incidents of mixed TGEV and PEDV/TGEV infection.