Detection and differentiation of five diarrhea related pig viruses utilizing a multiplex PCR assay

Porcine viral diarrhea, mainly caused by porcine epidemic diarrhea virus (PEDV), transmissible gastroenteritis virus (TGEV), porcine group A rotaviruses (RVA), porcine group C rotaviruses (RVC) and porcine circovirus 2 (PCV2), is a serious global problem, resulting in substantial economic losses to the swine industry. For fast and reliable diagnosis of the causative agent associated with viral diarrhea in pigs, an inexpensive and easy to perform gel-based multiplex PCR assay was developed in this study to detect and differentiate the different viruses by amplicon size. The assay was able to distinguish between all five viral agents without cross-reacting with other non-target pig viruses. The detection limits of the assay per reaction were 5 copies for PEDV, TGEV, RVC and PCV2 and 50 copies for RVA for the singleplex assays and 50 copies when all five viruses were multiplexed. Sixty-nine field samples were used to validate the developed multiplex assay. The overall prevalence of positive samples was 44.9% (31/69). PCV2 was detected in 37.7% of the samples, PEDV and RVC each in 4.3%, TGEV in 2.9%, and RVA was detected in 1.4% of the samples tested. A total of 5.8% of the samples were co-infected by two or more viruses, and the results of the multiplex assay were in agreement to those obtained by single PCR assays. These findings suggest that the developed cost-effective multiplex assay is specific, sensitive, and will serve as a valuable diagnostic tool for the rapid differential detection of these five viruses and for molecular epidemiological studies and diarrhea disease management.