Development and Application of a Triplex RT-qPCR Assay for Differentiating Major Lineages of Porcine Reproductive and Respiratory Syndrome Virus.

Porcine reproductive and respiratory syndrome (PRRS) represents a critical infectious disease caused by the PRRS virus (PRRSV), posing a substantial threat to the global swine industry. In China, there is currently an epidemic trend characterized by the coexistence of multiple evolving genotypes. Effective prevention and control measures are contingent upon the availability of rapid, precise, and sensitive pathogen detection technologies. Addressing the need for swift differentiation of the predominant circulating strains, including the classical strains (PRRSV-C), the highly pathogenic strains (PRRSV-HP), and NADC30-like strains (PRRSV-NA), this study focuses on the NSP2 region of each lineage. It establishes a triple TaqMan-qPCR method capable of simultaneously genotyping these three lineages. The method demonstrated no cross-reactivity with other viruses, including porcine parvovirus (PPV), porcine transmissible gastroenteritis virus (TGEV), porcine pseudorabies virus (PRV), classical swine fever virus (CFSV), African swine fever virus (ASFV), porcine epidemic diarrhea virus (PEDV), porcine rotavirus (RV), and porcine circovirus (PCV2), thereby fully affirming its specificity. The sensitivity analysis demonstrated that the limit of detection (LOD) for the NSP2 gene in each lineage was 1 copy/μL based on the purified plasmids. Both inter-group and intra-group coefficients of variation (CV) were less than 4%, indicating high reproducibility. Comparative studies with commercial kits revealed that the developed TaqMan-qPCR method exhibited 100% relative sensitivity and a relative conformity rate exceeding 98%, suggesting its potential as a viable alternative to commercial kits. Furthermore, the analysis of 1049 clinical samples using the qPCR method indicated that the PRRSV-NADC30-like strains are currently the predominant circulating strain in clinical settings in Hebei Province. In conclusion, this study developed a triple TaqMan-qPCR method capable of simultaneously identifying PRRSV-C, PRRSV-HP and PRRSV-NA, enabling rapid and accurate identification of the PRRSV genotypes prevalent in pig populations. This provides a robust technical tool for the development of targeted immunization and prevention strategies.