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

Abstract

Simple Summary Porcine reproductive and respiratory syndrome virus (PRRSV) is a major pathogen in the swine industry, presenting a longstanding and significant threat to global pig production. In China, there is currently an epidemic trend characterized by the coexistence of multiple evolving genotypes. To address the need for rapid 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 focused on the NSP2 region of each strain and established a triple TaqMan-qPCR method capable of simultaneously genotyping the three strains. This detection method has high specificity and shows no cross-reaction with various pig-susceptible viruses. Moreover, its relative detection accuracy compared to the mainstream commercial kits in the market exceeds 98%. By using the qPCR method to analyze 1049 clinical samples, it was found that the NADC30-like strains are currently the main prevalent strain of PRRSV in the clinical environment of Hebei Province. The triple TaqMan-qPCR method developed in this study can quickly and accurately identify the prevalent PRRSV genotypes in pig populations. This provides a reliable technical tool for formulating targeted immunization and prevention strategies.