Molecular Epidemiology, Genetic Diversity, and Isolation of Porcine Reproductive and Respiratory Syndrome Virus in Hubei Province, Central China, 2024–2025

Porcine reproductive and respiratory syndrome virus (PRRSV) remains the most economically devastating pathogen of the global swine industry, with frequent genetic recombination and continuous lineage replacement driving its rapid evolution. Hubei Province, a major swine-producing hub in central China, endures substantial PRRSV disease pressure, yet the current epidemiological and evolutionary landscape of circulating strains remains poorly characterized. In this study, 1478 clinical samples were collected from 12 prefecture-level cities between 2024 and 2025 and subjected to RT-PCR detection, ORF5 sequencing, virus isolation, and complete genome analysis. The detection rate among clinical samples was 26.32%, highest in nursery pigs (32.65%). Phylogenetic analysis of 136 ORF5 sequences revealed lineage 1 dominance (66.18%), comprising NADC30-like (38.24%) and NADC34-like (27.94%) strains, followed by lineage 8 (24.26%), lineage 5 (5.15%), and lineage 3 (4.41%). Six isolates were recovered, and whole-genome analysis identified lineage-specific NSP2 deletion patterns and a recombinant strain (LW HP) bearing a JXA1-like backbone with NADC30-like insertions. Selection pressure analysis ranked Nsp2 as the least-constrained gene (dN/dS = 0.3065; purifying selection), with positively selected codons in GP5 and the NSP2 hypervariable region. These findings delineate the current epidemic status and genetic characteristics of PRRSV in central China, providing critical data for regional prevention and vaccine development.