Molecular Epidemiology, Lineage Evolutionary Dynamics, and Antigenic Variation Analysis of Type II PRRSV in China During 2024–2025

Porcine reproductive and respiratory syndrome virus (PRRSV) represents one of the major threats to the global swine industry, with its rapid evolution and antigenic variation posing persistent challenges to disease control. Based on 328 clinical samples collected from PRRSV symptomatic (respiratory disorders, reproductive failures, and high fever) pigs across 27 provinces in China during 2024–2025, this study employed open reading frame (ORF) 5 gene sequencing, complete genome sequencing of representative strains from key lineages (including a rapidly spreading NADC30-like Lineage 1.8 strain, a vaccine-related Lineage 8.7 strain, and a genetically distinct Lineage 3 strain), phylogenetic analysis, transmission dynamics analysis, intrahost single nucleotide variant (iSNV) analysis, and recombination detection to systematically reveal the molecular epidemiological characteristics and evolutionary dynamics of type II PRRSV currently circulating in China. The results demonstrated a complex pattern of coexistence among five major lineages of type II PRRSV in China, including Lineage 1.5, Lineage 1.8, Lineage 3, Lineage 5, and Lineage 8.7, with Lineage 1.8 emerging as the predominant circulating strain (48.5% of positive samples), followed by Lineage 1.5 (23.2%), while Lineages 3, 5, and 8.7 showed more restricted geographical distribution. Spatial transmission analysis identified Guangdong and Henan as key transmission nodes, forming “viral exchange centers” connecting northern and southern regions, while Hubei, Shanxi, and Jiangsu have become new viral aggregation sites. Genetic diversity analysis revealed high haplotype diversity (Hd) across all lineages except Lineage 5, with Lineage 5 showing a remarkable 106.6% increase in nucleotide diversity within 1 year, indicating rapid adaptive evolution. Tajima’s D test results revealed negative values for most lineages, with Lineage 5 and 8.7 reaching statistical significance, suggesting these viral populations have undergone recent population expansion or directional selection. Multidimensional scaling (MDS) analysis based on genetic distance revealed a potential antigenic divergence between the predominant circulating lineages (1.8 and 3) and current vaccine strains, which may compromise vaccine efficacy. In-depth analysis of three representative genomes revealed complex recombination patterns involving vaccine-related strains and identified the ORF2-ORF3 region as a potential recombination hotspot. The findings of this study provide a scientific basis for understanding the evolutionary mechanisms of type II PRRSV in China and offer important references for formulating targeted control strategies and optimizing vaccine design, which has significant value for ensuring the healthy development of China’s swine industry in the post-African swine fever era.