Longitudinal Molecular Epidemiology and Genomic Evolution of Porcine Reproductive and Respiratory Syndrome Virus in a Large-Scale Swine Production System in Northern China, 2023-2026.

Porcine reproductive and respiratory syndrome virus (PRRSV) remains a major threat to swine production because of its persistent circulation, genetic diversity, and frequent recombination. However, longitudinal molecular surveillance within large-scale integrated production systems remains limited. In this study, we investigated the epidemiological and genomic characteristics of PRRSV in a large-scale swine production system in Chifeng, Inner Mongolia, northern China, from January 2023 to May 2026. A total of 380,050 PRRSV nucleic acid testing records were analyzed, and 36,474 were positive, yielding an overall positivity rate of 9.60%. PRRSV detection showed marked temporal fluctuations, with increased positivity from late 2025 to early 2026, and substantial heterogeneity among farms. Nursery pigs showed the highest positivity rate among production stages, followed by finishing pigs and gilts, whereas boars had the lowest positivity. Among sample types, castration/tail-docking fluid, tongue-tip fluid, and tissue/organ samples had relatively high positivity rates. ORF5-based phylogenetic analysis revealed that all the study-derived sequences belonged to PRRSV-2, with sublineage 1.8 accounting for 53.74% and sublineage 1.5 accounting for 34.69%, indicating the predominance of lineage 1 strains. Whole-genome phylogenetic analysis of the 11 successfully assembled PRRSV genomes confirmed that they were NADC30-like PRRSVs and carried the characteristic 111 + 1 + 19 discontinuous deletion pattern in Nsp2. GP5 amino acid alignment revealed substitutions in antigenically relevant regions, including epitope A, epitope B, and predicted glycosylation-related sites. Recombination analysis revealed potential recombination events involving lineage 8-related fragments in CF-k141-31, CF-k141-560, and CF-k141-2190. These findings demonstrate that PRRSV circulation in this production system is characterized by temporal clustering, farm-level heterogeneity, lineage 1 predominance, and genomic diversification of NADC30-like strains. These results support the integration of routine real-time reverse transcription quantitative PCR (RT-qPCR) surveillance, ORF5 sequencing, and periodic whole-genome sequencing for targeted PRRSV monitoring and control in large-scale swine production systems.