Porcine reproductive and respiratory syndrome virus (PRRSV) poses a significant threat to the global swine industry. In this study, the genetic diversity, evolutionary dynamics, and key antigenic characteristics of the PRRSV-1 GP5 gene in China were systematically investigated. A total of 114 Chinese PRRSV-1 GP5 sequences, isolated between 1999 and 2024, were analyzed alongside global reference strains. The nucleotide and amino acid sequence similarities ranged from 60.03% to 100% and from 48.72% to 100%, respectively, with mutation and deletion hotspots concentrated in the N-terminal hypervariable region. Phylogenetic analysis further classified the Chinese strains into four major lineages: Amervac-like, BJEU06-1-like, HKEU16-like, and NMEU09-1-like. Notably, a preliminary phylogenetic observation indicated that several recent Chinese PRRSV-1 isolates clustered topologically close to PRRSV-2 strains. However, as this finding is based solely on a single-gene tree and has not been validated by formal tests for convergent evolution, homoplasy, or selection pressure, it should be interpreted with caution and warrants further investigation using whole-genome data. A Bayesian evolutionary analysis estimated the evolutionary rate at 1.94 × 10⁻³ substitutions per site per year and the time to the most recent common ancestor at approximately 1910. No statistically significant recombination events were identified within the GP5 gene. The transmembrane topology of GP5 was highly conserved, whereas B-cell linear epitopes were enriched in the N-terminal extracellular region. This study establishes a useful molecular foundation for understanding PRRSV-1 evolution in China and offers valuable insights for the development of broad-spectrum vaccines and effective control strategies.

Background/Objectives: Porcine reproductive and respiratory syndrome virus type 2 (PRRSV-2) remains the predominant genotype circulating in China and continues to evolve through mutation and recombination. Although NSP1 is recognized as a multifunctional nonstructural protein involved in immune regulation, its genetic variation among PRRSV-2 strains circulating in China has not been comprehensively characterized. Methods: In this study, 425 complete NSP1 sequences, primarily representing PRRSV-2 strains circulating in China, were analyzed, and 48 representative strains were selected for pairwise percent-identity visualization. Results: Pairwise nucleotide identity among the 48 representative strains was found to range from 80.1% to 100.0%, with the lowest value detected between AHBZ and SD-R, whereas pairwise amino-acid identity ranged from 79.6% to 100.0%, with the lowest value detected between AHBZ and HNhx. Among the 425 aligned amino-acid sequences, 290 variable sites and 93 completely conserved sites were identified. The broad-lineage distribution was composed of Lineage 1 (n = 79), Lineage 3 (n = 4), Lineage 5 (n = 21), and Lineage 8 (n = 321). A global FEL dN/dS of approximately 0.2979 was estimated from 379 non-recombinant unique haplotypes, and seven high-confidence candidate positively selected sites—42, 239, 255, 302, 367, 370, and 378—were supported by MEME, FEL, and FUBAR. A descriptive lineage-biased pattern concentrated in Lineage 5 was observed for NSP1β Val19Ile, corresponding to full-length NSP1 V199I. Eight candidate recombination events were identified using RDP4, and six representative events were further examined using SimPlot. Conclusions: Overall, NSP1 was found to be under predominant purifying selection while retaining localized variability, lineage-biased residue patterns, and candidate recombination signals that should be interpreted cautiously and validated experimentally.