On September 27, 2025, a research team from the College of Veterinary Medicine at South China Agricultural University published a new study on the molecular epidemiology and evolutionary dynamics of porcine reproductive and respiratory syndrome virus type II (PRRSV-2) in the journal *Transboundary and Emerging Diseases*.
Based on 328 clinical samples from 27 provinces across China in 2024-2025, this study is the first to systematically reveal the current lineage distribution, transmission patterns, antigenic variation, and recombination hotspots of PRRSV-2 in China, providing important scientific evidence for vaccine optimization and epidemic prevention and control.
Research Highlights
* The study is the first to systematically reveal the coexistence of five major PRRSV-2 lineages in China in 2024–2025, including lineages 1.5, 1.8, 3, 5, and 8.7, with lineage 1.8 (NADC30-like) becoming the dominant circulating strain (accounting for 48.5% of positive samples).
• Guangdong (southern core) and Henan (central hub) are the "spreading origins" of the two dominant lineages, 1.8 and 1.5. The virus radiated from these two regions to surrounding provinces to the north and south, with Hubei, Shanxi, and Jiangsu becoming new clusters.
• The ORF2-ORF3 region was identified as a recombination hotspot, with frequent recombination between vaccine strains and wild-type strains.
• Based on MDS genetic distance analysis, the current vaccine strain shows significant antigenic differences from the main circulating lineages (1.8 and 3), suggesting a potential decrease in vaccine protective efficacy.
• Lineage 5 saw a 106.6% increase in nucleotide diversity within one year, indicating a significantly accelerated evolutionary rate.
Studies show that five major PRRSV-II lineages are simultaneously circulating in Chinese fields in 2024-2025, with lineage 1.8 (NADC30-like) accounting for nearly half, exhibiting significant antigenic differences from vaccine strains. The virus has formed a north-south transmission hub in Guangdong and Henan provinces, with high-frequency recombination in the ORF2-ORF3 regions. Lineage 5 showed a doubling of genetic diversity within one year, indicating new challenges to the protective efficacy of current vaccines.
Introduction
PRRSV, one of the most destructive viruses in the global swine industry, has been prevalent in China for nearly 30 years. In recent years, with the accelerated reconstruction of the industry after African swine fever, the issues of PRRSV lineage diversification, cross-regional transmission, and vaccine-related recombination have become increasingly prominent. However, systematic studies targeting this critical phase of 2024-2025 remain lacking.
Research Results
1. Five lineages coexist, with lineage 1.8 being dominant:
The study categorized the currently circulating PRRSV-2 into five lineages: 1.5 (NADC34-like), 1.8 (NADC30-like), 3, 5, and 8.7. Lineage 1.8 accounted for 48.5% of positive samples, making it the absolutely dominant strain and the most widely distributed; lineage 1.5 accounted for 23.2%, second only to 1.8 in terms of prevalence. Lineages 3, 5, and 8.7 exhibited regionally limited distributions.
Figure 1. Sample collection and phylogenetic analysis.
(a) The size of the circles in each province represents the number of samples, and different colors represent different lineages. (b) Maximum likelihood (ML) phylogenetic tree of the type II genotype of Chinese porcine reproductive and respiratory syndrome virus (PRRSV). Red circles represent sequences obtained in this study, and blue asterisks represent obtained whole genome sequences.
2. Guangdong and Henan as "virus exchange centers":
Spatiotemporal transmission dynamics analysis clearly identifies Guangdong and Henan as "virus exchange centers" for type II PRRSV, serving as key transmission nodes connecting the north and south. The dominant strain, lineage 1.8, first spread extensively in these two regions and subsequently continued to spread to neighboring provinces such as Hunan, Hubei, Jiangsu, and Shaanxi; lineage 1.5, centered in Henan, radiated to central and northern provinces such as Shanxi, Hebei, and Zhejiang. Leveraging their cross-regional virus circulation advantages, these two regions formed a clustered transmission network covering the north and south, further promoting genetic exchange and diffusion between different lineages. Their pivotal role was also validated by both sample proportion (ranking among the top five) and transmission path tracing.
Figure 2. Transmission Analysis.
(a1, b1, c1, d1): Phylogenetic tree constructed using Nextstrain software with maximum likelihood estimation based on ORF5. Different regions on the branches are marked with different colors. (a2, b2, c2, d2): Phylogenetic reconstruction of PRRSV ORF5. The size of the circle represents the number of samples, and the color corresponds to the ancestor node.
3. Significant Antigenic Differences, Challenging Vaccine Efficacy:
Multidimensional scaling analysis revealed that the dominant strain 1.8 (48.5%) and the 3 strain (high antigenic diversity) in the current prevalent PRRSV lineages are significantly separated from commonly used vaccine strains such as JXA1, CH-1R, and VR2332 in antigenic space. Conversely, the 5 and 8.7 lineages show high antigenic similarity to vaccine strains. This antigenic divergence suggests that existing vaccines may not provide complete protection against the two major prevalent lineages, 1.8 and 3, posing a challenge to disease control. This conclusion requires further verification through subsequent serological trials.
Figure 3. MDS cluster analysis of vaccine strains, prototype strains, and field samples.
4. Accelerated evolution and a surge in genetic diversity in lineage 5:
Type II PRRSV lineage 5 exhibits significant evolutionary characteristics, with a 106.6% surge in nucleotide diversity within one year, indicating a rapid increase in genetic diversity. Its Tajima's D test shows a significantly negative value, suggesting that this lineage may be undergoing rapid population expansion or directional selection, with a significantly accelerated evolutionary rate. Close monitoring of its epidemic status and variation trends is necessary.
Figure 4. Recombination analysis.
(a) Recombination analysis of strain R24121302heyuan241213. Different colors represent different strains; a red asterisk indicates R24121302heyuan241213.
(b) Recombination analysis of strain P24110708wuhan241107. Different colors represent different strains; a red asterisk indicates P24110708wuhan241107.
(c) Recombination analysis of strain P25012805heyuan250128. Different colors represent different strains; a red asterisk indicates P25012805heyuan250128.
Figure 5. Genetic diversity analysis of the ORF5 gene of type II porcine reproductive and respiratory syndrome virus in five major lineages in China (2024-2025).
(a) Haplotype diversity (Hd) analysis of lineages 1.5, 1.8, 3, 5, and 8.7. (b) Nucleotide diversity (Pi) analysis. (c) Tajima's D test results; well numbers and asterisks indicate statistical significance (p < 0.05).
Summary
This study fills a gap in the 2024-2025 PRRSV type II epidemiological data in China, and for the first time systematically reveals the recombination characteristics and antigenic variation patterns of dominant strains. The study confirms that PRRSV type II has entered a new stage of "recombination-driven variation," posing a serious challenge to the traditional single-strain-based vaccine control system.
The research findings not only provide a scientific basis for developing targeted surveillance programs but also point the way for the development of novel broad-spectrum vaccines—future vaccines should focus on covering key antigenic epitopes of L1C sublineage recombinant strains, while strengthening sequence design for recombination hotspot regions. Furthermore, the lineage classification and variation monitoring methods established in this study can provide a reference paradigm for global PRRSV epidemiological research.
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