International Journal of Molecular Veterinary Research, 2025, Vol.15, No.1, 32-42 http://animalscipublisher.com/index.php/ijmvr 38 are most prevalent. They have high polymorphism in immune epitopes and seasonal variation in prevalence. Globally, sequential domination and displacement of lineages are shaped by immune-mediated selection, and fresh sub-lineages emerge every 1-4 years. The same pattern occurs in the United States, with lineage 1 replacing lineage 9 as the most prevalent form, which demonstrates ongoing diversification and immune-driven selection pressures (Paploski et al., 2019; Yuan et al., 2025). 6.2 Mechanisms underlying recombination and emergence of highly pathogenic strains Recombination is one of the major driving forces of PRRSV, occurring within and across lineages, and even between wild-type and vaccine viruses. Recombination hotspots are found in nonstructural protein (e.g., NSP1, NSP2, NSP9) and structural protein genes (e.g., ORF2-ORF6, GP2-GP6). Recombination may generate new variants with greater virulence, immune evasion, and altered tissue tropism. Interestingly, recombination after the administration of modified live vaccine (MLV) has caused virulence reversion in some cases. It is believed that these recombination processes are mediated by the copy-choice mechanism of RNA replication, but more mechanistic research is needed (Guo et al., 2021; Cui et al., 2024; Yang et al., 2024). 6.3 Phylogenetic analysis of regional PRRSV lineages Phylogenetic reconstruction on the basis of ORF5 and genomic information classified PRRSV-2 in China into four main lineages (1, 3, 5, 8) among which the sub-lineage 1.8 and 1.5 dominate currently. Regional studies reveal that certain sub-lineages, i.e., NADC30-like (1.8), show limited inter-provincial transmissions, while others, e.g., NADC34-like (1.5), possess increased cross-regional as well as international transmissibility. Longitudinal monitoring in the US has followed the rise and fall of different sub-lineages, with lineage fitness and immune escape triggered by positive selection and glycosylation evolution in GP5 and other proteins (Zhang et al., 2024; Yuan et al., 2025). 6.4 Applications of molecular epidemiology in prevention and control strategies Molecular epidemiology, founded upon high-throughput sequencing and phylogenetic analysis, underpins real-time surveillance, transmission chain tracking, and emerging variant detection. It informs targeted vaccination, biosecurity, and outbreak response. Recombination dynamics and genetic diversity analysis predict the emergence of highly pathogenic or immune-evading strains and guide vaccine and control measure updates. Ongoing genomic surveillance is critical for the early warning and effective containment of PRRSV at both local and international levels (Guo et al., 2021; Wu et al., 2024). 7 Research Challenges and Limitations 7.1 Unresolved key mechanisms in PRRSV pathogenesis While much advancement has been made in the area of the biology and pathogenicity mechanisms of PRRSV, certain fundamental aspects continue to be mysterious. The precise molecular processes of viral entry, replication, and persistence within host macrophages continue to be unclear. While receptors such as CD163 and Siglec-1 have been identified as being central to viral attachment and internalization, the allied signal transduction mechanisms for inducing immunosuppression and cell reprogramming still need to be more clearly defined. In addition, the processes by which PRRSV causes long-term persistence and tolerance of the immune system are not yet understood. The complex interactions between viral proteins and host immune components including pattern recognition receptors, cytokine networks, and apoptotic pathways are major hurdles in understanding the full complement of PRRSV pathogenesis (Yuan et al., 2025). 7.2 Standardization and sensitivity issues in molecular diagnostic technologies Despite increased development in molecular tests like qRT-PCR, RT-LAMP, and next-generation sequencing, there is significant heterogeneity among laboratories and detection systems. Lack of global harmonization regarding assay design, sample preparation, and result interpretation has given rise to heterogeneity in terms of detection sensitivity and specificity. Additionally, RNA degradation, genetic variability of field strains, and viral load variations during the course of infection also tend to compromise the accuracy of diagnosis. Creation of reference materials, standard operating procedures, and inter-laboratory quality control programs remains crucial
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