Porcine reproductive and respiratory syndrome virus (PRRSV) is a significant pathogen causing substantial financial losses in the global swine industry. The prevention of PRRSV is hampered due to frequent gene recombination among different strains of PRRSV. In this study, a new PRRSV strain, PRRSV-HQ-2020, was identified from nursery piglets in Yunnan Province, China, in 2020. The complete genome analysis revealed that PRRSV-HQ-2020 is highly similar to JXA1-like (lineage 8.7 PRRSV, isolated from China in 2008) in the 5′UTR, nsp1–9, and nsp11 coding regions. Additionally, it has a resemblance to JM (lineage 3 PRRSV, isolated from Taiwan, China, in 2010) in the nsp12-M coding region and NADC30 (lineage 1.8 PRRSV, isolated from North American in 2008) in the nsp10, N, and 3′UTR, suggesting a natural recombination event. Furthermore, recombination analyses showed three interlineage recombination events among lineages 8.7, 1.8, and 3. Notably, the GP5 protein of PRRSV-HQ-2020 exhibited a crucial mutation at position 44, leading to the deletion of a key glycosylation site. These findings provide direct evidence for the natural occurrence of recombination events among three lineages of PRRSV-2 in Chinese swine herds, leading to the emergence of unique genetic properties of PRRSV variants, and providing a theoretical basis for developing better PRRSV prevention strategies.

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