Molecular and pathological characteristics of co-infection with PRRSV-1 and PRRSV-2 recombinant strains in a pig farm in Xinjiang, China

This study aimed to conduct an integrated diagnosis of a severe Porcine Reproductive and Respiratory Syndrome (PRRS) outbreak occurring in China’s Xinjiang region in 2025, to elucidate its molecular characteristics, etiological complexity, and potential evolutionary risks. First, pathogen screening was performed via clinical investigation combined with subtype-specific fluorescent quantitative RT-PCR, and samples with lower cycle threshold (Ct) values were selected for high-throughput metatranscriptomic sequencing. Based on the obtained complete viral genome sequences, phylogenetic analysis, homology assessment, analysis of key amino acid variations, and recombination event analysis were further conducted. This was combined with histopathology (H&E staining) and immunohistochemical (IHC) staining targeting the PRRSV nucleocapsid protein to confirm infection and localize viral antigen at the pathological level. Molecular diagnostic results confirmed, for the first time, the co-infection of PRRSV-1 (European type) and PRRSV-2 (North American type) in this pig farm. Both complete viral genomes obtained (XJ/PRRSV1/2025 and XJ/PRRSV2/2025) exhibited recombinant genomic structures. Phylogenetic and recombination analysis indicated that XJ/PRRSV1/2025 belongs to PRRSV-1 subtype S1.3, with its major parental origin remaining unclear, while minor recombinant fragments were derived from BJEU06-1-like strains; XJ/PRRSV2/2025 clusters within sublineage 1.8 of lineage 1 and is a recombinant of NADC30-like and JXA1-like strains. Homology analysis revealed significant differences in nucleotide and amino acid sequence identities between the two strains and their respective reference strains in key genes such as ORF5. Characteristic amino acid substitutions were also detected within the neutralizing epitope region of the GP5 protein for both strains. Pathological examination confirmed diffuse interstitial pneumonia, and IHC results showed PRRSV antigen specifically distributed in alveolar macrophages and type II alveolar epithelial cells. This study systematically reports, for the first time, the molecular and pathological characteristics of co-infection with PRRSV-1 and PRRSV-2 recombinant genomes in swine populations in Northwest China. This discovery highlights the high-risk evolutionary mode of “mixed infection-dual recombination” in PRRSV epidemiology, marking a new stage of increased ecological complexity for PRRSV in China. It also poses significant challenges to the current PRRSV-2-centric strategies for diagnosis, vaccination, and surveillance.