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Porcine reproductive and respiratory syndrome virus （PRRSV） remains a pathogen causing substantial economic losses to China’s swine industry. Porcine reproductive and respiratory syndrome virus type 2 （PRRSV-2） currently predominates in China， exhibiting a complex epidemiological pattern characterized by co-circulating multiple lineages， which significantly complicates disease control measures. This study aimed to evaluate the diagnostic potential of metatranscriptomic sequencing in discriminating PRRSV-2 mixed infections involving multiple lineages. A PRRSV-2-positive serum sample collected from a swine farm in Sichuan Province was subjected to metatranscriptomic sequencing. This approach successfully recovered complete viral genome sequences. Subsequent comprehensive analysis， including phylogenetic reconstruction （IQ-TREE）， similarity comparison （Megalign）， and recombination analysis （RDP4/SimPlot）， was employed to elucidate the evolutionary and recombination characteristics of the viruses. The results demonstrate the successful identification of three distinct PRRSV-2 strains from this single serum sample： SC01-2025 （15 023 bp）， SC02-2025 （14 954 bp）， and SC03-2025 （15 293 bp）—the phylogenetic classification assigned these strains to lineages 1.8， 3， and 8.7， respectively.SC01-2025 was identified as a recombinant between lineage 1.8 （NADC30） and lineage 5 （VR2332）. While its full genome shared 88.09% nucleotide similarity with the NADC30 strain， regions encompassing NSP3-7， NSP9-12， and ORF3 exhibited higher similarity to the VR2332 strain. SC02-2025 was found to be a triple-recombinant virus （lineages 1.8/3/8.7）. This strain displayed the highest similarity to the NADC30 strain within the NSP2 and NSP3 regions， to the JXA1 strain within NSP1 and NSP7-10 regions， and the QYYZ strain in the remaining genomic segments. SC03-2025 showed 99% full-genome nucleotide similarity to the JXA1-P80 vaccine strain， with no evidence of recombination detected. This study， leveraging metatranscriptomic sequencing， precisely identified a mixed infection involving multiple PRRSV-2 lineages within a single pig farm in Sichuan. It revealed the complex epidemiological scenario involving the concurrent presence of a vaccine strain （JXA1-P80） and field strains （NADC30-like and QYYZ-like viruses）. These findings demonstrate that metatranscriptomic sequencing provides high-resolution diagnostic support for PRRSV disease surveillance and monitoring.
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| 科 Family | 属数 Number of genus | 种数 Number of species | 占总种数比例 Percentage of total species (%) | 属 Genus | 种数 Number of species | 占总种数比例 Percentage of total species (%) |
|---|---|---|---|---|---|---|
| 鹅膏菌科Amanitaceae | 2 | 11 | 5.26 | 鹅膏菌属 Amanita | 10 | 4.78 |
| 小菇科 Mycenaceae | 2 | 12 | 5.74 | 丝盖伞属 Inocybe | 5 | 2.39 |
| 多孔菌科 Polyporaceae | 8 | 14 | 6.70 | 蜡蘑属 Laccaria | 5 | 2.39 |
| 红菇科 Russulaceae | 3 | 23 | 11.00 | 小皮伞属 Marasmius | 6 | 2.87 |
| 小菇属 Mycena | 11 | 5.26 | ||||
| 光柄菇属 Pluteus | 5 | 2.39 | ||||
| 红菇属 Russula | 17 | 8.13 | ||||
| 栓菌属 Trametes | 5 | 2.39 |
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