Abstract: This study investigated the epidemiology, genomic characteristics, and genetic variability of porcine circovirus type 2 (PCV2) and type 3 (PCV3) across five large-scale sow farms in Hunan Province. From January 2022 to December 2024, a total of 9 760 tissue samples (including aborted fetuses, castration fluids, and umbilical cord blood) were collected from these farms. And one sample of lung tissue was from a pig that died of suspected circovirus infection. Real-time quantitative PCR (qPCR) was employed to detect PCV2 and PCV3 infections. The results revealed: (1) The overall positive rates were 1.78% (174/9 760) for PCV2 and 27.88% (2 721/9 760) for PCV3, with a co-infection rate of 0.67% (65/9 760). (2) Farm C exhibited the highest detection rates: 3.74% (30/802) for PCV2 and 52.62% (422/802) for PCV3. (3) Among sample types, castration fluids showed the highest positive rates: 2.07% (139/6 701) for PCV2 and 34.73% (2 327/6 701) for PCV3. Through PCR amplification and sequencing, one complete PCV3 genome was assembled from a PCR-positive lung samples. Phylogenetic analysis classified this strain as PCV3a, a predominant sub type in the region. Monitoring findings PCV3 demonstrated higher significantly prevalence than PCV2 in the surveyed farms, a PCV3 isolated strain was sequenced and genotyped as PCV3a. These findings provided critical insights for PCV3 surveillance and control strategies in large-scale pig farms.

Key words: PCV2, PCV3, qRT-PCR, whole genome amplification, genetic evolution analysis