Molecular Surveillance and Evolutionary Dynamics of Porcine Circovirus Types 2 and 3 in China, 2022-2025

Porcine circovirus types 2 (PCV2) and 3 (PCV3) are globally distributed pathogens associated with reproductive disorders, subclinical infections, and multifactorial disease complexes in swine. To elucidate their epidemiological and evolutionary patterns in China, we examined 8426 clinical samples collected from 28 provincial-level regions between 2022 and 2025. PCV2 showed substantially higher prevalence than PCV3 across production stages and clinical categories and exhibited pronounced seasonal peaks in autumn. PCV2 was most frequently detected in tissue samples and presented high viral loads in systemic wasting and enteric cases, whereas PCV3 occurred at lower viral loads and was predominantly identified in swabs, semen, and milk. A total of 181 PCV2 and 106 PCV3 ORF2 sequences were obtained for genetic analysis. PCV2d was confirmed as the overwhelmingly dominant genotype nationwide, while PCV3c predominated among circulating PCV3 lineages alongside coexisting PCV3a and PCV3b clusters. Selection pressure analyses indicated that both viruses were largely shaped by purifying selection, although PCV2 harbored a greater number of positively selected sites located in surface-exposed regions of the Cap protein. Phylodynamic inference revealed long-term stability in the effective population size of PCV2, whereas PCV3 experienced a recent expansion followed by stabilization. Spatial phylogeographic reconstruction demonstrated a centralized diffusion pattern for PCV2, with Hebei serving as a major transmission hub, in contrast to the multicentered and geographically admixed spread of PCV3. Collectively, these findings indicate that PCV2 remains the primary pathogenic burden in Chinese swine herds. In contrast, the more diffuse dissemination of PCV3 from multiple sources warrants sustained molecular monitoring, particularly in breeding populations.