Epidemiological and genetic variation analysis of emerging porcine circovirus type 3 in Henan Province, 2023–2024

BACKGROUND: Porcine circovirus type 3 (PCV3) is an emerging pathogen with high genetic variability, posing a continuous challenge to swine health and disease control. Ongoing viral evolution highlights the need for molecular surveillance to monitor circulating PCV3 strains. RESULTS: From 2023 to 2024, 257 blood and tissue samples from pigs with reproductive and respiratory disorders were collected in Henan Province, China. PCV3 was detected in 21.79% (56/257) of samples by quantitative real-time PCR (qPCR). Genetic characterization of 15 new PCV3 strains showed 98.95-99.95% nucleotide (nt) identity among themselves and 98.70-99.85% identity with global reference strains. Phylogenetic analysis of the ORF2 genes identified PCV3a-1, PCV3a-2, PCV3a-IM, PCV3b, and PCV3c subtypes, with PCV3b predominating. Notably, a genetically divergent strain, HN240609, clustered within the PCV3c subgroup. Additionally, multiple unique amino acid (aa) mutations were observed in the predicted T-cell and B-cell epitope regions of the capsid (Cap) protein (R10K, A35V, T102A, T102S, F104Y, T170A, and V180I). CONCLUSIONS: Genetically diverse PCV3 strains are co-circulating in Henan Province, and mutations in antigenic regions of the Cap protein may facilitate immune evasion. Continuous molecular surveillance is therefore essential for effective PCV3 prevention and control.