First Molecular Detection and Genetic Characterization of Porcine Circovirus 5 in Diagnostic Swine Samples from China

Porcine circovirus type 5 (PCV5) is a recently reported porcine-associated CRESS DNA virus, but information regarding its occurrence, genomic characteristics, and evolutionary relationship remains limited. In this study, a total of 100 diagnostic samples collected from clinically diseased pigs from 27 commercial swine farms in 16 cities across seven provinces of China during 2025 were screened for PCV5 using quantitative PCR. PCV5 was detected in 22% (22/100) of the tested samples, with positive samples identified in Henan and Fujian provinces among the sampled regions. PCV5-positive samples were mainly fecal samples and were obtained from pigs showing diarrhea, respiratory signs, wasting, or systemic disease. Co-detection analysis showed that most PCV5-positive samples were also positive for other swine viral pathogens, particularly PCV3, PCV2, and PEDV, indicating that the clinical significance of PCV5 should be interpreted cautiously. Complete genome amplification and sequencing yielded two identical PCV5 genomes from Henan and Fujian provinces. A representative strain, designated PCV5-Henan2025-ZJQ01, was further characterized and deposited in GenBank under accession number PZ496079. The complete genome was 2903 nt in length and contained a positive-sense ORF encoding Cap and a negative-sense ORF encoding Rep, showing a distinct genomic organization compared with classical porcine circoviruses. Phylogenetic analysis based on Rep and Cap amino acid sequences showed that PCV5-Henan2025-ZJQ01 was closely related to previously reported PCV5-related sequences but distinct from classical PCV1–PCV4. These findings provide additional molecular and genomic evidence for PCV5 in Chinese swine diagnostic samples and support the need for continued surveillance and further studies on its epidemiological and pathogenic significance.