Objective  The study was carried out to investigate the prevalence of porcine circovirus Type 2 (PCV2) in pigs and cattle in Yunnan Province, and to identify the genetic variation and molecular evolution trend of PCV2 strains in Yunnan Province.

Method  PCR method was used to detect the etiology of PCV2 in 783 blood and manure samples of pigs and cattle from 11 regions of Yunnan Province. The whole genome amplification, cloning and sequencing of 6 PCV2 positive samples were carried out. The whole gene and ORF2 amino acid sequences were compared and analyzed by DNAStar software, and the genetic evolution tree was drawn by MEGA software.

Result  The positive rate of PCV2 of detected samples was 48.73%. A total of 6 strain PCV2 genome sequences were measured, of which 5 strain were 1 767 bp and 1 strain was 1 768 bp. The genetic development analysis showed that there were 2 strains of PCV2a subtype, 2 strains of PCV2b subtype and 2 strains of PCV2d subtype. The homology of 6 strains PCV2 was 94.6%-99.9%, and the homology with 20 national reference strains in GenBank database was 91.4 %-99.8 %. The ORF2 of 6 strains PCV2 had their typical amino acid sites. The amino acid site of PCV2a strain was mutated to be consistent with PCV2 (b/d) at the 80th (V80L) amino acid site, and the amino acid site of PCV2b strain was mutated to be consistent with PCV2d at the 59th (R59K), 63rd (K63R), 190th (A190T) and other amino acid sites.

Conclusion  PCV2 commonly exists in pigs in Yunnan, and the three gene subtypes of PCV2a, PCV2b and PCV2d coexist, and PCV2 (a/b) has a tendency to mutate to PCV2d. Holstein cows have not been infected with PCV2.