Abstract: [Objective] To understand the genome characteristics and variation of pigeon circovirus (PiCV) circulating in Beijing. [Method] Used the liver and spleen tissues of 3 diseased pigeons as templates, the pathogen was detected by PCR technology. Using the DNA of the positive liver tissue as a template, PCR technology was used to amplify the whole gene sequence of PiCV. DNAStar and Mega 7.0 softwares were used to splice and compare the nucleotide sequence of the amplified sequence, and construct evolutionary tree. The nucleotide sequence and amino acid sequence of the two open reading frames of the virus genome were compared, and the phylogenetic tree was constructed. [Result] The PCR test showed that PiCV positive was detected in the tissues of one of the three sick pigeons, but no other viruses were detected. The whole genome sequence of a PiCV strain was successfully obtained by PCR fragmented amplification, named PiCV BJ. The virus genome was 2 034 bp in size and contained 2 main open reading frames (ORFs), ORF-V1 encodes the Rep protein, ORF-C1 encodes the Cap protein. The similarity comparison results showed that the nucleotide similarity between the genome sequence of PiCV BJ strain and other reference sequences registered on GenBank was 86.0% to 97.0%, and the homology with PL53 isolated from Poland in 2011 was 97.0%. The genetic evolution results showed that the PiCV BJ strain was in the same branch as PL124 isolated from Poland in 2014, and was closely related;It was not in the same branch with other avian circoviruses, and was relatively distant. The start codon of Cap gene of PiCV BJ strain was ATG, which had 95.8% and 85.2% nucleotide and amino acid similarity with 11-08304 strain isolated from Belgium in 2011. The Rep gene had 94.6% and 96.2% nucleotide and amino acid similarity with PL53 isolated from Poland in 2011. The similarity of nucleotide and amino acid was 94.6% and 96.2%, respectively. The phylogenetic tree analysis of Cap and Rep genes also showed that PiCV BJ strains was in the same branch as PL53 and 11-08304, which was close to the results of similarity analysis. [Conclusion] PiCV BJ strain was from abroad and might be introduced into China by racing pigeons, which suggested that virus monitoring should be done well in external introduction. This study enriched the genetic research data of PiCV, provided a reference basis for further exploring the genetic variation and transmission mechanism of PiCV, and also provided an important theoretical basis for the prevention and control of PiCV.

Key words: Pigeon circovirus (PiCV); whole genome; phylogenetic analysis