Circovirus infections have been documented in adult and nestling canaries but the distribution of the virus in the world is not yet known. In captive canary flocks, circovirus infections have been reported based on the clinical observations. In this study the presence of both canary circovirus (CaCV) and Chicken anemia virus (CAV) in canary flocks were investigated. Virus strains were detected by polymerase chain reaction (PCR) and direct sequencing of amplified products. Nucleotide sequences were aligned and compared with existing data in gene bank. PCR identified CaCV-positive birds giving an overall positivity rate of 25 % but all samples were negative for CAV. According to the sequencing data three distinct strains were identified.
Our results indicated a relationship between genetic variation in replicase gene (rep) and the geographical regions, as well as the feasibility use of rep gene for virus detection and molecular epidemiology investigations. We are reporting detection and characterization of Canary circovirus based on the replicase (REP) gene. Sequencing results and sequence identity analysis revealed that replicase gene could be used for detecting and discriminating the members of family Circoviridae. This manuscript is the first report of canary circovirus in Iran and three new strains in the world.