Identification of chicken anemia virus putative intergenotype recombinants

Chicken anemia virus (CAV), the only member of the genus Gyrovirus in the family Circoviridae is the pathogen of chicken infectious anemia. It is unknown whether homologous recombination happens between CAV strains. In order to gain insight into this matter, we have performed a phylogenetic analysis of full-length CAV strains isolated to detect possible recombination events. Two putative recombinants, SD24, SD22 and the putative parental-like strains were identified with the use of SimPlot program. The two mosaic CAV consist of a novel genotype in the phylogenetic tree. It suggests that homologous recombinant plays roles in generating genetic diversity in natural populations of CAV.