Duck Circovirus in Northern Vietnam: Genetic Characterization of the Complete Genome and Epidemiological Analysis of the Causative Agent

Abstract In the present study, tissue samples collected from a total of 130 commercial ducks collected from clinically suspected flocks and diseased birds in six provinces of northern Vietnam were tested for DuCV infection. The DuCV genome was detected in 56 out of 130 (43.08%) duck samples by PCR. Of 38 tested farms, 26 (68.42%) were positive for the DuCV genome. The rate of the DuCV genome detection in ducks at 3–4 (54.17%) is significantly higher (p<0.05) than that of <3 (32.43%) and >7 (33.33%), insignificantly higher than that of 5–7 (43.33%) (p=0.11) weeks of age. Length of the six Vietnamese DuCV genomes obtained ranged from 1,988 to 1,995 nucleotides. Among the six Vietnamese DuCV genomes, nucleotide identities were from 83.24% to 99.69%. Phylogenetic analysis of the complete genomes indicated that the DuCVs circulating in northern Vietnam were divided into two main genotypes I and II, and several subgenotypes. The Vietnamese DuCVs were closely related to the Chinese, Taiwanese, and Korean strains. One positive selection site of capsid protein was detected.