title: Genetic diversity and genotype analysis of duck circovirus.
abstract: To investigate the genetic diversity and genotype of duck circovirus (DuCV), nine full-length DuCV genomes were determined from clinical samples. Multiple sequence alignment and phylogenetic analyses were performed on the nine viral genome sequences as well as on 27 genome sequences retrieved from the GenBank database. Pairwise analysis showed that the determined genome sequences have a genome organization identical to the 27 sequences and share 83.3%-99.8% identity among themselves and 82.6%-99.9% with the other 27 sequences. Phylogenetic analysis revealed that all 36 viral genome sequences are divided into two lineages, DuCV1 and DuCV2, in which the nucleotide diversity between genome sequences in these two lineages ranged from 13.2%-17.4%; these may be regarded as two types of viruses. Viruses under DuCV1 and DuCV2 are further clustered into different sublineages. When analyzed using the method for genotype definition proposed by Grau-Roma et al, these different sublineages can be defined as genotypes DuCV1a, DuCV1b, DuCV2a, DuCV2b, and DuCV2c. In addition, the viral sequences obtained from mainland China are different in genomic size and share a diversity of no less than 13.2%, including the sequences that came from all genotypes. This suggests that the DuCVs prevalent in domestic duck flocks in China are ecologically divergent.
authors.affiliation: Institution of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350013, People's Republic of China.
authors.forename: Guanghua
authors.initials: G
authors.lastname: Fu
authors.forename: Shaohua
authors.initials: S
authors.lastname: Shi
authors.forename: Yu
authors.initials: Y
authors.lastname: Huang
authors.forename: Longfei
authors.initials: L
authors.lastname: Cheng
authors.forename: Chunxiang
authors.initials: C
authors.lastname: Peng
authors.forename: Chunhe
authors.initials: C
authors.lastname: Wan
authors.forename: Hongmei
authors.initials: H
authors.lastname: Chen
authors.forename: Fang
authors.initials: F
authors.lastname: Lin
authors.forename: Jiansheng
authors.initials: J
authors.lastname: Lin
mesh_terms: D000595:Amino Acid Sequence; D019943:Amino Acid Substitution; D000818:Animals; D018173:Circoviridae Infections / Q000662:veterinary* / Q000821:virology; D017925:Circovirus / Q000145:classification* / Q000235:genetics*; D004372:Ducks; D014644:Genetic Variation; D016679:Genome, Viral; D005838:Genotype; D010802:Phylogeny; D011201:Poultry Diseases / Q000821:virology*; D014764:Viral Proteins / Q000235:genetics / Q000378:metabolism
chemical_list: D014764:Viral Proteins