Identification, genotyping, and molecular evolution analysis of duck circovirus.
Duck circovirus (DuCV) is a contagious immunosuppressive virus affecting many duck species, which is responsible for multiple outbreaks in poultry industries worldwide. In this study, the first DuCV isolate GH01 was identified in Sichuan by PCR, which shared a high level of nucleotide identity (81.8-99.4%) with sequences of other DuCV isolates available in GenBank. Comparative phylogenetic and pairwise sequence comparison analyses indicated that DuCV could be divided into two genotypes (DuCV-1 and DuCV-2) and six subtypes (1a, 1b, 1c, 2a, 2b and 2c) based on the complete genome sequence. The results revealed that both DuCV-1 and DuCV-2 had evolved from the same ancestor but undergone divergent evolution. Interestingly, phylogenetic analyses indicated that three isolates were classified into a cluster DuCV-2a using complete DuCV genome sequence and cap gene, except rep gene. Recombination analyses revealed that DuCV-2a arose from recombination between DuCV-1a and DuCV-2b isolates within the rep genes, and the recombination events mainly occur both in non-structural protein coding region and structural protein coding region. In addition, the mechanisms of recombination supporting the genetic variability in DuCV isolates were investigated. Likewise, selective pressure indicated that purifying selection had been a major driving force in maintaining diversity among the DuCV isolates. Because eradicating the virus from commercial ducks is impossible, it is necessary to take effective control measures and implement them throughout the world.
Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China; College of Veterinary Medicine, Sichuan Agricultural University, 46 Xinkang Road, Ya'an, Sichuan 625014, China. Electronic address: zhangzhilong0518@163.com.
Zhilong
Z
Zhang
Renyong
R
Jia
Yanyan
Y
Lu
Mingshu
M
Wang
Dekang
D
Zhu
Shun
S
Chen
Zhongqiong
Z
Yin
Xiaoyue
X
Chen
Anchun
A
Cheng
D000818:Animals; D017925:Circovirus / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D004372:Ducks / Q000821:virology*; D019143:Evolution, Molecular; D005814:Genes, Viral; D014644:Genetic Variation; D005838:Genotype; D010802:Phylogeny; D011995:Recombination, Genetic
DuCV; Duck circovirus; Evolution; Genotype; ML; MP; NJ; PASC; PCR; PRE; Phylogenetic; Recombination; Selective pressure; dN; dS; duck circovirus; maximum parsimony; maximum-likelihood; neighbor-joining; non-synonymous substitutions; nt; nucleotide; pairwise sequence comparison; polymerase chain reaction; potential recombination event; synonymous substitutions