title: The phylogenetic and recombinational analysis of beak and feather disease virus Taiwan isolates.
abstract: Beak and feather disease virus (BFDV) is an avian circovirus, and it has a single-stranded DNA genome. It causes a fatal disease in parrots called psittacine beak and feather disease (PBFD). After screening of samples collected from Taiwan using PCR, complete genome sequences of isolates from 21 samples from various species of parrot were obtained. The nucleotide sequences of the replication-associated protein gene (rep) and the amino acid sequences of the replication-associated protein (Rep) were more conserved than the nucleotide sequences of the capsid protein gene (cp) and the amino acid sequences of the capsid protein (CP). In Bayesian phylogenetic analysis, the topology of the complete genome sequence was similar to that of the rep gene alone. Recombination events were identified in Taiwan isolates. Recombination hot spots were mainly located in the intergenic region between the 3' ends of the rep and cp genes and at the 5' end of the cp gene. The 5' end and the middle of the rep gene were found to be recombination cold spots. Despite the overall negative selection that was observed for the rep and cp genes, one and 18 positive selected sites were found for the rep and cp gene, respectively.
authors.affiliation: Department of Veterinary Medicine, College of Veterinary Medicine, National Chung Hsing University, 250 Kuo Kuang Road, Taichung, 40227, Taiwan.
authors.forename: Shr-Wei
authors.initials: SW
authors.lastname: Huang
authors.affiliation: Department of Biological Sciences, National Sun Yat-Sen University, 70 Lienhai Road, Kaohsiung, 80424, Taiwan.
authors.forename: Yu-Chung
authors.initials: YC
authors.lastname: Chiang
authors.affiliation: Department of Veterinary Medicine, College of Veterinary Medicine, National Chung Hsing University, 250 Kuo Kuang Road, Taichung, 40227, Taiwan.
authors.forename: Chien-Yu
authors.initials: CY
authors.lastname: Chin
authors.affiliation: Department of Animal Sciences, National Chung Hsing University, 250 Kuo Kuang Road, Taichung, 40227, Taiwan.
authors.forename: Pin-Chi
authors.initials: PC
authors.lastname: Tang
authors.affiliation: Department of Veterinary Medicine, College of Veterinary Medicine, National Chung Hsing University, 250 Kuo Kuang Road, Taichung, 40227, Taiwan.
authors.forename: Pan-Chen
authors.initials: PC
authors.lastname: Liu
authors.affiliation: Department of Veterinary Medicine, College of Veterinary Medicine, National Chung Hsing University, 250 Kuo Kuang Road, Taichung, 40227, Taiwan. cyoungwang@dragon.nchu.edu.tw.
authors.forename: Chi-Young
authors.initials: CY
authors.lastname: Wang
mesh_terms: D000818:Animals; D001715:Bird Diseases / Q000821:virology*; D036022:Capsid Proteins / Q000235:genetics; D018173:Circoviridae Infections / Q000662:veterinary* / Q000821:virology; D017925:Circovirus / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D004265:DNA Helicases / Q000235:genetics; D004279:DNA, Viral / Q000737:chemistry / Q000235:genetics; D016679:Genome, Viral; D010311:Parrots; D010802:Phylogeny; D011995:Recombination, Genetic; D017422:Sequence Analysis, DNA; D013624:Taiwan; D015534:Trans-Activators / Q000235:genetics
chemical_list: D036022:Capsid Proteins; D004279:DNA, Viral; D015534:Trans-Activators; C045264:replication initiator protein; D004265:DNA Helicases