Recurrent positive selection and heterogeneous codon usage bias events leading to coexistence of divergent pigeon circoviruses.
The capsid genes from 14 pigeon circovirus (PiCV) sequences, collected from Taiwan between 2009 and 2010, were sequenced and compared with 14 PiCV capsid gene sequences from GenBank. Based on pairwise comparison, PiCV strains from Taiwan shared 73.9-100% nucleotide identity and 72-100% amino acid identity with those of the 14 reported PiCV sequences. Phylogenetic analyses revealed that Taiwanese PiCV isolates can be grouped into two clades: clade 1 comprising isolates from Belgium, Australia, USA, Italy and China, and clade 2 showing close relation to isolates from Germany and France. Recurrent positive selection was detected in clade 1 PiCV lineages, which may contribute to the diversification of predominant PiCV sequences in Taiwan. Further observations suggest that synonymous codon usage variations between PiCV clade 1 and clade 2 may reflect the adaptive divergence on translation efficiency of capsid genes in infectious hosts. Variation in selective pressures acting on the evolutionary divergence and codon usage bias of both clades explains the regional coexistence of virus sequences congeners prevented from competitive exclusion within an island such as Taiwan. Our genotyping results also provide insight into the aetiological agents of PiCV outbreak in Taiwan and we present a comparative analysis of the central coding region of PiCV genome. From the sequence comparison results of 28 PiCVs which differs in regard to the geographical origin and columbid species, we identified conserved regions within the capsid gene that are likely to be suitable for primer selection and vaccine development.
Department of Life Science, National Taiwan Normal University, Taipei 11677, Taiwan, ROC.
Pei-Chun
PC
Liao
Graduate Institute of Animal Vaccine Technology, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung 91201, Taiwan, ROC.
Kung-Kai
KK
Wang
Department of Veterinary Medicine, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung 91201, Taiwan, ROC.
Shinn-Shyong
SS
Tsai
Institute of Molecular Biology, National Chung Hsing University, 40227 Taichung, Taiwan, ROC.
Hung-Jen
HJ
Liu
Department of Life Science, National Taiwan Normal University, Taipei 11677, Taiwan, ROC.
Bing-Hong
BH
Huang
Animal Biologics Pilot Production Center, National Pingtung University of Science and Technology, Pingtung 91201, Taiwan, ROC.|Graduate Institute of Animal Vaccine Technology, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung 91201, Taiwan, ROC.
Kuo-Pin
KP
Chuang
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; D003062:Codon; D010856:Columbidae / Q000821:virology*; D019143:Evolution, Molecular; D016679:Genome, Viral; D005838:Genotype; D008969:Molecular Sequence Data; D016366:Open Reading Frames; D010802:Phylogeny
D036022:Capsid Proteins; D003062:Codon