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.
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Acknowledgments
This study was supported by grants from the National Science Council, Taiwan (NSC 102-2313-13-005-011 and MOST 103-2313-B-005-039). We thank Dr. Kirby for his editing of this manuscript.
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All authors declares no conflict of interest. This article does not contain any studies with human participants or animals that were performed by any of the authors.
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An erratum to this article can be found at http://dx.doi.org/10.1007/s00705-016-3006-5.
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705_2016_2963_MOESM1_ESM.xlsx
Supplementary material 1 (XLSX 34 kb) Supplemental Table 1 The breakpoint number at the aligned positions showing both 95% and 99% confidence intervals (95% and 99% CI)
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Huang, SW., Chiang, YC., Chin, CY. et al. The phylogenetic and recombinational analysis of beak and feather disease virus Taiwan isolates. Arch Virol 161, 2969–2988 (2016). https://doi.org/10.1007/s00705-016-2963-z
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DOI: https://doi.org/10.1007/s00705-016-2963-z