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Mutability dynamics of an emergent single stranded DNA Virus in a naïve host

Citation

Sarker, S and Patterson, EI and Peters, A and Baker, GB and Forwood, JK and Ghorashi, SA and Holdsworth, M and Baker, R and Murray, N and Raidal, SR, Mutability dynamics of an emergent single stranded DNA Virus in a naïve host, PLoS ONE, 9, (1) Article e85370. ISSN 1932-6203 (2014) [Refereed Article]


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Copyright Statement

Copyright 2014 The Authors-This is an open-access article distributed under the terms of the Creative Commons Attribution License, (CC BY 3.0 AU) which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

DOI: doi:10.1371/journal.pone.0085370

Abstract

Quasispecies variants and recombination were studied longitudinally in an emergent outbreak of beak and feather disease virus (BFDV) infection in the orange-bellied parrot (Neophema chrysogaster). Detailed health monitoring and the small population size (<300 individuals) of this critically endangered bird provided an opportunity to longitudinally track viral replication and mutation events occurring in a circular, single-stranded DNA virus over a period of four years within a novel bottleneck population. Optimized PCR was used with different combinations of primers, primer walking, direct amplicon sequencing and sequencing of cloned amplicons to analyze BFDV genome variants. Analysis of complete viral genomes (n = 16) and Rep gene sequences (n = 35) revealed that the outbreak was associated with mutations in functionally important regions of the normally conserved Rep gene and immunogenic capsid (Cap) gene with a high evolutionary rate (3.41 x 10-3 subs/site/year) approaching that for RNA viruses; simultaneously we observed significant evidence of recombination hotspots between two distinct progenitor genotypes within orange-bellied parrots indicating early cross-transmission of BFDV in the population. Multiple quasispecies variants were also demonstrated with at least 13 genotypic variants identified in four different individual birds, with one containing up to seven genetic variants. Preferential PCR amplification of variants was also detected. Our findings suggest that the high degree of genetic variation within the BFDV species as a whole is reflected in evolutionary dynamics within individually infected birds as quasispecies variation, particularly when BFDV jumps from one host species to another.

Item Details

Item Type:Refereed Article
Research Division:Biological Sciences
Research Group:Ecology
Research Field:Behavioural Ecology
Objective Division:Environment
Objective Group:Ecosystem Assessment and Management
Objective Field:Ecosystem Assessment and Management of Antarctic and Sub-Antarctic Environments
Author:Baker, GB (Dr Barry Baker)
ID Code:91557
Year Published:2014
Web of Science® Times Cited:21
Deposited By:IMAS Research and Education Centre
Deposited On:2014-05-21
Last Modified:2017-11-08
Downloads:179 View Download Statistics

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