Mutability dynamics of an emergent single stranded DNA virus in a naive host

Subir Sarker, Edward Patterson, Andrew Peters, G. Barry Baker, Jade Forwood, Seyed Ghorashi, Mark Holdsworth, Rupert Baker, Neil Murray, Shane Raidal

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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 (3.41Ã'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.
Original languageEnglish
Pages (from-to)1-11
Number of pages11
JournalPLoS One
Volume9
Issue number1
DOIs
Publication statusPublished - Jan 2014

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Beak and feather disease virus
ssDNA viruses
Circovirus
DNA Viruses
Single-Stranded DNA
Viruses
Parrots
Genes
Birds
Genetic Recombination
Disease Outbreaks
genome walking
mutation
Polymerase Chain Reaction
Mutation
capsid
genome
Viral Genome
Capsid
birds

Grant Number

  • FT120100242

Cite this

Sarker, Subir ; Patterson, Edward ; Peters, Andrew ; Baker, G. Barry ; Forwood, Jade ; Ghorashi, Seyed ; Holdsworth, Mark ; Baker, Rupert ; Murray, Neil ; Raidal, Shane. / Mutability dynamics of an emergent single stranded DNA virus in a naive host. In: PLoS One. 2014 ; Vol. 9, No. 1. pp. 1-11.
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Mutability dynamics of an emergent single stranded DNA virus in a naive host. / Sarker, Subir; Patterson, Edward; Peters, Andrew; Baker, G. Barry; Forwood, Jade; Ghorashi, Seyed; Holdsworth, Mark; Baker, Rupert; Murray, Neil; Raidal, Shane.

In: PLoS One, Vol. 9, No. 1, 01.2014, p. 1-11.

Research output: Contribution to journalArticle

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AU - Holdsworth, Mark

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AU - Murray, Neil

AU - Raidal, Shane

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