title: Mutability dynamics of an emergent single stranded DNA virus in a naïve host.
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 (3.41×10(-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.
authors.affiliation: School of Animal and Veterinary Sciences, Charles Sturt University, Wagga Wagga, New South Wales, Australia ; Graham Centre for Agricultural Innovation (NSW Department of Primary Industries and Charles Sturt University), Wagga Wagga, New South Wales, Australia.
authors.forename: Subir
authors.initials: S
authors.lastname: Sarker
authors.affiliation: School of Animal and Veterinary Sciences, Charles Sturt University, Wagga Wagga, New South Wales, Australia ; Graham Centre for Agricultural Innovation (NSW Department of Primary Industries and Charles Sturt University), Wagga Wagga, New South Wales, Australia.
authors.forename: Edward I
authors.initials: EI
authors.lastname: Patterson
authors.affiliation: School of Animal and Veterinary Sciences, Charles Sturt University, Wagga Wagga, New South Wales, Australia ; Graham Centre for Agricultural Innovation (NSW Department of Primary Industries and Charles Sturt University), Wagga Wagga, New South Wales, Australia.
authors.forename: Andrew
authors.initials: A
authors.lastname: Peters
authors.affiliation: Institute of Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania, Australia.
authors.forename: G Barry
authors.initials: GB
authors.lastname: Baker
authors.affiliation: School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, New South Wales, Australia ; Graham Centre for Agricultural Innovation (NSW Department of Primary Industries and Charles Sturt University), Wagga Wagga, New South Wales, Australia.
authors.forename: Jade K
authors.initials: JK
authors.lastname: Forwood
authors.affiliation: School of Animal and Veterinary Sciences, Charles Sturt University, Wagga Wagga, New South Wales, Australia ; Graham Centre for Agricultural Innovation (NSW Department of Primary Industries and Charles Sturt University), Wagga Wagga, New South Wales, Australia.
authors.forename: Seyed A
authors.initials: SA
authors.lastname: Ghorashi
authors.affiliation: Biodiversity Conservation Branch, Department of Primary Industries, Parks, Water and Environment, Hobart, Tasmania, Australia.
authors.forename: Mark
authors.initials: M
authors.lastname: Holdsworth
authors.affiliation: Healesville Sanctuary, Zoos Victoria, Healesville, Victoria, Australia.
authors.forename: Rupert
authors.initials: R
authors.lastname: Baker
authors.affiliation: Department of Genetics, La Trobe University, Bundoora, Victoria, Australia.
authors.forename: Neil
authors.initials: N
authors.lastname: Murray
authors.affiliation: School of Animal and Veterinary Sciences, Charles Sturt University, Wagga Wagga, New South Wales, Australia ; Graham Centre for Agricultural Innovation (NSW Department of Primary Industries and Charles Sturt University), Wagga Wagga, New South Wales, Australia.
authors.forename: Shane R
authors.initials: SR
authors.lastname: Raidal
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D036022:Capsid Proteins / Q000235:genetics; D018173:Circoviridae Infections / Q000635:transmission / Q000662:veterinary* / Q000821:virology; D017925:Circovirus / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D004277:DNA, Single-Stranded / Q000145:classification / Q000235:genetics*; D004279:DNA, Viral / Q000145:classification / Q000235:genetics*; D019143:Evolution, Molecular; D014644:Genetic Variation; D016679:Genome, Viral; D008969:Molecular Sequence Data; D059645:Mutation Rate; D009690:Nucleic Acid Conformation; D010311:Parrots / Q000821:virology*; D010802:Phylogeny; D011995:Recombination, Genetic; D016415:Sequence Alignment; D014779:Virus Replication
chemical_list: D036022:Capsid Proteins; D004277:DNA, Single-Stranded; D004279:DNA, Viral