Mutability Dynamics of an Emergent Single Stranded DNA Virus in a Naïve Host

• DOI: 10.1371/journal.pone.0085370
• Publication Date: 2014-01-08T17:13:17Z
• Authors: Subir Sarker; Edward I. Patterson; Andrew Peters; G. Barry Baker; Jade K. Forwood; Seyed A. Ghorashi; Mark Holdsworth; Rupert Baker; Neil Murray; Shane R. Raidal
• Keywords: Viral quasispecies; Amplicon

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