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

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 endan...

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Autores principales:	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
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2014
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/84100c9fc96f4468beaac55313304e1d
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spelling	oai:doaj.org-article:84100c9fc96f4468beaac55313304e1d2021-11-18T08:38:23ZMutability dynamics of an emergent single stranded DNA virus in a naïve host.1932-620310.1371/journal.pone.0085370https://doaj.org/article/84100c9fc96f4468beaac55313304e1d2014-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/24416396/?tool=EBIhttps://doaj.org/toc/1932-6203Quasispecies 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.Subir SarkerEdward I PattersonAndrew PetersG Barry BakerJade K ForwoodSeyed A GhorashiMark HoldsworthRupert BakerNeil MurrayShane R RaidalPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 9, Iss 1, p e85370 (2014)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q 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 Mutability dynamics of an emergent single stranded DNA virus in a naïve host.
description	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.
format	article
author	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
author_facet	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
author_sort	Subir Sarker
title	Mutability dynamics of an emergent single stranded DNA virus in a naïve host.
title_short	Mutability dynamics of an emergent single stranded DNA virus in a naïve host.
title_full	Mutability dynamics of an emergent single stranded DNA virus in a naïve host.
title_fullStr	Mutability dynamics of an emergent single stranded DNA virus in a naïve host.
title_full_unstemmed	Mutability dynamics of an emergent single stranded DNA virus in a naïve host.
title_sort	mutability dynamics of an emergent single stranded dna virus in a naïve host.
publisher	Public Library of Science (PLoS)
publishDate	2014
url	https://doaj.org/article/84100c9fc96f4468beaac55313304e1d
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Mutability dynamics of an emergent single stranded DNA virus in a naïve host.

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