Efficient and unbiased metagenomic recovery of RNA virus genomes from human plasma samples

Abstract RNA viruses cause significant human pathology and are responsible for the majority of emerging zoonoses. Mainstream diagnostic assays are challenged by their intrinsic diversity, leading to false negatives and incomplete characterisation. New sequencing techniques are expanding our ability...

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Autores principales:	Carmen F. Manso, David F. Bibby, Jean L. Mbisa
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2017
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/fb41f3d700174360bc9925d1f2619c98
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spelling	oai:doaj.org-article:fb41f3d700174360bc9925d1f2619c982021-12-02T11:40:21ZEfficient and unbiased metagenomic recovery of RNA virus genomes from human plasma samples10.1038/s41598-017-02239-52045-2322https://doaj.org/article/fb41f3d700174360bc9925d1f2619c982017-06-01T00:00:00Zhttps://doi.org/10.1038/s41598-017-02239-5https://doaj.org/toc/2045-2322Abstract RNA viruses cause significant human pathology and are responsible for the majority of emerging zoonoses. Mainstream diagnostic assays are challenged by their intrinsic diversity, leading to false negatives and incomplete characterisation. New sequencing techniques are expanding our ability to agnostically interrogate nucleic acids within diverse sample types, but in the clinical setting are limited by overwhelming host material and ultra-low target frequency. Through selective host RNA depletion and compensatory protocol adjustments for ultra-low RNA inputs, we are able to detect three major blood-borne RNA viruses – HIV, HCV and HEV. We recovered complete genomes and up to 43% of the genome from samples with viral loads of 104 and 103 IU/ml respectively. Additionally, we demonstrated the utility of this method in detecting and characterising members of diverse RNA virus families within a human plasma background, some present at very low levels. By applying this method to a patient sample series, we have simultaneously determined the full genome of both a novel subtype of HCV genotype 6, and a co-infecting human pegivirus. This method builds upon earlier RNA metagenomic techniques and can play an important role in the surveillance and diagnostics of blood-borne viruses.Carmen F. MansoDavid F. BibbyJean L. MbisaNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 7, Iss 1, Pp 1-13 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Carmen F. Manso David F. Bibby Jean L. Mbisa Efficient and unbiased metagenomic recovery of RNA virus genomes from human plasma samples
description	Abstract RNA viruses cause significant human pathology and are responsible for the majority of emerging zoonoses. Mainstream diagnostic assays are challenged by their intrinsic diversity, leading to false negatives and incomplete characterisation. New sequencing techniques are expanding our ability to agnostically interrogate nucleic acids within diverse sample types, but in the clinical setting are limited by overwhelming host material and ultra-low target frequency. Through selective host RNA depletion and compensatory protocol adjustments for ultra-low RNA inputs, we are able to detect three major blood-borne RNA viruses – HIV, HCV and HEV. We recovered complete genomes and up to 43% of the genome from samples with viral loads of 104 and 103 IU/ml respectively. Additionally, we demonstrated the utility of this method in detecting and characterising members of diverse RNA virus families within a human plasma background, some present at very low levels. By applying this method to a patient sample series, we have simultaneously determined the full genome of both a novel subtype of HCV genotype 6, and a co-infecting human pegivirus. This method builds upon earlier RNA metagenomic techniques and can play an important role in the surveillance and diagnostics of blood-borne viruses.
format	article
author	Carmen F. Manso David F. Bibby Jean L. Mbisa
author_facet	Carmen F. Manso David F. Bibby Jean L. Mbisa
author_sort	Carmen F. Manso
title	Efficient and unbiased metagenomic recovery of RNA virus genomes from human plasma samples
title_short	Efficient and unbiased metagenomic recovery of RNA virus genomes from human plasma samples
title_full	Efficient and unbiased metagenomic recovery of RNA virus genomes from human plasma samples
title_fullStr	Efficient and unbiased metagenomic recovery of RNA virus genomes from human plasma samples
title_full_unstemmed	Efficient and unbiased metagenomic recovery of RNA virus genomes from human plasma samples
title_sort	efficient and unbiased metagenomic recovery of rna virus genomes from human plasma samples
publisher	Nature Portfolio
publishDate	2017
url	https://doaj.org/article/fb41f3d700174360bc9925d1f2619c98
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_version_	1718395681162395648

Efficient and unbiased metagenomic recovery of RNA virus genomes from human plasma samples

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