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Specific Capture and Whole-Genome Sequencing of Viruses from Clinical Samples

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Title: Specific Capture and Whole-Genome Sequencing of Viruses from Clinical Samples
Authors: Depledge, DP
Palser, AL
Watson, SJ
Lai, IY-C
Gray, ER
Grant, P
Kanda, RK
Leproust, E
Kellam, P
Breuer, J
Item Type: Journal Article
Abstract: Whole genome sequencing of viruses directly from clinical samples is integral for understanding the genetics of host-virus interactions. Here, we report the use of sample sparing target enrichment (by hybridisation) for viral nucleic acid separation and deep-sequencing of herpesvirus genomes directly from a range of clinical samples including saliva, blood, virus vesicles, cerebrospinal fluid, and tumour cell lines. We demonstrate the effectiveness of the method by deep-sequencing 13 highly cell-associated human herpesvirus genomes and generating full length genome alignments at high read depth. Moreover, we show the specificity of the method enables the study of viral population structures and their diversity within a range of clinical samples types.
Issue Date: 18-Nov-2011
Date of Acceptance: 25-Oct-2011
URI: http://hdl.handle.net/10044/1/62232
DOI: https://dx.doi.org/10.1371/journal.pone.0027805
ISSN: 1932-6203
Publisher: PUBLIC LIBRARY OF SCIENCE
Journal / Book Title: PLOS ONE
Volume: 6
Issue: 11
Copyright Statement: © 2011 Depledge et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Keywords: Science & Technology
Multidisciplinary Sciences
Science & Technology - Other Topics
VARICELLA-ZOSTER-VIRUS
EPSTEIN-BARR-VIRUS
COMPLETE DNA-SEQUENCES
VACCINE
IDENTIFICATION
CARCINOMA
GENOTYPES
RECOMBINATION
AMPLIFICATION
VARIABILITY
Cell Line, Tumor
DNA, Viral
Genome, Viral
Herpesviridae
Herpesviridae Infections
Herpesvirus 3, Human
Herpesvirus 4, Human
Herpesvirus 8, Human
Humans
Mutation
Polymerase Chain Reaction
Reproducibility of Results
Saliva
Sequence Analysis, DNA
Species Specificity
MD Multidisciplinary
General Science & Technology
Publication Status: Published
Article Number: ARTN e27805
Online Publication Date: 2011-11-18
Appears in Collections:Department of Medicine
Faculty of Medicine



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