publication . Article . 2015

ve-SEQ: Robust, unbiased enrichment for streamlined detection and whole-genome sequencing of HCV and other highly diverse pathogens.

Paolo Piazza; Camilla L. C. Ip; Rory Bowden; Amy Trebes; David Bonsall; Paul Klenerman; Paul Klenerman; Anthony Brown; Eleanor Barnes; Eleanor Barnes; ...
Open Access English
  • Published: 13 Oct 2015 Journal: F1000Research, volume 4 (eissn: 2046-1402, Copyright policy)
  • Publisher: F1000Research
  • Country: United Kingdom
Abstract
<ns4:p>The routine availability of high-depth virus sequence data would allow the sensitive detection of resistance-associated variants that can jeopardize HIV or hepatitis C virus (HCV) treatment. We introduce ve-SEQ, a high-throughput method for sequence-specific enrichment and characterization of whole-virus genomes at up to 20% divergence from a reference sequence and 1,000-fold greater sensitivity than direct sequencing. The extreme genetic diversity of HCV led us to implement an algorithm for the efficient design of panels of oligonucleotide probes to capture any sequence among a defined set of targets without detectable bias. ve-SEQ enables efficient dete...
Subjects
free text keywords: Research Article, Articles, Genomics, HIV Infection & AIDS: Basic Science, Viral Infections (without HIV), Virus genome sequencing, Sequence capture and enrichment, Anti-viral resistance, Hepatitis C virus, Medicine, R, Science, Q, Reference genome, Genetic diversity, Genome, Genetics, Virus, Biology, Oligonucleotide, Data sequences, Metagenomics, Whole genome sequencing
Funded by
WT| Understanding the genetic basis of common human diseases: core funding for the Wellcome Trust Centre for Human Genetics.
Project
  • Funder: Wellcome Trust (WT)
  • Project Code: 090532
  • Funding stream: Cellular and Molecular Neuroscience
,
WT| Function and specificity of T cells in persistent virus infection.
Project
  • Funder: Wellcome Trust (WT)
  • Project Code: 091663
  • Funding stream: Immune System in Health and Disease
,
NIH| Reversal of Immune Failure with Viral Cure in Chronic HCV Infection
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 2U19AI082630-06
  • Funding stream: NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES
34 references, page 1 of 3

1 Mohd Hanafiah K Groeger J Flaxman AD: Global epidemiology of hepatitis C virus infection: new estimates of age-specific antibody to HCV seroprevalence.Hepatology.2013;57(4):1333–1342. 10.1002/hep.26141 23172780 [OpenAIRE] [PubMed] [DOI]

2 Messina JP Humphreys I Flaxman A: Global distribution and prevalence of hepatitis C virus genotypes.Hepatology.2015;61(1):77–87. 10.1002/hep.27259 25069599 [OpenAIRE] [PubMed] [DOI]

3 Jacobson IM Gordon SC Kowdley KV: Sofosbuvir for hepatitis C genotype 2 or 3 in patients without treatment options.N Engl J Med.2013;368(20):1867–1877. 10.1056/NEJMoa1214854 23607593 [PubMed] [DOI]

4 Lawitz E Mangia A Wyles D: Sofosbuvir for previously untreated chronic hepatitis C infection.N Engl J Med.2013;368(20):1878–1887. 10.1056/NEJMoa1214853 23607594 [PubMed] [DOI]

5 Shah N Pierce T Kowdley KV: Review of direct-acting antiviral agents for the treatment of chronic hepatitis C.Expert Opin Investig Drugs.2013;22(9):1107–1121. 10.1517/13543784.2013.806482 23735127 [OpenAIRE] [PubMed] [DOI]

6 Asboe D Aitken C Boffito M: British HIV Association guidelines for the routine investigation and monitoring of adult HIV-1-infected individuals 2011.HIV Med.2012;13(1):1–44. 10.1111/j.1468-1293.2011.00971.x 22171742 [OpenAIRE] [PubMed] [DOI]

7 Gordon SC Muir AJ Lim JK: Safety profile of boceprevir and telaprevir in chronic hepatitis C: real world experience from HCV-TARGET.J Hepatol.2015;62(2):286–293. 10.1016/j.jhep.2014.08.052 25218 788 [OpenAIRE] [PubMed] [DOI]

8 Hutchison C Kwong A Ray S: Accelerating drug development through collaboration: the Hepatitis C Drug Development Advisory Group.Clin Pharmacol Ther.2014;96(2):162–165. 10.1038/clpt.2014.113 24853733 [OpenAIRE] [PubMed] [DOI]

9 Hedskog C Chodavarapu K Ku KS: Genotype- and Subtype-Independent Full-Genome Sequencing Assay for Hepatitis C Virus.J Clin Microbiol.2015;53(7):2049–59. 10.1128/JCM.02624-14 25878342 [OpenAIRE] [PubMed] [DOI]

10 Smith DB Bukh J Kuiken C: Expanded classification of hepatitis C virus into 7 genotypes and 67 subtypes: updated criteria and genotype assignment web resource.Hepatology.2014;59(1):318–327. 10.1002/hep.26744 24115039 [OpenAIRE] [PubMed] [DOI]

11 Humphreys I Fleming V Fabris P: Full-length characterization of hepatitis C virus subtype 3a reveals novel hypervariable regions under positive selection during acute infection.J Virol.2009;83(22):11456–11466. 10.1128/JVI.00884-09 19740991 [OpenAIRE] [PubMed] [DOI]

12 Lauck M Alvarado-Mora MV Becker EA: Analysis of hepatitis C virus intrahost diversity across the coding region by ultradeep pyrosequencing.J Virol.2012;86(7):39 52–3960. 10.1128/JVI.06627-11 22278255 [OpenAIRE] [PubMed] [DOI]

13 Batty EM Wong TH Trebes A: A modified RNA-Seq approach for whole genome sequencing of RNA viruses from faecal and blood samples.PLoS One.2013;8(6):e66129. 10.1371/journal.pone.0066129 23762474 [OpenAIRE] [PubMed] [DOI]

14 Ninomiya M Ueno Y Funayama R: Use of Illumina deep sequencing technology to differentiate hepatitis C virus variants.J Clin Microbiol.2012;50(3):857–866. 10.1128/JCM.05715-11 22205816 [OpenAIRE] [PubMed] [DOI]

15 Iles JC Njouom R Foupouapouognigni Y: Characterization of Hepatitis C Virus Recombination in Cameroon by Use of Nonspecific Next-Generation Sequencing.J Clin Microbiol.2015;53(10):3155–64. 10.1128/JCM.00483-15 26202126 [OpenAIRE] [PubMed] [DOI]

34 references, page 1 of 3
Abstract
<ns4:p>The routine availability of high-depth virus sequence data would allow the sensitive detection of resistance-associated variants that can jeopardize HIV or hepatitis C virus (HCV) treatment. We introduce ve-SEQ, a high-throughput method for sequence-specific enrichment and characterization of whole-virus genomes at up to 20% divergence from a reference sequence and 1,000-fold greater sensitivity than direct sequencing. The extreme genetic diversity of HCV led us to implement an algorithm for the efficient design of panels of oligonucleotide probes to capture any sequence among a defined set of targets without detectable bias. ve-SEQ enables efficient dete...
Subjects
free text keywords: Research Article, Articles, Genomics, HIV Infection & AIDS: Basic Science, Viral Infections (without HIV), Virus genome sequencing, Sequence capture and enrichment, Anti-viral resistance, Hepatitis C virus, Medicine, R, Science, Q, Reference genome, Genetic diversity, Genome, Genetics, Virus, Biology, Oligonucleotide, Data sequences, Metagenomics, Whole genome sequencing
Funded by
WT| Understanding the genetic basis of common human diseases: core funding for the Wellcome Trust Centre for Human Genetics.
Project
  • Funder: Wellcome Trust (WT)
  • Project Code: 090532
  • Funding stream: Cellular and Molecular Neuroscience
,
WT| Function and specificity of T cells in persistent virus infection.
Project
  • Funder: Wellcome Trust (WT)
  • Project Code: 091663
  • Funding stream: Immune System in Health and Disease
,
NIH| Reversal of Immune Failure with Viral Cure in Chronic HCV Infection
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 2U19AI082630-06
  • Funding stream: NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES
34 references, page 1 of 3

1 Mohd Hanafiah K Groeger J Flaxman AD: Global epidemiology of hepatitis C virus infection: new estimates of age-specific antibody to HCV seroprevalence.Hepatology.2013;57(4):1333–1342. 10.1002/hep.26141 23172780 [OpenAIRE] [PubMed] [DOI]

2 Messina JP Humphreys I Flaxman A: Global distribution and prevalence of hepatitis C virus genotypes.Hepatology.2015;61(1):77–87. 10.1002/hep.27259 25069599 [OpenAIRE] [PubMed] [DOI]

3 Jacobson IM Gordon SC Kowdley KV: Sofosbuvir for hepatitis C genotype 2 or 3 in patients without treatment options.N Engl J Med.2013;368(20):1867–1877. 10.1056/NEJMoa1214854 23607593 [PubMed] [DOI]

4 Lawitz E Mangia A Wyles D: Sofosbuvir for previously untreated chronic hepatitis C infection.N Engl J Med.2013;368(20):1878–1887. 10.1056/NEJMoa1214853 23607594 [PubMed] [DOI]

5 Shah N Pierce T Kowdley KV: Review of direct-acting antiviral agents for the treatment of chronic hepatitis C.Expert Opin Investig Drugs.2013;22(9):1107–1121. 10.1517/13543784.2013.806482 23735127 [OpenAIRE] [PubMed] [DOI]

6 Asboe D Aitken C Boffito M: British HIV Association guidelines for the routine investigation and monitoring of adult HIV-1-infected individuals 2011.HIV Med.2012;13(1):1–44. 10.1111/j.1468-1293.2011.00971.x 22171742 [OpenAIRE] [PubMed] [DOI]

7 Gordon SC Muir AJ Lim JK: Safety profile of boceprevir and telaprevir in chronic hepatitis C: real world experience from HCV-TARGET.J Hepatol.2015;62(2):286–293. 10.1016/j.jhep.2014.08.052 25218 788 [OpenAIRE] [PubMed] [DOI]

8 Hutchison C Kwong A Ray S: Accelerating drug development through collaboration: the Hepatitis C Drug Development Advisory Group.Clin Pharmacol Ther.2014;96(2):162–165. 10.1038/clpt.2014.113 24853733 [OpenAIRE] [PubMed] [DOI]

9 Hedskog C Chodavarapu K Ku KS: Genotype- and Subtype-Independent Full-Genome Sequencing Assay for Hepatitis C Virus.J Clin Microbiol.2015;53(7):2049–59. 10.1128/JCM.02624-14 25878342 [OpenAIRE] [PubMed] [DOI]

10 Smith DB Bukh J Kuiken C: Expanded classification of hepatitis C virus into 7 genotypes and 67 subtypes: updated criteria and genotype assignment web resource.Hepatology.2014;59(1):318–327. 10.1002/hep.26744 24115039 [OpenAIRE] [PubMed] [DOI]

11 Humphreys I Fleming V Fabris P: Full-length characterization of hepatitis C virus subtype 3a reveals novel hypervariable regions under positive selection during acute infection.J Virol.2009;83(22):11456–11466. 10.1128/JVI.00884-09 19740991 [OpenAIRE] [PubMed] [DOI]

12 Lauck M Alvarado-Mora MV Becker EA: Analysis of hepatitis C virus intrahost diversity across the coding region by ultradeep pyrosequencing.J Virol.2012;86(7):39 52–3960. 10.1128/JVI.06627-11 22278255 [OpenAIRE] [PubMed] [DOI]

13 Batty EM Wong TH Trebes A: A modified RNA-Seq approach for whole genome sequencing of RNA viruses from faecal and blood samples.PLoS One.2013;8(6):e66129. 10.1371/journal.pone.0066129 23762474 [OpenAIRE] [PubMed] [DOI]

14 Ninomiya M Ueno Y Funayama R: Use of Illumina deep sequencing technology to differentiate hepatitis C virus variants.J Clin Microbiol.2012;50(3):857–866. 10.1128/JCM.05715-11 22205816 [OpenAIRE] [PubMed] [DOI]

15 Iles JC Njouom R Foupouapouognigni Y: Characterization of Hepatitis C Virus Recombination in Cameroon by Use of Nonspecific Next-Generation Sequencing.J Clin Microbiol.2015;53(10):3155–64. 10.1128/JCM.00483-15 26202126 [OpenAIRE] [PubMed] [DOI]

34 references, page 1 of 3
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