ve-SEQ: Robust, unbiased enrichment for streamlined detection and whole-genome sequencing of HCV and other highly diverse pathogens.
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 detection and sequencing of any HCV genome, including mixtures and intra-host variants, in a single experiment, with greater tolerance of sequence diversity than standard amplification methods and greater sensitivity than metagenomic sequencing, features that are directly applicable to other pathogens or arbitrary groups of target organisms, allowing the combination of sensitive detection with sequencing in many settings.
Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, OX1 4BH, UK.
David
D
Bonsall
Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, OX1 4BH, UK.|Oxford Martin School, University of Oxford, Oxford, OX1 4BH, UK.
M Azim
MA
Ansari
Oxford Genomics Centre, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX1 4BH, UK.
Camilla
C
Ip
Oxford Genomics Centre, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX1 4BH, UK.
Amy
A
Trebes
Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, OX1 4BH, UK.
Anthony
A
Brown
Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, OX1 4BH, UK.|National Institute for Health Research Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK.
Paul
P
Klenerman
Oxford Genomics Centre, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX1 4BH, UK.
David
D
Buck
Oxford Genomics Centre, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX1 4BH, UK.
Paolo
P
Piazza
Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, OX1 4BH, UK.|National Institute for Health Research Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK.
Eleanor
E
Barnes
Oxford Genomics Centre, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX1 4BH, UK.
Rory
R
Bowden
Anti-viral resistance; Hepatitis C virus; Sequence capture and enrichment; Virus genome sequencing