ArticleF1000Research2015
ve-SEQ: Robust, unbiased enrichment for streamlined detection and whole-genome sequencing of HCV and other highly diverse pathogens.
Article in F1000Research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 papers.
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Who cites it
45 citing papers in PubMed.
- Identification and masking of artifactual and misleading within-host variants in deep-sequencing SARS-CoV-2 data.Molecular biology and evolution · 2026Article
- Rapid phylogenomic analysis for viral surveillance and metagenomic profiling with Omni2Tree.bioRxiv : the preprint server for biology · 2026Article
- Clinical metagenomics for diagnosis and surveillance of viral pathogens.Nature reviews. Microbiology · 2026Review
- teamNGS Balances Sensitivity for Viruses with Comprehensive Microbial Detection in Clinical Specimens.Microorganisms · 2025Article
- Genetically distinct within-host subpopulations of hepatitis C virus persist after Direct-Acting Antiviral treatment failure.PLoS pathogens · 2025Article
- Whole genome sequencing of hepatitis B virus using tiled amplicon (HEPTILE) and probe based enrichment on Illumina and Nanopore platforms.Scientific reports · 2025Article
- The Evolution of Nucleic Acid-Based Diagnosis Methods from the (pre-)CRISPR to CRISPR era and the Associated Machine/Deep Learning Approaches in Relevant RNA Design.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Castanet: a pipeline for rapid analysis of targeted multi-pathogen genomic data.Bioinformatics (Oxford, England) · 2024Article
- Hybrid-Capture Target Enrichment in Human Pathogens: Identification, Evolution, Biosurveillance, and Genomic Epidemiology.Pathogens (Basel, Switzerland) · 2024Review
- Targeted metagenomics reveals association between severity and pathogen co-detection in infants with respiratory syncytial virus.Nature communications · 2024Article
- A robust, scalable, and cost-efficient approach to whole genome sequencing of RSV directly from clinical samples.Journal of clinical microbiology · 2024Article
- High-performance enrichment-based genome sequencing to support the investigation of hepatitis A virus outbreaks.Microbiology spectrum · 2024Article
- Longitudinal population-level HIV epidemiologic and genomic surveillance highlights growing gender disparity of HIV transmission in Uganda.Nature microbiology · 2024Article
- A proof of concept for a targeted enrichment approach to the simultaneous detection and characterization of rickettsial pathogens from clinical specimens.Frontiers in microbiology · 2024Article
- Article
- An enrichment protocol and analysis pipeline for long read sequencing of the hepatitis B virus transcriptome.The Journal of general virology · 2023Article
- Targeted genomic sequencing with probe capture for discovery and surveillance of coronaviruses in bats.eLife · 2022Article
- ProbeTools: designing hybridization probes for targeted genomic sequencing of diverse and hypervariable viral taxa.BMC genomics · 2022Article
- Probe Capture Enrichment Methods for HIV and HCV Genome Sequencing and Drug Resistance Genotyping.Pathogens (Basel, Switzerland) · 2022Review
- Viral genome wide association study identifies novel hepatitis C virus polymorphisms associated with sofosbuvir treatment failure.Nature communications · 2021Article
Corrections and comments
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Authors and funding
11 authors.
Funding
Abstract
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.