ArticleJournal of clinical microbiology2012
Use of illumina deep sequencing technology to differentiate hepatitis C virus variants.
Article in Journal of clinical microbiology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
25 citing papers in PubMed, 50 citations in OpenAlex.
- Genotype- and Subtype-Independent Full-Genome Sequencing Assay for Hepatitis C Virus.Journal of clinical microbiology · 2015Trial
- Ultradeep sequencing study of chronic hepatitis C virus genotype 1 infection in patients treated with daclatasvir, peginterferon, and ribavirin.Antimicrobial agents and chemotherapy · 2014Trial
- Trial
- Managing Viral Emerging Infectious Diseases via Current and Future Molecular Diagnostics.Diagnostics (Basel, Switzerland) · 2023Review
- Low-Bias RNA Sequencing of the HIV-2 Genome from Blood Plasma.Journal of virology · 2019Article
- Identification of HCV Resistant Variants against Direct Acting Antivirals in Plasma and Liver of Treatment Naïve Patients.Scientific reports · 2017Article
- A metagenomics study for the identification of respiratory viruses in mixed clinical specimens: an application of the iterative mapping approach.Archives of virology · 2017Article
- The new frontier of diagnostics: Molecular assays and their role in infection prevention and control.American journal of infection control · 2017Review
- Genomic Analysis of Viral Outbreaks.Annual review of virology · 2016Review
- Update on hepatitis B and C virus diagnosis.World journal of virology · 2015Review
- Hepatitis C virus genetic variability and evolution.World journal of hepatology · 2015Review
- Advanced molecular surveillance of hepatitis C virus.Viruses · 2015Review
- ve-SEQ: Robust, unbiased enrichment for streamlined detection and whole-genome sequencing of HCV and other highly diverse pathogens.F1000Research · 2015Article
- Deep sequencing: becoming a critical tool in clinical virology.Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology · 2014Review
- Deep sequencing of evolving pathogen populations: applications, errors, and bioinformatic solutions.Microbial informatics and experimentation · 2014Article
- Hepatitis C virus protease inhibitor-resistance mutations: our experience and review.World journal of gastroenterology · 2013Review
- Prediction of treatment efficacy and telaprevir-resistant variants after triple therapy in patients infected with hepatitis C virus genotype 1.Journal of clinical microbiology · 2013Article
- Next generation sequencing of viral RNA genomes.BMC genomics · 2013Article
- Multicenter quality control of hepatitis C virus protease inhibitor resistance genotyping.Journal of clinical microbiology · 2013Article
- Complete viral RNA genome sequencing of ultra-low copy samples by sequence-independent amplification.Nucleic acids research · 2013Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
11 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Hepatitis C virus (HCV) is a positive-strand enveloped RNA virus that shows diverse viral populations even in one individual. Though Sanger sequencing has been used to determine viral sequences, deep sequencing technologies are much faster and can perform large-scale sequencing. We demonstrate the successful use of Illumina deep sequencing technology and subsequent analyses to determine the genetic variants and amino acid substitutions in both treatment-naïve (patient 1) and treatment-experienced (patient 7) isolates from HCV-infected patients. As a result, almost the full nucleotide sequence of HCV was detectable for patients 1 and 7. The reads were mapped to the HCV reference sequence. The coverage was 99.8% and the average depth was 69.5× for patient 7, with values of 99.4% (coverage) and 51.1× (average depth) for patient 1. In patient 7, amino acid (aa) 70 in the core region showed arginine, with methionine at aa 91, by Sanger sequencing. Major variants showed the same amino acid sequence, but minor variants were detectable in 18% (6/34 sequences) of sequences, with replacement of methionine by leucine at aa 91. In NS3, 8 amino acid positions showed mixed variants (T72T/I, K213K/R, G237G/S, P264P/S/A, S297S/A, A358A/T, S457S/C, and I615I/M) in patient 7. In patient 1, 3 amino acid positions showed mixed variants (L14L/F/V, S61S/A, and I586T/I). In conclusion, deep sequencing technologies are powerful tools for obtaining more profound insight into the dynamics of variants in the HCV quasispecies in human serum.
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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.