ArticleThe Journal of infectious diseases2013
Whole genome pyrosequencing of rare hepatitis C virus genotypes enhances subtype classification and identification of naturally occurring drug resistance variants.
Article in The Journal of infectious diseases, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- Trial
- Genotype- and Subtype-Independent Full-Genome Sequencing Assay for Hepatitis C Virus.Journal of clinical microbiology · 2015Trial
- Rapid phylogenomic analysis for viral surveillance and metagenomic profiling with Omni2Tree.bioRxiv : the preprint server for biology · 2026Article
- Reducing haystacks to needles-ViralClust: a Nextflow pipeline to cluster viral sequences.GigaScience · 2026Article
- Full-length sequence analysis of hepatitis C virus genotype 3b strains and development of anJournal of virology · 2023Article
- Hepatitis C subtyping assay failure in UK patients born in sub-Saharan Africa: Implications for global treatment and elimination.Journal of medical virology · 2023Article
- Cell Culture Studies of the Efficacy and Barrier to Resistance of Sofosbuvir-Velpatasvir and Glecaprevir-Pibrentasvir against Hepatitis C Virus Genotypes 2a, 2b, and 2c.Antimicrobial agents and chemotherapy · 2020Article
- Review
- Clinical and biological insights from viral genome sequencing.Nature reviews. Microbiology · 2017Review
- Antiviral drug resistance as an adaptive process.Virus evolution · 2016Review
- High incidence of the hepatitis C virus recombinant 2k/1b in Georgia: Recommendations for testing and treatment.Hepatology research : the official journal of the Japan Society of Hepatology · 2015Article
- The full-length genome sequences of nine HCV genotype 4 variants representing a new subtype 4s and eight unclassified lineages.Virology · 2015Article
- High-resolution hepatitis C virus subtyping using NS5B deep sequencing and phylogeny, an alternative to current methods.Journal of clinical microbiology · 2015Article
- Article
- 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
- Origin of hepatitis C virus genotype 3 in Africa as estimated through an evolutionary analysis of the full-length genomes of nine subtypes, including the newly sequenced 3d and 3e.The Journal of general virology · 2014Article
- Expanded classification of hepatitis C virus into 7 genotypes and 67 subtypes: updated criteria and genotype assignment web resource.Hepatology (Baltimore, Md.) · 2014Article
- Comparison of pyrosequencing, Sanger sequencing, and melting curve analysis for detection of low-frequency macrolide-resistant mycoplasma pneumoniae quasispecies in respiratory specimens.Journal of clinical microbiology · 2013Article
- Advances in the development of nucleoside and nucleotide analogues for cancer and viral diseases.Nature reviews. Drug discovery · 2013Review
- Article
Corrections and comments
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Authors and funding
14 authors.
Funding
Abstract
backgroundInfection with hepatitis C virus (HCV) is a burgeoning worldwide public health problem, with 170 million infected individuals and an estimated 20 million deaths in the coming decades. While 6 main genotypes generally distinguish the global geographic diversity of HCV, a multitude of closely related subtypes within these genotypes are poorly defined and may influence clinical outcome and treatment options. Unfortunately, the paucity of genetic data from many of these subtypes makes time-consuming primer walking the limiting step for sequencing understudied subtypes.
methodsHere we combined long-range polymerase chain reaction amplification with pyrosequencing for a rapid approach to generate the complete viral coding region of 31 samples representing poorly defined HCV subtypes.
resultsPhylogenetic classification based on full genome sequences validated previously identified HCV subtypes, identified a recombinant sequence, and identified a new distinct subtype of genotype 4. Unlike conventional sequencing methods, use of deep sequencing also facilitated characterization of minor drug resistance variants within these uncommon or, in some cases, previously uncharacterized HCV subtypes.
conclusionsThese data aid in the classification of uncommon HCV subtypes while also providing a high-resolution view of viral diversity within infected patients, which may be relevant to the development of therapeutic regimens to minimize drug resistance.
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