ArticleJournal of clinical microbiology2004
Accurate representation of the hepatitis C virus quasispecies in 5.2-kilobase amplicons.
Article in Journal of clinical microbiology, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 25 citations in OpenAlex.
- Elucidation of hepatitis C virus transmission and early diversification by single genome sequencing.PLoS pathogens · 2012Trial
- Hepatitis C virus (HCV) genotype 1b displays higher genetic variability of hypervariable region 1 (HVR1) than genotype 3.Scientific reports · 2019Article
- Next-generation sequencing analysis of a cluster of hepatitis C virus infections in a haematology and oncology center.PloS one · 2018Article
- Trace amounts of sporadically reappearing HCV RNA can cause infection.The Journal of clinical investigation · 2014Article
- HIV populations are large and accumulate high genetic diversity in a nonlinear fashion.Journal of virology · 2013Article
- Development of a sensitive RT-PCR method for amplifying and sequencing near full-length HCV genotype 1 RNA from patient samples.Virology journal · 2013Article
- Spontaneous clearance of primary acute hepatitis C virus infection correlated with high initial viral RNA level and rapid HVR1 evolution.Hepatology (Baltimore, Md.) · 2012Article
- Immunogenicity and cross-reactivity of a representative ancestral sequence in hepatitis C virus infection.Journal of immunology (Baltimore, Md. : 1950) · 2012Article
- Spontaneous clearance of chronic hepatitis C virus infection is associated with appearance of neutralizing antibodies and reversal of T-cell exhaustion.The Journal of infectious diseases · 2012Article
- Virological footprint of CD4+ T-cell responses during chronic hepatitis C virus infection.The Journal of general virology · 2010Article
- Acceleration of hepatitis C virus envelope evolution in humans is consistent with progressive humoral immune selection during the transition from acute to chronic infection.Journal of virology · 2010Article
- Functional characterization of core genes from patients with acute hepatitis C virus infection.The Journal of infectious diseases · 2010Article
- Full-length characterization of hepatitis C virus subtype 3a reveals novel hypervariable regions under positive selection during acute infection.Journal of virology · 2009Article
- Selection pressure from neutralizing antibodies drives sequence evolution during acute infection with hepatitis C virus.Gastroenterology · 2009Article
- High-programmed death-1 levels on hepatitis C virus-specific T cells during acute infection are associated with viral persistence and require preservation of cognate antigen during chronic infection.Journal of immunology (Baltimore, Md. : 1950) · 2008Article
- Hepatitis C virus immune escape via exploitation of a hole in the T cell repertoire.Journal of immunology (Baltimore, Md. : 1950) · 2008Article
- Progression of fibrosis during chronic hepatitis C is associated with rapid virus evolution.Journal of virology · 2007Article
- Efficient amplification and cloning of near full-length hepatitis C virus genome from clinical samples.Biochemical and biophysical research communications · 2006Article
- Comprehensive analyses of CD8+ T cell responses during longitudinal study of acute human hepatitis C.Hepatology (Baltimore, Md.) · 2005Article
- Divergent and convergent evolution after a common-source outbreak of hepatitis C virus.The Journal of experimental medicine · 2005Article
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Authors and funding
8 authors at 3 institutions in 2 countries.
Funding
Abstract
Hepatitis C virus (HCV) exists as a swarm of genetically distinct but related variants, or a quasispecies, whose complexity and sequence evolution are critical to studies of viral pathogenesis. Because most studies of the HCV quasispecies have focused on a relatively small genomic segment, the first hypervariable region of the E2 gene, it is possible that viral complexity is occasionally underestimated (due to primer mismatch) and that sequence evolution is misperceived due to unrecognized covariation. This report describes a sensitive and reproducible method to amplify most of the HCV genome as a single 5.2-kb amplicon by using primers directed at relatively conserved genomic segments. Using 52 specimens obtained during acute infection over a range of viral RNA concentrations, the overall rate of successful amplification was 94% and varied in a concentration-dependent manner, with successful amplification in 26 of 26 (100%) specimens at greater than 10(5) IU/ml, 15 of 16 (94%) at 10(4) to 10(5) IU/ml, 6 of 7 (86%) at 10(3) to 10(4) IU/ml, and 2 of 3 (67%) at less than 10(3) IU/ml. Quasispecies complexity, determined by using this novel long-amplicon method followed by heteroduplex mobility assay combined with single-stranded conformational polymorphism (HDA+SSCP) analysis, was very high, even during acute HCV infection, when 10 to 21 (median, 16) different HDA+SSCP patterns were detected among 33 cDNA clones examined. Replicate analyses indicate that this diversity is not dominated by random errors generated during amplification. Therefore, the HCV quasispecies is highly complex even during acute infection and is accurately represented in amplicons representing more than half of the viral genome.
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