scholarly journals Acute Hepatitis C Virus Structural Gene Sequences as Predictors of Persistent Viremia: Hypervariable Region 1 as a Decoy

1999 ◽  
Vol 73 (4) ◽  
pp. 2938-2946 ◽  
Author(s):  
Stuart C. Ray ◽  
Yu-Ming Wang ◽  
Oliver Laeyendecker ◽  
John R. Ticehurst ◽  
Stephen A. Villano ◽  
...  
Keyword(s):  
Hepatitis C Virus ◽  
Hepatitis C ◽  
Selective Pressure ◽  
Hypervariable Region ◽  
Amino Acid Sequences ◽  
Heteroduplex Analysis ◽  
Acute Hepatitis C ◽  
Hypervariable Region 1 ◽  
Persistent Viremia ◽  
Quasispecies Complexity

ABSTRACT We hypothesized that hepatitis C virus (HCV) persistence is related to the sequence variability of putative envelope genes. This hypothesis was tested by characterizing quasispecies in specimens collected every six months from a cohort of acutely HCV-infected subjects (mean duration of specimen collection, 72 months after seroconversion). We evaluated 5 individuals who spontaneously cleared viremia and 10 individuals with persistent viremia by cloning 33 1-kb amplicons that spanned E1 and the 5′ half of E2, including hypervariable region 1 (HVR1). To assess the quasispecies complexity and to detect variants for sequencing, the first PCR-positive sample was examined by using a previously described method that combines heteroduplex analysis and analysis of single-stranded conformational polymorphisms. The ratio of nonsynonymous to synonymous substitutions (dN/dS ) within each sample was evaluated as an indicator of relative selective pressure. Amino acid sequences were analyzed for signature patterns, glycosylation signals, and charge. Quasispecies complexity was higher and E1dN/dS ratios (selective pressure) were lower in those with persistent viremia; the association with persistence was strengthened by the presence of a combination of both characteristics. In contrast, a trend toward higher HVR1dN/dS ratios was detected among those with persistent viremia. We did not detect any such association for factors that may affect complexity such as serum HCV RNA concentration. HVR1 had a lower positive charge in subjects with persistent viremia, although no consistent motifs were detected. Our data suggest that HCV persistence is associated with a complex quasispecies and immune response to HVR1.

scholarly journals Hypervariable Region 1 Sequence Stability during Hepatitis C Virus Replication in Chimpanzees

2000 ◽  
Vol 74 (7) ◽  
pp. 3058-3066 ◽  
Author(s):  
Stuart C. Ray ◽  
Qing Mao ◽  
Robert E. Lanford ◽  
Suzanne Bassett ◽  
Oliver Laeyendecker ◽  
...  
Keyword(s):  
Hepatitis C Virus ◽  
Hepatitis C ◽  
Selection Pressure ◽  
Hypervariable Region ◽  
Variable Region ◽  
Nonsynonymous Substitution ◽  
Hypervariable Region 1 ◽  
Single Stranded Conformational Polymorphism ◽  
Quasispecies Complexity ◽  
Selection Of

ABSTRACT The putative envelope 2 (E2) gene of hepatitis C virus (HCV) contains a highly variable region referred to as hypervariable region 1 (HVR1). We hypothesized that this genetic variability is driven by immune selection pressure, rather than representing the accumulation of random mutations in a region with relatively little functional constraint. To test this hypothesis, we examined the E2 sequence of a human inoculum that was passaged through eight chimpanzees, which appear to have a replicative rate (opportunity for chance mutation) similar to that of humans. Acute-phase plasma samples from a human (the inoculum) and six of eight serially infected chimpanzees were studied. For each, 33 cloned cDNAs were examined by a combined heteroduplex–single-stranded conformational polymorphism assay to assess quasispecies complexity and optimize selection of clones with unique gel shift patterns (clonotypes) for sequencing. The sequence diversity of HCV was significantly lower in the chimpanzees than in the humans, and during eight serial passages there was no change in the sequence of the majority clonotype from each animal examined. Similarly, the rates of protein sequence altering (nonsynonymous) substitution were lower in the chimpanzees than in the humans. These findings demonstrate that nonsynonymous mutations indicate selection pressure rather than being an incidental result of HCV replication.

scholarly journals Hypervariable region 1 variant acting as TCR antagonist affects hepatitis C virus-specific CD4+T cell repertoire by favoring CD95-mediated apoptosis

2005 ◽  
Vol 78 (2) ◽  
pp. 372-382 ◽  
Author(s):  
Cristiano Scottà ◽  
Loretta Tuosto ◽  
Anna Maria Masci ◽  
Luigi Racioppi ◽  
Enza Piccolella ◽  
...  
Keyword(s):  
Hepatitis C Virus ◽  
Hepatitis C ◽  
T Cell ◽  
Hypervariable Region ◽  
Cd4 T Cell ◽  
T Cell Repertoire ◽  
Cell Repertoire ◽  
Hypervariable Region 1

scholarly journals Ultradeep Pyrosequencing of Hepatitis C Virus Hypervariable Region 1 in Quasispecies Analysis

2013 ◽  
Vol 2013 ◽  
pp. 1-10 ◽  
Author(s):  
Kamila Caraballo Cortés ◽  
Osvaldo Zagordi ◽  
Tomasz Laskus ◽  
Rafał Płoski ◽  
Iwona Bukowska-Ośko ◽  
...  
Keyword(s):  
Hepatitis C Virus ◽  
Hepatitis C ◽  
Hypervariable Region ◽  
454 Sequencing ◽  
Correction Method ◽  
Sequencing Error ◽  
Hypervariable Region 1 ◽  
Reconstruction Methods ◽  
Sequencing Strategy

Genetic variability of hepatitis C virus (HCV) determines pathogenesis of infection, including viral persistence and resistance to treatment. The aim of the present study was to characterize HCV genetic heterogeneity within a hypervariable region 1 (HVR1) of a chronically infected patient by ultradeep 454 sequencing strategy. Three independent sequencing error correction methods were applied. First correction method (Method I) implemented cut-off for genetic variants present in less than 1%. In the second method (Method II), a condition to call a variant was bidirectional coverage of sequencing reads. Third method (Method III) usedShort Read Assembly into Haplotypes(ShoRAH) program. After the application of these three different algorithms, HVR1 population consisted of 8, 40, and 186 genetic haplotypes. The most sensitive method was ShoRAH, allowing to reconstruct haplotypes constituting as little as 0.013% of the population. The most abundant genetic variant constituted only 10.5%. Seventeen haplotypes were present in a frequency above 1%, and there was wide dispersion of the population into very sparse haplotypes. Our results indicate that HCV HVR1 heterogeneity andquasispeciespopulation structure may be reconstructed by ultradeep sequencing. However, credible analysis requires proper reconstruction methods, which would distinguish sequencing error from real variabilityin vivo.

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