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Dynamic analysis of heterogeneous hepatitis C virus populations by direct solid-phase sequencing
J Odeberg1, Z Yun, A Sönnerborg
1Department of Biochemistry, Royal Institute of Technology, Stockholm, Sweden.
Journal of Clinical Microbiology
|July 1, 1995
Summary
Hepatitis C virus (HCV) exhibits rapid sequence variation in its E2/NS1 region, with nucleotide changes occurring at 0.1-0.2 per site annually. Direct sequencing effectively tracks these dynamic viral changes in patients.
Area of Science:
- Virology
- Molecular Biology
- Genetics
Background:
- Hepatitis C virus (HCV) poses a significant global health challenge.
- Understanding HCV genome diversity is crucial for developing effective treatments and vaccines.
- The hypervariable E2/NS1 region is key to HCV's adaptability and immune evasion.
Purpose of the Study:
- To analyze sequence diversity and variation in the HCV E2/NS1 region.
- To determine the nucleotide substitution rate in HCV isolates.
- To compare direct solid-phase sequencing with RT-PCR clone sequencing for HCV analysis.
Main Methods:
- Semiautomated solid-phase direct sequencing of the HCV E2/NS1 region.
- Sequencing of 24 HCV isolates from seropositive patients.
- Longitudinal monitoring of six untreated patients over 14 months.
- Comparative analysis of direct sequencing versus RT-PCR clone sequencing.
Main Results:
- Significant sequence variations were observed in the HCV E2/NS1 region over time.
- The nucleotide change rate was quantified at 0.1 to 0.2 nucleotide substitutions per genome site per year.
- Direct solid-phase sequencing proved advantageous for studying dynamic changes in heterogeneous HCV populations.
Conclusions:
- The HCV E2/NS1 region demonstrates rapid evolution.
- Semiautomated solid-phase direct sequencing is a valuable tool for tracking viral dynamics.
- This method offers advantages over traditional clone sequencing for studying viral heterogeneity.