Acute hepatitis C in a chronically HIV-infected patient: Evolution of different viral genomic regions

Single-Tube Method for Nucleic Acid Extraction, Amplification, Purification, and Sequencing

Background: The hepatitis C virus (HCV) genotype determines patient prognosis and duration of treatment, but sequencing of the gene is lengthy and labor-intensive. We used a commercially available nucleic acid extraction system to develop a single-tube extraction-to-sequencing (STETS) method for HCV genotyping.

Methods: HCV RNA was purified and amplified in tubes coated with a solid-phase matrix that irreversibly bound nucleic acid during the extraction step. After reverse transcription-PCR, the amplicon was adsorbed to the original extraction matrix for purification and use in the subsequent sequencing reactions.

Results: The STETS method generated genotyping-quality sequence for a range of HCV titers from 500 to 6 000 000 IU/mL. If a viral sample was detected during real-time reverse transcription-PCR, it could be sequenced and genotyped. Read lengths >600 bases were observed with the STETS method. Mixed infections were detected and genotyped if at least 15% of the minor species was present. Combining the STETS method with consecutive sequencing provided a means of performing both forward and reverse sequencing in a single tube.

Conclusions: A single-tube nucleic acid extraction-to-sequencing method, which requires less time and labor than conventional methods, generates HCV sequence data that are equivalent to conventional methods and can be used to genotype HCV.

Dynamic determination and analysis of serum virus load in patients with chronic HBV infection

AIM: To observe the variation of viral load and characteristics of within-host dynamics in patients with chronic hepatitis B virus infection without receiving antiviral therapy.

METHODS: Serum was collected consecutively from 3 patients with different clinical phenotype, ALT and total bilirubin were determined, and HBV DNA was measured by quantitative TaqMan fluorogenic PCR.

RESULTS: Spontaneous fluctuations of HBV DNA load were observed when measured daily, wkly and moly in our untreated patients with chronic HBV infection, but there was no determinate correlation between HBV DNA loads and ALT values.

CONCLUSION: The spontaneous fluctuation of viral load in untreated patients with different clinical phenotype displays some characteristic patterns. Here we propose a PID pattern for host feedback to virus using population quantity of HBV as variant, which may be used for the prediction of virus-host ecological evolution in persistent HBV infection.