Using high-throughput sequencing for investigating intra-host hepatitis C evolution over long retrospective periods

Area of Science:

• Virology
• Evolutionary Biology
• Genetics

Background:

• Hospital biological sample collections are crucial for studying chronic infection evolution.
• High-throughput sequencing enables analysis of within-host viral genetic diversity and treatment resistance over time.

Purpose of the Study:

• To investigate the evolutionary dynamics of hepatitis C virus (HCV) populations in patients unresponsive to dual therapies.
• To analyze genomic variation in HCV over a 13-year period using stored blood samples.

Main Methods:

• Utilized amplicon sequencing to survey genomic variation in the Core and NS5B regions of HCV.
• Analyzed viral populations from blood samples collected at multiple time points over 13 years.
• Assessed genetic heterogeneity and sample composition to understand viral population changes during treatment.

Main Results:

• Observed mixed infections with multiple HCV genotypes in both patients.
• Noted an increase in genetic diversity in the NS5B region after treatment initiation.
• Estimated secondary infections predated treatment and identified diversifying selection post-treatment, maintaining high viral heterogeneity.

Conclusions:

• Viral diversity maintenance in multi-genotype HCV infections can be explained by soft selective sweeps initiated concurrently with antiviral treatment.
• Understanding viral evolution under treatment pressure is key for managing chronic infections.