High-resolution hepatitis C virus subtyping using NS5B deep sequencing and phylogeny, an alternative to current...

Area of Science:

• Virology
• Molecular Diagnostics
• Infectious Diseases

Background:

• Hepatitis C virus (HCV) has seven genotypes and 67 subtypes.
• Treatment response to direct-acting antivirals (DAAs) in genotype 1 HCV is subtype-dependent.
• Existing HCV subtyping methods lack sufficient accuracy.

Purpose of the Study:

• To evaluate a deep-sequencing assay for Hepatitis C virus (HCV) subtyping.
• To compare its performance against commercial assays and direct sequencing.
• To assess its utility in identifying mixed HCV infections.

Main Methods:

• Deep sequencing on the 454/GS-Junior platform was used for HCV subtyping.
• Performance was compared with Versant HCV Genotype 2.0 and Abbott Real-time HCV Genotype II assays.
• Direct NS5B sequencing served as the gold standard for 114 clinical specimens.

Main Results:

• Deep sequencing accurately identified HCV subtypes, matching Sanger sequencing results.
• It detected mixed-subtype infections missed by commercial assays.
• Commercial assays showed lower accuracy, failing to subtype numerous samples.

Conclusions:

• Deep sequencing is a more efficient and accurate method for HCV subtyping.
• It reliably identifies mixed infections, crucial for DAA treatment decisions.
• This method supports optimized DAA-based treatment strategies across all HCV subtypes.