Ion Torrent Genexus as a Fast and Reliable Solution for HIV-1 Drug Resistance Testing: Comparison with the GeneStudio...

Area of Science:

• Molecular Biology
• Virology
• Clinical Diagnostics

Background:

• Next-generation sequencing (NGS) enhances HIV-1 genotypic resistance testing (GRT) for detecting low-frequency drug-resistance variants.
• Interpreting low-frequency mutations in HIV-1 GRT is challenging due to potential sequencing artifacts.

Purpose of the Study:

• To compare the analytical performance and workflow efficiency of two Ion Torrent platforms, GeneStudio S5 (S5) and Genexus (GX), for routine HIV-1 GRT.
• To evaluate the reliability of variant interpretation using a standardized confirmation algorithm.

Main Methods:

• Prospective collection of 134 plasma samples from people with HIV.
• Comparative sequencing analysis of 100 samples on both S5 and GX platforms.
• Application of a standardized confirmation algorithm integrating Stanford HIVdb and Geneious software for discordant mutation analysis.

Main Results:

• Overall concordance for resistance-associated mutations was 88.0% between the S5 and GX platforms.
• High agreement rates were observed for protease (97.0%), reverse transcriptase (90.0%), and integrase (100%).
• The Genexus (GX) platform demonstrated a significantly faster turnaround time (approx. 24 h) and more automated workflow compared to the GeneStudio S5 (S5) (approx. 72 h).

Conclusions:

• Both GeneStudio S5 and Genexus platforms are suitable for routine HIV-1 GRT.
• A standardized bioinformatic review process is crucial for the reliable interpretation of HIV-1 resistance variants, especially discordant ones.
• The Genexus platform offers improved workflow efficiency for HIV-1 GRT.