Hybrid next-generation sequencing protocol for testing HIV-2 drug resistance

Area of Science:

• Virology
• Genetics
• Clinical Diagnostics

Background:

• HIV-2 infection impacts over a million individuals globally, with treatment complicated by inherent drug resistance.
• Monitoring drug resistance mutations (DRM) is crucial for managing treatment failure in people living with HIV-2 (PLHIV-2).
• Lack of commercial tests necessitates the development of in-house methods for DRM detection.

Purpose of the Study:

• To evaluate a hybrid next-generation sequencing (NGS) Ion Torrent protocol for detecting DRM in PLHIV-2.
• To assess the clinical utility of this NGS protocol in managing HIV-2 treatment.

Main Methods:

• A hybrid NGS Ion Torrent protocol was used to analyze 100 samples from PLHIV-2 in Portugal.
• Sanger sequencing was performed on 48 samples for comparative analysis.
• NGS successfully amplified key viral regions: 92% protease, 91% reverse transcriptase, and 49% integrase.

Main Results:

• NGS demonstrated high amplification rates for crucial HIV-2 drug resistance regions.
• The NGS protocol showed strong statistical agreement with Sanger sequencing for DRM identification.
• NGS identified two reverse transcriptase mutations (K70E, M184V) not detected by Sanger, highlighting its superior sensitivity for minority variants.

Conclusions:

• Hybrid NGS is effective for detecting DRM in PLHIV-2, including minority variants.
• This NGS protocol offers comprehensive data for adjusting antiretroviral therapy (ART) regimens.
• Implementing NGS can improve patient outcomes and the quality of care for PLHIV-2.