Performance of the Applied Biosystems HIV-1 Genotyping Kit with Integrase

Area of Science:

• Virology
• Molecular Biology
• Genetics

Background:

• HIV genotyping is crucial for determining antiretroviral drug susceptibility.
• The Applied Biosystems HIV-1 Genotyping Kit with Integrase (AB kit) identifies resistance mutations in HIV protease, reverse transcriptase, and integrase.
• Previous studies utilized the ViroSeq HIV-1 Genotyping System for HIV resistance detection.

Purpose of the Study:

• To compare the performance of the AB kit against the ViroSeq system.
• To evaluate the utility of AB kit amplicons for next-generation sequencing (NGS).
• To assess the sensitivity of different methods in detecting resistance-associated mutations (RAMs).

Main Methods:

• HIV RNA extraction from 96 plasma samples using the MagNA Pure 24 instrument.
• HIV genotyping using the AB kit and ViroSeq system.
• Analysis of AB kit DNA amplicons by NGS using the Nextera XT kit.
• Drug resistance prediction using the Stanford HIV Drug Resistance Database.

Main Results:

• High concordance between AB kit and ViroSeq for protease/reverse transcriptase and integrase sequences (mean genetic distance 0.02% and 0.04%).
• Both methods detected 103 major RAMs; the AB kit identified four additional major RAMs also detected by NGS.
• NGS identified 27 major RAMs missed by both Sanger-based kits, highlighting its enhanced sensitivity.

Conclusions:

• The AB kit demonstrates comparable performance to ViroSeq for detecting known RAMs.
• Utilizing AB kit amplicons with NGS significantly enhances the detection sensitivity for RAMs.
• NGS offers a more comprehensive approach to identifying HIV drug resistance mutations.