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Updated: Sep 11, 2025
An Affordable HIV-1 Drug Resistance Monitoring Method for Resource Limited Settings
Published on: March 30, 2014
Design and Evaluation of Next-Generation HIV Genotyping for Detection of Resistance Mutations to 28 Antiretroviral
Sung Yong Park1, Christian Takayama2, Jenica Ryu3
1Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, California, USA.
Background:
The emergence and spread of human immunodeficiency virus (HIV) drug-resistant strains present a major barrier to effective lifelong antiretroviral therapy. The anticipated rise in long-acting subcutaneous lenacapavir (LEN) use, along with the increased risk of transmitted resistance and pre-exposure prophylaxis-associated resistance, underscore the urgent need for advanced genotyping methods to enhance clinical care and prevention strategies.
Methods:
We developed the portable HIV genotyping (PHG) platform, which combines cost-effective next-generation sequencing with cloud computing to screen for resistance to 28 antiretroviral drugs across 5 major classes, including LEN. We analyzed 3 study cohorts and compared our drug-resistance findings with standard-care testing results and high-fidelity sequencing data obtained through unique molecular identifier (UMI) labeling.
Results:
PHG identified 2 major LEN-resistance mutations in 1 participant, confirmed by an additional independent sequencing run. Across 3 study cohorts, PHG consistently detected the same drug-resistance mutations as standard-care genotyping and high-fidelity UMI labeling in most tested specimens. PHG's 10% limit of detection minimized false-positive results and enabled identification of minority variants with less than 20% frequency, pointing to underdiagnosis of drug resistance in clinical care. Furthermore, PHG identified linked cross-class resistance mutations, confirmed by UMI labeling, including linked cross-resistance in a participant who reported use of long-acting cabotegravir and rilpivirine. We also observed multiyear persistence of linked cross-class resistance mutations.
Conclusions:
PHG demonstrates significant improvements over standard-care HIV genotyping, offering deeper insights into LEN resistance, minority variants, and cross-class resistance using a low-cost, high-throughput portable sequencing technology and publicly available cloud computing.
