ArticleClinical infectious diseases : an official publication of the Infectious Diseases Society of America2025
Design and Evaluation of Next-Generation HIV Genotyping for Detection of Resistance Mutations to 28 Antiretroviral Drugs Across 5 Major Classes Including Lenacapavir.
Article in Clinical infectious diseases : an official publication of the Infectious Diseases Society of America, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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Abstract
backgroundThe 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.
methodsWe 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.
resultsPHG 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.
conclusionsPHG 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.
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