Clinical Significance of Minority HIV-1 Drug Resistance Variants

Robert Shafer, Stanford University, Palo Alto
Clinical Sciences
Thematic Priority Area: Therapeutic Strategies for HIV
Innovative, Developmental, Exploratory Award (IDEA)

The high mutation rate of HIV-1 and the complex population genetics of HIV-1 within infected patients complicates the use of antiretroviral (ARV) drug resistance testing in both previously untreated and treated patients because standard genotypic resistance tests are unable to detect minority drug-resistant variants present at levels below 20% to 30% of the virus population within a clinical sample. This inability to detect minority drug-resistant variants may threaten the success of first-line ARV therapy at a time in which transmitted HIV-1 drug resistance has become common and may have a negative influence on the success of salvage therapy regimens.

The first aim of this proposal is to use a new sequencing technology (ultra-deep pyrosequencing) – which can reliably detect variants present in as few as one percent of a virus population – to determine the prevalence, proportions, and clinical significance of minority drug-resistant variants in ARV-naive patients with and without evidence of genotypic resistance by standard direct PCR dideoxynucleotide cycle sequencing. The second aim is to use ultra-deep pyrosequencing to determine the prevalence and proportions of minority drug-resistant variants in ARV-treated patients in whom decisions about salvage therapy would be influenced by the presence of minority drug-resistance variants. The third aim is to evaluate the potential of ultra-deep sequencing for detecting minority CXCR4-tropic HIV-1 variants in a background of a predominant CCR5-tropic HIV-1 population.

The insights gained from the studies outlined in this proposal will lead to the more effective use of initial ARV therapy in areas where transmitted HIV-1 drug resistance is common and to a better understanding of how to design salvage therapy regimens for patients in whom previous ARV treatments have been successful. The results of the studies outlined in this proposal will be pivotal in planning future larger studies of the clinical relevance of minority drug-resistant variants in a variety of different clinical settings. Follow-up studies will require larger numbers of patients including patients from clinical cohorts and clinical trials. Although the population of patients being studied in this proposal is large, no single population is able to provide answers for most clinical questions because of the confounding variables that make it difficult to distinguish association from causation when examining the relationship between minority drug-resistance mutations and virological outcome.