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Research Focus: Studies of Clinical Resistance

The Translational Research Unit (TRU) is primarily responsible for advancing the clinical and translational research efforts of the Host-Virus Interaction Branch by developing and applying new technologies to characterize and identify the sources of persistent HIV-1 viremia despite antiretroviral therapy (ART) and to evaluate the effect of HIV-1 genetic diversity and low-frequency drug resistance mutations on the response to ART.  Working closely with Dr. Frank Maldarelli in the Clinical Retrovirology Section, in consultation with Dr. John Coffin of Tufts University and Dr. John Mellors of the University of Pittsburgh, the TRU collaborates with research groups worldwide to perform studies of HIV-host interactions, viral persistence during therapy, and the evolution of resistance.

HIV-1 viremia persists in patients on ART despite suppression to very low levels and usually rebounds to pretherapy levels if ART is stopped.  The mechanisms that allow viremia to persist during therapy are not well understood.  Their elucidation is imperative if HIV-1 infection is ever to be cured.  Cellular reservoirs that harbor HIV-1 genomes and express viral RNA during ART are likely long-lived, proliferating cells that were infected prior to initiating therapy.  By measuring the levels of HIV-1 plasma RNA and levels of cellular HIV-1 DNA and RNA during treatment and by sequencing virus populations in cells and plasma, the TRU aims to reveal sources of persistent virus production on ART.  We previously developed assays in the TRU that are capable of measuring very low levels of viremia and of sequencing HIV-1 populations in patient plasma and tissues.  We have now combined these techniques to enable sequencing of virus populations in patients with very low levels of viremia and have applied these methods to characterize the genetics of persistent viremia in patients on short- and long-term ART and to characterize proviral and intracellular viral RNA in different tissues and cellular subsets.

Determining the frequency of rare, drug-resistant variants in untreated patients can provide important insights into the emergence of drug resistance and into the effective population size of HIV-1.  We previously developed an allele-specific PCR (ASP) assay capable of detecting specific drug resistance mutations present in 0.1% of the total virus population.  Recently, we have increased the sensitivity of this assay 100-fold to 0.001%, and applied this improved technology to samples from RT-SHIV-infected macaques to estimate mutant frequencies before ART and to estimate replicating population sizes.  Ongoing studies include applying these and other ultrasensitive methods under development to samples collected from women before and after exposure to single-dose nevirapine (NVP) and in patients initiating standard-of-care ART to investigate the impacts of HIV-1 diversity, low-frequency drug-resistant variants, and effective population size on the response to ART.

Last modified: 13 March 2014

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