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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 despite antiretroviral therapy (ART) and to evaluate the effect of HIV-1 genetic diversity, expression, 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, sources of rebound viremia, and the evolution of resistance.

HIV-1 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 investigating the genetics of HIV-1 plasma RNA and cellular HIV-1 DNA and RNA, the TRU aims to reveal sources of persistent virus production on ART and the sources of rebound viremia after stopping ART.  The TRU developed the gold-standard assays that allow for sequencing of HIV RNA and DNA in single virions and in single infected cells.  These assays are applied to blood and tissues from HIV-1-infected donors to characterize the genetics of viremia in patients on and off ART.

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.  The TRU previously developed an allele-specific PCR (ASP) assay capable of detecting specific drug resistance mutations present in 0.1-0.001% of the total virus population.  More recently, the TRU developed an ultrasensitive single-genome sequencing (uSGS) assay that provides sequence information from thousands of HIV variants present in donors' plasma, providing templates to investigate the linkage of drug resistance mutations and to perform studies on HIV-1 evolution.  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: 21 October 2015

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