Dynamic Shifts in the HIV Proviral Landscape During Long Term Combination Antiretroviral Therapy: Implications for Persistence and Control of HIV Infections
Elizabeth M. Anderson,
Francesco R. Simonetti,
Robert J. Gorelick,
Shawn Hill,
Monica A. Gouzoulis,
Jennifer Bell,
Catherine Rehm,
Liliana Pérez,
Eli Boritz,
Xiaolin Wu,
Daria Wells,
Stephen H. Hughes,
Venigalla Rao,
John M. Coffin,
Mary F. Kearney,
Frank Maldarelli
Affiliations
Elizabeth M. Anderson
HIV Dynamics and Replication Program, NCI, NIH, Frederick, MD 21702, USA
Francesco R. Simonetti
HIV Dynamics and Replication Program, NCI, NIH, Frederick, MD 21702, USA
Robert J. Gorelick
Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
Shawn Hill
HIV Dynamics and Replication Program, NCI, NIH, Frederick, MD 21702, USA
Monica A. Gouzoulis
HIV Dynamics and Replication Program, NCI, NIH, Frederick, MD 21702, USA
Jennifer Bell
Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
Catherine Rehm
Laboratory of Immunoregulation, NIAID, NIH, Bethesda, MD 20814, USA
Liliana Pérez
Virus Persistence and Dynamics Section, VRC, NIAID, NIH, Bethesda, MD 20814, USA
Eli Boritz
Virus Persistence and Dynamics Section, VRC, NIAID, NIH, Bethesda, MD 20814, USA
Xiaolin Wu
Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
Daria Wells
Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
Stephen H. Hughes
HIV Dynamics and Replication Program, NCI, NIH, Frederick, MD 21702, USA
Venigalla Rao
Department of Biology, The Catholic University of America, Washington, DC 20064, USA
John M. Coffin
Department of Biology, Tufts University, Boston, MA 02155, USA
Mary F. Kearney
HIV Dynamics and Replication Program, NCI, NIH, Frederick, MD 21702, USA
Frank Maldarelli
HIV Dynamics and Replication Program, NCI, NIH, Frederick, MD 21702, USA
Combination antiretroviral therapy (cART) controls but does not eradicate HIV infection; HIV persistence is the principal obstacle to curing infections. The proportion of defective proviruses increases during cART, but the dynamics of this process are not well understood, and a quantitative analysis of how the proviral landscape is reshaped after cART is initiated is critical to understanding how HIV persists. Here, we studied longitudinal samples from HIV infected individuals undergoing long term cART using multiplexed Droplet Digital PCR (ddPCR) approaches to quantify the proportion of deleted proviruses in lymphocytes. In most individuals undergoing cART, HIV proviruses that contain gag are lost more quickly than those that lack gag. Increases in the fraction of gag-deleted proviruses occurred only after 1−2 years of therapy, suggesting that the immune system, and/or toxicity of viral re-activation helps to gradually shape the proviral landscape. After 10−15 years on therapy, there were as many as 3.5−5 times more proviruses in which gag was deleted or highly defective than those containing intact gag. We developed a provirus-specific ddPCR approach to quantify individual clones. Investigation of a clone of cells containing a deleted HIV provirus integrated in the HORMAD2 gene revealed that the cells underwent a massive expansion shortly after cART was initiated until the clone, which was primarily in effector memory cells, dominated the population of proviruses for over 6 years. The expansion of this HIV-infected clone had substantial effects on the overall proviral population.
