Biphasic decay of intact SHIV genomes following initiation of antiretroviral therapy complicates analysis of interventions targeting the reservoir

Journal Article · 15 October 2023 · Proceedings of the National Academy of Sciences of the United States of America

DOI: https://doi.org/10.1073/pnas.2313209120 · OSTI ID:2246852

Kumar, Mithra R.  ^[1]; Fray, Emily J.  ^[1]; Bender, Alexandra M. ^[1]; Zitzmann, Carolin ^[2]; Ribeiro, Ruy M.  ^[2]; Perelson, Alan S.  ^[2]; Barouch, Dan H. ^[3]; Siliciano, Janet D. ^[1]; Siliciano, Robert F.  ^[4]

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1. Johns Hopkins University, Baltimore, MD (United States). School of Medicine
2. Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)
3. Beth Israel Deaconess Medical Center, Boston, MA (United States)
4. Johns Hopkins University, Baltimore, MD (United States). School of Medicine; Howard Hughes Medical Institute (HHMI), Baltimore, MD (United States)

The latent reservoir for HIV-1 in resting CD4⁺ T cells persists despite antiretroviral therapy (ART) and precludes cure. Reservoir-targeting interventions are evaluated in ART-treated macaques infected with simian immunodeficiency virus (SIV) or simian-human immunodeficiency virus (SHIV). Efficacy is determined by reservoir measurements before and after the intervention. However, most proviruses persisting in the setting of ART are defective. In addition, intact HIV-1 and SIV genomes undergo complex, multiphasic decay observable when new infection events are blocked by ART. Intervention-induced elimination of latently infected cells must be distinguished from natural decay. Here, we address these issues for SHIV. We describe an intact proviral DNA assay that allows digital counting of SHIV genomes lacking common fatal defects. We show that intact SHIV genomes in circulating CD4⁺ T cells undergo biphasic decay during the first year of ART, with a rapid first phase (t_1/2 = 30.1 d) and a slower second phase (t_1/2 = 8.1 mo) that is still more rapid that the slow decay observed in people with HIV-1 on long-term ART (t_1/2 = 3.7 y). In SHIV models, most interventions are tested during 2nd phase decay. Natural 2nd phase decay must be considered in evaluating interventions as most infected cells present at this time do not become part of the stable reservoir. In addition, for interventions tested during 2nd phase decay, a caveat is that the intervention may not be equally effective in people with HIV on long-term ART whose reservoirs are dominated by latently infected cells with a slower decay rate.

• Research Organization: Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)
• Sponsoring Organization: USDOE National Nuclear Security Administration (NNSA); National Institutes of Health (NIH); Johns Hopkins Center for AIDS Research
• Grant/Contract Number: 89233218CNA000001
• OSTI ID: 2246852
• Report Number(s): LA-UR--23-28914
• Journal Information: Proceedings of the National Academy of Sciences of the United States of America, Journal Name: Proceedings of the National Academy of Sciences of the United States of America Journal Issue: 43 Vol. 120; ISSN 0027-8424
• Publisher: National Academy of SciencesCopyright Statement
• Country of Publication: United States
• Language: English