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Cited by 718HIV Research and TreatmentVirus-based gene therapy researchHIV/AIDS drug development and treatment

A quantitative approach for measuring the reservoir of latent HIV-1 proviruses

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Bruner, Katherine M., Wang, Zheng, Simonetti, Francesco R., Bender, Alexandra M., Kwon, Kyungyoon J., Sengupta, Srona, Fray, Emily J., Beg, Subul A. +18 more·2019·Nature
DOI 10.1038/s41586-019-0898-8PMC PMC6447073
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Abstract

A stable latent reservoir for HIV-1 in resting CD4+ T cells is the principal barrier to a cure 1-3. Curative strategies that target the reservoir are being tested 4,5 and require accurate, scalable reservoir assays. The reservoir was defined with quantitative viral outgrowth assays for cells that release infectious virus after one round of T cell activation 1. However, these quantitative outgrowth assays and newer assays for cells that produce viral RNA after activation 6 may underestimate the reservoir size because one round of activation does not induce all proviruses 7. Many studies rely on simple assays based on polymerase chain reaction to detect proviral DNA regardless of transcriptional status, but the clinical relevance of these assays is unclear, as the vast majority of proviruses are defective 7-9. Here we describe a more accurate method of measuring the HIV-1 reservoir that separately quantifies intact and defective proviruses. We show that the dynamics of cells that carry intact and defective proviruses are different in vitro and in vivo. These findings have implications for targeting the intact proviruses that are a barrier to curing HIV infection.

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  • The combination of Gag and Env detection covers the functionality of most of the viral genome length, avoiding a 5' or 3' constrained bias.

    “Thereby, the combination covers the functionality of most of the viral genome length, thus avoiding a 5 0 or 3 0 constrained bias”

    From Revealing viral and cellular dynamics of HIV-1 at the single-cell level during early treatment periods (2023) · cites this paper as [36]

    The Methods (Bioinformatic analysis; page unavailable) place the assay’s two amplicons at 5′ Ψ and 3′ env, and the Abstract says they jointly identify more than 90% of deleted proviruses as defective. This supports using targets at opposite ends to detect defects, but the paper uses Ψ—not gag—and does not establish that the assay tests the functionality of most of the genome or eliminates 5′/3′ bias. (LLM, conf=0.86)

    Experimental — accuracy not yet measured

  • Env expression alone is more affected by genetic defects than the gag region, and assay formats exclusively based on free Gag protein as a reservoir marker only insufficiently assess the presence of infectious particles.

    “Moreover, Env expression alone is more affected by genetic defects than the gag region, 36,53 and assay formats exclusively based on free Gag protein as a reservoir marker only insufficiently assess the presence of infectious particles.”

    From Revealing viral and cellular dynamics of HIV-1 at the single-cell level during early treatment periods (2023) · cites this paper as [36]

    The paper reports genetic defects affecting Env and finds that gag PCR excludes only 30% of defective proviruses (main text, page unavailable). It does not directly compare how often defects impair Env versus Gag expression. The citation follows the Env–gag comparison; the separate claim about free Gag protein assays is also not tested in this paper. (LLM, conf=0.80)

    Experimental — accuracy not yet measured

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Cites

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Research works printed but not linked: 33

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Authors
Bruner, K. M., Wang, Z., Simonetti, F. R., Bender, A. M., Kwon, K. J., Sengupta, S., Fray, E. J., Beg, S. A., Antar, A. A. R., Jenike, K. M., Bertagnolli, L. N., Capoferri, A. A., Kufera, J. T., Timmons, A., Nobles, C., Gregg, J., Wada, N., Ho, Y.-C., Zhang, H., Margolick, J. B., Blankson, J. N., Deeks, S. G., Bushman, F. D., Siliciano, J. D., Laird, G. M., & Siliciano, R. F.
Affiliations
  • Johns Hopkins University (US)
  • University of Pennsylvania (US)
  • University of California, San Francisco (US)
  • Howard Hughes Medical Institute (US)
Corresponding author
Siliciano, Robert F.
ORCID
Venue
Nature
Publisher
Springer Science and Business Media LLC
Published
2019-01-30
Volume
566
Issue
7742
Pages
120-125
ISSN
  • 0028-0836 (ISSN-L)
  • 1476-4687
DOI
10.1038/s41586-019-0898-8
PMC
PMC6447073
OpenAlex
W2911228036
Cited by
718
References
2
Citations by year
2026: 81 · 2025: 109 · 2024: 106 · 2023: 107 · 2022: 79 · 2021: 98 · 2020: 93 · 2019: 45
FWCI
44.40
Type
journal article
Language
en
Open access
Licence
www.springer.com/tdm (tdm)
Locations
  • Nature (publishedVersion)
  • PubMed (publishedVersion)
  • PubMed Central (acceptedVersion)
  • eScholarship (California Digital Library) (submittedVersion)
  • RePEc: Research Papers in Economics (submittedVersion)
Funders
  • National Science Foundation (1738428, 1621633)
  • Howard Hughes Medical Institute
  • Bill and Melinda Gates Foundation (OPP1115715)
  • National Institutes of Health (43222, UM1 AI12661)
  • National Heart, Lung, and Blood Institute (U01HL146201)
  • National Institute on Drug Abuse (R61DA047022)
  • National Institute of General Medical Sciences (T32GM007445)
  • National Institute of Allergy and Infectious Diseases (P01AI131374, P01AI131306, UM1AI126620, R01AI043222, R44AI124996, UM1AI126603, R43AI124996, AI126620, AI126603, U01AI035042, UM1 AI12661, P30AI027763)
  • National Center for Research Resources (UL1RR025005)
Topics
  • Life Sciences › Immunology and Microbiology › Virology › HIV Research and Treatment
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Virus-based gene therapy research
  • Health Sciences › Medicine › Infectious Diseases › HIV/AIDS drug development and treatment
Keywords
HIV-1 latent reservoir, proviral DNA, resting CD4+ T cells, HIV cure strategies, viral outgrowth assay, reservoir dynamics
MeSH terms
Carrier State, Cell Line, Defective Viruses, DNA, Viral, Humans, Lymphocyte Activation, Proviruses, CD4-Positive T-Lymphocytes, HIV-1, HIV Infections, Polymerase Chain Reaction, Virus Latency

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