Certain infected individuals suppress human immunodeficiency virus (HIV) in the absence of anti-retroviral therapy (ART). Elucidating the underlying mechanism(s) is of high interest. Here we present two contrasting case reports of HIV-infected individuals who controlled plasma viremia for extended periods after undergoing analytical treatment interruption (ATI). In Participant 04, who experienced viral blips and initiated undisclosed self-administration of suboptimal ART detected shortly before day 1,250, phylogenetic analyses of plasma HIV env sequences suggested continuous viral evolution and/or reactivation of pre-existing viral reservoirs over time. Antiviral CD8+ T cell activities were higher in Participant 04 than in Participant 30. In contrast, Participant 30 exhibited potent plasma-IgG-mediated neutralization activity against autologous virus that became ineffective when he experienced sudden plasma viral rebound 1,434 d after ATI due to HIV superinfection. Our data provide insight into distinct mechanisms of post-treatment interruption control and highlight the importance of frequent monitoring of undisclosed use of ART and superinfection during the ATI phase.
This is a preview of subscription content, access via your institution
Access Nature and 54 other Nature Portfolio journals
Get Nature+, our best-value online-access subscription
$29.99 / 30 days
cancel any time
Subscribe to this journal
Receive 12 print issues and online access
$209.00 per year
only $17.42 per issue
Rent or buy this article
Prices vary by article type
Prices may be subject to local taxes which are calculated during checkout
HIV sequences are available in GenBank under accession numbers MT998681–MT998840 (Participant 04) and MW865486–MW865605 (Participant 30). All HIV integration site sequences are available in BioProject under accession number PRJNA720555. External requests for data will be evaluated by the corresponding author, and requests might be subject to National Institutes of Health policies.
The pipeline for annotated HIV integration site sequences is available at https://github.com/NCBR-FNLCR/NCBR_hiv_integration.
Deeks, S. G., Lewin, S. R. & Havlir, D. V. The end of AIDS: HIV infection as a chronic disease. Lancet 382, 1525–1533 (2013).
Chun, T. W., Moir, S. & Fauci, A. S. HIV reservoirs as obstacles and opportunities for an HIV cure. Nat. Immunol. 16, 584–589 (2015).
Margolis, D. M. et al. Curing HIV: seeking to target and clear persistent infection. Cell 181, 189–206 (2020).
Lewin, S. R. & Rasmussen, T. A. Kick and kill for HIV latency. Lancet 395, 844–846 (2020).
Barouch, D. H. & Deeks, S. G. Immunologic strategies for HIV-1 remission and eradication. Science 345, 169–174 (2014).
Namazi, G. et al. The Control of HIV After Antiretroviral Medication Pause (CHAMP) study: posttreatment controllers identified from 14 clinical studies. J. Infect. Dis. 218, 1954–1963 (2018).
Sáez-Cirión, A. et al. Post-treatment HIV-1 controllers with a long-term virological remission after the interruption of early initiated antiretroviral therapy ANRS VISCONTI Study. PLoS Pathog. 9, e1003211 (2013).
Etemad, B., Esmaeilzadeh, E. & Li, J. Z. Learning from the exceptions: HIV remission in post-treatment controllers. Front. Immunol. 10, 1749 (2019).
Fogel, J. M. et al. Undisclosed antiretroviral drug use in a multinational clinical trial (HIV Prevention Trials Network 052). J. Infect. Dis. 208, 1624–1628 (2013).
Sykes, W. et al. Discovery of false elite controllers: HIV antibody-positive RNA-negative blood donors found to be on antiretroviral therapy. J. Infect. Dis. 220, 643–647 (2019).
Altfeld, M. et al. HIV-1 superinfection despite broad CD8+ T-cell responses containing replication of the primary virus. Nature 420, 434–439 (2002).
Smith, D. M., Richman, D. D. & Little, S. J. HIV superinfection. J. Infect. Dis. 192, 438–444 (2005).
Redd, A. D., Quinn, T. C. & Tobian, A. A. Frequency and implications of HIV superinfection. Lancet Infect. Dis. 13, 622–628 (2013).
Sneller, M. C. et al. A randomized controlled safety/efficacy trial of therapeutic vaccination in HIV-infected individuals who initiated antiretroviral therapy early in infection. Sci. Transl. Med. 9, eaan8848 (2017).
Jiang, C. et al. Distinct viral reservoirs in individuals with spontaneous control of HIV-1. Nature 585, 261–267 (2020).
Van Gassen, S. et al. FlowSOM: using self-organizing maps for visualization and interpretation of cytometry data. Cytom. A 87, 636–645 (2015).
Mascola, J. R. & Haynes, B. F. HIV-1 neutralizing antibodies: understanding nature’s pathways. Immunol. Rev. 254, 225–244 (2013).
Caskey, M., Klein, F. & Nussenzweig, M. C. Broadly neutralizing anti-HIV-1 monoclonal antibodies in the clinic. Nat. Med. 25, 547–553 (2019).
Sok, D. & Burton, D. R. Recent progress in broadly neutralizing antibodies to HIV. Nat. Immunol. 19, 1179–1188 (2018).
Gondim, M. V. P. et al. Heightened resistance to host type 1 interferons characterizes HIV-1 at transmission and after antiretroviral therapy interruption. Sci. Transl. Med. 13, eabd8179 (2021).
Song, H. et al. Tracking HIV-1 recombination to resolve its contribution to HIV-1 evolution in natural infection. Nat. Commun. 9, 1928 (2018).
Weber, M. D. et al. Virological and immunological responses to raltegravir and dolutegravir in the gut-associated lymphoid tissue of HIV-infected men and women. Antivir. Ther. 23, 495–504 (2018).
Imaz, A. et al. Seminal tenofovir concentrations, viral suppression, and semen quality with tenofovir alafenamide, compared with tenofovir disoproxil fumarate (Spanish HIV/AIDS Research Network, PreEC/RIS 40). Clin. Infect. Dis. 69, 1403–1409 (2019).
Lee, S. A. et al. Antiretroviral therapy concentrations differ in gut vs. lymph node tissues and are associated with HIV viral transcription by a novel RT–ddPCR assay. J. Acquir. Immune Defic. Syndr. 83, 530–537 (2020).
Chun, T. W. et al. HIV-infected individuals receiving effective antiviral therapy for extended periods of time continually replenish their viral reservoir. J. Clin. Invest. 115, 3250–3255 (2005).
Myers, L. E., McQuay, L. J. & Hollinger, F. B. Dilution assay statistics. J. Clin. Microbiol. 32, 732–739 (1994).
McLaren, W. et al. The Ensembl variant effect predictor. Genome Biol. 17, 122 (2016).
Quinlan, A. R. & Hall, I. M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841–842 (2010).
Qu, K. et al. Individuality and variation of personal regulomes in primary human T cells. Cell Syst. 1, 51–61 (2015).
We are grateful to the study volunteers for their participation in this study. We thank the National Institute of Allergy and Infectious Diseases HIV Outpatient Clinic staff for their assistance in the execution of this study. This work was supported by the Intramural Research Program of the National Institute of Allergy and Infectious Diseases, National Institutes of Health.
The authors declare no competing interests.
Peer review information Nature Medicine thanks Timothy Henrich, Joseph Wong and Morgane Rolland for their contribution to the peer review of this work. Alison Farrell is the primary editor on this article and managed its editorial process and peer review in collaboration with the rest of the editorial team.
Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Levels of CD4+ and CD8+ T cell counts of study participants are shown following discontinuation of ART.
a. Phylogenetic tree analysis of the 3’-half of HIV sequences. The phylogenetic tree without subtype B reference sequences was constructed using the neighbor-joining method and was rooted with the predominant sequences from day 56. The tree reliability was estimated by 1000 bootstrap replicates. The nodes that were supported by more than 80% of bootstrap replicates are indicated by asterisks. The sequences derived at multiple time points are shown in different symbols/colors. b. Genetic divergence of the 3’-half of HIV sequences of rebounding plasma HIV from each time point compared to that from day 56. c. Mutations identified in previously known HLA-restricted CD8+ T cell epitopes. Amino acid substitutions in all seven viral proteins (Vif, Vpr, Vpu, Tat, Rev, Env, and Nef) in the 3’-half of HIV sequences obtained at the time of plasma viral rebound (days 56, 581, 862, and 875) were examined to identify potential escape mutations at previously known HLA (A*03 and B*40)-restricted CD8+ T cell epitopes over time.
Frequencies of CD4+ T cells carrying total HIV DNA, cell-associated HIV RNA, and replication-competent HIV are shown following discontinuation of ART.
Extended Data Fig. 4 Characterization of HIV-integration landscape/features in the post-treatment controllers.
Integration sites of all HIV proviruses were analyzed in CD4+ T cells from the 2 post-treatment controllers, Participants 04 and 30 (D0) and from 3 chronic-treated HIV-infected individuals on suppressive ART (N01-N03) as controls. a. The relative proportion of HIV integration sites per chromosome in each participant is expressed by the heatmap. Contribution of each chromosome to the total size of human genome (first row of the heatmap) and to the genic regions (expressed by the black bars) are included as references. Distribution of individual HIV-integration sites in each chromosome is depicted by red bars for Participants 04 and 30, and blue bars for Participants N01-N03. b. Proportion of HIV proviruses integrated in the indicated genomic regions. c. Distance in bp between individual HIV-integration sites and the most proximal transcriptional start site (TSS) peak (left) or to the most proximal ATAC-Seq peak indicating accessible chromatin (right). The numbers of unique HIV integration events were 51, 53, 223, 80, and 100 for Participant 04, Participant 30, N01, N02, and N03, respectively.
High-dimensional flow cytometric analyses of longitudinal peripheral blood mononuclear cells (PBMCs) of study participants. a. Frequencies of the activation/exhaustion markers TIGIT, PD-1, CD38 and HLA-DR on CD8+ T cells in Participant 04 (red) and Participant 30 (blue) are shown. P values were determined using an unpaired two-tailed Mann-Whitney test; ns, P > 0.05; **, P = 0.0063; ***, P < 0.001, ns, not significant. P values were adjusted for multiple comparisons. b. Global opt-SNE plots of CD3 + T cells of pooled time points from each study participant (left) and opt-SNE visualization of expression of the indicated markers (right) are shown. c. Opt-SNE map of T cell clusters identified by FlowSOM clustering. Each number indicates a distinct cluster. d. Heatmap showing the level of expression (MFI) within individual clusters. e. Comparison of frequencies of T cells expressing markers associated with indicated clusters are shown. Ten time points per study participant were analyzed. Each measurement was performed once at each time point. P values were determined using an unpaired two-tailed Mann-Whitney test; *, P = 0.011; ***, P < 0.001. P values were adjusted for multiple comparisons.
Extended Data Fig. 6 Neutralization capacity of bNAbs and autologous plasma against replication-competent HIV isolates.
a. Sensitivity of infectious viral isolates to bNAbs. The concentration of all infectious viral isolates was initially determined by HIV p24 ELISA and titration using standard TZM-bl target cells. Each viral isolate was incubated with 10 µg/ml of bNAbs for 90 minutes followed by incubation with TZM-bl cells for 48 hours. Cells were then lysed and substrate was added to measure the luciferase activity. The level of viral suppression by each antibody was determined over media controls. The numbers of independent viral isolates examined on each day were as follows: 12 (day 117) and 11 (day 1,093) for Participant 04 and 10 (day 117), 11 (day 517), 9 (day 705), 12 (day 1,223), 12 (day 1,405), and 24 (day 1,447) for Participant 30. P values were determined using an unpaired two-tailed Mann-Whitney test; ns, P > 0.05; **, P = 0.004; ***, P < 0.001; ns, not significant. P values were adjusted for multiple comparisons. b. Neutralization curves for heat-inactivated plasma against autologous infectious HIV. Heat-inactivated, serially diluted plasma was subjected to the neutralization assay against replication-competent virus at multiple time points. Each measurement was performed in duplicate at each time point.
About this article
Cite this article
Blazkova, J., Gao, F., Marichannegowda, M.H. et al. Distinct mechanisms of long-term virologic control in two HIV-infected individuals after treatment interruption of anti-retroviral therapy. Nat Med 27, 1893–1898 (2021). https://doi.org/10.1038/s41591-021-01503-6
This article is cited by
Nature Reviews Microbiology (2023)
Chronic brain damage in HIV-infected individuals under antiretroviral therapy is associated with viral reservoirs, sulfatide release, and compromised cell-to-cell communication
Cellular and Molecular Life Sciences (2023)
Current HIV/AIDS Reports (2022)