Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Distinct mechanisms of long-term virologic control in two HIV-infected individuals after treatment interruption of anti-retroviral therapy

Abstract

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 options

Buy article

Get time limited or full article access on ReadCube.

$32.00

All prices are NET prices.

Fig. 1: Levels of plasma viremia after discontinuation of ART and phylogenetic analysis of HIV sequences.
Fig. 2: CD8+ T cell responses to HIV and neutralization capacity of autologous plasma against replication-competent viral isolates.

Data availability

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.

Code availability

The pipeline for annotated HIV integration site sequences is available at https://github.com/NCBR-FNLCR/NCBR_hiv_integration.

References

  1. Deeks, S. G., Lewin, S. R. & Havlir, D. V. The end of AIDS: HIV infection as a chronic disease. Lancet 382, 1525–1533 (2013).

    Article  Google Scholar 

  2. Chun, T. W., Moir, S. & Fauci, A. S. HIV reservoirs as obstacles and opportunities for an HIV cure. Nat. Immunol. 16, 584–589 (2015).

    Article  CAS  Google Scholar 

  3. Margolis, D. M. et al. Curing HIV: seeking to target and clear persistent infection. Cell 181, 189–206 (2020).

    Article  CAS  Google Scholar 

  4. Lewin, S. R. & Rasmussen, T. A. Kick and kill for HIV latency. Lancet 395, 844–846 (2020).

    Article  Google Scholar 

  5. Barouch, D. H. & Deeks, S. G. Immunologic strategies for HIV-1 remission and eradication. Science 345, 169–174 (2014).

    Article  CAS  Google Scholar 

  6. 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).

    Article  Google Scholar 

  7. 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).

    Article  Google Scholar 

  8. Etemad, B., Esmaeilzadeh, E. & Li, J. Z. Learning from the exceptions: HIV remission in post-treatment controllers. Front. Immunol. 10, 1749 (2019).

    Article  Google Scholar 

  9. 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).

    Article  CAS  Google Scholar 

  10. 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).

    Article  CAS  Google Scholar 

  11. Altfeld, M. et al. HIV-1 superinfection despite broad CD8+ T-cell responses containing replication of the primary virus. Nature 420, 434–439 (2002).

    Article  CAS  Google Scholar 

  12. Smith, D. M., Richman, D. D. & Little, S. J. HIV superinfection. J. Infect. Dis. 192, 438–444 (2005).

    Article  Google Scholar 

  13. Redd, A. D., Quinn, T. C. & Tobian, A. A. Frequency and implications of HIV superinfection. Lancet Infect. Dis. 13, 622–628 (2013).

    Article  Google Scholar 

  14. 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).

  15. Jiang, C. et al. Distinct viral reservoirs in individuals with spontaneous control of HIV-1. Nature 585, 261–267 (2020).

    Article  CAS  Google Scholar 

  16. Van Gassen, S. et al. FlowSOM: using self-organizing maps for visualization and interpretation of cytometry data. Cytom. A 87, 636–645 (2015).

    Article  Google Scholar 

  17. Mascola, J. R. & Haynes, B. F. HIV-1 neutralizing antibodies: understanding nature’s pathways. Immunol. Rev. 254, 225–244 (2013).

    Article  Google Scholar 

  18. Caskey, M., Klein, F. & Nussenzweig, M. C. Broadly neutralizing anti-HIV-1 monoclonal antibodies in the clinic. Nat. Med. 25, 547–553 (2019).

    Article  CAS  Google Scholar 

  19. Sok, D. & Burton, D. R. Recent progress in broadly neutralizing antibodies to HIV. Nat. Immunol. 19, 1179–1188 (2018).

    Article  CAS  Google Scholar 

  20. 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).

    Article  CAS  Google Scholar 

  21. Song, H. et al. Tracking HIV-1 recombination to resolve its contribution to HIV-1 evolution in natural infection. Nat. Commun. 9, 1928 (2018).

    Article  Google Scholar 

  22. 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).

    Article  Google Scholar 

  23. 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).

    Article  CAS  Google Scholar 

  24. 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).

    Article  CAS  Google Scholar 

  25. 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).

    Article  CAS  Google Scholar 

  26. Myers, L. E., McQuay, L. J. & Hollinger, F. B. Dilution assay statistics. J. Clin. Microbiol. 32, 732–739 (1994).

    Article  CAS  Google Scholar 

  27. McLaren, W. et al. The Ensembl variant effect predictor. Genome Biol. 17, 122 (2016).

    Article  Google Scholar 

  28. Quinlan, A. R. & Hall, I. M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841–842 (2010).

    Article  CAS  Google Scholar 

  29. Qu, K. et al. Individuality and variation of personal regulomes in primary human T cells. Cell Syst. 1, 51–61 (2015).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

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.

Author information

Authors and Affiliations

Authors

Contributions

J.B., F.G., S.M., A.S.F. and T.-W.C. designed the research. J.B., F.G., M.H.M., J.S.J., V.S., E.J.W., R.F.S., E.D.H., M.C. and T.-W.C. performed experiments. J.B., F.G., M.H.M. and J.L. performed bioinformatic analysis. K.G., E.B., C.K. and M.C.S. contributed to recruitment of study participants. J.B., F.G., M.H.M., J.L., S.M. and T.-W.C. analyzed data. J.B., S.M., A.S.F. and T.-W.C. wrote the manuscript.

Corresponding author

Correspondence to Tae-Wook Chun.

Ethics declarations

Competing interests

The authors declare no competing interests.

Additional information

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.

Extended data

Extended Data Fig. 1 Longitudinal measurements of CD4+ and CD8+ T cell counts.

Levels of CD4+ and CD8+ T cell counts of study participants are shown following discontinuation of ART.

Extended Data Fig. 2 Genetic analyses of rebounding plasma HIV in Participant 04.

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.

Extended Data Fig. 3 Dynamics of HIV reservoirs.

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.

Extended Data Fig. 5 Phenotypic characterization of T cells.

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.

Extended Data Table 1 Baseline characteristics of study participants

Supplementary information

Supplementary Information

Supplementary Table 1: Antibodies used for T cell phenotyping and intracellular cytokine staining. Supplementary Fig. 1: Gating strategy for T cell subsets and intracellular cytokine staining

Reporting Summary

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

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

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/s41591-021-01503-6

This article is cited by

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing