1
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Ngo MH, Pankrac J, Ho RCY, Ndashimye E, Pawa R, Ceccacci R, Biru T, Olabode AS, Klein K, Li Y, Kovacs C, Assad R, Jacobson JM, Canaday DH, Tomusange S, Jamiru S, Anok A, Kityamuweesi T, Buule P, Galiwango RM, Reynolds SJ, Quinn TC, Redd AD, Prodger JL, Mann JFS, Arts EJ. Effective and targeted latency reversal in CD4 + T cells from individuals on long term combined antiretroviral therapy initiated during chronic HIV-1 infection. Emerg Microbes Infect 2024; 13:2327371. [PMID: 38444369 DOI: 10.1080/22221751.2024.2327371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Accepted: 03/01/2024] [Indexed: 03/07/2024]
Abstract
To date, an affordable, effective treatment for an HIV-1 cure remains only a concept with most "latency reversal" agents (LRAs) lacking specificity for the latent HIV-1 reservoir and failing in early clinical trials. We assessed HIV-1 latency reversal using a multivalent HIV-1-derived virus-like particle (HLP) to treat samples from 32 people living with HIV-1 (PLWH) in Uganda, US and Canada who initiated combined antiretroviral therapy (cART) during chronic infection. Even after 5-20 years on stable cART, HLP could target CD4+ T cells harbouring latent HIV-1 reservoir resulting in 100-fold more HIV-1 release into culture supernatant than by common recall antigens, and 1000-fold more than by chemotherapeutic LRAs. HLP induced release of a divergent and replication-competent HIV-1 population from PLWH on cART. These findings suggest HLP provides a targeted approach to reactivate the majority of latent HIV-1 proviruses among individuals infected with HIV-1.
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Affiliation(s)
- Minh Ha Ngo
- Department of Microbiology and Immunology, University of Western Ontario, London, Canada
- College of Veterinary Medicine, Vietnam National University of Agriculture, Hanoi, Vietnam
| | - Joshua Pankrac
- Department of Microbiology and Immunology, University of Western Ontario, London, Canada
| | - Ryan C Y Ho
- Department of Microbiology and Immunology, University of Western Ontario, London, Canada
| | - Emmanuel Ndashimye
- Department of Microbiology and Immunology, University of Western Ontario, London, Canada
| | - Rahul Pawa
- Department of Microbiology and Immunology, University of Western Ontario, London, Canada
| | - Renata Ceccacci
- Department of Microbiology and Immunology, University of Western Ontario, London, Canada
| | - Tsigereda Biru
- Department of Microbiology and Immunology, University of Western Ontario, London, Canada
- Special Immunology Unit and Division of Infectious Diseases, Department of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Abayomi S Olabode
- Department of Microbiology and Immunology, University of Western Ontario, London, Canada
| | - Katja Klein
- Department of Microbiology and Immunology, University of Western Ontario, London, Canada
- Bristol Veterinary School, University of Bristol, Bristol, UK
| | - Yue Li
- Department of Microbiology and Immunology, University of Western Ontario, London, Canada
| | - Colin Kovacs
- Maple Leaf Medical Clinic and Division of Infectious Diseases, Department of Medicine, University of Toronto, Toronto, Canada
| | - Robert Assad
- Special Immunology Unit and Division of Infectious Diseases, Department of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Jeffrey M Jacobson
- Special Immunology Unit and Division of Infectious Diseases, Department of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - David H Canaday
- Special Immunology Unit and Division of Infectious Diseases, Department of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | | | | | - Aggrey Anok
- Rakai Health Sciences Program, Kalisizo, Uganda
| | | | - Paul Buule
- Rakai Health Sciences Program, Kalisizo, Uganda
| | | | - Steven J Reynolds
- Rakai Health Sciences Program, Kalisizo, Uganda
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Thomas C Quinn
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Andrew D Redd
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Jessica L Prodger
- Department of Microbiology and Immunology, University of Western Ontario, London, Canada
| | - Jamie F S Mann
- Department of Microbiology and Immunology, University of Western Ontario, London, Canada
- Bristol Veterinary School, University of Bristol, Bristol, UK
| | - Eric J Arts
- Department of Microbiology and Immunology, University of Western Ontario, London, Canada
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2
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Lee GQ, Khadka P, Gowanlock SN, Copertino DC, Duncan MC, Omondi FH, Kinloch NN, Kasule J, Kityamuweesi T, Buule P, Jamiru S, Tomusange S, Anok A, Chen Z, Jones RB, Galiwango RM, Reynolds SJ, Quinn TC, Brumme ZL, Redd AD, Prodger JL. HIV-1 subtype A1, D, and recombinant proviral genome landscapes during long-term suppressive therapy. Nat Commun 2024; 15:5480. [PMID: 38956017 PMCID: PMC11219899 DOI: 10.1038/s41467-024-48985-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 05/13/2024] [Indexed: 07/04/2024] Open
Abstract
The primary obstacle to curing HIV-1 is a reservoir of CD4+ cells that contain stably integrated provirus. Previous studies characterizing the proviral landscape, which have been predominantly conducted in males in the United States and Europe living with HIV-1 subtype B, have revealed that most proviruses that persist during antiretroviral therapy (ART) are defective. In contrast, less is known about proviral landscapes in females with non-B subtypes, which represents the largest group of individuals living with HIV-1. Here, we analyze genomic DNA from resting CD4+ T-cells from 16 female and seven male Ugandans with HIV-1 receiving suppressive ART (n = 23). We perform near-full-length proviral sequencing at limiting dilution to examine the proviral genetic landscape, yielding 607 HIV-1 subtype A1, D, and recombinant proviral sequences (mean 26/person). We observe that intact genomes are relatively rare and clonal expansion occurs in both intact and defective genomes. Our modification of the primers and probes of the Intact Proviral DNA Assay (IPDA), developed for subtype B, rescues intact provirus detection in Ugandan samples for which the original IPDA fails. This work will facilitate research on HIV-1 persistence and cure strategies in Africa, where the burden of HIV-1 is heaviest.
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Affiliation(s)
- Guinevere Q Lee
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York, NY, USA.
| | - Pragya Khadka
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York, NY, USA
| | - Sarah N Gowanlock
- Department of Microbiology and Immunology, Western University, London, ON, Canada
| | - Dennis C Copertino
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York, NY, USA
| | - Maggie C Duncan
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - F Harrison Omondi
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Natalie N Kinloch
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | | | | | - Paul Buule
- Rakai Health Sciences Program, Kalisizo, Uganda
| | | | | | - Aggrey Anok
- Rakai Health Sciences Program, Kalisizo, Uganda
| | - Zhengming Chen
- Department of Population Health Sciences, Division of Biostatistics, Weill Cornell Medicine, New York, NY, USA
| | - R Brad Jones
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York, NY, USA
| | | | - Steven J Reynolds
- Rakai Health Sciences Program, Kalisizo, Uganda
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Thomas C Quinn
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Zabrina L Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Andrew D Redd
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Jessica L Prodger
- Department of Microbiology and Immunology, Western University, London, ON, Canada
- Department of Epidemiology and Biostatistics, Western University, London, ON, Canada
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3
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Ferreira RC, Reynolds SJ, Capoferri AA, Baker OR, Brown EE, Klock E, Miller J, Lai J, Saraf S, Kirby C, Lynch B, Hackman J, Gowanlock SN, Tomusange S, Jamiru S, Anok A, Kityamuweesi T, Buule P, Bruno D, Martens C, Rose R, Lamers SL, Galiwango RM, Poon AFY, Quinn TC, Prodger JL, Redd AD. Temporary increase in circulating replication-competent latent HIV-infected resting CD4+ T cells after switch to an integrase inhibitor based antiretroviral regimen. EBioMedicine 2024; 102:105040. [PMID: 38485563 PMCID: PMC11026949 DOI: 10.1016/j.ebiom.2024.105040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 02/16/2024] [Accepted: 02/16/2024] [Indexed: 03/26/2024] Open
Abstract
BACKGROUND The principal barrier to an HIV cure is the presence of the latent viral reservoir (LVR), which has been understudied in African populations. From 2018 to 2019, Uganda instituted a nationwide rollout of ART consisting of Dolutegravir (DTG) with two NRTI, which replaced the previous regimen of one NNRTI and the same two NRTI. METHODS Changes in the inducible replication-competent LVR (RC-LVR) of ART-suppressed Ugandans with HIV (n = 88) from 2015 to 2020 were examined using the quantitative viral outgrowth assay. Outgrowth viruses were examined for viral evolution. Changes in the RC-LVR were analyzed using three versions of a Bayesian model that estimated the decay rate over time as a single, linear rate (model A), or allowing for a change at time of DTG initiation (model B&C). FINDINGS Model A estimated the slope of RC-LVR change as a non-significant positive increase, which was due to a temporary spike in the RC-LVR that occurred 0-12 months post-DTG initiation (p < 0.005). This was confirmed with models B and C; for instance, model B estimated a significant decay pre-DTG initiation with a half-life of 6.9 years, and an ∼1.7-fold increase in the size of the RC-LVR post-DTG initiation. There was no evidence of viral failure or consistent evolution in the cohort. INTERPRETATION These data suggest that the change from NNRTI- to DTG-based ART is associated with a significant temporary increase in the circulating RC-LVR. FUNDING Supported by the NIH (grant 1-UM1AI164565); Gilead HIV Cure Grants Program (90072171); Canadian Institutes of Health Research (PJT-155990); and Ontario Genomics-Canadian Statistical Sciences Institute.
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Affiliation(s)
- Roux-Cil Ferreira
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Steven J Reynolds
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA; Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Rakai Health Sciences Program, Kalisizo, Uganda
| | - Adam A Capoferri
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Owen R Baker
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Erin E Brown
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Ethan Klock
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jernelle Miller
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jun Lai
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Sharada Saraf
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Charles Kirby
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Briana Lynch
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Jada Hackman
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Sarah N Gowanlock
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | | | | | - Aggrey Anok
- Rakai Health Sciences Program, Kalisizo, Uganda
| | | | - Paul Buule
- Rakai Health Sciences Program, Kalisizo, Uganda
| | - Daniel Bruno
- Genomics Research Section, Rocky Mountain Laboratories, NIAID, NIH, Hamilton, MT, USA
| | - Craig Martens
- Genomics Research Section, Rocky Mountain Laboratories, NIAID, NIH, Hamilton, MT, USA
| | | | | | | | - Art F Y Poon
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada; Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Thomas C Quinn
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA; Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jessica L Prodger
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada; Department of Epidemiology and Biostatistics, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Andrew D Redd
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA; Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa.
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4
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Ranga U, Panchapakesan A, Saini C. HIV-1 subtypes and latent reservoirs. Curr Opin HIV AIDS 2024; 19:87-92. [PMID: 38169308 DOI: 10.1097/coh.0000000000000835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
PURPOSE OF REVIEW We explore the current status of research on HIV-1 subtype-specific variations and their impact on HIV-1 latency. We also briefly address the controversy surrounding the decision-making process governing the ON/OFF states of HIV-1 transcription, specifically focusing on the regulatory elements, the long terminal repeat (LTR), and Tat. Understanding the decision-making process is crucial for developing effective intervention strategies, such as the 'shock-and-kill' approach, to reactivate latent HIV-1. RECENT FINDINGS Attention has been drawn to subtype-specific transcription factor binding site (TFBS) variations and the possible impact of these variations on viral latency. Further, diverse subtype-specific assays have been developed to quantify the latent viral reservoirs. One interesting observation is the relatively larger latent reservoirs in HIV-1B infection than those of other viral subtypes, which needs rigorous validation. The emergence of LTR-variant viral strains in HIV-1C demonstrating significantly higher levels of latency reversal has been reported. SUMMARY Despite persistent and substantial efforts, latent HIV-1 remains a formidable challenge to a functional cure. Determined and continued commitment is needed to understand the ON/OFF decision-making process of HIV-1 latency, develop rigorous assays for accurately quantifying the latent reservoirs, and identify potent latency-reversing agents and cocktails targeting multiple latency stages. The review emphasizes the importance of including diverse viral subtypes in future latency research.
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Affiliation(s)
- Udaykumar Ranga
- HIV-AIDS Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore, Karnataka
| | - Arun Panchapakesan
- Molecular Biology Laboratory, Y R Gaitonde Centre for AIDS Research and Education (YRG CARE), Chennai, Tamil Nadu, India
| | - Chhavi Saini
- HIV-AIDS Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore, Karnataka
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5
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Kankaka EN, Redd AD, Khan A, Reynolds SJ, Saraf S, Kirby C, Lynch B, Hackman J, Tomusange S, Kityamuweesi T, Jamiru S, Anok A, Buule P, Bruno D, Martens C, Chang LW, Quinn TC, Prodger JL, Poon A. Dating reservoir formation in virologically suppressed people living with HIV-1 in Rakai, Uganda. Virus Evol 2023; 9:vead046. [PMID: 37547379 PMCID: PMC10399970 DOI: 10.1093/ve/vead046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 06/15/2023] [Accepted: 07/25/2023] [Indexed: 08/08/2023] Open
Abstract
The timing of the establishment of the HIV latent viral reservoir (LVR) is of particular interest, as there is evidence that proviruses are preferentially archived at the time of antiretroviral therapy (ART) initiation. Quantitative viral outgrowth assays (QVOAs) were performed using Peripheral Blood Mononuclear Cells (PBMC) collected from Ugandans living with HIV who were virally suppressed on ART for >1 year, had known seroconversion windows, and at least two archived ART-naïve plasma samples. QVOA outgrowth populations and pre-ART plasma samples were deep sequenced for the pol and gp41 genes. The bayroot program was used to estimate the date that each outgrowth virus was incorporated into the reservoir. Bayroot was also applied to previously published data from a South African cohort. In the Ugandan cohort (n = 11), 87.9 per cent pre-ART and 56.3 per cent viral outgrowth sequences were unique. Integration dates were estimated to be relatively evenly distributed throughout viremia in 9/11 participants. In contrast, sequences from the South African cohort (n = 9) were more commonly estimated to have entered the LVR close to ART initiation, as previously reported. Timing of LVR establishment is variable between populations and potentially viral subtypes, which could limit the effectiveness of interventions that target the LVR only at ART initiation.
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Affiliation(s)
- Edward Nelson Kankaka
- Research Department, Rakai Health Sciences Program, 4-6 Sanitary Lane, Old Bukoba Road, Kalisizo 256, Uganda
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, 615 N. Wolfe Street, Baltimore, MD 21211, USA
| | - Andrew D Redd
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, 615 N. Wolfe Street, Baltimore, MD 21211, USA
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 5601 Fishers Lane, MSC, Bethesda, MD 9806, USA
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Faculty of Health Sciences, Anzio Rd, Observatory, Cape Town 7925, South Africa
| | - Amjad Khan
- Department of Pathology, Schulich School of Medicine and Dentistry, Western University, 1151 Richmond Street, London, Ontario N6A 5K8, Canada
| | - Steven J Reynolds
- Research Department, Rakai Health Sciences Program, 4-6 Sanitary Lane, Old Bukoba Road, Kalisizo 256, Uganda
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, 615 N. Wolfe Street, Baltimore, MD 21211, USA
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 5601 Fishers Lane, MSC, Bethesda, MD 9806, USA
| | - Sharada Saraf
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 5601 Fishers Lane, MSC, Bethesda, MD 9806, USA
| | - Charles Kirby
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, 615 N. Wolfe Street, Baltimore, MD 21211, USA
| | - Briana Lynch
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 5601 Fishers Lane, MSC, Bethesda, MD 9806, USA
| | - Jada Hackman
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 5601 Fishers Lane, MSC, Bethesda, MD 9806, USA
| | - Stephen Tomusange
- Research Department, Rakai Health Sciences Program, 4-6 Sanitary Lane, Old Bukoba Road, Kalisizo 256, Uganda
| | - Taddeo Kityamuweesi
- Research Department, Rakai Health Sciences Program, 4-6 Sanitary Lane, Old Bukoba Road, Kalisizo 256, Uganda
| | - Samiri Jamiru
- Research Department, Rakai Health Sciences Program, 4-6 Sanitary Lane, Old Bukoba Road, Kalisizo 256, Uganda
| | - Aggrey Anok
- Research Department, Rakai Health Sciences Program, 4-6 Sanitary Lane, Old Bukoba Road, Kalisizo 256, Uganda
| | - Paul Buule
- Research Department, Rakai Health Sciences Program, 4-6 Sanitary Lane, Old Bukoba Road, Kalisizo 256, Uganda
| | - Daniel Bruno
- Genomic Unit, Rocky Mountain Laboratories, NIAID, NIH, 904 South Fourth Street, Hamilton, MT 59840, USA
| | - Craig Martens
- Genomic Unit, Rocky Mountain Laboratories, NIAID, NIH, 904 South Fourth Street, Hamilton, MT 59840, USA
| | - Larry W Chang
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, 615 N. Wolfe Street, Baltimore, MD 21211, USA
| | - Thomas C Quinn
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, 615 N. Wolfe Street, Baltimore, MD 21211, USA
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 5601 Fishers Lane, MSC, Bethesda, MD 9806, USA
| | - Jessica L Prodger
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, Western University, 1151 Richmond Street, London, Ontario N6A 5K8, Canada
| | - Art Poon
- Department of Pathology, Schulich School of Medicine and Dentistry, Western University, 1151 Richmond Street, London, Ontario N6A 5K8, Canada
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6
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Ferreira RC, Reynolds SJ, Capoferri AA, Baker O, Brown EE, Klock E, Miller J, Lai J, Saraf S, Kirby C, Lynch B, Hackman J, Gowanlock SN, Tomusange S, Jamiru S, Anok A, Kityamuweesi T, Buule P, Bruno D, Martens C, Rose R, Lamers SL, Galiwango RM, Poon AFY, Quinn TC, Prodger JL, Redd AD. Temporary increase in circulating replication-competent latent HIV-infected resting CD4+ T cells after switch to an integrase inhibitor based antiretroviral regimen. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.05.12.23289896. [PMID: 37292785 PMCID: PMC10246077 DOI: 10.1101/2023.05.12.23289896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The principal barrier to an HIV cure is the presence of a latent viral reservoir (LVR) made up primarily of latently infected resting CD4+ (rCD4) T-cells. Studies in the United States have shown that the LVR decays slowly (half-life=3.8 years), but this rate in African populations has been understudied. This study examined longitudinal changes in the inducible replication competent LVR (RC-LVR) of ART-suppressed Ugandans living with HIV (n=88) from 2015-2020 using the quantitative viral outgrowth assay, which measures infectious units per million (IUPM) rCD4 T-cells. In addition, outgrowth viruses were examined with site-directed next-generation sequencing to assess for possible ongoing viral evolution. During the study period (2018-19), Uganda instituted a nationwide rollout of first-line ART consisting of Dolutegravir (DTG) with two NRTI, which replaced the previous regimen that consisted of one NNRTI and the same two NRTI. Changes in the RC-LVR were analyzed using two versions of a novel Bayesian model that estimated the decay rate over time on ART as a single, linear rate (model A) or allowing for an inflection at time of DTG initiation (model B). Model A estimated the population-level slope of RC-LVR change as a non-significant positive increase. This positive slope was due to a temporary increase in the RC-LVR that occurred 0-12 months post-DTG initiation (p<0.0001). This was confirmed with model B, which estimated a significant decay pre-DTG initiation with a half-life of 7.7 years, but a significant positive slope post-DTG initiation leading to a transient estimated doubling-time of 8.1 years. There was no evidence of viral failure in the cohort, or consistent evolution in the outgrowth sequences associated with DTG initiation. These data suggest that either the initiation of DTG, or cessation of NNRTI use, is associated with a significant temporary increase in the circulating RC-LVR.
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Affiliation(s)
- Roux-Cil Ferreira
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Steven J. Reynolds
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD
- Rakai Health Sciences Program, Kalisizo, Uganda
| | - Adam A. Capoferri
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Owen Baker
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Erin E. Brown
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Ethan Klock
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Jernelle Miller
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Jun Lai
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Sharada Saraf
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Charles Kirby
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Briana Lynch
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Jada Hackman
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Sarah N. Gowanlock
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, Western University, London, Ontario
| | | | | | - Aggrey Anok
- Rakai Health Sciences Program, Kalisizo, Uganda
| | | | - Paul Buule
- Rakai Health Sciences Program, Kalisizo, Uganda
| | - Daniel Bruno
- Genomic Unit, Rocky Mountain Laboratories, NIAID, NIH, Hamilton, MT
| | - Craig Martens
- Genomic Unit, Rocky Mountain Laboratories, NIAID, NIH, Hamilton, MT
| | | | | | | | - Art F. Y. Poon
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, Western University, London, Ontario
| | - Thomas C. Quinn
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Jessica L. Prodger
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, Western University, London, Ontario
- Department of Epidemiology and Biostatistics, Schulich School of Medicine and Dentistry, Western University, London, Ontario
| | - Andrew D. Redd
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
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7
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Adair JE, Androski L, Bayigga L, Bazira D, Brandon E, Dee L, Deeks S, Draz M, Dubé K, Dybul M, Gurkan U, Harlow E, Kityo C, Louella M, Malik P, Mathews V, McKemey A, Mugerwa H, Muyanja D, Olayiwola O, Orentas RJ, Popovski A, Sheehy J, Ssali F, Nsubuga MS, Tisdale JF, Verhoeyen E, Dropulić B. Towards access for all: 1st Working Group Report for the Global Gene Therapy Initiative (GGTI). Gene Ther 2023; 30:216-221. [PMID: 34493840 PMCID: PMC10113145 DOI: 10.1038/s41434-021-00284-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 07/09/2021] [Accepted: 07/21/2021] [Indexed: 11/09/2022]
Abstract
The gene and cell therapy field saw its first approved treatments in Europe in 2012 and the United States in 2017 and is projected to be at least a $10B USD industry by 2025. Despite this success, a massive gap exists between the companies, clinics, and researchers developing these therapeutic approaches, and their availability to the patients who need them. The unacceptable reality is a geographic exclusion of low-and middle-income countries (LMIC) in gene therapy development and ultimately the provision of gene therapies to patients in LMIC. This is particularly relevant for gene therapies to treat human immunodeficiency virus infection and hemoglobinopathies, global health crises impacting tens of millions of people primarily located in LMIC. Bridging this divide will require research, clinical and regulatory infrastructural development, capacity-building, training, an approval pathway and community adoption for success and sustainable affordability. In 2020, the Global Gene Therapy Initiative was formed to tackle the barriers to LMIC inclusion in gene therapy development. This working group includes diverse stakeholders from all sectors and has set a goal of introducing two gene therapy Phase I clinical trials in two LMIC, Uganda and India, by 2024. Here we report on progress to date for this initiative.
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Affiliation(s)
- Jennifer E Adair
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
- University of Washington, Seattle, WA, USA.
| | | | | | - Deus Bazira
- Georgetown University Medical Center, Washington, District of Columbia, USA
| | | | - Lynda Dee
- AIDS Action Baltimore, Baltimore, MD, USA
- amFAR Institute for HIV Cure Community Advisory Board, New York, NY, USA
- Delaney AIDS Research Enterprise Community Advisory Board, San Francisco, CA, USA
- Martin Delaney Collaboratory Community Advisory Board, Bethesda, MD, USA
| | - Steven Deeks
- University of California at San Francisco, San Francisco, CA, USA
| | - Mohamed Draz
- Case Western Reserve University, Cleveland, OH, USA
| | - Karine Dubé
- University of North Carolina, Chapel Hill, NC, USA
| | - Mark Dybul
- Georgetown University Medical Center, Washington, District of Columbia, USA
| | - Umut Gurkan
- Case Western Reserve University, Cleveland, OH, USA
| | | | - Cissy Kityo
- Joint Clinical Research Centre, Kampala, Uganda
| | | | - Punam Malik
- Cincinnati Children's Medical Hospital, Cincinnati, OH, USA
| | | | | | | | | | | | - Rimas J Orentas
- University of Washington, Seattle, WA, USA
- Caring Cross, Gaithersburg, MD, USA
- Seattle Children's Research Institute, Seattle, WA, USA
| | | | | | | | | | - John F Tisdale
- National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Els Verhoeyen
- Université Côte d'Azur, INSERM, C3M, Nice, France
- CIRI, INSERM, Université Lyon, CNRS, ENS de Lyon, Lyon, France
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Kankaka EN, Nalugoda F, Serwadda D, Makumbi F, Wawer MJ, Gray RH, Quinn TC, Reynolds SJ, Nakigozi G, Lutalo T, Kigozi G, Sewankambo NK, Kagaayi J. Makerere's contribution to the development of a high impact HIV research population-based cohort in the Rakai Region, Uganda. Afr Health Sci 2022; 22:42-50. [PMID: 36321125 PMCID: PMC9590336 DOI: 10.4314/ahs.v22i2.7s] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Longitudinal population-based cohort studies can provide critical insights on temporal, spatial and sociodemographic changes in health status and health determinants that are not obtained by other study designs. However, establishing and maintaining such a cohort study can be challenging and expensive. Here, we describe the role of Makerere University in the development and conduct of such a cohort. We chronicle the first academia-led reports of HIV in East Africa; how this led to initiation of the Rakai Community Cohort Study in 1988, the first and oldest HIV cohort in sub-Saharan Africa; its impact on HIV prevention, care and treatment; how the cohort has been maintained; and opportunities, challenges, and future directions including non-communicable diseases.
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Affiliation(s)
| | | | - David Serwadda
- Rakai Health Sciences Program
- Makerere University College of Health Sciences, School of Public Health
| | - Fredrick Makumbi
- Rakai Health Sciences Program
- Makerere University College of Health Sciences, School of Public Health
| | - Maria J Wawer
- Rakai Health Sciences Program
- Johns Hopkins Bloomberg School of Public Health
- Johns Hopkins University School of Medicine
| | - Ronald H Gray
- Rakai Health Sciences Program
- Johns Hopkins Bloomberg School of Public Health
| | - Thomas C Quinn
- Johns Hopkins University School of Medicine
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH
| | - Steven J Reynolds
- Johns Hopkins University School of Medicine
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH
| | | | - Tom Lutalo
- Rakai Health Sciences Program
- Uganda Virus Research Institute
| | | | - Nelson K Sewankambo
- Rakai Health Sciences Program
- Makerere University College of Health Sciences, School of Medicine
| | - Joseph Kagaayi
- Rakai Health Sciences Program
- Makerere University College of Health Sciences, School of Public Health
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9
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Joussef-Piña S, Nankya I, Nalukwago S, Baseke J, Rwambuya S, Winner D, Kyeyune F, Chervenak K, Thiel B, Asaad R, Dobrowolski C, Luttge B, Lawley B, Kityo CM, Boom WH, Karn J, Quiñones-Mateu ME. Reduced and highly diverse peripheral HIV-1 reservoir in virally suppressed patients infected with non-B HIV-1 strains in Uganda. Retrovirology 2022; 19:1. [PMID: 35033105 PMCID: PMC8760765 DOI: 10.1186/s12977-022-00587-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 01/03/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Our understanding of the peripheral human immunodeficiency virus type 1 (HIV-1) reservoir is strongly biased towards subtype B HIV-1 strains, with only limited information available from patients infected with non-B HIV-1 subtypes, which are the predominant viruses seen in low- and middle-income countries (LMIC) in Africa and Asia. RESULTS In this study, blood samples were obtained from well-suppressed ART-experienced HIV-1 patients monitored in Uganda (n = 62) or the U.S. (n = 50), with plasma HIV-1 loads < 50 copies/ml and CD4+ T-cell counts > 300 cells/ml. The peripheral HIV-1 reservoir, i.e., cell-associated HIV-1 RNA and proviral DNA, was characterized using our novel deep sequencing-based EDITS assay. Ugandan patients were slightly younger (median age 43 vs 49 years) and had slightly lower CD4+ counts (508 vs 772 cells/ml) than U.S. individuals. All Ugandan patients were infected with non-B HIV-1 subtypes (31% A1, 64% D, or 5% C), while all U.S. individuals were infected with subtype B viruses. Unexpectedly, we observed a significantly larger peripheral inducible HIV-1 reservoir in U.S. patients compared to Ugandan individuals (48 vs. 11 cell equivalents/million cells, p < 0.0001). This divergence in reservoir size was verified measuring proviral DNA (206 vs. 88 cell equivalents/million cells, p < 0.0001). However, the peripheral HIV-1 reservoir was more diverse in Ugandan than in U.S. individuals (8.6 vs. 4.7 p-distance, p < 0.0001). CONCLUSIONS The smaller, but more diverse, peripheral HIV-1 reservoir in Ugandan patients might be associated with viral (e.g., non-B subtype with higher cytopathicity) and/or host (e.g., higher incidence of co-infections or co-morbidities leading to less clonal expansion) factors. This highlights the need to understand reservoir dynamics in diverse populations as part of ongoing efforts to find a functional cure for HIV-1 infection in LMICs.
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Affiliation(s)
- Samira Joussef-Piña
- Departments of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, OH, USA
| | - Immaculate Nankya
- Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda
| | - Sophie Nalukwago
- Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda
| | - Joy Baseke
- Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda
| | - Sandra Rwambuya
- Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda
| | - Dane Winner
- Departments of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, OH, USA
| | - Fred Kyeyune
- Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda
| | - Keith Chervenak
- Departments of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Bonnie Thiel
- Departments of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Robert Asaad
- Departments of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Curtis Dobrowolski
- Departments of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, OH, USA
| | - Benjamin Luttge
- Departments of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, OH, USA
| | - Blair Lawley
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, 720 Cumberland Street, P.O. Box 56, Dunedin, New Zealand
| | - Cissy M Kityo
- Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda
| | - W Henry Boom
- Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda
- Departments of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Jonathan Karn
- Departments of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, OH, USA
- Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda
| | - Miguel E Quiñones-Mateu
- Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda.
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, 720 Cumberland Street, P.O. Box 56, Dunedin, New Zealand.
- Webster Centre for Infectious Diseases, University of Otago, Dunedin, New Zealand.
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10
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Ismail SD, Pankrac J, Ndashimye E, Prodger JL, Abrahams MR, Mann JFS, Redd AD, Arts EJ. Addressing an HIV cure in LMIC. Retrovirology 2021; 18:21. [PMID: 34344423 PMCID: PMC8330180 DOI: 10.1186/s12977-021-00565-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 07/19/2021] [Indexed: 12/15/2022] Open
Abstract
HIV-1 persists in infected individuals despite years of antiretroviral therapy (ART), due to the formation of a stable and long-lived latent viral reservoir. Early ART can reduce the latent reservoir and is associated with post-treatment control in people living with HIV (PLWH). However, even in post-treatment controllers, ART cessation after a period of time inevitably results in rebound of plasma viraemia, thus lifelong treatment for viral suppression is indicated. Due to the difficulties of sustained life-long treatment in the millions of PLWH worldwide, a cure is undeniably necessary. This requires an in-depth understanding of reservoir formation and dynamics. Differences exist in treatment guidelines and accessibility to treatment as well as social stigma between low- and-middle income countries (LMICs) and high-income countries. In addition, demographic differences exist in PLWH from different geographical regions such as infecting viral subtype and host genetics, which can contribute to differences in the viral reservoir between different populations. Here, we review topics relevant to HIV-1 cure research in LMICs, with a focus on sub-Saharan Africa, the region of the world bearing the greatest burden of HIV-1. We present a summary of ART in LMICs, highlighting challenges that may be experienced in implementing a HIV-1 cure therapeutic. Furthermore, we discuss current research on the HIV-1 latent reservoir in different populations, highlighting research in LMIC and gaps in the research that may facilitate a global cure. Finally, we discuss current experimental cure strategies in the context of their potential application in LMICs.
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Affiliation(s)
- Sherazaan D Ismail
- Division of Medical Virology, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, 7925, South Africa
| | - Joshua Pankrac
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, N6A5C1, Canada
| | - Emmanuel Ndashimye
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, N6A5C1, Canada
- Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda
| | - Jessica L Prodger
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, N6A5C1, Canada
- Department of Epidemiology and Biostatistics, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, N6A 5C1, Canada
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Melissa-Rose Abrahams
- Division of Medical Virology, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, 7925, South Africa
| | - Jamie F S Mann
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, N6A5C1, Canada
- Bristol Veterinary School, University of Bristol, Langford House, Langford, Bristol, BS40 5DU, UK
| | - Andrew D Redd
- Division of Medical Virology, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, 7925, South Africa
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA
| | - Eric J Arts
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, N6A5C1, Canada.
- Division of Infectious Diseases, Department of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA.
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11
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The Intact Non-Inducible Latent HIV-1 Reservoir is Established In an In Vitro Primary T CM Cell Model of Latency. J Virol 2021; 95:JVI.01297-20. [PMID: 33441346 PMCID: PMC8092701 DOI: 10.1128/jvi.01297-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The establishment of HIV-1 latency has hindered an HIV-1 cure. "Shock and Kill" strategies to target this reservoir aim to induce the latent provirus with latency reversing agents (LRAs). However, recent studies have shown that the majority of the intact HIV-1 viral reservoir found in ART-suppressed HIV infected individuals is not inducible. We sought to understand whether this non-inducible reservoir is established, and thus able to be studied, in an in vitro primary TCM model of latency. Furthermore, we wanted to expand this model system to include R5-tropic and non-B subtype viruses. To that end, we generated our TCM model of latency with an R5 subtype B virus, AD8 and an R5 subtype C virus, MJ4. Our results demonstrate that both intact and defective proviruses are generated in this model. Less than 50% of intact proviruses are inducible regardless of viral strain in the context of maximal stimulation through the TCR or with different clinically relevant LRAs including the HDAC inhibitors SAHA and MS-275, the PKC agonist Ingenol 3,20-dibenzoate or the SMAC mimetic AZD-5582. Our findings suggest that current LRA strategies are insufficient to effectively reactivate intact latent HIV-1 proviruses in primary CD4 TCM cells and that the mechanisms involved in the generation of the non-inducible HIV-1 reservoir can be studied using this primary in vitro model.Importance: HIV-1 establishes a latent reservoir that persists under antiretroviral therapy. Antiretroviral therapy is able to stop the spread of the virus and the progression of the disease but does not target this latent reservoir. If antiretroviral therapy is stopped, the virus is able to resume replication and the disease progresses. Recently, it has been demonstrated that most of the latent reservoir capable of generating replication competent virus cannot be induced in the laboratory setting. However, the mechanisms that influence the generation of this intact and non-inducible latent reservoir are still under investigation. Here we demonstrate the generation of defective, intact and intact non-inducible latent HIV-1 in a TCM model of latency using different HIV-1 strains. Thus, the mechanisms which control inducibility can be studied using this primary cell model of latency, which may accelerate our understanding of the latent reservoir and the development of curative strategies.
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12
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Cohn LB, Chomont N, Deeks SG. The Biology of the HIV-1 Latent Reservoir and Implications for Cure Strategies. Cell Host Microbe 2020; 27:519-530. [PMID: 32272077 DOI: 10.1016/j.chom.2020.03.014] [Citation(s) in RCA: 163] [Impact Index Per Article: 40.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Antiretroviral therapy (ART) inhibits HIV replication but is not curative. During ART, the integrated HIV genome persists indefinitely within CD4+ T cells and perhaps other cells. Here, we describe the mechanisms thought to contribute to its persistence during treatment and highlight findings from numerous recent studies describing the importance of cell proliferation in that process. Continued progress elucidating the biology will enhance our ability to develop effective curative interventions.
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Affiliation(s)
- Lillian B Cohn
- Chan Zuckerberg Biohub, San Francisco, CA; Department of Medicine, University of California, San Francisco, CA
| | - Nicolas Chomont
- Centre de recherche du CHUM and Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal, QC, Canada
| | - Steven G Deeks
- Department of Medicine, University of California, San Francisco, CA.
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13
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Novelli S, Delobel P, Bouchaud O, Avettand-Fenoel V, Fialaire P, Cabié A, Souala F, Raffi F, Catalan P, Weiss L, Meyer L, Goujard C. Enhanced immunovirological response in women compared to men after antiretroviral therapy initiation during acute and early HIV-1 infection: results from a longitudinal study in the French ANRS Primo cohort. J Int AIDS Soc 2020; 23:e25485. [PMID: 32333726 PMCID: PMC7183251 DOI: 10.1002/jia2.25485] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Revised: 12/05/2019] [Accepted: 03/04/2020] [Indexed: 01/03/2023] Open
Abstract
Introduction Previous studies have reported better immunovirological characteristics in women compared with men after HIV seroconversion. We investigated whether differences persisted under long‐term antiretroviral therapy (ART) in individuals treated since acute and early HIV‐1 infection (AHI). Methods Data were obtained for 262 women and 1783 men enrolled between 1996 and 2017 in the French multicentre ANRS PRIMO cohort. We modelled the viral response, long‐term immune recovery and HIV DNA decay in the 143 women and 1126 men who initiated ART within the first three months of infection. Results The participants were mostly white. The mean age was 37 years at AHI diagnosis. Pre‐ART viral loads were lower in women than men, 5.2 and 5.6 log10 copies/mL (p = 0.001). After ART initiation, women more rapidly achieved viral suppression than men (adjusted hazard ratio: 1.33, 95% confidence interval 1.09 to 1.69). They also experienced a faster increase in CD4+ T‐cell count and CD4:CD8 ratio during the first months of treatment. Sex‐related differences in CD4+ T‐cell counts were more pronounced with increasing age. This led to a sustained mean difference of 99 to 168 CD4+ T‐cells/µL depending on age between women and men at 150 months of ART. Moreover, CD4:CD8 ratio of women was higher than that of men by 0.31, at 150 months of ART. There was no statistically significant difference between sexes for the levels of HIV DNA over time (mean estimate at the last modelling point: 1.9 log10 copies/106 PBMCs after 70 months of ART for both sexes). Conclusions The high level of immune recovery and decrease in total HIV DNA levels achieved after ART initiation during AHI reinforce the importance of early diagnosis of HIV infection and immediate ART initiation. The immunological benefit of being female increased throughout prolonged ART duration, which may give women additional protection from adverse clinical events and premature ageing.
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Affiliation(s)
- Sophie Novelli
- Paris-Saclay University, UVSQ, Inserm, CESP, U1018, Le Kremlin-Bicêtre, France
| | - Pierre Delobel
- Department of Infectious and Tropical Diseases, Toulouse University Hospital, Toulouse, France
| | - Olivier Bouchaud
- Department of Infectious and Tropical Diseases, Avicenne Hospital, Assistance Publique-Hôpitaux de Paris (AP-HP), Bobigny, France
| | - Véronique Avettand-Fenoel
- Institut Cochin - CNRS 8104, INSERM U1016, AP-HP, Laboratoire de Microbiologie clinique, Hôpital Necker-Enfants Malades, Université Paris Descartes, Paris, France
| | - Pascale Fialaire
- Department of Infectious and Tropical Diseases, Angers University Hospital, Angers, France
| | - André Cabié
- Department of Infectious Diseases, University Hospital of Martinique, Fort-de-France, France
| | - Faouzi Souala
- Department of Infectious and Tropical Diseases, Rennes University Hospital, Rennes, France
| | - François Raffi
- Infectious diseases department and Inserm CIC 1413, University Hospital of Nantes, Nantes, France
| | - Pilartxo Catalan
- Department of Internal Medicine, AP-HP, Bicêtre Hospital, Le Kremlin-Bicêtre, France
| | - Laurence Weiss
- Service d'Immunologie Clinique, AP-HP, Hôpital Européen Georges Pompidou, Paris, France
| | - Laurence Meyer
- Inserm, CESP, U1018, Department of Public Health and Epidemiology, AP-HP, Bicêtre Hospital, Paris-Saclay University, Le Kremlin-Bicêtre, France
| | - Cécile Goujard
- Inserm, CESP, U1018, Department of Internal Medicine, AP-HP, Bicêtre Hospital, Paris-Saclay University, Le Kremlin-Bicêtre, France
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14
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Falcinelli SD, Shook-Sa BE, Dewey MG, Sridhar S, Read J, Kirchherr J, James KS, Allard B, Ghofrani S, Stuelke E, Baker C, Roan NR, Eron JJ, Kuruc JD, Ramirez C, Gay C, Mollan KR, Margolis DM, Adimora AA, Archin NM. Impact of Biological Sex on Immune Activation and Frequency of the Latent HIV Reservoir During Suppressive Antiretroviral Therapy. J Infect Dis 2020; 222:1843-1852. [PMID: 32496542 PMCID: PMC7653086 DOI: 10.1093/infdis/jiaa298] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 05/27/2020] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Persistent HIV infection of long-lived resting CD4 T cells, despite antiretroviral therapy (ART), remains a barrier to HIV cure. Women have a more robust type 1 interferon response during HIV infection relative to men, contributing to lower initial plasma viremia. As lower viremia during acute infection is associated with reduced frequency of latent HIV infection, we hypothesized that women on ART would have a lower frequency of latent HIV compared to men. METHODS ART-suppressed, HIV seropositive women (n = 22) were matched 1:1 to 22 of 39 ART-suppressed men. We also compared the 22 women to all 39 men, adjusting for age and race as covariates. We measured the frequency of latent HIV using the quantitative viral outgrowth assay, the intact proviral DNA assay, and total HIV gag DNA. We also performed activation/exhaustion immunophenotyping on peripheral blood mononuclear cells and quantified interferon-stimulated gene (ISG) expression in CD4 T cells. RESULTS We did not observe evident sex differences in the frequency of persistent HIV in resting CD4 T cells. Immunophenotyping and CD4 T-cell ISG expression analysis revealed marginal differences across the sexes. CONCLUSIONS Differences in HIV reservoir frequency and immune activation appear to be small across sexes during long-term suppressive therapy.
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Affiliation(s)
- Shane D Falcinelli
- HIV Cure Center, University of North Carolina, Chapel Hill, North Carolina, USA
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Bonnie E Shook-Sa
- Biostatistics Core, Center for AIDS Research, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Morgan G Dewey
- HIV Cure Center, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Sumati Sridhar
- Biostatistics Core, Center for AIDS Research, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Jenna Read
- HIV Cure Center, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Jennifer Kirchherr
- HIV Cure Center, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Katherine S James
- HIV Cure Center, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Brigitte Allard
- HIV Cure Center, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Simon Ghofrani
- HIV Cure Center, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Erin Stuelke
- HIV Cure Center, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Caroline Baker
- Department of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Nadia R Roan
- Department of Urology, University of California San Francisco, San Francisco, California, USA
- Gladstone Institutes, San Francisco, California, USA
| | - Joseph J Eron
- Department of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
| | - JoAnn D Kuruc
- Department of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Catalina Ramirez
- Department of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Cynthia Gay
- Department of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Katie R Mollan
- Biostatistics Core, Center for AIDS Research, University of North Carolina, Chapel Hill, North Carolina, USA
| | - David M Margolis
- HIV Cure Center, University of North Carolina, Chapel Hill, North Carolina, USA
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, North Carolina, USA
- Department of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Adaora A Adimora
- Department of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Nancie M Archin
- HIV Cure Center, University of North Carolina, Chapel Hill, North Carolina, USA
- Department of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
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15
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Heritability of the HIV-1 reservoir size and decay under long-term suppressive ART. Nat Commun 2020; 11:5542. [PMID: 33139735 PMCID: PMC7608612 DOI: 10.1038/s41467-020-19198-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 09/23/2020] [Indexed: 12/02/2022] Open
Abstract
The HIV-1 reservoir is the major hurdle to curing HIV-1. However, the impact of the viral genome on the HIV-1 reservoir, i.e. its heritability, remains unknown. We investigate the heritability of the HIV-1 reservoir size and its long-term decay by analyzing the distribution of those traits on viral phylogenies from both partial-pol and viral near full-length genome sequences. We use a unique nationwide cohort of 610 well-characterized HIV-1 subtype-B infected individuals on suppressive ART for a median of 5.4 years. We find that a moderate but significant fraction of the HIV-1 reservoir size 1.5 years after the initiation of ART is explained by genetic factors. At the same time, we find more tentative evidence for the heritability of the long-term HIV-1 reservoir decay. Our findings indicate that viral genetic factors contribute to the HIV-1 reservoir size and hence the infecting HIV-1 strain may affect individual patients’ hurdle towards a cure. The HIV reservoir is a major hurdle for a cure of HIV, but the factors determining its size and dynamics remain unclear. Here the authors show in a large cohort of 610 HIV-1 infected individuals, who are on suppressive ART for a median of 5.4 years, that viral genetic factors contribute substantially to the HIV-1 reservoir size.
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Barr L, Jefferys R. A landscape analysis of HIV cure-related clinical research in 2019. J Virus Erad 2020; 6:100010. [PMID: 33294212 PMCID: PMC7695817 DOI: 10.1016/j.jve.2020.100010] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 08/26/2020] [Accepted: 08/27/2020] [Indexed: 11/28/2022] Open
Abstract
Objectives In 2018, we surveyed investigators conducting HIV cure-related clinical research, drawing on information from the online listing established by Treatment Action Group (TAG). The purpose of the survey was to facilitate a landscape analysis of the field. In 2019, we fielded a second survey in order to provide updated information and assess any shifts in the landscape. Methods Trials and observational studies listed as of August 16, 2019 formed the sample set. Survey questions addressed funding, trial development, recruitment, enrollment, participant demographics, antiretroviral therapy status, HIV reservoir assays, invasive procedures, study completion, data sharing and dissemination plans. A survey was sent to the contact(s) for each study. Supplemental information was collected from clinicaltrials.gov and available presentations/publications of study results. Results A total of 97 interventional trials and 36 observational studies were identified, with 30 including analytical treatment interruptions. Total projected enrollment is 13,732 participants, with observational studies contributing the majority (8,325). Most interventional trials are in early phases. The majority of current research is located in the USA, involves predominately male participants and is limited in racial and ethnic diversity. Prespecified demographic enrollment targets are rare. Two thirds of respondents to our previous survey reported that enrollment is progressing more slowly than anticipated. Conclusions A diverse range of interventions are being evaluated in HIV cure research, but participant diversity is far from optimal with a continuing underrepresentation of women. Broadening inclusion and geographic reach will be necessary to achieve the goal of developing widely effective, safe and accessible curative interventions.
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Affiliation(s)
- Liz Barr
- AIDS Clinical Trials Group (ACTG), Baltimore, MD, USA.,University of Maryland, Baltimore County (UMBC), USA.,Treatment Action Group (TAG), New York, USA
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Prodger JL, Capoferri AA, Yu K, Lai J, Reynolds SJ, Kasule J, Kityamuweesi T, Buule P, Serwadda D, Kwon KJ, Schlusser K, Martens C, Scully E, Choi YH, Redd AD, Quinn TC. Reduced HIV-1 latent reservoir outgrowth and distinct immune correlates among women in Rakai, Uganda. JCI Insight 2020; 5:139287. [PMID: 32544096 DOI: 10.1172/jci.insight.139287] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 06/03/2020] [Indexed: 01/22/2023] Open
Abstract
HIV-1 infection remains incurable owing to the persistence of a viral reservoir that harbors integrated provirus within host cellular DNA. Increasing evidence links sex-based differences in HIV-1 immune responses and pathogenesis; however, little is known about differences in HIV-1 infection persistence. Here, we quantified persistent HIV-1 infection in 90 adults on suppressive antiretroviral therapy in Rakai, Uganda (57 female patients). Total HIV-1 DNA was quantified by PCR, and replication-competent provirus by quantitative viral outgrowth assay (QVOA). Immune phenotyping of T cell subsets and plasma biomarkers was also performed. We found that whereas both sexes had similar total HIV DNA levels, female patients had significantly fewer resting CD4+ T cells harboring replication-competent virus, as measured by viral outgrowth in the QVOA. Factors associated with viral outgrowth differed by sex; notably, frequency of programmed cell death 1 (PD1+) CD4+ T cells correlated with reservoir size in male but not female patients. The sex-based differences in HIV-1 persistence observed in this cohort warrant additional research, especially given the widespread use of the QVOA to assess reservoir size and current explorations of PD1 agonists in cure protocols. Efforts should be made to power future cure studies to assess outcomes in both male and female patients.
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Affiliation(s)
- Jessica L Prodger
- Department of Microbiology and Immunology and.,Department of Epidemiology and Biostatistics, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada.,Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Adam A Capoferri
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Katherine Yu
- Department of Epidemiology and Biostatistics, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Jun Lai
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Steven J Reynolds
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland, USA.,Rakai Health Sciences Program, Kalisizo, Uganda
| | | | | | - Paul Buule
- Rakai Health Sciences Program, Kalisizo, Uganda
| | - David Serwadda
- Rakai Health Sciences Program, Kalisizo, Uganda.,Makerere University, Kampala, Uganda
| | - Kyungyoon J Kwon
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Katherine Schlusser
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Craig Martens
- Genomic Unit, Rocky Mountain Laboratories, NIAID, NIH, Hamilton, Montana, USA
| | - Eileen Scully
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Yun-Hee Choi
- Department of Epidemiology and Biostatistics, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Andrew D Redd
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland, USA
| | - Thomas C Quinn
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland, USA
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HIV-1 Latency and Latency Reversal: Does Subtype Matter? Viruses 2019; 11:v11121104. [PMID: 31795223 PMCID: PMC6950696 DOI: 10.3390/v11121104] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 11/22/2019] [Accepted: 11/27/2019] [Indexed: 02/06/2023] Open
Abstract
Cells that are latently infected with HIV-1 preclude an HIV-1 cure, as antiretroviral therapy does not target this latent population. HIV-1 is highly genetically diverse, with over 10 subtypes and numerous recombinant forms circulating worldwide. In spite of this vast diversity, much of our understanding of latency and latency reversal is largely based on subtype B viruses. As such, most of the development of cure strategies targeting HIV-1 are solely based on subtype B. It is currently assumed that subtype does not influence the establishment or reactivation of latent viruses. However, this has not been conclusively proven one way or the other. A better understanding of the factors that influence HIV-1 latency in all viral subtypes will help develop therapeutic strategies that can be applied worldwide. Here, we review the latest literature on subtype-specific factors that affect viral replication, pathogenesis, and, most importantly, latency and its reversal.
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Brief Report: Pulmonary Tuberculosis Is Associated With Persistent Systemic Inflammation and Decreased HIV-1 Reservoir Markers in Coinfected Ugandans. J Acquir Immune Defic Syndr 2019; 79:407-411. [PMID: 30063648 DOI: 10.1097/qai.0000000000001823] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
BACKGROUND Mycobacterium tuberculosis (TB) infection induces systemic inflammation that could impact HIV-1 persistence. SETTING HIV-1-seropositive individuals either with or without pulmonary TB disease were recruited in Kampala, Uganda. METHODS Plasma cytokines, HIV-1 DNA, and cell-associated (ca)-RNA were compared among those coinfected with TB (cases) to those without TB (controls). TB-coinfected cases and controls were compared at presentation (n = 15 and n = 16, respectively) and at around 6 months after HIV-1 treatment initiation among those who had achieved virologic suppression (n = 6 and n = 8, respectively). At follow-up, the TB-coinfected cases had also finished TB treatment. RESULTS Before treatment, the TB-coinfected cases as compared to the controls had higher levels of soluble(s)-CD163 (P = 0.0002) and interleukin-6 (P = 0.006) but lower levels of macrophage chemoattractant protein-1 (P = 0.04). After treatment, the TB-coinfected cases as compared to controls still had higher plasma s-CD163 levels (P = 0007). Controls as compared to the coinfected cases had higher ca-RNA per DNA template both at baseline (P = 0.03) and at follow-up (P = 0.07). Levels of ca-RNA per DNA copy at follow-up showed a negative correlation with baseline plasma s-CD163 (P = 0.008) and interleukin-6 (P = 0.05) levels. CONCLUSIONS TB disease is associated with inflammation and decreased HIV-1 RNA expression relative to the number of infected cells, both before and after viral suppression. Infections present before antiretroviral initiation impact HIV-1 latency.
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HIV Subtype and Nef-Mediated Immune Evasion Function Correlate with Viral Reservoir Size in Early-Treated Individuals. J Virol 2019; 93:JVI.01832-18. [PMID: 30602611 DOI: 10.1128/jvi.01832-18] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 11/30/2018] [Indexed: 11/20/2022] Open
Abstract
The HIV accessory protein Nef modulates key immune evasion and pathogenic functions, and its encoding gene region exhibits high sequence diversity. Given the recent identification of early HIV-specific adaptive immune responses as novel correlates of HIV reservoir size, we hypothesized that viral factors that facilitate the evasion of such responses-namely, Nef genetic and functional diversity-might also influence reservoir establishment and/or persistence. We isolated baseline plasma HIV RNA-derived nef clones from 30 acute/early-infected individuals who participated in a clinical trial of early combination antiretroviral therapy (cART) (<6 months following infection) and assessed each Nef clone's ability to downregulate CD4 and human leukocyte antigen (HLA) class I in vitro We then explored the relationships between baseline clinical, immunological, and virological characteristics and the HIV reservoir size measured 48 weeks following initiation of suppressive cART (where the reservoir size was quantified in terms of the proviral DNA loads as well as the levels of replication-competent HIV in CD4+ T cells). Maximal within-host Nef-mediated downregulation of HLA, but not CD4, correlated positively with post-cART proviral DNA levels (Spearman's R = 0.61, P = 0.0004) and replication-competent reservoir sizes (Spearman's R = 0.36, P = 0.056) in univariable analyses. Furthermore, the Nef-mediated HLA downregulation function was retained in final multivariable models adjusting for established clinical and immunological correlates of reservoir size. Finally, HIV subtype B-infected persons (n = 25) harbored significantly larger viral reservoirs than non-subtype B-infected persons (2 infected with subtype CRF01_AE and 3 infected with subtype G). Our results highlight a potentially important role of viral factors-in particular, HIV subtype and accessory protein function-in modulating viral reservoir establishment and persistence.IMPORTANCE While combination antiretroviral therapies (cART) have transformed HIV infection into a chronic manageable condition, they do not act upon the latent HIV reservoir and are therefore not curative. As HIV cure or remission should be more readily achievable in individuals with smaller HIV reservoirs, achieving a deeper understanding of the clinical, immunological, and virological determinants of reservoir size is critical to eradication efforts. We performed a post hoc analysis of 30 participants of a clinical trial of early cART who had previously been assessed in detail for their clinical, immunological, and reservoir size characteristics. We observed that the HIV subtype and autologous Nef-mediated HLA downregulation function correlated with the viral reservoir size measured approximately 1 year post-cART initiation. Our findings highlight virological characteristics-both genetic and functional-as possible novel determinants of HIV reservoir establishment and persistence.
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Poon AFY, Prodger JL, Lynch BA, Lai J, Reynolds SJ, Kasule J, Capoferri AA, Lamers SL, Rodriguez CW, Bruno D, Porcella SF, Martens C, Quinn TC, Redd AD. Quantitation of the latent HIV-1 reservoir from the sequence diversity in viral outgrowth assays. Retrovirology 2018; 15:47. [PMID: 29976219 PMCID: PMC6034329 DOI: 10.1186/s12977-018-0426-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 06/14/2018] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND The ability of HIV-1 to integrate into the genomes of quiescent host immune cells, establishing a long-lived latent viral reservoir (LVR), is the primary obstacle to curing these infections. Quantitative viral outgrowth assays (QVOAs) are the gold standard for estimating the size of the replication-competent HIV-1 LVR, measured by the number of infectious units per million (IUPM) cells. QVOAs are time-consuming because they rely on culturing replicate wells to amplify the production of virus antigen or nucleic acid to reproducibly detectable levels. Sequence analysis can reduce the required number of culture wells because the virus genetic diversity within the LVR provides an internal replication and dilution series. Here we develop a Bayesian method to jointly estimate the IUPM and variant frequencies (a measure of clonality) from the sequence diversity of QVOAs. RESULTS Using simulation experiments, we find our Bayesian approach confers significantly greater accuracy over current methods to estimate the IUPM, particularly for reduced numbers of QVOA replicates and/or increasing actual IUPM. Furthermore, we determine that the improvement in accuracy is greater with increasing genetic diversity in the sample population. We contrast results of these different methods applied to new HIV-1 sequence data derived from QVOAs from two individuals with suppressed viral loads from the Rakai Health Sciences Program in Uganda. CONCLUSIONS Utilizing sequence variation has the additional benefit of providing information on the contribution of clonality of the LVR, where high clonality (the predominance of a single genetic variant) suggests a role for cell division in the long-term persistence of the reservoir. In addition, our Bayesian approach can be adapted to other limiting dilution assays where positive outcomes can be partitioned by their genetic heterogeneity, such as immune cell populations and other viruses.
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Affiliation(s)
- Art F Y Poon
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada.
| | - Jessica L Prodger
- Department of Microbiology and Immunology, Western University, London, ON, Canada.,Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Briana A Lynch
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Baltimore, MD, USA
| | - Jun Lai
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Steven J Reynolds
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA.,Rakai Health Sciences Program, Kalisizo, Uganda
| | | | - Adam A Capoferri
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | | | | | - Daniel Bruno
- Genomics Unit, Research Technologies Branch, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Stephen F Porcella
- Genomics Unit, Research Technologies Branch, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Craig Martens
- Genomics Unit, Research Technologies Branch, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Thomas C Quinn
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Baltimore, MD, USA.,Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Andrew D Redd
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Baltimore, MD, USA.,Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
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