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Shahid A, MacLennan S, Jones BR, Sudderuddin H, Dang Z, Cobarrubias K, Duncan MC, Kinloch NN, Dapp MJ, Archin NM, Fischl MA, Ofotokun I, Adimora A, Gange S, Aouizerat B, Kuniholm MH, Kassaye S, Mullins JI, Goldstein H, Joy JB, Anastos K, Brumme ZL. The replication-competent HIV reservoir is a genetically restricted, younger subset of the overall pool of HIV proviruses persisting during therapy, which is highly genetically stable over time. J Virol 2024; 98:e0165523. [PMID: 38214547 PMCID: PMC10878278 DOI: 10.1128/jvi.01655-23] [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: 10/24/2023] [Accepted: 12/07/2023] [Indexed: 01/13/2024] Open
Abstract
Within-host HIV populations continually diversify during untreated infection, and this diversity persists within infected cell reservoirs during antiretroviral therapy (ART). Achieving a better understanding of on-ART proviral evolutionary dynamics, and a better appreciation of how the overall persisting pool of (largely genetically defective) proviruses differs from the much smaller replication-competent HIV reservoir, is critical to HIV cure efforts. We reconstructed within-host HIV evolutionary histories in blood from seven participants of the Women's Interagency HIV Study who experienced HIV seroconversion, and used these data to characterize the diversity, lineage origins, and ages of proviral env-gp120 sequences sampled longitudinally up to 12 years on ART. We also studied HIV sequences emerging from the reservoir in two participants. We observed that proviral clonality generally increased over time on ART, with clones frequently persisting long term. While on-ART proviral integration dates generally spanned the duration of untreated infection, HIV emerging in plasma was exclusively younger (i.e., dated to the years immediately pre-ART). The genetic and age distributions of distinct proviral sequences remained stable during ART in all but one participant, in whom there was evidence that younger proviruses had been preferentially eliminated after 12 years on ART. Analysis of the gag region in three participants corroborated our env-gp120-based observations, indicating that our observations are not influenced by the HIV region studied. Our results underscore the remarkable genetic stability of the distinct proviral sequences that persist in blood during ART. Our results also suggest that the replication-competent HIV reservoir is a genetically restricted, younger subset of this overall proviral pool.IMPORTANCECharacterizing the genetically diverse HIV sequences that persist in the reservoir despite antiretroviral therapy (ART) is critical to cure efforts. Our observations confirm that proviruses persisting in blood on ART, which are largely genetically defective, broadly reflect the extent of within-host HIV evolution pre-ART. Moreover, on-ART clonal expansion is not appreciably accompanied by the loss of distinct proviral lineages. In fact, on-ART proviral genetic composition remained stable in all but one participant, in whom, after 12 years on ART, proviruses dating to around near ART initiation had been preferentially eliminated. We also identified recombinant proviruses between parental sequence fragments of different ages. Though rare, such sequences suggest that reservoir cells can be superinfected with HIV from another infection era. Overall, our finding that the replication-competent reservoir in blood is a genetically restricted, younger subset of all persisting proviruses suggests that HIV cure strategies will need to eliminate a reservoir that differs in key respects from the overall proviral pool.
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Affiliation(s)
- Aniqa Shahid
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Signe MacLennan
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Bradley R. Jones
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
- Bioinformatics Program, University of British Columbia, Vancouver, British Columbia, Canada
| | - Hanwei Sudderuddin
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Zhong Dang
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Kyle Cobarrubias
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Maggie C. Duncan
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Natalie N. Kinloch
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Michael J. Dapp
- Department of Microbiology, University of Washington, School of Medicine, Seattle, Washington, USA
| | - Nancie M. Archin
- UNC HIV Cure Center, Institute of Global Health and Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Margaret A. Fischl
- Department of Medicine, University of Miami School of Medicine, Miami, Florida, USA
| | - Igho Ofotokun
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Adaora Adimora
- Department of Epidemiology, UNC Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Stephen Gange
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | | | - Mark H. Kuniholm
- Department of Epidemiology and Biostatistics, University at Albany, State University of New York, Rensselaer, New York, New York, USA
| | - Seble Kassaye
- Division of Infectious Diseases and Tropical Medicine, Georgetown University, Washington, DC, USA
| | - James I. Mullins
- Department of Microbiology, University of Washington, School of Medicine, Seattle, Washington, USA
- Department of Global Health, University of Washington, School of Medicine, Seattle, Washington, USA
- Department of Medicine, University of Washington, School of Medicine, Seattle, Washington, USA
| | - Harris Goldstein
- Departments of Microbiology and Immunology and Pediatrics, Albert Einstein College of Medicine, Bronx, New York, New York, USA
| | - Jeffrey B. Joy
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
- Bioinformatics Program, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Kathryn Anastos
- Department of Medicine, Albert Einstein College of Medicine, New York, New York, USA
| | - Zabrina L. Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - the MACS/WIHS combined cohort study (MWCSS)OfotokunIghovwerha1ShethAnandi1WingoodGina1BrownTodd2MargolickJoseph2AnastosKathryn3HannaDavid3SharmaAnjali3GustafsonDeborah4WilsonTracey4D’SouzaGypsyamber5GangeStephen5TopperElizabeth5CohenMardge6FrenchAudrey6WolinskySteven7PalellaFrank7StosorValentina7AouizeratBradley8PriceJennifer8TienPhyllis8DetelsRoger9MimiagaMatthew9KassayeSeble10MerensteinDaniel10AlcaideMaria11FischlMargaret11JonesDeborah11MartinsonJeremy12RinaldoCharles12KempfMirjam-Colette13Dionne-OdomJodie13Konkle-ParkerDeborah13BrockJames B.13AdimoraAdaora14Floris-MooreMichelle14Emory University, Atlanta, Georgia, USAJohns Hopkins University, Baltimore, Maryland, USAAlbert Einstein College of Medicine, Bronx, New York, USASuny Downstate Medical Center, Brooklyn, New York, USAJohns Hopkins University, Baltimore, Maryland, USAHektoen Institute for Medical Research, Chicago, Illinois, USANorthwestern University at Chicago, Chicago, Illinois, USAUniversity of California San Francisco, San Francisco, California, USAUniversity of California Los Angeles, Los Angeles, California, USAGeorgetown University, Washington, DC, USAUniversity of Miami School of Medicine, Coral Gables, Florida, USAUniversity of Pittsburgh, Pittsburgh, Pennsylvania, USAUniversity of Alabama Birmingham, Birmingham, Alabama, USAUniversity of North Carolina Chapel Hill, Chapel Hill, North Carolina, USA
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
- Bioinformatics Program, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Microbiology, University of Washington, School of Medicine, Seattle, Washington, USA
- UNC HIV Cure Center, Institute of Global Health and Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Medicine, University of Miami School of Medicine, Miami, Florida, USA
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
- Department of Epidemiology, UNC Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
- College of Dentistry, New York University, New York, New York, USA
- Department of Epidemiology and Biostatistics, University at Albany, State University of New York, Rensselaer, New York, New York, USA
- Division of Infectious Diseases and Tropical Medicine, Georgetown University, Washington, DC, USA
- Department of Global Health, University of Washington, School of Medicine, Seattle, Washington, USA
- Department of Medicine, University of Washington, School of Medicine, Seattle, Washington, USA
- Departments of Microbiology and Immunology and Pediatrics, Albert Einstein College of Medicine, Bronx, New York, New York, USA
- Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Medicine, Albert Einstein College of Medicine, New York, New York, USA
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2
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Gebremedhin T, Aynalem M, Adem M, Geremew D, Aleka Y, Kiflie A. Dolutegravir based therapy showed CD4 + T cell count recovery and viral load suppression among ART naïve people living with HIV AIDS: a pilot evaluation. Sci Rep 2024; 14:3297. [PMID: 38331983 PMCID: PMC10853173 DOI: 10.1038/s41598-024-53282-y] [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: 11/01/2022] [Accepted: 01/30/2024] [Indexed: 02/10/2024] Open
Abstract
Recently, dolutegravir (DTG)-based combined therapy, a more effective and safer first-line antiretroviral therapy (ART), has been recommended by the World Health Organization for the treatment of Human Immunodeficiency Virus (HIV) since July 2018. However, its effectiveness in CD4+ T-cells count recovery and viral load suppression has not been studied yet in Ethiopia, where HIV is endemic. Therefore, we aimed to conduct a pilot assessment on the effect of DTG-based therapy on CD4+ T-cell count and viral load count among people living with HIV (PLWH) in Ethiopia. A longitudinal prospective cohort study was conducted from July 2020 to February 2021. 109 PLWH who are ART naive but plan to initiate DTG-based therapy were recruited. HIV viral ribonucleic acid (RNA) copies were determined using polymerase chain reaction. To compute the difference in viral load and CD4+ T-cell counts between the baseline, 3rd, and 6th months, a Friedman test was used. The study included 109 PLWH who had never received antiretroviral medication. Participants taking DTG-based treatment showed significantly decreasing median (IQR) values of viral load count (copies/mL) from 446,812 (237649.5-732994.5) at baseline to 34 (23.5-46) at 3 months and 0.0 (0-19) at 6 months of treatment follow-up. Although the treatment increases the proportion of participants with HIV-1 RNA 50 copies/mL from 0 (0% at baseline) to 87 (79.8%) and 100 (91.7%) at the 3rd and 6th months of treatment, respectively, On the other hand, the CD4+ T-cell count increased significantly during treatment: median (IQR): 209 (81.5-417.5) versus 291 (132-522) versus 378 (181-632.5) cells/L at baseline, the 3rd and 6th months of the treatment follow-up period, respectively. We found dolutegravir-based therapy was a promising option with high virological suppression rates and CD4+ T-cell count recovery, demonstrating a restoration of cellular immunity. Moreover, Viral load suppression rates were high after the initiation of the treatment. We recommend further research should be conducted with a larger number of participants to acquire greater awareness of the treatment outcomes.
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Affiliation(s)
| | - Melak Aynalem
- Department of Hematology and Immunohematology, University of Gondar, Gondar, Ethiopia
| | - Mohammed Adem
- Department of Immunology and Molecular Biology, University of Gondar, Gondar, Ethiopia
| | - Demeke Geremew
- Department of Medical Laboratory Sciences, Immunology and Molecular Biology Unit, College of Medicine and Health Sciences, Bahir Dar University, Bahir Dar, Ethiopia
| | - Yetemwork Aleka
- Department of Immunology and Molecular Biology, University of Gondar, Gondar, Ethiopia.
| | - Amare Kiflie
- Department of Immunology and Molecular Biology, University of Gondar, Gondar, Ethiopia
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3
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Joseph SB, Abrahams MR, Moeser M, Tyers L, Archin NM, Council OD, Sondgeroth A, Spielvogel E, Emery A, Zhou S, Doolabh D, Ismail SD, Karim SA, Margolis DM, Pond SK, Garrett N, Swanstrom R, Williamson C. The timing of HIV-1 infection of cells that persist on therapy is not strongly influenced by replication competency or cellular tropism of the provirus. PLoS Pathog 2024; 20:e1011974. [PMID: 38422171 DOI: 10.1371/journal.ppat.1011974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 03/12/2024] [Accepted: 01/16/2024] [Indexed: 03/02/2024] Open
Abstract
People with HIV-1 (PWH) on antiretroviral therapy (ART) can maintain undetectable virus levels, but a small pool of infected cells persists. This pool is largely comprised of defective proviruses that may produce HIV-1 proteins but are incapable of making infectious virus, with only a fraction (~10%) of these cells harboring intact viral genomes, some of which produce infectious virus following ex vivo stimulation (i.e. inducible intact proviruses). A majority of the inducible proviruses that persist on ART are formed near the time of therapy initiation. Here we compared proviral DNA (assessed here as 3' half genomes amplified from total cellular DNA) and inducible replication competent viruses in the pool of infected cells that persists during ART to determine if the original infection of these cells occurred at comparable times prior to therapy initiation. Overall, the average percent of proviruses that formed late (i.e. around the time of ART initiation, 60%) did not differ from the average percent of replication competent inducible viruses that formed late (69%), and this was also true for proviral DNA that was hypermutated (57%). Further, there was no evidence that entry into the long-lived infected cell pool was impeded by the ability to use the CXCR4 coreceptor, nor was the formation of long-lived infected cells enhanced during primary infection, when viral loads are exceptionally high. We observed that infection of cells that transitioned to be long-lived was enhanced among people with a lower nadir CD4+ T cell count. Together these data suggest that the timing of infection of cells that become long-lived is impacted more by biological processes associated with immunodeficiency before ART than the replication competency and/or cellular tropism of the infecting virus or the intactness of the provirus. Further research is needed to determine the mechanistic link between immunodeficiency and the timing of infected cells transitioning to the long-lived pool, particularly whether this is due to differences in infected cell clearance, turnover rates and/or homeostatic proliferation before and after ART.
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Affiliation(s)
- Sarah B Joseph
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- UNC HIV Cure Center and Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Melissa-Rose Abrahams
- Division of Medical Virology, Institute of Infectious Diseases and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Matthew Moeser
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Lynn Tyers
- Division of Medical Virology, Institute of Infectious Diseases and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Nancie M Archin
- UNC HIV Cure Center and Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Olivia D Council
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- UNC HIV Cure Center and Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Amy Sondgeroth
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Ean Spielvogel
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Ann Emery
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Shuntai Zhou
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Deelan Doolabh
- Division of Medical Virology, Institute of Infectious Diseases and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Sherazaan D Ismail
- Division of Medical Virology, Institute of Infectious Diseases and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Salim Abdool Karim
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu- Natal, Durban, South Africa
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | - David M Margolis
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- UNC HIV Cure Center and Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Sergei Kosakovsky Pond
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, Pennsylvania, United States of America
| | - Nigel Garrett
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu- Natal, Durban, South Africa
- Discipline of Public Health Medicine, School of Nursing and Public Health, University of KwaZulu-Natal, Durban, South Africa
| | - Ronald Swanstrom
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Carolyn Williamson
- Division of Medical Virology, Institute of Infectious Diseases and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu- Natal, Durban, South Africa
- National Health Laboratory Services of South Africa, Johannesburg, South Africa
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4
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Min AK, Javidfar B, Missall R, Doanman D, Durens M, Graziani M, Mordelt A, Marro SG, de Witte L, Chen BK, Swartz TH, Akbarian S. HIV-1 infection of genetically engineered iPSC-derived central nervous system-engrafted microglia in a humanized mouse model. J Virol 2023; 97:e0159523. [PMID: 38032195 PMCID: PMC10734545 DOI: 10.1128/jvi.01595-23] [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: 10/13/2023] [Accepted: 11/05/2023] [Indexed: 12/01/2023] Open
Abstract
IMPORTANCE Our mouse model is a powerful tool for investigating the genetic mechanisms governing central nervous system (CNS) human immunodeficiency virus type-1 (HIV-1) infection and latency in the CNS at a single-cell level. A major advantage of our model is that it uses induced pluripotent stem cell-derived microglia, which enables human genetics, including gene function and therapeutic gene manipulation, to be explored in vivo, which is more challenging to study with current hematopoietic stem cell-based models for neuroHIV. Our transgenic tracing of xenografted human cells will provide a quantitative medium to develop new molecular and epigenetic strategies for reducing the HIV-1 latent reservoir and to test the impact of therapeutic inflammation-targeting drug interventions on CNS HIV-1 latency.
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Affiliation(s)
- Alice K. Min
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Behnam Javidfar
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Roy Missall
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Donald Doanman
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Madel Durens
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Mara Graziani
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Annika Mordelt
- Department of Human Genetics and Department of Cognitive Neuroscience, Radboud UMC, Nijmegen, the Netherlands
- Centre for Neuroscience, Donders Institute for Brain, Cognition, and Behavior, Nijmegen, the Netherlands
| | - Samuele G. Marro
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Lotje de Witte
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Human Genetics and Department of Cognitive Neuroscience, Radboud UMC, Nijmegen, the Netherlands
- Centre for Neuroscience, Donders Institute for Brain, Cognition, and Behavior, Nijmegen, the Netherlands
| | - Benjamin K. Chen
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Talia H. Swartz
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Schahram Akbarian
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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5
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Kinloch NN, Shahid A, Dong W, Kirkby D, Jones BR, Beelen CJ, MacMillan D, Lee GQ, Mota TM, Sudderuddin H, Barad E, Harris M, Brumme CJ, Jones RB, Brockman MA, Joy JB, Brumme ZL. HIV reservoirs are dominated by genetically younger and clonally enriched proviruses. mBio 2023; 14:e0241723. [PMID: 37971267 PMCID: PMC10746175 DOI: 10.1128/mbio.02417-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 10/09/2023] [Indexed: 11/19/2023] Open
Abstract
IMPORTANCE Characterizing the human immunodeficiency virus (HIV) reservoir that endures despite antiretroviral therapy (ART) is critical to cure efforts. We observed that the oldest proviruses persisting during ART were exclusively defective, while intact proviruses (and rebound HIV) dated to nearer ART initiation. This helps explain why studies that sampled sub-genomic proviruses on-ART (which are largely defective) routinely found sequences dating to early infection, whereas those that sampled replication-competent HIV found almost none. Together with our findings that intact proviruses were more likely to be clonal, and that on-ART low-level/isolated viremia originated from proviruses of varying ages (including possibly defective ones), our observations indicate that (i) on-ART and rebound viremia can have distinct within-host origins, (ii) intact proviruses have shorter lifespans than grossly defective ones and thus depend more heavily on clonal expansion for persistence, and (iii) an HIV reservoir predominantly "dating" to near ART initiation will be substantially adapted to within-host pressures, complicating immune-based cure strategies.
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Affiliation(s)
- Natalie N. Kinloch
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Aniqa Shahid
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Winnie Dong
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Don Kirkby
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Bradley R. Jones
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
- Bioinformatics Program, University of British Columbia, Vancouver, British Columbia, Canada
| | - Charlotte J. Beelen
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Daniel MacMillan
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Guinevere Q. Lee
- Infectious Diseases Division, Department of Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Talia M. Mota
- Infectious Diseases Division, Department of Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Hanwei Sudderuddin
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
- Experimental Medicine Program, University of British Columbia, Vancouver, British Columbia, Canada
| | - Evan Barad
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Marianne Harris
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
- Department of Family Practice, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Chanson J. Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
- Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - R. Brad Jones
- Infectious Diseases Division, Department of Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Mark A. Brockman
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
- Department of Molecular Biology and Biochemistry, Faculty of Science, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Jeffrey B. Joy
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
- Bioinformatics Program, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Zabrina L. Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
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6
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Docken SS, McCormick K, Pampena MB, Samer S, Lindemuth E, Pinkevych M, Viox EG, Wu Y, Schlub TE, Cromer D, Keele BF, Paiardini M, Betts MR, Bar KJ, Davenport MP. Preferential selection of viral escape mutants by CD8+ T cell 'sieving' of SIV reactivation from latency. PLoS Pathog 2023; 19:e1011755. [PMID: 38032851 PMCID: PMC10688670 DOI: 10.1371/journal.ppat.1011755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 10/15/2023] [Indexed: 12/02/2023] Open
Abstract
HIV rapidly rebounds after interruption of antiretroviral therapy (ART). HIV-specific CD8+ T cells may act to prevent early events in viral reactivation. However, the presence of viral immune escape mutations may limit the effect of CD8+ T cells on viral rebound. Here, we studied the impact of CD8 immune pressure on post-treatment rebound of barcoded SIVmac293M in 14 Mamu-A*01 positive rhesus macaques that initiated ART on day 14, and subsequently underwent two analytic treatment interruptions (ATIs). Rebound following the first ATI (seven months after ART initiation) was dominated by virus that retained the wild-type sequence at the Mamu-A*01 restricted Tat-SL8 epitope. By the end of the two-month treatment interruption, the replicating virus was predominantly escaped at the Tat-SL8 epitope. Animals reinitiated ART for 3 months prior to a second treatment interruption. Time-to-rebound and viral reactivation rate were significantly slower during the second treatment interruption compared to the first. Tat-SL8 escape mutants dominated early rebound during the second treatment interruption, despite the dominance of wild-type virus in the proviral reservoir. Furthermore, the escape mutations detected early in the second treatment interruption were well predicted by those replicating at the end of the first, indicating that escape mutant virus in the second interruption originated from the latent reservoir as opposed to evolving de novo post rebound. SL8-specific CD8+ T cell levels in blood prior to the second interruption were marginally, but significantly, higher (median 0.73% vs 0.60%, p = 0.016). CD8+ T cell depletion approximately 95 days after the second treatment interruption led to the reappearance of wild-type virus. This work suggests that CD8+ T cells can actively suppress the rebound of wild-type virus, leading to the dominance of escape mutant virus after treatment interruption.
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Affiliation(s)
- Steffen S. Docken
- Infection Analytics Program, Kirby Institute, UNSW Sydney, Sydney, New South Wales, Australia
| | - Kevin McCormick
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - M. Betina Pampena
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Center for AIDS Research and Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Sadia Samer
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | - Emily Lindemuth
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Mykola Pinkevych
- Infection Analytics Program, Kirby Institute, UNSW Sydney, Sydney, New South Wales, Australia
| | - Elise G. Viox
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | - Yuhuang Wu
- Infection Analytics Program, Kirby Institute, UNSW Sydney, Sydney, New South Wales, Australia
| | - Timothy E. Schlub
- Sydney School of Public Health, Faculty of Medicine and Health, University of Sydney, Sydney, New South Wales, Australia
| | - Deborah Cromer
- Infection Analytics Program, Kirby Institute, UNSW Sydney, Sydney, New South Wales, Australia
| | - Brandon F. Keele
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Mirko Paiardini
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
- Department of Pathology and Laboratory Medicine, School of Medicine, Emory University, Atlanta, Georgia, United States of America
| | - Michael R. Betts
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Center for AIDS Research and Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Katharine J. Bar
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Miles P. Davenport
- Infection Analytics Program, Kirby Institute, UNSW Sydney, Sydney, New South Wales, Australia
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7
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Shahid A, MacLennan S, Jones BR, Sudderuddin H, Dang Z, Cobamibias K, Duncan MC, Kinloch NN, Dapp MJ, Archin NM, Fischl MA, Ofotokun I, Adimora A, Gange S, Aouizerat B, Kuniholm MH, Kassaye S, Mullins JI, Goldstein H, Joy JB, Anastos K, Brumme ZL. The replication-competent HIV reservoir is a genetically restricted, younger subset of the overall pool of HIV proviruses persisting during therapy, which is highly genetically stable over time. RESEARCH SQUARE 2023:rs.3.rs-3259040. [PMID: 37645749 PMCID: PMC10462229 DOI: 10.21203/rs.3.rs-3259040/v1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Within-host HIV populations continually diversify during untreated infection, and members of these diverse forms persist within infected cell reservoirs, even during antiretroviral therapy (ART). Characterizing the diverse viral sequences that persist during ART is critical to HIV cure efforts, but our knowledge of on-ART proviral evolutionary dynamics remains incomplete, as does our understanding of the differences between the overall pool of persisting proviral DNA (which is largely genetically defective) and the subset of intact HIV sequences capable of reactivating. Here, we reconstructed within-host HIV evolutionary histories in blood from seven participants of the Women's Interagency HIV Study (WIHS) who experienced HIV seroconversion. We measured diversity, lineage origins and ages of proviral sequences (env-gp120) sampled up to four times, up to 12 years on ART. We used the same techniques to study HIV sequences emerging from the reservoir in two participants. Proviral clonality generally increased over time on ART, with clones frequently persisting across multiple time points. The integration dates of proviruses persisting on ART generally spanned the duration of untreated infection (though were often skewed towards years immediately pre-ART), while in contrast, reservoir-origin viremia emerging in plasma was exclusively "younger" (i.e., dated to the years immediately pre-ART). The genetic and age distributions of distinct proviral sequences remained highly stable during ART in all but one participant in whom, after 12 years, there was evidence that "younger" proviruses had been preferentially eliminated. Analysis of within-host recombinant proviral sequences also suggested that HIV reservoirs can be superinfected with virus reactivated from an older era, yielding infectious viral progeny with mosaic genomes of sequences with different ages. Overall, results underscore the remarkable genetic stability of distinct proviral sequences that persist on ART, yet suggest that replication-competent HIV reservoir represents a genetically-restricted and overall "younger" subset of the overall persisting proviral pool in blood.
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Affiliation(s)
- Aniqa Shahid
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Signe MacLennan
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Bradley R Jones
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Hanwei Sudderuddin
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Zhong Dang
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Kyle Cobamibias
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Maggie C Duncan
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Natalie N Kinloch
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Michael J Dapp
- Department of Microbiology, University of Washington, School of Medicine, Seattle, WA, USA
| | - Nande M Archin
- UNC HIV Cure Center, Institute of Global Health and Infectious Diseases, University of North Carolina at Chapel Hill, NC, USA
| | - Margaret A Fischl
- Department of Medicine, University of Miami School of Medicine, Miami, FL, USA
| | - Igho Ofotokun
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Adaora Adimora
- Departments of Medicine and Epidemiology, University of North Carolina School of Medicine, UNC Gillings School of Global Public Health, Chapel Hill, NC, USA
| | - Stephen Gange
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | | | - Mark H Kuniholm
- Department of Epidemiology and Biostatistics, University at Albany, State University of New York, Rensselaer, New York, NY, USA
| | - Seble Kassaye
- Division of Infectious Diseases and Tropical Medicine, Georgetown University, Washington, DC, USA
| | - James I Mullins
- Department of Microbiology, University of Washington, School of Medicine, Seattle, WA, USA
| | - Harris Goldstein
- Departments of Microbiology and Immunology and Pediatrics, Albert Einstein College of Medicine, Bronx, New York, NY, USA
| | - Jeffrey B Joy
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Kathryn Anastos
- Department of Medicine, Albert Einstein College of Medicine, New York, NY, USA
| | - Zabrina L Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
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8
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de Azevedo SSD, Côrtes FH, Villela LM, Hoagland B, Grinsztejn B, Veloso VG, Morgado MG, Bello G. Ongoing HIV-1 evolution and reservoir reseeding in two elite controllers with genetically diverse peripheral proviral quasispecies. Mem Inst Oswaldo Cruz 2023; 118:e230066. [PMID: 37283423 DOI: 10.1590/0074-02760230066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 05/15/2023] [Indexed: 06/08/2023] Open
Abstract
BACKGROUND Elite controllers (EC) are human immunodeficiency virus (HIV)-positive individuals who can maintain low viral loads for extended periods without antiretroviral therapy due to multifactorial and individual characteristics. Most have a small HIV-1 reservoir composed of identical proviral sequences maintained by clonal expansion of infected CD4+ T cells. However, some have a more diverse peripheral blood mononuclear cell (PBMC)-associated HIV-1 reservoir with unique sequences. OBJECTIVES To understand the turnover dynamics of the PBMC-associated viral quasispecies in ECs with relatively diverse circulating proviral reservoirs. METHODS We performed single genome amplification of the env gene at three time points during six years in two EC with high intra-host HIV DNA diversity. FINDINGS Both EC displayed quite diverse PBMCs-associated viral quasispecies (mean env diversity = 1.9-4.1%) across all time-points comprising both identical proviruses that are probably clonally expanded and unique proviruses with evidence of ongoing evolution. HIV-1 env glycosylation pattern suggests that ancestral and evolving proviruses may display different phenotypes of resistance to broadly neutralising antibodies consistent with persistent immune pressure. Evolving viruses may progressively replace the ancestral ones or may remain as minor variants in the circulating proviral population. MAIN CONCLUSIONS These findings support that the high intra-host HIV-1 diversity of some EC resulted from long-term persistence of archival proviruses combined with the continuous reservoir's reseeding and low, but measurable, viral evolution despite undetectable viremia.
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Affiliation(s)
| | - Fernanda Heloise Côrtes
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório de AIDS & Imunologia Molecular, Rio de Janeiro, RJ, Brasil
| | - Larissa M Villela
- Fundação Oswaldo Cruz-Fiocruz, Instituto Nacional de Infectologia Evandro Chagas, Rio de Janeiro, RJ, Brasil
| | - Brenda Hoagland
- Fundação Oswaldo Cruz-Fiocruz, Instituto Nacional de Infectologia Evandro Chagas, Rio de Janeiro, RJ, Brasil
| | - Beatriz Grinsztejn
- Fundação Oswaldo Cruz-Fiocruz, Instituto Nacional de Infectologia Evandro Chagas, Rio de Janeiro, RJ, Brasil
| | - Valdilea Gonçalvez Veloso
- Fundação Oswaldo Cruz-Fiocruz, Instituto Nacional de Infectologia Evandro Chagas, Rio de Janeiro, RJ, Brasil
| | - Mariza G Morgado
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório de AIDS & Imunologia Molecular, Rio de Janeiro, RJ, Brasil
| | - Gonzalo Bello
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório de AIDS & Imunologia Molecular, Rio de Janeiro, RJ, Brasil
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9
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Kinloch NN, Shahid A, Dong W, Kirkby D, Jones BR, Beelen CJ, MacMillan D, Lee GQ, Mota TM, Sudderuddin H, Barad E, Harris M, Brumme CJ, Jones RB, Brockman MA, Joy JB, Brumme ZL. HIV reservoirs are dominated by genetically younger and clonally enriched proviruses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.12.536611. [PMID: 37090500 PMCID: PMC10120704 DOI: 10.1101/2023.04.12.536611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
In order to cure HIV, we need to better understand the within-host evolutionary origins of the small reservoir of genome-intact proviruses that persists within infected cells during antiretroviral therapy (ART). Most prior studies on reservoir evolutionary dynamics however did not discriminate genome-intact proviruses from the vast background of defective ones. We reconstructed within-host pre-ART HIV evolutionary histories in six individuals and leveraged this information to infer the ages of intact and defective proviruses sampled after an average >9 years on ART, along with the ages of rebound and low-level/isolated viremia occurring during this time. We observed that the longest-lived proviruses persisting on ART were exclusively defective, usually due to large deletions. In contrast, intact proviruses and rebound HIV exclusively dated to the years immediately preceding ART. These observations are consistent with genome-intact proviruses having shorter lifespans, likely due to the cumulative risk of elimination following viral reactivation and protein production. Consistent with this, intact proviruses (and those with packaging signal defects) were three times more likely to be genetically identical compared to other proviral types, highlighting clonal expansion as particularly important in ensuring their survival. By contrast, low-level/isolated viremia sequences were genetically heterogeneous and sometimes ancestral, where viremia may have originated from defective proviruses. Results reveal that the HIV reservoir is dominated by clonally-enriched and genetically younger sequences that date to the untreated infection period when viral populations had been under within-host selection pressures for the longest duration. Knowledge of these qualities may help focus strategies for reservoir elimination.
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Affiliation(s)
- Natalie N. Kinloch
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC
| | - Aniqa Shahid
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC
| | - Winnie Dong
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC
| | - Don Kirkby
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC
| | - Bradley R. Jones
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC
- Bioinformatics Program, University of British Columbia, Vancouver, BC
| | | | - Daniel MacMillan
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC
| | - Guinevere Q. Lee
- Infectious Diseases Division, Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Talia M. Mota
- Infectious Diseases Division, Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Hanwei Sudderuddin
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC
- Experimental Medicine Program, University of British Columbia, Vancouver, BC
| | - Evan Barad
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC
| | - Marianne Harris
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC
- Department of Family Practice, Faculty of Medicine, University of British Columbia, Vancouver, BC
| | - Chanson J. Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC
- Department of Medicine, University of British Columbia, Vancouver, BC
| | - R. Brad Jones
- Infectious Diseases Division, Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Mark A. Brockman
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC
- Department of Molecular Biology and Biochemistry, Faculty of Science, Simon Fraser University, Burnaby BC
| | - Jeffrey B. Joy
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC
- Bioinformatics Program, University of British Columbia, Vancouver, BC
- Department of Medicine, University of British Columbia, Vancouver, BC
| | - Zabrina L. Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC
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10
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de Azevedo SSD, Côrtes FH, Villela LM, Hoagland B, Grinsztejn B, Veloso VG, Morgado MG, Bello G. Comparative HIV-1 Proviral Dynamics in Two Individuals That Maintained Viral Replication Control with or without Antiretroviral Therapy following Superinfection. Viruses 2022; 14:v14122802. [PMID: 36560806 PMCID: PMC9783199 DOI: 10.3390/v14122802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 09/12/2022] [Accepted: 09/21/2022] [Indexed: 12/23/2022] Open
Abstract
The analysis of the HIV-1 proviral dynamics after superinfection in the context of both natural and antiretroviral therapy (ART)-mediated suppression could yield unique insights into understanding the persistence of viral variants that seeded the infected cells at different times. In this study, we performed a longitudinal analysis of the env diversity of PBMC-associated HIV DNA quasispecies in two HIV controllers (EEC09 and VC32) that were superinfected with subtype F1 viruses several years after primoinfection with subtype B viruses. Patient EEC09 started ART soon after superinfection, while patient VC32 maintained a natural control of virus replication for at least six years following the superinfection. Our analysis revealed no significant temporal changes in the overall proportion of primo-infecting and superinfecting proviral variants over 2-3 years after superinfection in both HIV controllers. Upon the introduction of ART, individual EEC09 displayed no evidence of HIV-infected cell turnover or viral evolution, while subject VC32 displayed some level of HIV-infected cell reseeding and detectable evolution (divergence) of both viral variants. These results confirm that proviral variants that seeded the reservoir at different times throughout infection could persist for long periods under fully suppressive ART or natural viremic control, but the HIV-1 proviral dynamics could be different in both settings.
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Affiliation(s)
- Suwellen Sardinha Dias de Azevedo
- Laboratório de AIDS and Imunologia Molecular, Instituto Oswaldo Cruz—FIOCRUZ, Rio de Janeiro 21040-360, Brazil
- Correspondence: or Auwellendias@gmail; Tel.: +55-21-3865-8147; Fax: +55-21-3865-8173
| | - Fernanda H. Côrtes
- Laboratório de AIDS and Imunologia Molecular, Instituto Oswaldo Cruz—FIOCRUZ, Rio de Janeiro 21040-360, Brazil
| | - Larissa M. Villela
- Instituto Nacional de Infectologia Evandro Chagas-INI, FIOCRUZ, Rio de Janeiro 21040-360, Brazil
| | - Brenda Hoagland
- Instituto Nacional de Infectologia Evandro Chagas-INI, FIOCRUZ, Rio de Janeiro 21040-360, Brazil
| | - Beatriz Grinsztejn
- Instituto Nacional de Infectologia Evandro Chagas-INI, FIOCRUZ, Rio de Janeiro 21040-360, Brazil
| | - Valdilea G. Veloso
- Instituto Nacional de Infectologia Evandro Chagas-INI, FIOCRUZ, Rio de Janeiro 21040-360, Brazil
| | - Mariza G. Morgado
- Laboratório de AIDS and Imunologia Molecular, Instituto Oswaldo Cruz—FIOCRUZ, Rio de Janeiro 21040-360, Brazil
| | - Gonzalo Bello
- Laboratório de AIDS and Imunologia Molecular, Instituto Oswaldo Cruz—FIOCRUZ, Rio de Janeiro 21040-360, Brazil
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11
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HIV proviral genetic diversity, compartmentalization and inferred dynamics in lung and blood during long-term suppressive antiretroviral therapy. PLoS Pathog 2022; 18:e1010613. [PMID: 36331974 PMCID: PMC9668181 DOI: 10.1371/journal.ppat.1010613] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 11/16/2022] [Accepted: 10/21/2022] [Indexed: 11/06/2022] Open
Abstract
The lung is an understudied site of HIV persistence. We isolated 898 subgenomic proviral sequences (nef) by single-genome approaches from blood and lung from nine individuals on long-term suppressive antiretroviral therapy (ART), and characterized genetic diversity and compartmentalization using formal tests. Consistent with clonal expansion as a driver of HIV persistence, identical sequences comprised between 8% to 86% of within-host datasets, though their location (blood vs. lung) followed no consistent pattern. The majority (77%) of participants harboured at least one sequence shared across blood and lung, supporting the migration of clonally-expanded cells between sites. The extent of blood proviral diversity on ART was also a strong indicator of diversity in lung (Spearman's ρ = 0.98, p<0.0001). For three participants, insufficient lung sequences were recovered to reliably investigate genetic compartmentalization. Of the remainder, only two participants showed statistically significant support for compartmentalization when analysis was restricted to distinct proviruses per site, and the extent of compartmentalization was modest in both cases. When all within-host sequences (including duplicates) were considered, the number of compartmentalized datasets increased to four. Thus, while a subset of individuals harbour somewhat distinctive proviral populations in blood and lung, this can simply be due to unequal distributions of clonally-expanded sequences. For two participants, on-ART proviruses were also phylogenetically analyzed in context of plasma HIV RNA populations sampled up to 18 years prior, including pre-ART and during previous treatment interruptions. In both participants, on-ART proviruses represented the most ancestral sequences sampled within-host, confirming that HIV sequences can persist in the body for decades. This analysis also revealed evidence of re-seeding of the reservoir during treatment interruptions. Results highlight the genetic complexity of proviruses persisting in lung and blood during ART, and the uniqueness of each individual's proviral composition. Personalized HIV remission and cure strategies may be needed to overcome these challenges.
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