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Immonen TT, Fennessey CM, Lipkey L, Newman L, Macairan A, Bosche M, Waltz N, Del Prete GQ, Lifson JD, Keele BF. No evidence for ongoing replication on ART in SIV-infected macaques. Nat Commun 2024; 15:5093. [PMID: 38877003 PMCID: PMC11178840 DOI: 10.1038/s41467-024-49369-9] [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: 02/27/2024] [Accepted: 06/04/2024] [Indexed: 06/16/2024] Open
Abstract
The capacity of HIV-1 to replicate during optimal antiretroviral therapy (ART) is challenging to assess directly. To gain greater sensitivity to detect evolution on ART, we used a nonhuman primate (NHP) model providing precise control over the level of pre-ART evolution and more comprehensive analyses than are possible with clinical samples. We infected 21 rhesus macaques (RMs) with the barcoded virus SIVmac239M and initiated ART early to minimize baseline genetic diversity. RMs were treated for 285-1200 days. We used several tests of molecular evolution to compare 1352 near-full-length (nFL) SIV DNA single genome sequences from PBMCs, lymph nodes, and spleen obtained near the time of ART initiation and those present after long-term ART, none of which showed significant changes to the SIV DNA population during ART in any animal. To investigate the possibility of ongoing replication in unsampled putative tissue sanctuaries during ART, we discontinued treatment in four animals and confirmed that none of the 336 nFL SIV RNA sequences obtained from rebound plasma viremia showed evidence of evolution. The rigorous nature of our analyses reinforced the emerging consensus of a lack of appreciable ongoing replication on effective ART and validates the relevance of this NHP model for cure studies.
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Affiliation(s)
- Taina T Immonen
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Christine M Fennessey
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Leslie Lipkey
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Laura Newman
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Agatha Macairan
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Marjorie Bosche
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Nora Waltz
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Gregory Q Del Prete
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Jeffrey D Lifson
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Brandon F Keele
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA.
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HIV drug resistance in various body compartments. Curr Opin HIV AIDS 2022; 17:205-212. [PMID: 35762375 DOI: 10.1097/coh.0000000000000741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
PURPOSE OF REVIEW HIV drug resistance testing using blood plasma or dried blood spots forms part of international guidelines. However, as the clinical utility of assessing drug resistance in other body compartments is less well established, we review this for blood cells and samples from other body compartments. RECENT EVIDENCE Although clinical benefit is not clear, drug resistance testing in blood cells is often performed when patients with suppressed plasma viral loads require a treatment substitution. In patients with HIV neurocognitive disease, cerebral spinal fluid (CSF) drug resistance is rarely discordant with plasma but has nevertheless been used to guide antiretroviral drug substitutions. Cases with HIV drug resistance in genital fluids have been documented but this does not appear to indicate transmission risk when blood plasma viral loads are suppressed. SUMMARY Drug-resistant variants, which may be selected in tissues under conditions of variable adherence and drug penetration, appear to disseminate quickly, and become detectable in blood. This may explain why drug resistance discordance between plasma and these compartments is rarely found. Partial compartmentalization of HIV populations is well established for the CSF and the genital tract but other than blood plasma, evidence is lacking to support drug resistance testing in body compartments.
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Abstract
Genetically-characterizing full-length HIV-1 RNA is critical for identifying genetically-intact genomes and for comparing these RNA genomes to proviral DNA. We have developed a method for sequencing plasma-derived RNA using long-range sequencing (PRLS assay; ∼8.3 kb from gag to the 3′ end or ∼5 kb from integrase to the 3′ end). We employed the gag-3′ PRLS assay to sequence HIV-1 RNA genomes from ART-naive participants during acute/early infection (n = 6) or chronic infection (n = 2). On average, only 65% of plasma-derived genomes were genetically-intact. Defects were found in all genomic regions but were concentrated in env and pol. We compared these genomes to near-full-length proviral sequences from paired peripheral blood mononuclear cell (PBMC) samples for the acute/early group and found that near-identical (>99.98% identical) sequences were identified only during acute infection. For three participants who initiated therapy during acute infection, we used the int-3′ PRLS assay to sequence plasma-derived genomes from an analytical treatment interruption and identified 100% identical genomes between pretherapy and rebound time points. The PRLS assay provides a new level of sensitivity for understanding the genetic composition of plasma-derived HIV-1 RNA from viremic individuals either pretherapy or after treatment interruption, which will be invaluable in assessing possible HIV-1 curative strategies. IMPORTANCE We developed novel plasma-derived RNA using long-range sequencing assays (PRLS assay; 8.3 kb, gag-3′, and 5.0 kb, int-3′). Employing the gag-3′ PRLS assay, we found that 26% to 51% of plasma-derived genomes are genetically-defective, largely as a result of frameshift mutations and deletions. These genetic defects were concentrated in the env region compared to gag and pol, likely a reflection of viral immune escape in env during untreated HIV-1 infection. Employing the int-3′ PRLS assay, we found that analytical treatment interruption (ATI) plasma-derived sequences were identical and genetically-intact. Several sequences from the ATI plasma samples were identical to viral sequences from pretherapy plasma and PBMC samples, indicating that HIV-1 reservoirs established prior to therapy contribute to viral rebound during an ATI. Therefore, near-full-length sequencing of HIV-1 particles is required to gain an accurate picture of the genetic landscape of plasma HIV-1 virions in studies of HIV-1 replication and persistence.
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White JA, Simonetti FR, Beg S, McMyn NF, Dai W, Bachmann N, Lai J, Ford WC, Bunch C, Jones JL, Ribeiro RM, Perelson AS, Siliciano JD, Siliciano RF. Complex decay dynamics of HIV virions, intact and defective proviruses, and 2LTR circles following initiation of antiretroviral therapy. Proc Natl Acad Sci U S A 2022; 119:e2120326119. [PMID: 35110411 PMCID: PMC8833145 DOI: 10.1073/pnas.2120326119] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Accepted: 12/21/2021] [Indexed: 02/07/2023] Open
Abstract
In persons living with HIV-1 (PLWH) who start antiretroviral therapy (ART), plasma virus decays in a biphasic fashion to below the detection limit. The first phase reflects the short half-life (<1 d) of cells that produce most of the plasma virus. The second phase represents the slower turnover (t1/2 = 14 d) of another infected cell population, whose identity is unclear. Using the intact proviral DNA assay (IPDA) to distinguish intact and defective proviruses, we analyzed viral decay in 17 PLWH initiating ART. Circulating CD4+ T cells with intact proviruses include few of the rapidly decaying first-phase cells. Instead, this population initially decays more slowly (t1/2 = 12.9 d) in a process that largely represents death or exit from the circulation rather than transition to latency. This more protracted decay potentially allows for immune selection. After ∼3 mo, the decay slope changes, and CD4+ T cells with intact proviruses decay with a half-life of 19 mo, which is still shorter than that of the latently infected cells that persist on long-term ART. Two-long-terminal repeat (2LTR) circles decay with fast and slow phases paralleling intact proviruses, a finding that precludes their use as a simple marker of ongoing viral replication. Proviruses with defects at the 5' or 3' end of the genome show equivalent monophasic decay at rates that vary among individuals. Understanding these complex early decay processes is important for correct use of reservoir assays and may provide insights into properties of surviving cells that can constitute the stable latent reservoir.
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Affiliation(s)
- Jennifer A White
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Francesco R Simonetti
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Subul Beg
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Natalie F McMyn
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Weiwei Dai
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Niklas Bachmann
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Jun Lai
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - William C Ford
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Christina Bunch
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Joyce L Jones
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Ruy M Ribeiro
- Department of Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545
| | - Alan S Perelson
- Department of Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545
| | - Janet D Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Robert F Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205;
- HHMI, Baltimore, MD 21205
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Siliciano JD, Siliciano RF. In Vivo Dynamics of the Latent Reservoir for HIV-1: New Insights and Implications for Cure. ANNUAL REVIEW OF PATHOLOGY-MECHANISMS OF DISEASE 2021; 17:271-294. [PMID: 34736342 DOI: 10.1146/annurev-pathol-050520-112001] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Although antiretroviral therapy (ART) can reduce viremia to below the limit of detection and allow persons living with HIV-1 (PLWH) to lead relatively normal lives, viremia rebounds when treatment is interrupted. Rebound reflects viral persistence in a stable latent reservoir in resting CD4+ T cells. This reservoir is now recognized as the major barrier to cure and is the focus of intense international research efforts. Strategies to cure HIV-1 infection include interventions to eliminate this reservoir, to prevent viral rebound from the reservoir, or to enhance immune responses such that viral replication is effectively controlled. Here we consider recent developments in understanding the composition of the reservoir and how it can be measured in clinical studies. We also discuss exciting new insights into the in vivo dynamics of the reservoir and the reasons for its remarkable stability. Finally we discuss recent discoveries on the complex processes that govern viral rebound. Expected final online publication date for the Annual Review of Pathology: Mechanisms of Disease, Volume 17 is January 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Janet D Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA;
| | - Robert F Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA; .,Howard Hughes Medical Institute, Baltimore, Maryland 21205, USA
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Musick A, Spindler J, Boritz E, Pérez L, Crespo-Vélez D, Patro SC, Sobolewski MD, Bale MJ, Reid C, Keele BF, Capoferri A, Shao W, Wiegand A, Simonetti FR, Mellors JW, Hughes SH, Coffin JM, Maldarelli F, Kearney MF. HIV Infected T Cells Can Proliferate in vivo Without Inducing Expression of the Integrated Provirus. Front Microbiol 2019; 10:2204. [PMID: 31632364 PMCID: PMC6781911 DOI: 10.3389/fmicb.2019.02204] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 09/09/2019] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND HIV-1 proviruses can persist during ART in clonally-expanded populations of CD4+ T cells. To date, few examples of an expanded clones containing replication-competent proviruses exist, although it is suspected to be common. One such clone, denoted AMBI-1 (Maldarelli et al., 2014), was also a source of persistent viremia on ART, begging the question of how the AMBI-1 clone can survive despite infection with a replication-competent, actively-expressing provirus. We hypothesized that only a small fraction of cells within the AMBI-1 clone are activated to produce virus particles during cell division while the majority remain latent despite division, ensuring their survival. To address this question, we determined the fraction of HIV-1 proviruses within the AMBI-1 clone that expresses unspliced cell-associated RNA during ART and compared this fraction to 33 other infected T cell clones within the same individual. RESULTS In total, 34 different clones carrying either intact or defective proviruses in "Patient 1" from Maldarelli et al. (2014) were assessed. We found that 2.3% of cells within the AMBI-1 clone contained unspliced HIV-1 RNA. Highest levels of HIV-1 RNA were found in the effector memory (EM) T cell subset. The fraction of cells within clones that contained HIV-1 RNA was not different in clones with intact (median 2.3%) versus defective (median 3.5%) proviruses (p = 0.2). However, higher fractions and levels of RNA were found in cells with proviruses containing multiple drug resistance mutations, including those contributing to rebound viremia. CONCLUSION These findings show that the vast majority of HIV-1 proviruses within expanded T cell clones, including intact proviruses, may be transcriptionally silent at any given time, implying that infected T cells may be able to be activated to proliferate without inducing the expression of the integrated provirus or, alternatelively, may be able to proliferate without cellular activation. The results of this study suggest that the long, presumed correlation between the level of cellular and proviral activation may not be accurate and, therefore, requires further investigation.
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Affiliation(s)
- Andrew Musick
- Human Immunodeficiency Virus (HIV) Dynamics and Replication Program, Center for Cancer Research (CCR), National Cancer Institute (NCI)-Frederick, Frederick, MD, United States
| | - Jonathan Spindler
- Human Immunodeficiency Virus (HIV) Dynamics and Replication Program, Center for Cancer Research (CCR), National Cancer Institute (NCI)-Frederick, Frederick, MD, United States
| | - Eli Boritz
- Virus Persistence and Dynamics Section, Vaccine Research Center, National Institute for Allergies and Infectious Diseases (NIAID), Bethesda, MD, United States
| | - Liliana Pérez
- Virus Persistence and Dynamics Section, Vaccine Research Center, National Institute for Allergies and Infectious Diseases (NIAID), Bethesda, MD, United States
| | - Daniel Crespo-Vélez
- Virus Persistence and Dynamics Section, Vaccine Research Center, National Institute for Allergies and Infectious Diseases (NIAID), Bethesda, MD, United States
| | - Sean C. Patro
- Human Immunodeficiency Virus (HIV) Dynamics and Replication Program, Center for Cancer Research (CCR), National Cancer Institute (NCI)-Frederick, Frederick, MD, United States
| | | | - Michael J. Bale
- Human Immunodeficiency Virus (HIV) Dynamics and Replication Program, Center for Cancer Research (CCR), National Cancer Institute (NCI)-Frederick, Frederick, MD, United States
| | - Carolyn Reid
- Frederick National Laboratory for Cancer Research, Aquired Immunodeficiency Syndrome (AIDS) and Cancer Virus Program, Leidos Biomedical Research Inc., Frederick, MD, United States
| | - Brandon F. Keele
- Frederick National Laboratory for Cancer Research, Aquired Immunodeficiency Syndrome (AIDS) and Cancer Virus Program, Leidos Biomedical Research Inc., Frederick, MD, United States
| | - Adam Capoferri
- Human Immunodeficiency Virus (HIV) Dynamics and Replication Program, Center for Cancer Research (CCR), National Cancer Institute (NCI)-Frederick, Frederick, MD, United States
| | - Wei Shao
- Frederick National Laboratory for Cancer Research, Advanced Biomedical Computing Center, Leidos Biomedical Research, Inc., Frederick, MD, United States
| | - Ann Wiegand
- Human Immunodeficiency Virus (HIV) Dynamics and Replication Program, Center for Cancer Research (CCR), National Cancer Institute (NCI)-Frederick, Frederick, MD, United States
| | - Francesco R. Simonetti
- Human Immunodeficiency Virus (HIV) Dynamics and Replication Program, Center for Cancer Research (CCR), National Cancer Institute (NCI)-Frederick, Frederick, MD, United States
| | - John W. Mellors
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Stephen H. Hughes
- Human Immunodeficiency Virus (HIV) Dynamics and Replication Program, Center for Cancer Research (CCR), National Cancer Institute (NCI)-Frederick, Frederick, MD, United States
| | - John M. Coffin
- Department of Molecular Biology and Microbiology, Tufts University, Boston, MA, United States
| | - Frank Maldarelli
- Human Immunodeficiency Virus (HIV) Dynamics and Replication Program, Center for Cancer Research (CCR), National Cancer Institute (NCI)-Frederick, Frederick, MD, United States
| | - Mary F. Kearney
- Human Immunodeficiency Virus (HIV) Dynamics and Replication Program, Center for Cancer Research (CCR), National Cancer Institute (NCI)-Frederick, Frederick, MD, United States
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7
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HIV Diversity and Genetic Compartmentalization in Blood and Testes during Suppressive Antiretroviral Therapy. J Virol 2019; 93:JVI.00755-19. [PMID: 31189714 DOI: 10.1128/jvi.00755-19] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 06/08/2019] [Indexed: 12/27/2022] Open
Abstract
HIV's ability to persist during suppressive antiretroviral therapy is the main barrier to cure. Immune-privileged tissues, such as the testes, may constitute distinctive sites of HIV persistence, but this has been challenging to study in humans. We analyzed the proviral burden and genetics in the blood and testes of 10 individuals on suppressive therapy who underwent elective gender-affirming surgery. HIV DNA levels in matched blood and testes were quantified by quantitative PCR, and subgenomic proviral sequences (nef region) were characterized from single templates. HIV diversity, compartmentalization, and immune escape burden were assessed using genetic and phylogenetic approaches. Diverse proviruses were recovered from the blood (396 sequences; 354 nef-intact sequences) and testes (326 sequences; 309 nef-intact sequences) of all participants. Notably, the frequency of identical HIV sequences varied markedly between and within individuals. Nevertheless, proviral loads, within-host unique HIV sequence diversity, and the immune escape burden correlated positively between blood and testes. When all intact nef sequences were evaluated, 60% of participants exhibited significant blood-testis genetic compartmentalization, but none did so when the evaluation was restricted to unique sequences per site, suggesting that compartmentalization, when present, is attributable to the clonal expansion of HIV-infected cells. Our observations confirm the testes as a site of HIV persistence and suggest that individuals with larger and more diverse blood reservoirs will have larger and more diverse testis reservoirs. Furthermore, while the testis microenvironment may not be sufficiently unique to facilitate the seeding of unique viral populations therein, differential clonal expansion dynamics may be at play, which may complicate HIV eradication.IMPORTANCE Two key questions in HIV reservoir biology are whether immune-privileged tissues, such as the testes, harbor distinctive proviral populations during suppressive therapy and, if so, by what mechanism. While our results indicated that blood-testis HIV genetic compartmentalization was reasonably common (60%), it was always attributable to differential frequencies of identical HIV sequences between sites. No blood-tissue data set retained evidence of compartmentalization when only unique HIV sequences per site were considered; moreover, HIV immune escape mutation burdens were highly concordant between sites. We conclude that the principal mechanism by which blood and testis reservoirs differ is not via seeding of divergent HIV sequences therein but, rather, via differential clonal expansion of latently infected cells. Thus, while viral diversity and escape-related barriers to HIV eradication are of a broadly similar magnitude across the blood and testes, clonal expansion represents a challenge. The results support individualized analysis of within-host reservoir diversity to inform curative approaches.
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8
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Ferris AL, Wells DW, Guo S, Del Prete GQ, Swanstrom AE, Coffin JM, Wu X, Lifson JD, Hughes SH. Clonal expansion of SIV-infected cells in macaques on antiretroviral therapy is similar to that of HIV-infected cells in humans. PLoS Pathog 2019; 15:e1007869. [PMID: 31291371 PMCID: PMC6619828 DOI: 10.1371/journal.ppat.1007869] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 05/24/2019] [Indexed: 12/11/2022] Open
Abstract
Clonal expansion of HIV infected cells plays an important role in the formation and persistence of the reservoir that allows the virus to persist, in DNA form, despite effective antiretroviral therapy. We used integration site analysis to ask if there is a similar clonal expansion of SIV infected cells in macaques. We show that the distribution of HIV and SIV integration sites in vitro is similar and that both viruses preferentially integrate in many of the same genes. We obtained approximately 8000 integration sites from blood samples taken from SIV-infected macaques prior to the initiation of ART, and from blood, spleen, and lymph node samples taken at necropsy. Seven clones were identified in the pre-ART samples; one persisted for a year on ART. An additional 100 clones were found only in on-ART samples; a number of these clones were found in more than one tissue. The timing and extent of clonal expansion of SIV-infected cells in macaques and HIV-infected cells in humans is quite similar. This suggests that SIV-infected macaques represent a useful model of the clonal expansion of HIV infected cells in humans that can be used to evaluate strategies intended to control or eradicate the viral reservoir.
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Affiliation(s)
- Andrea L. Ferris
- HIV Dynamics and Replication Program, National Cancer Institute Frederick, National Institutes of Health, Frederick, MD, United States of America
| | - David W. Wells
- Cancer Research Technology Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick MD, United States of America
| | - Shuang Guo
- Cancer Research Technology Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick MD, United States of America
| | - Gregory Q. Del Prete
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, United States of America
| | - Adrienne E. Swanstrom
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, United States of America
| | - John M. Coffin
- Department of Molecular Biology and Microbiology, Tufts University, Boston MA, United States of America
| | - Xiaolin Wu
- Cancer Research Technology Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick MD, United States of America
| | - Jeffrey D. Lifson
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, United States of America
| | - Stephen H. Hughes
- HIV Dynamics and Replication Program, National Cancer Institute Frederick, National Institutes of Health, Frederick, MD, United States of America
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9
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Coffin JM, Wells DW, Zerbato JM, Kuruc JD, Guo S, Luke BT, Eron JJ, Bale M, Spindler J, Simonetti FR, Hill S, Kearney MF, Maldarelli F, Wu X, Mellors JW, Hughes SH. Clones of infected cells arise early in HIV-infected individuals. JCI Insight 2019; 4:128432. [PMID: 31217357 PMCID: PMC6629130 DOI: 10.1172/jci.insight.128432] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 05/16/2019] [Indexed: 01/30/2023] Open
Abstract
In HIV-infected individuals on long-term antiretroviral therapy (ART), more than 40% of the infected cells are in clones. Although most HIV proviruses present in individuals on long-term ART are defective, including those in clonally expanded cells, there is increasing evidence that clones carrying replication-competent proviruses are common in patients on long-term ART and form part of the HIV reservoir that makes it impossible to cure HIV infection with current ART alone. Given the importance of clonal expansion in HIV persistence, we determined how soon after HIV acquisition infected clones can grow large enough to be detected (clones larger than ca. 1 × 105 cells). We studied 12 individuals sampled in early HIV infection (Fiebig stage III-V/VI) and 5 who were chronically infected. The recently infected individuals were started on ART at or near the time of diagnosis. We isolated more than 6,500 independent integration sites from peripheral blood mononuclear cells before ART was initiated and after 0.5-18 years of suppressive ART. Some infected clones could be detected approximately 4 weeks after HIV infection and some of these clones persisted for years. The results help to explain how the reservoir is established early and persists for years.
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Affiliation(s)
- John M. Coffin
- Department of Molecular Biology and Microbiology, Tufts University, Boston, Massachusetts, USA
| | | | - Jennifer M. Zerbato
- Department of Medicine, Division of Infectious Diseases, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Joann D. Kuruc
- Department of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
| | | | - Brian T. Luke
- Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick Maryland, USA
| | - Joseph J. Eron
- Department of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Michael Bale
- HIV Dynamics and Replication Program, NCI-Frederick, Frederick, Maryland, USA
| | - Jonathan Spindler
- HIV Dynamics and Replication Program, NCI-Frederick, Frederick, Maryland, USA
| | | | - Shawn Hill
- HIV Dynamics and Replication Program, NCI-Frederick, Frederick, Maryland, USA
| | - Mary F. Kearney
- HIV Dynamics and Replication Program, NCI-Frederick, Frederick, Maryland, USA
| | - Frank Maldarelli
- HIV Dynamics and Replication Program, NCI-Frederick, Frederick, Maryland, USA
| | | | - John W. Mellors
- Department of Medicine, Division of Infectious Diseases, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Stephen H. Hughes
- HIV Dynamics and Replication Program, NCI-Frederick, Frederick, Maryland, USA
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10
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Phylogenetic inference for the study of within-host HIV-1 dynamics and persistence on antiretroviral therapy. Lancet HIV 2019; 6:e325-e333. [PMID: 30962119 DOI: 10.1016/s2352-3018(19)30051-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 02/02/2019] [Accepted: 02/19/2019] [Indexed: 01/22/2023]
Abstract
Although antiretroviral therapy (ART) is highly effective at inhibiting HIV-1 replication and preventing AIDS, it cannot eradicate the infection. Many studies have used viral genetic information from single-genome and deep sequencing of blood and tissue samples to investigate the mechanisms that sustain the HIV-1 reservoir. Sequence data are analysed by use of measurements of population diversity and divergence and by exploration of phylogenetic associations. The study of intrahost HIV-1 populations on ART requires specific considerations as their dynamics can be shaped by host factors such as cell death and proliferation. Hence, understanding both the biology of HIV-1 persistence and the phylogenetic methods that can be applied to this field is crucial. We conclude that the most suitable phylogenetic methods and evolutionary models for characterising HIV-1 populations on ART include using neighbour-joining trees to identify identical proviral sequences that might result from T-cell proliferation, and using maximum-likelihood analysis to investigate the possibility of ongoing viral replication on ART. Characterising the reservoir for HIV-1 on ART is a high priority for the design of curative interventions.
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11
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Capone A, Lo Presti A, Sernicola L, Farcomeni S, Ferrantelli F, Maggiorella MT, Mee ET, Rose NJ, Cella E, Ciccozzi M, Ensoli B, Borsetti A. Genetic diversity in the env V1-V2 region of proviral quasispecies from long-term controller MHC-typed cynomolgus macaques infected with SHIVSF162P4cy. J Gen Virol 2018; 99:1717-1728. [PMID: 30311877 DOI: 10.1099/jgv.0.001159] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Intra-host evolution of human immunodeficiency virus (HIV) and simian immunodeficiency virus (SIV) has been shown by viral RNA analysis in subjects who naturally suppress plasma viremia to low levels, known as controllers. However, little is known about the variability of proviral DNA and the inter-relationships among contained systemic viremia, rate of reservoir reseeding and specific major histocompatibility complex (MHC) genotypes, in controllers. Here, we analysed the proviral DNA quasispecies of the env V1-V2 region, in PBMCs and in anatomical compartments of 13 long-term controller monkeys after 3.2 years of infection with simian/human immunodeficiency virus (SHIV)SF162P4cy. A considerable variation in the genetic diversity of proviral quasispecies was present among animals. Seven monkeys exhibited env V1-V2 proviral populations composed of both clusters of identical ancestral sequences and new variants, whereas the other six monkeys displayed relatively high env V1-V2 genetic diversity with a large proportion of diverse novel sequences. Our results demonstrate that in SHIVSF162P4cy-infected monkeys there exists a disparate pattern of intra-host viral diversity and that reseeding of the proviral reservoir occurs in some animals. Moreover, even though no particular association has been observed between MHC haplotypes and the long-term control of infection, a remarkably similar pattern of intra-host viral diversity and divergence was found within animals carrying the M3 haplotype. This suggests that in animals bearing the same MHC haplotype and infected with the same virus, viral diversity follows a similar pattern with similar outcomes and control of infection.
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Affiliation(s)
- Alessia Capone
- 1National HIV/AIDS Research Center, Istituto Superiore di Sanità, V.le Regina Elena 299, 00161 Rome, Italy.,2Neuroimmunology Laboratory, Fondazione Santa Lucia, Rome, Italy.,3Department of Biology and Biotechnology Charles Darwin, Sapienza University, Rome, Italy
| | - Alessandra Lo Presti
- 4Department of Infectious Diseases, Istituto Superiore di Sanità, V.le Regina Elena 299, 00161 Rome, Italy
| | - Leonardo Sernicola
- 1National HIV/AIDS Research Center, Istituto Superiore di Sanità, V.le Regina Elena 299, 00161 Rome, Italy
| | - Stefania Farcomeni
- 1National HIV/AIDS Research Center, Istituto Superiore di Sanità, V.le Regina Elena 299, 00161 Rome, Italy
| | - Flavia Ferrantelli
- 5National Center for Global Health, Istituto Superiore di Sanità, V.le Regina Elena 299, 00161 Rome, Italy
| | - Maria T Maggiorella
- 1National HIV/AIDS Research Center, Istituto Superiore di Sanità, V.le Regina Elena 299, 00161 Rome, Italy
| | - Edward T Mee
- 6Division of Virology, National Institute for Biological Standards and Control, Medicines and Healthcare product Regulatory Agency, South Mimms, Hertfordshire, EN6 3QG, UK
| | - Nicola J Rose
- 6Division of Virology, National Institute for Biological Standards and Control, Medicines and Healthcare product Regulatory Agency, South Mimms, Hertfordshire, EN6 3QG, UK
| | - Eleonora Cella
- 7Medical statistic and molecular epidemiology unit, University campus bio medico, Roma, Italy
| | - Massimo Ciccozzi
- 7Medical statistic and molecular epidemiology unit, University campus bio medico, Roma, Italy
| | - Barbara Ensoli
- 1National HIV/AIDS Research Center, Istituto Superiore di Sanità, V.le Regina Elena 299, 00161 Rome, Italy
| | - Alessandra Borsetti
- 1National HIV/AIDS Research Center, Istituto Superiore di Sanità, V.le Regina Elena 299, 00161 Rome, Italy
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12
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van Zyl G, Bale MJ, Kearney MF. HIV evolution and diversity in ART-treated patients. Retrovirology 2018; 15:14. [PMID: 29378595 PMCID: PMC5789667 DOI: 10.1186/s12977-018-0395-4] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 01/18/2018] [Indexed: 12/21/2022] Open
Abstract
Characterizing HIV genetic diversity and evolution during antiretroviral therapy (ART) provides insights into the mechanisms that maintain the viral reservoir during ART. This review describes common methods used to obtain and analyze intra-patient HIV sequence data, the accumulation of diversity prior to ART and how it is affected by suppressive ART, the debate on viral replication and evolution in the presence of ART, HIV compartmentalization across various tissues, and mechanisms for the emergence of drug resistance. It also describes how CD4+ T cells that were likely infected with latent proviruses prior to initiating treatment can proliferate before and during ART, providing a renewable source of infected cells despite therapy. Some expanded cell clones carry intact and replication-competent proviruses with a small fraction of the clonal siblings being transcriptionally active and a source for residual viremia on ART. Such cells may also be the source for viral rebound after interrupting ART. The identical viral sequences observed for many years in both the plasma and infected cells of patients on long-term ART are likely due to the proliferation of infected cells both prior to and during treatment. Studies on HIV diversity may reveal targets that can be exploited in efforts to eradicate or control the infection without ART.
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Affiliation(s)
- Gert van Zyl
- Division of Medical Virology, Stellenbosch University and NHLS Tygerberg, Cape Town, South Africa
| | - Michael J Bale
- HIV Dynamic and Replication Program, Center for Cancer Research, National Cancer Institute at Frederick, 1050 Boyles Street, Building 535, Room 109, Frederick, MD, 21702-1201, USA
| | - Mary F Kearney
- HIV Dynamic and Replication Program, Center for Cancer Research, National Cancer Institute at Frederick, 1050 Boyles Street, Building 535, Room 109, Frederick, MD, 21702-1201, USA.
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13
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Van Zyl GU, Katusiime MG, Wiegand A, McManus WR, Bale MJ, Halvas EK, Luke B, Boltz VF, Spindler J, Laughton B, Engelbrecht S, Coffin JM, Cotton MF, Shao W, Mellors JW, Kearney MF. No evidence of HIV replication in children on antiretroviral therapy. J Clin Invest 2017; 127:3827-3834. [PMID: 28891813 PMCID: PMC5617669 DOI: 10.1172/jci94582] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 07/26/2017] [Indexed: 12/21/2022] Open
Abstract
It remains controversial whether current antiretroviral therapy (ART) fully suppresses the cycles of HIV replication and viral evolution in vivo. If replication persists in sanctuary sites such as the lymph nodes, a high priority should be placed on improving ART regimes to target these sites. To investigate the question of ongoing viral replication on current ART regimens, we analyzed HIV populations in longitudinal samples from 10 HIV-1-infected children who initiated ART when viral diversity was low. Eight children started ART at less than ten months of age and showed suppression of plasma viremia for seven to nine years. Two children had uncontrolled viremia for fifteen and thirty months, respectively, before viremia suppression, and served as positive controls for HIV replication and evolution. These latter 2 children showed clear evidence of virus evolution, whereas multiple methods of analysis bore no evidence of virus evolution in any of the 8 children with viremia suppression on ART. Phylogenetic trees simulated with the recently reported evolutionary rate of HIV-1 on ART of 6 × 10-4 substitutions/site/month bore no resemblance to the observed data. Taken together, these data refute the concept that ongoing HIV replication is common with ART and is the major barrier to curing HIV-1 infection.
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Affiliation(s)
- Gert U. Van Zyl
- Division of Medical Virology, Stellenbosch University and National Health Laboratory Service (NHLS) Tygerberg, Cape Town, South Africa
| | - Mary Grace Katusiime
- Division of Medical Virology, Stellenbosch University and National Health Laboratory Service (NHLS) Tygerberg, Cape Town, South Africa
| | - Ann Wiegand
- HIV Dynamics and Replication Program, National Cancer Institute (NCI), Frederick, Maryland, USA
| | - William R. McManus
- HIV Dynamics and Replication Program, National Cancer Institute (NCI), Frederick, Maryland, USA
| | - Michael J. Bale
- HIV Dynamics and Replication Program, National Cancer Institute (NCI), Frederick, Maryland, USA
| | - Elias K. Halvas
- Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Brian Luke
- Advanced Biomedical Computing Center, Leidos Biomedical Research Inc. and Frederick National Laboratories for Cancer Research, Frederick, Maryland, USA
| | - Valerie F. Boltz
- HIV Dynamics and Replication Program, National Cancer Institute (NCI), Frederick, Maryland, USA
| | - Jonathan Spindler
- HIV Dynamics and Replication Program, National Cancer Institute (NCI), Frederick, Maryland, USA
| | - Barbara Laughton
- Department Pediatrics and Child Health, Tygerberg Children’s Hospital and Family Clinical Research Unit, Stellenbosch University, Cape Town, South Africa
| | - Susan Engelbrecht
- Division of Medical Virology, Stellenbosch University and National Health Laboratory Service (NHLS) Tygerberg, Cape Town, South Africa
| | - John M. Coffin
- Department of Molecular Biology and Microbiology, Tufts University, Boston, Massachusetts, USA
| | - Mark F. Cotton
- Department Pediatrics and Child Health, Tygerberg Children’s Hospital and Family Clinical Research Unit, Stellenbosch University, Cape Town, South Africa
| | - Wei Shao
- Advanced Biomedical Computing Center, Leidos Biomedical Research Inc. and Frederick National Laboratories for Cancer Research, Frederick, Maryland, USA
| | - John W. Mellors
- Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Mary F. Kearney
- HIV Dynamics and Replication Program, National Cancer Institute (NCI), Frederick, Maryland, USA
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14
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Boritz EA, Douek DC. Perspectives on Human Immunodeficiency Virus (HIV) Cure: HIV Persistence in Tissue. J Infect Dis 2017; 215:S128-S133. [PMID: 28520970 DOI: 10.1093/infdis/jix005] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The uneven anatomic distribution of cell subsets that harbor human immunodeficiency virus (HIV) during antiretroviral therapy (ART) complicates investigation of the barriers to HIV cure. Here we propose that while previous studies done largely in blood cells have led to important investigations into HIV latency, other important mechanisms of HIV persistence during ART may not be readily apparent in the bloodstream. We specifically consider as an example the question of ongoing HIV replication during ART. We discuss how growing understanding of key anatomic sanctuaries for the virus can inform future experiments aimed at further clarifying this issue.
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Affiliation(s)
- Eli A Boritz
- Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Daniel C Douek
- Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
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15
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Feder AF, Kline C, Polacino P, Cottrell M, Kashuba ADM, Keele BF, Hu SL, Petrov DA, Pennings PS, Ambrose Z. A spatio-temporal assessment of simian/human immunodeficiency virus (SHIV) evolution reveals a highly dynamic process within the host. PLoS Pathog 2017; 13:e1006358. [PMID: 28542550 PMCID: PMC5444849 DOI: 10.1371/journal.ppat.1006358] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 04/17/2017] [Indexed: 12/25/2022] Open
Abstract
The process by which drug-resistant HIV-1 arises and spreads spatially within an infected individual is poorly understood. Studies have found variable results relating how HIV-1 in the blood differs from virus sampled in tissues, offering conflicting findings about whether HIV-1 throughout the body is homogeneously distributed. However, most of these studies sample only two compartments and few have data from multiple time points. To directly measure how drug resistance spreads within a host and to assess how spatial structure impacts its emergence, we examined serial sequences from four macaques infected with RT-SHIVmne027, a simian immunodeficiency virus encoding HIV-1 reverse transcriptase (RT), and treated with RT inhibitors. Both viral DNA and RNA (vDNA and vRNA) were isolated from the blood (including plasma and peripheral blood mononuclear cells), lymph nodes, gut, and vagina at a median of four time points and RT was characterized via single-genome sequencing. The resulting sequences reveal a dynamic system in which vRNA rapidly acquires drug resistance concomitantly across compartments through multiple independent mutations. Fast migration results in the same viral genotypes present across compartments, but not so fast as to equilibrate their frequencies immediately. The blood and lymph nodes were found to be compartmentalized rarely, while both the blood and lymph node were more frequently different from mucosal tissues. This study suggests that even oft-sampled blood does not fully capture the viral dynamics in other parts of the body, especially the gut where vRNA turnover was faster than the plasma and vDNA retained fewer wild-type viruses than other sampled compartments. Our findings of transient compartmentalization across multiple tissues may help explain the varied results of previous compartmentalization studies in HIV-1. HIV-1 is difficult to treat because the virus can evolve to become drug-resistant within the body, but we have an incomplete understanding of where drug-resistant viruses originate and how they spread within a person. In this study, four macaques were infected with RT-SHIV, a simian immunodeficiency virus with an HIV-1 reverse transcriptase coding region, which can be targeted with standard HIV drugs. We sampled virus from the macaques before, during and after their viral population became resistant to administered drugs and determined the genetic viral sequences in several parts of the body: blood, lymph nodes, gut, and vagina. We found that drug resistance emerged across compartments nearly simultaneously, and drug resistance evolved multiple independent times within each macaque. Although migration of RT-SHIV between compartments is fast, compartments do not have the same distribution of viral genotypes. This is important because although studies typically sample virus from the blood to study how HIV-1 evolution in humans, our study suggests that it is not fully representative of other parts of the body, particularly the gut.
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Affiliation(s)
- Alison F. Feder
- Department of Biology, Stanford University, Stanford, CA, United States
| | - Christopher Kline
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Patricia Polacino
- Washington National Primate Research Center, University of Washington, Seattle, WA, United States
| | - Mackenzie Cottrell
- Division of Pharmacotherapy and Experimental Therapeutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Angela D. M. Kashuba
- Division of Pharmacotherapy and Experimental Therapeutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Brandon F. Keele
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, United States
| | - Shiu-Lok Hu
- Washington National Primate Research Center, University of Washington, Seattle, WA, United States
| | - Dmitri A. Petrov
- Department of Biology, Stanford University, Stanford, CA, United States
| | - Pleuni S. Pennings
- Department of Biology, San Francisco State University, San Francisco, CA, United States
- * E-mail: (PSP); (ZA)
| | - Zandrea Ambrose
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
- * E-mail: (PSP); (ZA)
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16
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Single-cell analysis of HIV-1 transcriptional activity reveals expression of proviruses in expanded clones during ART. Proc Natl Acad Sci U S A 2017; 114:E3659-E3668. [PMID: 28416661 DOI: 10.1073/pnas.1617961114] [Citation(s) in RCA: 118] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Little is known about the fraction of human immunodeficiency virus type 1 (HIV-1) proviruses that express unspliced viral RNA in vivo or about the levels of HIV RNA expression within single infected cells. We developed a sensitive cell-associated HIV RNA and DNA single-genome sequencing (CARD-SGS) method to investigate fractional proviral expression of HIV RNA (1.3-kb fragment of p6, protease, and reverse transcriptase) and the levels of HIV RNA in single HIV-infected cells from blood samples obtained from individuals with viremia or individuals on long-term suppressive antiretroviral therapy (ART). Spiking experiments show that the CARD-SGS method can detect a single cell expressing HIV RNA. Applying CARD-SGS to blood mononuclear cells in six samples from four HIV-infected donors (one with viremia and not on ART and three with viremia suppressed on ART) revealed that an average of 7% of proviruses (range: 2-18%) expressed HIV RNA. Levels of expression varied from one to 62 HIV RNA molecules per cell (median of 1). CARD-SGS also revealed the frequent expression of identical HIV RNA sequences across multiple single cells and across multiple time points in donors on suppressive ART consistent with constitutive expression of HIV RNA in infected cell clones. Defective proviruses were found to express HIV RNA at levels similar to those proviruses that had no obvious defects. CARD-SGS is a useful tool to characterize fractional proviral expression in single infected cells that persist despite ART and to assess the impact of experimental interventions on proviral populations and their expression.
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17
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Proviruses with identical sequences comprise a large fraction of the replication-competent HIV reservoir. PLoS Pathog 2017; 13:e1006283. [PMID: 28328934 PMCID: PMC5378418 DOI: 10.1371/journal.ppat.1006283] [Citation(s) in RCA: 196] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 04/03/2017] [Accepted: 03/08/2017] [Indexed: 11/19/2022] Open
Abstract
The major obstacle to curing HIV infection is the persistence of cells with intact proviruses that can produce replication-competent virus. This HIV reservoir is believed to exist primarily in CD4+ T-cells and is stable despite years of suppressive antiretroviral therapy. A potential mechanism for HIV persistence is clonal expansion of infected cells, but how often such clones carry replication-competent proviruses has been controversial. Here, we used single-genome sequencing to probe for identical HIV sequence matches among viruses recovered in different viral outgrowth cultures and between the sequences of outgrowth viruses and proviral or intracellular HIV RNA sequences in uncultured blood mononuclear cells from eight donors on suppressive ART with diverse proviral populations. All eight donors had viral outgrowth virus that was fully susceptible to their current ART drug regimen. Six of eight donors studied had identical near full-length HIV RNA sequences recovered from different viral outgrowth cultures, and one of the two remaining donors had identical partial viral sequence matches between outgrowth virus and intracellular HIV RNA. These findings provide evidence that clonal expansion of HIV-infected cells is an important mechanism of reservoir persistence that should be targeted to cure HIV infection. Antiretroviral therapy (ART) can reduce plasma HIV viral loads to undetectable levels. However, HIV-infected cells can persist despite years of antiretroviral suppression and contribute to rebound viremia following cessation of ART. It is unclear whether HIV-infected cells are maintained by ongoing viral replication, prolonged survival of infected cells, or clonal expansion of infected cells. No studies to date have definitively determined whether clonal expansion is a common mechanism of persistence for replication-competent HIV. To investigate, we used single-genome sequencing to detect identical HIV sequence matches between replication-competent viruses, proviruses, and/or cell-associated RNA from eight donors who were on long-term suppressive ART without evidence of ongoing viral replication. Six of eight donors had identical near full-length sequences between unique replication-competent viruses. One of the two remaining donors had identical partial viral sequences between a replication-competent virus and cell-associated HIV RNA. These findings suggest that clonal expansion is an important mechanism of persistence of replication-competent HIV and should be targeted by HIV cure efforts.
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18
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Araínga M, Edagwa B, Mosley RL, Poluektova LY, Gorantla S, Gendelman HE. A mature macrophage is a principal HIV-1 cellular reservoir in humanized mice after treatment with long acting antiretroviral therapy. Retrovirology 2017; 14:17. [PMID: 28279181 PMCID: PMC5345240 DOI: 10.1186/s12977-017-0344-7] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 03/06/2017] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Despite improved clinical outcomes seen following antiretroviral therapy (ART), resting CD4+ T cells continue to harbor latent human immunodeficiency virus type one (HIV-1). However, such cells are not likely the solitary viral reservoir and as such defining where and how others harbor virus is imperative for eradication measures. To such ends, we used HIV-1ADA-infected NOD.Cg-Prkdc scid Il2rg tm1Wjl /SzJ mice reconstituted with a human immune system to explore two long-acting ART regimens investigating their abilities to affect viral cell infection and latency. At 6 weeks of infection animals were divided into four groups. One received long-acting (LA) cabotegravir (CAB) and rilpivirine (RVP) (2ART), a second received LA CAB, lamivudine, abacavir and RVP (4ART), a third were left untreated and a fourth served as an uninfected control. After 4 weeks of LA ART treatment, blood, spleen and bone marrow (BM) cells were collected then phenotypically characterized. CD4+ T cell subsets, macrophages and hematopoietic progenitor cells were analyzed for HIV-1 nucleic acids by droplet digital PCR. RESULTS Plasma viral loads were reduced by two log10 or to undetectable levels in the 2 and 4ART regimens, respectively. Numbers and distributions of CD4+ memory and regulatory T cells, macrophages and hematopoietic progenitor cells were significantly altered by HIV-1 infection and by both ART regimens. ART reduced viral DNA and RNA in all cell and tissue compartments. While memory cells were the dominant T cell reservoir, integrated HIV-1 DNA was also detected in the BM and spleen macrophages in both regimen-treated mice. CONCLUSION Despite vigorous ART regimens, HIV-1 DNA and RNA were easily detected in mature macrophages supporting their potential role as an infectious viral reservoir.
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Affiliation(s)
- Mariluz Araínga
- Department of Pharmacology and Experimental Neuroscience, 985880 Nebraska Medical Center, College of Medicine, University of Nebraska Medical Center, Omaha, NE, 68198-5880, USA
| | - Benson Edagwa
- Department of Pharmacology and Experimental Neuroscience, 985880 Nebraska Medical Center, College of Medicine, University of Nebraska Medical Center, Omaha, NE, 68198-5880, USA
| | - R Lee Mosley
- Department of Pharmacology and Experimental Neuroscience, 985880 Nebraska Medical Center, College of Medicine, University of Nebraska Medical Center, Omaha, NE, 68198-5880, USA
| | - Larisa Y Poluektova
- Department of Pharmacology and Experimental Neuroscience, 985880 Nebraska Medical Center, College of Medicine, University of Nebraska Medical Center, Omaha, NE, 68198-5880, USA
| | - Santhi Gorantla
- Department of Pharmacology and Experimental Neuroscience, 985880 Nebraska Medical Center, College of Medicine, University of Nebraska Medical Center, Omaha, NE, 68198-5880, USA
| | - Howard E Gendelman
- Department of Pharmacology and Experimental Neuroscience, 985880 Nebraska Medical Center, College of Medicine, University of Nebraska Medical Center, Omaha, NE, 68198-5880, USA.
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19
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Policicchio BB, Pandrea I, Apetrei C. Animal Models for HIV Cure Research. Front Immunol 2016; 7:12. [PMID: 26858716 PMCID: PMC4729870 DOI: 10.3389/fimmu.2016.00012] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 01/12/2016] [Indexed: 12/17/2022] Open
Abstract
The HIV-1/AIDS pandemic continues to spread unabated worldwide, and no vaccine exists within our grasp. Effective antiretroviral therapy (ART) has been developed, but ART cannot clear the virus from the infected patient. A cure for HIV-1 is badly needed to stop both the spread of the virus in human populations and disease progression in infected individuals. A safe and effective cure strategy for human immunodeficiency virus (HIV) infection will require multiple tools, and appropriate animal models are tools that are central to cure research. An ideal animal model should recapitulate the essential aspects of HIV pathogenesis and associated immune responses, while permitting invasive studies, thus allowing a thorough evaluation of strategies aimed at reducing the size of the reservoir (functional cure) or eliminating the reservoir altogether (sterilizing cure). Since there is no perfect animal model for cure research, multiple models have been tailored and tested to address specific quintessential questions of virus persistence and eradication. The development of new non-human primate and mouse models, along with a certain interest in the feline model, has the potential to fuel cure research. In this review, we highlight the major animal models currently utilized for cure research and the contributions of each model to this goal.
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Affiliation(s)
| | - Ivona Pandrea
- Center for Vaccine Research, University of Pittsburgh , Pittsburgh, PA , USA
| | - Cristian Apetrei
- Center for Vaccine Research, University of Pittsburgh , Pittsburgh, PA , USA
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20
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Gabriel B, Fiebig U, Hohn O, Plesker R, Coulibaly C, Cichutek K, Mühlebach MD, Bannert N, Kurth R, Norley S. Suppressing active replication of a live attenuated simian immunodeficiency virus vaccine does not abrogate protection from challenge. Virology 2015; 489:1-11. [PMID: 26685794 DOI: 10.1016/j.virol.2015.11.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Revised: 10/14/2015] [Accepted: 11/28/2015] [Indexed: 10/22/2022]
Abstract
Although safety concerns preclude the use of live attenuated HIV vaccines in humans, they provide a useful system for identifying the elusive correlates of protective immunity in the SIV/macaque animal model. However, a number of pieces of evidence suggest that protection may result from prior occupancy of susceptible target cells by the vaccine virus rather than the immune response. To address this, we developed a Nef-deletion variant of an RT-SHIV whose active replication could be shut off by treatment with RT-inhibitors. Groups of macaques were inoculated with the ∆Nef-RT-SHIV and immune responses allowed to develop before antiretroviral treatment and subsequent challenge with wild-type SIVmac239. Vaccinated animals either resisted infection fully or significantly controlled the subsequent viremia. However, there was no difference between animals undergoing replication of the vaccine virus and those without. This strongly suggests that competition for available target cells does not play a role in protection.
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