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Sun X, Zhang H, Kong X, Li N, Zhang T, An M, Ding H, Shang H, Han X. Low-level viremia episodes appear to affect the provirus composition of the circulating cellular HIV reservoir during antiretroviral therapy. Front Microbiol 2024; 15:1376144. [PMID: 38841056 PMCID: PMC11150674 DOI: 10.3389/fmicb.2024.1376144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 04/12/2024] [Indexed: 06/07/2024] Open
Abstract
Low-level viremia (LLV) ranging from 50 to 1,000 copies/ml is common in most HIV-1-infected patients receiving antiretroviral therapy (ART). However, the source of LLV and the impact of LLV on the HIV-1 reservoir during ART remain uncertain. We hypothesized that LLV may arise from the HIV reservoir and its occurrence affect the composition of the reservoir after LLV episodes. Accordingly, we investigated the genetic linkage of sequences obtained from plasma at LLV and pre-ART time points and from peripheral blood mononuclear cells (PBMCs) at pre-ART, pre-LLV, LLV, and post-LLV time points. We found that LLV sequences were populated with a predominant viral quasispecies that accounted for 67.29%∼100% of all sequences. Two episodes of LLV in subject 1, spaced 6 months apart, appeared to have originated from the stochastic reactivation of latently HIV-1-infected cells. Moreover, 3.77% of pre-ART plasma sequences were identical to 67.29% of LLV-3 plasma sequences in subject 1, suggesting that LLV may have arisen from a subset of cells that were infected before ART was initiated. No direct evidence of sequence linkage was found between LLV viruses and circulating cellular reservoirs in all subjects. The reservoir size, diversity, and divergence of the PBMC DNA did not differ significantly between the pre- and post-LLV sampling points (P > 0.05), but the composition of viral reservoir quasispecies shifted markedly before and after LLV episodes. Indeed, subjects with LLV had a higher total PBMC DNA level, greater viral diversity, a lower proportion of variants with identical sequences detected at two or more time points, and a shorter variant duration during ART compared with subjects without LLV. Overall, our findings suggested that LLV viruses may stem from an unidentified source other than circulating cellular reservoirs. LLV episodes may introduce great complexity into the HIV reservoir, which brings challenges to the development of treatment strategies.
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Affiliation(s)
- Xiao Sun
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Health Commission (NHC) Key Laboratory of AIDS Prevention and Treatment, National Clinical Research Center for Laboratory Medicine, The First Hospital of China Medical University, China Medical University, Shenyang, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Hui Zhang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Health Commission (NHC) Key Laboratory of AIDS Prevention and Treatment, National Clinical Research Center for Laboratory Medicine, The First Hospital of China Medical University, China Medical University, Shenyang, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Xiangchen Kong
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Health Commission (NHC) Key Laboratory of AIDS Prevention and Treatment, National Clinical Research Center for Laboratory Medicine, The First Hospital of China Medical University, China Medical University, Shenyang, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Nan Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Health Commission (NHC) Key Laboratory of AIDS Prevention and Treatment, National Clinical Research Center for Laboratory Medicine, The First Hospital of China Medical University, China Medical University, Shenyang, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Tong Zhang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Health Commission (NHC) Key Laboratory of AIDS Prevention and Treatment, National Clinical Research Center for Laboratory Medicine, The First Hospital of China Medical University, China Medical University, Shenyang, China
- Clinical Laboratory, Shenyang Women’s and Children’s Hospital, Shenyang, China
| | - Minghui An
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Health Commission (NHC) Key Laboratory of AIDS Prevention and Treatment, National Clinical Research Center for Laboratory Medicine, The First Hospital of China Medical University, China Medical University, Shenyang, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Haibo Ding
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Health Commission (NHC) Key Laboratory of AIDS Prevention and Treatment, National Clinical Research Center for Laboratory Medicine, The First Hospital of China Medical University, China Medical University, Shenyang, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Hong Shang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Health Commission (NHC) Key Laboratory of AIDS Prevention and Treatment, National Clinical Research Center for Laboratory Medicine, The First Hospital of China Medical University, China Medical University, Shenyang, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Xiaoxu Han
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Health Commission (NHC) Key Laboratory of AIDS Prevention and Treatment, National Clinical Research Center for Laboratory Medicine, The First Hospital of China Medical University, China Medical University, Shenyang, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
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2
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Li JZ, Melberg M, Kittilson A, Abdel-Mohsen M, Li Y, Aga E, Bosch RJ, Wonderlich ER, Kinslow J, Giron LB, Di Germanio C, Pilkinton M, MacLaren L, Keefer M, Fox L, Barr L, Acosta E, Ananworanich J, Coombs R, Mellors J, Deeks S, Gandhi RT, Busch M, Landay A, Macatangay B, Smith DM. Predictors of HIV rebound differ by timing of antiretroviral therapy initiation. JCI Insight 2024; 9:e173864. [PMID: 38329130 PMCID: PMC10967395 DOI: 10.1172/jci.insight.173864] [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: 07/12/2023] [Accepted: 12/19/2023] [Indexed: 02/09/2024] Open
Abstract
BACKGROUNDIdentifying factors that predict the timing of HIV rebound after treatment interruption will be crucial for designing and evaluating interventions for HIV remission.METHODSWe performed a broad evaluation of viral and immune factors that predict viral rebound (AIDS Clinical Trials Group A5345). Participants initiated antiretroviral therapy (ART) during chronic (N = 33) or early (N = 12) HIV infection with ≥ 2 years of suppressive ART and restarted ART if they had 2 viral loads ≥ 1,000 copies/mL after treatment interruption.RESULTSCompared with chronic-treated participants, early-treated individuals had smaller and fewer transcriptionally active HIV reservoirs. A higher percentage of HIV Gag-specific CD8+ T cell cytotoxic response was associated with lower intact proviral DNA. Predictors of HIV rebound timing differed between early- versus chronic-treated participants, as the strongest reservoir predictor of time to HIV rebound was level of residual viremia in early-treated participants and intact DNA level in chronic-treated individuals. We also identified distinct sets of pre-treatment interruption viral, immune, and inflammatory markers that differentiated participants who had rapid versus slow rebound.CONCLUSIONThe results provide an in-depth overview of the complex interplay of viral, immunologic, and inflammatory predictors of viral rebound and demonstrate that the timing of ART initiation modifies the features of rapid and slow viral rebound.TRIAL REGISTRATIONClinicalTrials.gov NCT03001128FUNDINGNIH National Institute of Allergy and Infectious Diseases, Merck.
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Affiliation(s)
- Jonathan Z. Li
- Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Meghan Melberg
- Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Autumn Kittilson
- Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Yijia Li
- Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
- University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Evgenia Aga
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Ronald J. Bosch
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | | | | | | | - Clara Di Germanio
- University of California, San Francisco, San Francisco, California, USA
- Vitalant Research Institute, San Francisco, California, USA
| | - Mark Pilkinton
- Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | | | | | - Lawrence Fox
- National Institute of Allergy and Infectious Diseases, NIH, Rockville, Maryland, USA
| | - Liz Barr
- AIDS Clinical Trials Group Community Scientific Subcommittee, Los Angeles, California, USA
| | | | | | | | - John Mellors
- University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Steven Deeks
- University of California, San Francisco, San Francisco, California, USA
| | - Rajesh T. Gandhi
- Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Michael Busch
- Vitalant Research Institute, San Francisco, California, USA
| | - Alan Landay
- Rush University Medical Center, Chicago, Illinois, USA
| | | | - Davey M. Smith
- University of California, San Diego, San Diego, California, USA
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3
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Lombardi F, Bruzzesi E, Bouba YR, Di Carlo D, Costabile V, Ranzenigo M, Maggiolo F, Castagna A, Callegaro AP, Zoncada A, Paolucci S, Micheli V, Renica S, Bezencheck A, Rossetti B, Santoro MM. Factors Associated with Low-Level Viremia in People Living with HIV in the Italian Antiviral Response Cohort Analysis Cohort: A Case-Control Study. AIDS Res Hum Retroviruses 2024; 40:80-89. [PMID: 37345697 DOI: 10.1089/aid.2023.0015] [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] [Indexed: 06/23/2023] Open
Abstract
Despite effective antiretroviral therapies (ARTs), a subset of people living with HIV (PLWH) still experience low-level viremia (LLV, i.e., 50-1,000 copies/mL). The present study compared PLWH experiencing LLV with those maintaining virological suppression (VS) and explored the potential impact of preexisting drug resistance and other factors on LLV. We conducted a retrospective, 1:1 matched case-control study within a cohort of drug-experienced VS subjects from the Italian Antiviral Response Cohort Analysis database, followed in the period 2009-2019. Cases were individuals experiencing LLV, while controls were those who maintained VS. Matching was for calendar year of first ART regimen. Preexisting drug resistance was calculated as cumulative genotypic susceptibility score (GSS) according to regimen administered at the observational period start. To explore the effect of cumulative GSS, treated as a binary variable (≥2 and <2) and other factors on LLV, we performed a logistic regression analysis. Within a main population of 3,455 PLWH, 337 cases were selected. Cases were comparable to the controls for both gender and age. However, cases showed that they had experienced a longer time since HIV diagnosis, a higher number of drugs previously administered, lower baseline CD4+ T cell count and a higher zenith viral load (VL). By multivariate analysis, we found that higher zenith VL [adjusted odds ratio (aOR) (95% confidence interval [CI]) 1.30 (1.14-1.48)], a cumulative usage of both PI [aOR (95% CI): 2.03 (1.19-3.48)] and InSTI [aOR (95% CI): 2.23 (1.47-3.38)] and a cumulative GSS <2 [aOR (95% CI) 0.67 (0.46-0.98)], were associated with a higher risk in developing LLV. In current high-efficacy ART era, in drug-experienced PLWH, the predictors of increased risk of LLV were the presence of preexisting drug resistance, higher zenith VL, and previous PI, and InSTI exposure.
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Affiliation(s)
- Francesca Lombardi
- UOC Malattie Infettive, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Elena Bruzzesi
- Infectious Diseases Unit, Università Vita-Salute San Raffaele, Milan, Italy
| | - Yagai Romeo Bouba
- Chantal BIYA International Reference Center for Research on HIV/AIDS Prevention and Management (CIRCB), Yaoundé, Cameroon
| | - Domenico Di Carlo
- Department of Biomedical and Clinical Sciences "L. Sacco", CRC Pediatric "Romeo and Enrica Invernizzi", University of Milan, Milan, Italy
| | - Valentino Costabile
- Department of Oncology and Hemato-oncology, University of Milan, Milan, Italy
| | - Martina Ranzenigo
- Infectious Diseases Unit, Università Vita-Salute San Raffaele, Milan, Italy
| | - Franco Maggiolo
- Department of Infectious Diseases, Azienda Ospedaliera Papa Giovanni XXIII, Bergamo, Italy
| | - Antonella Castagna
- Infectious Diseases Unit, Università Vita-Salute San Raffaele, Milan, Italy
- Infectious Diseases Unit, San Raffaele Scientific Institute, Milan, Italy
| | | | | | - Stefania Paolucci
- Molecular Virology Unit, Division of Microbiology and Virology, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Valeria Micheli
- Laboratory of Clinical Microbiology, Virology, and Bioemergencies, ASST Fatebenefratelli Sacco, L. Sacco University Hospital, Milan, Italy
| | - Silvia Renica
- Department of Oncology and Hemato-oncology, University of Milan, Milan, Italy
| | | | - Barbara Rossetti
- Infectious Diseases Unit, AUSL Toscana Sud-Est, Ospedale Misericordia Grosseto, Siena, Italy
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4
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Wu F, Simonetti FR. Learning from Persistent Viremia: Mechanisms and Implications for Clinical Care and HIV-1 Cure. Curr HIV/AIDS Rep 2023; 20:428-439. [PMID: 37955826 PMCID: PMC10719122 DOI: 10.1007/s11904-023-00674-w] [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] [Accepted: 10/11/2023] [Indexed: 11/14/2023]
Abstract
PURPOSE OF REVIEW In this review, we discuss what persistent viremia has taught us about the biology of the HIV-1 reservoir during antiretroviral therapy (ART). We will also discuss the implications of this phenomenon for HIV-1 cure research and its clinical management. RECENT FINDINGS While residual viremia (RV, 1-3 HIV-1 RNA copies/ml) can be detected in most of people on ART, some individuals experience non-suppressible viremia (NSV, > 20-50 copies/mL) despite optimal adherence. When issues of drug resistance and pharmacokinetics are ruled out, this persistent virus in plasma is the reflection of virus production from clonally expanded CD4+ T cells carrying proviruses. Recent work has shown that a fraction of the proviruses source of NSV are not infectious, due to defects in the 5'-Leader sequence. However, additional viruses and host determinants of NSV are not fully understood. The study of NSV is of prime importance because it represents a challenge for the clinical care of people on ART, and it sheds light on virus-host interactions that could advance HIV-1 remission research.
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Affiliation(s)
- Fengting Wu
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, 733 N Broadway, Baltimore, MD, 21205, USA
| | - Francesco R Simonetti
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, 733 N Broadway, Baltimore, MD, 21205, USA.
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5
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Botha JC, Demirov D, Gordijn C, Katusiime MG, Bale MJ, Wu X, Wells D, Hughes SH, Cotton MF, Mellors JW, Kearney MF, van Zyl GU. The largest HIV-1-infected T cell clones in children on long-term combination antiretroviral therapy contain solo LTRs. mBio 2023; 14:e0111623. [PMID: 37530525 PMCID: PMC10470503 DOI: 10.1128/mbio.01116-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 06/26/2023] [Indexed: 08/03/2023] Open
Abstract
Combination antiretroviral therapy (cART) suppresses viral replication but does not cure HIV infection because a reservoir of infectious (intact) HIV proviruses persists in long-lived CD4+T cells. However, a large majority (>95%) of HIV-infected cells that persist on effective cART carry defective (non-infectious) proviruses. Defective proviruses consisting of only a single LTR (solo long terminal repeat) are commonly found as endogenous retroviruses in many animal species, but the frequency of solo-LTR HIV proviruses has not been well defined. Here we show that, in five pediatric donors whose viremia was suppressed on cART for at least 5 years, the proviruses in the nine largest clones of HIV-infected cells were solo LTRs. The sizes of five of these clones were assayed longitudinally by integration site-specific quantitative PCR. Minor waxing and waning of the clones was observed, suggesting that these clones are generally stable over time. Our findings show that solo LTRs comprise a large fraction of the proviruses in infected cell clones that persist in children on long-term cART. IMPORTANCE This work highlights that severely deleted HIV-1 proviruses comprise a significant proportion of the proviral landscape and are often overlooked.
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Affiliation(s)
| | - Dimiter Demirov
- Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | | | - Mary Grace Katusiime
- HIV Dynamics and Replication Program, National Cancer Institute, Frederick, Maryland, USA
| | - Michael J. Bale
- Laboratory of Epigenetics and Immunity, Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Xiaolin Wu
- HIV Dynamics and Replication Program, National Cancer Institute, Frederick, Maryland, USA
| | - Daria Wells
- HIV Dynamics and Replication Program, National Cancer Institute, Frederick, Maryland, USA
| | - Stephen H. Hughes
- HIV Dynamics and Replication Program, National Cancer Institute, Frederick, Maryland, USA
| | | | - John W. Mellors
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Mary F. Kearney
- HIV Dynamics and Replication Program, National Cancer Institute, Frederick, Maryland, USA
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6
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Chen J, He Y, Zhong H, Hu F, Li Y, Zhang Y, Zhang X, Lin W, Li Q, Xu F, Chen S, Zhang H, Cai W, Li L. Transcriptome analysis of CD4+ T cells from HIV-infected individuals receiving ART with LLV revealed novel transcription factors regulating HIV-1 promoter activity. Virol Sin 2023:S1995-820X(23)00022-6. [PMID: 36907331 DOI: 10.1016/j.virs.2023.03.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 03/06/2023] [Indexed: 03/12/2023] Open
Abstract
Some HIV-infected individuals receiving ART develop low-level viremia (LLV), with a plasma viral load of 50-1000 copies/mL. Persistent low-level viremia is associated with subsequent virologic failure. The peripheral blood CD4+ T cell pool is a source of LLV. However, the intrinsic characteristics of CD4+ T cells in LLV which may contribute to low-level viremia are largely unknown. We analyzed the transcriptome profiling of peripheral blood CD4+ T cells from healthy controls (HC) and HIV-infected patients receiving ART with either virologic suppression (VS) or LLV. To identify pathways potentially responding to increasing viral loads from HC to VS and to LLV, KEGG pathways of differentially expressed genes (DEGs) were acquired by comparing VS with HC (VS-HC group) and LLV with VS (LLV-VS group). Characterization of DEGs in key overlapping pathways showed that CD4+ T cells in LLV expressed higher levels of Th1 signature transcription factors (TBX21), toll-like receptors (TLR-4, -6, -7 and -8), anti-HIV entry chemokines (CCL3 and CCL4), and anti-IL-1β factors (ILRN and IL1R2) compared to VS. Our results also indicated activation of the NF-κB and TNF signaling pathways that could promote HIV-1 transcription. Finally, we evaluated the effects of 4 and 17 transcription factors that were upregulated in the VS-HC and LLV-VS groups, respectively, on HIV-1 promoter activity. Functional studies revealed that CXXC5 significantly increased, while SOX5 markedly suppressed HIV-1 transcription. In summary, we found that CD4+ T cells in LLV displayed a distinct mRNA profiling compared to that in VS, which promoted HIV-1 replication and reactivation of viral latency and may eventually contribute to virologic failure in patients with persistent LLV. CXXC5 and SOX5 may serve as targets for the development of latency-reversing agents.
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Affiliation(s)
- Jingliang Chen
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, 510440, China
| | - Yaozu He
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, 510440, China
| | - Huolin Zhong
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, 510440, China
| | - Fengyu Hu
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, 510440, China
| | - Yonghong Li
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, 510440, China
| | - Yeyang Zhang
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, 510440, China
| | - Xia Zhang
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, 510440, China
| | - Weiyin Lin
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, 510440, China
| | - Quanmin Li
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, 510440, China
| | - Feilong Xu
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, 510440, China
| | - Shaozhen Chen
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, 510440, China
| | - Hui Zhang
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China; Guangzhou Laboratory, Guangzhou International Bio-Island, Guangzhou, 510005, China.
| | - Weiping Cai
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, 510440, China.
| | - Linghua Li
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, 510440, China.
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7
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Joussef-Piña S, Nankya I, Nalukwago S, Baseke J, Rwambuya S, Winner D, Kyeyune F, Chervenak K, Thiel B, Asaad R, Dobrowolski C, Luttge B, Lawley B, Kityo CM, Boom WH, Karn J, Quiñones-Mateu ME. Reduced and highly diverse peripheral HIV-1 reservoir in virally suppressed patients infected with non-B HIV-1 strains in Uganda. Retrovirology 2022; 19:1. [PMID: 35033105 PMCID: PMC8760765 DOI: 10.1186/s12977-022-00587-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 01/03/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Our understanding of the peripheral human immunodeficiency virus type 1 (HIV-1) reservoir is strongly biased towards subtype B HIV-1 strains, with only limited information available from patients infected with non-B HIV-1 subtypes, which are the predominant viruses seen in low- and middle-income countries (LMIC) in Africa and Asia. RESULTS In this study, blood samples were obtained from well-suppressed ART-experienced HIV-1 patients monitored in Uganda (n = 62) or the U.S. (n = 50), with plasma HIV-1 loads < 50 copies/ml and CD4+ T-cell counts > 300 cells/ml. The peripheral HIV-1 reservoir, i.e., cell-associated HIV-1 RNA and proviral DNA, was characterized using our novel deep sequencing-based EDITS assay. Ugandan patients were slightly younger (median age 43 vs 49 years) and had slightly lower CD4+ counts (508 vs 772 cells/ml) than U.S. individuals. All Ugandan patients were infected with non-B HIV-1 subtypes (31% A1, 64% D, or 5% C), while all U.S. individuals were infected with subtype B viruses. Unexpectedly, we observed a significantly larger peripheral inducible HIV-1 reservoir in U.S. patients compared to Ugandan individuals (48 vs. 11 cell equivalents/million cells, p < 0.0001). This divergence in reservoir size was verified measuring proviral DNA (206 vs. 88 cell equivalents/million cells, p < 0.0001). However, the peripheral HIV-1 reservoir was more diverse in Ugandan than in U.S. individuals (8.6 vs. 4.7 p-distance, p < 0.0001). CONCLUSIONS The smaller, but more diverse, peripheral HIV-1 reservoir in Ugandan patients might be associated with viral (e.g., non-B subtype with higher cytopathicity) and/or host (e.g., higher incidence of co-infections or co-morbidities leading to less clonal expansion) factors. This highlights the need to understand reservoir dynamics in diverse populations as part of ongoing efforts to find a functional cure for HIV-1 infection in LMICs.
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Affiliation(s)
- Samira Joussef-Piña
- Departments of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, OH, USA
| | - Immaculate Nankya
- Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda
| | - Sophie Nalukwago
- Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda
| | - Joy Baseke
- Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda
| | - Sandra Rwambuya
- Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda
| | - Dane Winner
- Departments of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, OH, USA
| | - Fred Kyeyune
- Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda
| | - Keith Chervenak
- Departments of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Bonnie Thiel
- Departments of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Robert Asaad
- Departments of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Curtis Dobrowolski
- Departments of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, OH, USA
| | - Benjamin Luttge
- Departments of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, OH, USA
| | - Blair Lawley
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, 720 Cumberland Street, P.O. Box 56, Dunedin, New Zealand
| | - Cissy M Kityo
- Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda
| | - W Henry Boom
- Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda
- Departments of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Jonathan Karn
- Departments of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, OH, USA
- Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda
| | - Miguel E Quiñones-Mateu
- Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda.
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, 720 Cumberland Street, P.O. Box 56, Dunedin, New Zealand.
- Webster Centre for Infectious Diseases, University of Otago, Dunedin, New Zealand.
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8
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Rausch JW, Le Grice SFJ. Characterizing the Latent HIV-1 Reservoir in Patients with Viremia Suppressed on cART: Progress, Challenges, and Opportunities. Curr HIV Res 2021; 18:99-113. [PMID: 31889490 PMCID: PMC7475929 DOI: 10.2174/1570162x18666191231105438] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 12/05/2019] [Accepted: 12/09/2019] [Indexed: 02/07/2023]
Abstract
Modern combination antiretroviral therapy (cART) can bring HIV-1 in blood plasma to level undetectable by standard tests, prevent the onset of acquired immune deficiency syndrome (AIDS), and allow a near-normal life expectancy for HIV-infected individuals. Unfortunately, cART is not curative, as within a few weeks of treatment cessation, HIV viremia in most patients rebounds to pre-cART levels. The primary source of this rebound, and the principal barrier to a cure, is the highly stable reservoir of latent yet replication-competent HIV-1 proviruses integrated into the genomic DNA of resting memory CD4+ T cells. In this review, prevailing models for how the latent reservoir is established and maintained, residual viremia and viremic rebound upon withdrawal of cART, and the types and characteristics of cells harboring latent HIV-1 will be discussed. Selected technologies currently being used to advance our understanding of HIV latency will also be presented, as will a perspective on which areas of advancement are most essential for producing the next generation of HIV-1 therapeutics.
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Affiliation(s)
- Jason W Rausch
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, National Institute of Health, Frederick, MD 21702, United States
| | - Stuart F J Le Grice
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, National Institute of Health, Frederick, MD 21702, United States
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Katusiime MG, Van Zyl GU, Cotton MF, Kearney MF. HIV-1 Persistence in Children during Suppressive ART. Viruses 2021; 13:v13061134. [PMID: 34204740 PMCID: PMC8231535 DOI: 10.3390/v13061134] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 06/06/2021] [Accepted: 06/08/2021] [Indexed: 12/16/2022] Open
Abstract
There is a growing number of perinatally HIV-1-infected children worldwide who must maintain life-long ART. In early life, HIV-1 infection is established in an immunologically inexperienced environment in which maternal ART and immune dynamics during pregnancy play a role in reservoir establishment. Children that initiated early antiretroviral therapy (ART) and maintained long-term suppression of viremia have smaller and less diverse HIV reservoirs than adults, although their proviral landscape during ART is reported to be similar to that of adults. The ability of these early infected cells to persist long-term through clonal expansion poses a major barrier to finding a cure. Furthermore, the effects of life-long HIV persistence and ART are yet to be understood, but growing evidence suggests that these individuals are at an increased risk for developing non-AIDS-related comorbidities, which underscores the need for an HIV cure.
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Affiliation(s)
- Mary Grace Katusiime
- HIV Dynamics and Replication Program, CCR, National Cancer Institute, Frederick, MD 21702, USA;
- Correspondence:
| | - Gert U. Van Zyl
- Division of Medical Virology, Stellenbosch University and National Health Laboratory Service Tygerberg, Cape Town 8000, South Africa;
| | - Mark F. Cotton
- Department of Pediatrics and Child Health, Tygerberg Children’s Hospital and Family Center for Research with Ubuntu, Stellenbosch University, Cape Town 7505, South Africa;
| | - Mary F. Kearney
- HIV Dynamics and Replication Program, CCR, National Cancer Institute, Frederick, MD 21702, USA;
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10
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Integration in oncogenes plays only a minor role in determining the in vivo distribution of HIV integration sites before or during suppressive antiretroviral therapy. PLoS Pathog 2021; 17:e1009141. [PMID: 33826675 PMCID: PMC8055010 DOI: 10.1371/journal.ppat.1009141] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 04/19/2021] [Accepted: 03/24/2021] [Indexed: 12/11/2022] Open
Abstract
HIV persists during antiretroviral therapy (ART) as integrated proviruses in cells descended from a small fraction of the CD4+ T cells infected prior to the initiation of ART. To better understand what controls HIV persistence and the distribution of integration sites (IS), we compared about 15,000 and 54,000 IS from individuals pre-ART and on ART, respectively, with approximately 395,000 IS from PBMC infected in vitro. The distribution of IS in vivo is quite similar to the distribution in PBMC, but modified by selection against proviruses in expressed genes, by selection for proviruses integrated into one of 7 specific genes, and by clonal expansion. Clones in which a provirus integrated in an oncogene contributed to cell survival comprised only a small fraction of the clones persisting in on ART. Mechanisms that do not involve the provirus, or its location in the host genome, are more important in determining which clones expand and persist. In HIV-infected individuals, a small fraction of the infected cells persist and divide. This reservoir persists during fully suppressive ART and can rekindle the infection if ART is discontinued. Because the number of possible sites of HIV DNA integration is very large, each infected cell, and all of its descendants, can be identified by the site where the provirus is integrated (IS). To understand the selective forces that determine the fates of infected cells in vivo, we compared the distribution of HIV IS in freshly-infected cells to cells from HIV-infected donors sampled both before and during ART. We found that, as previously reported, integration favors highly-expressed genes. However, over time, the fraction of cells with proviruses integrated in highly-expressed genes decreases, implying that they grow less well. There are exceptions to this broad negative selection. When a provirus is integrated in a specific region in one of seven genes, the proviruses affect the expression of the target gene, promoting growth and/or survival of the cell. Although this effect is striking, it is only a minor component of the forces that promote the growth and survival of the population of infected cells during ART.
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11
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Bacchus-Souffan C, Fitch M, Symons J, Abdel-Mohsen M, Reeves DB, Hoh R, Stone M, Hiatt J, Kim P, Chopra A, Ahn H, York VA, Cameron DL, Hecht FM, Martin JN, Yukl SA, Mallal S, Cameron PU, Deeks SG, Schiffer JT, Lewin SR, Hellerstein MK, McCune JM, Hunt PW. Relationship between CD4 T cell turnover, cellular differentiation and HIV persistence during ART. PLoS Pathog 2021; 17:e1009214. [PMID: 33465157 PMCID: PMC7846027 DOI: 10.1371/journal.ppat.1009214] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 01/29/2021] [Accepted: 12/04/2020] [Indexed: 12/17/2022] Open
Abstract
The precise role of CD4 T cell turnover in maintaining HIV persistence during antiretroviral therapy (ART) has not yet been well characterized. In resting CD4 T cell subpopulations from 24 HIV-infected ART-suppressed and 6 HIV-uninfected individuals, we directly measured cellular turnover by heavy water labeling, HIV reservoir size by integrated HIV-DNA (intDNA) and cell-associated HIV-RNA (caRNA), and HIV reservoir clonality by proviral integration site sequencing. Compared to HIV-negatives, ART-suppressed individuals had similar fractional replacement rates in all subpopulations, but lower absolute proliferation rates of all subpopulations other than effector memory (TEM) cells, and lower plasma IL-7 levels (p = 0.0004). Median CD4 T cell half-lives decreased with cell differentiation from naïve to TEM cells (3 years to 3 months, p<0.001). TEM had the fastest replacement rates, were most highly enriched for intDNA and caRNA, and contained the most clonal proviral expansion. Clonal proviruses detected in less mature subpopulations were more expanded in TEM, suggesting that they were maintained through cell differentiation. Earlier ART initiation was associated with lower levels of intDNA, caRNA and fractional replacement rates. In conclusion, circulating integrated HIV proviruses appear to be maintained both by slow turnover of immature CD4 subpopulations, and by clonal expansion as well as cell differentiation into effector cells with faster replacement rates.
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Affiliation(s)
- Charline Bacchus-Souffan
- Division of Experimental Medicine, Department of Medicine, University of California, San Francisco, California, United States of America
| | - Mark Fitch
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, California, United States of America
| | - Jori Symons
- The Peter Doherty Institute for Infection and Immunity, University of Melbourne and Royal Melbourne Hospital, Melbourne, Australia
| | | | - Daniel B. Reeves
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Rebecca Hoh
- Division of HIV, Infectious Diseases and Global Medicine, Department of Medicine, Zuckerberg San Francisco General Hospital, University of California, San Francisco, California, United States of America
| | - Mars Stone
- Vitalant Research Institute and Department of Laboratory Medicine at the University of California, San Francisco, California, United States of America
| | - Joseph Hiatt
- Medical Scientist Training Program & Biomedical Sciences Graduate Program, University of California, San Francisco, California, United States of America
| | - Peggy Kim
- Infectious Diseases Section, Medical Service, San Francisco Veterans Affairs Medical Center, California, United States of America
| | - Abha Chopra
- Institute for Immunology and Infectious Diseases, Murdoch University, Perth, Australia
- Center for Translational Immunology and Infectious Diseases, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Haelee Ahn
- Division of Experimental Medicine, Department of Medicine, University of California, San Francisco, California, United States of America
| | - Vanessa A. York
- Division of Experimental Medicine, Department of Medicine, University of California, San Francisco, California, United States of America
| | - Daniel L. Cameron
- Division of Bioinformatics, Walter & Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Frederick M. Hecht
- Division of HIV, Infectious Diseases and Global Medicine, Department of Medicine, Zuckerberg San Francisco General Hospital, University of California, San Francisco, California, United States of America
| | - Jeffrey N. Martin
- Division of HIV, Infectious Diseases and Global Medicine, Department of Medicine, Zuckerberg San Francisco General Hospital, University of California, San Francisco, California, United States of America
| | - Steven A. Yukl
- Division of HIV, Infectious Diseases and Global Medicine, Department of Medicine, Zuckerberg San Francisco General Hospital, University of California, San Francisco, California, United States of America
- Infectious Diseases Section, Medical Service, San Francisco Veterans Affairs Medical Center, California, United States of America
| | - Simon Mallal
- Institute for Immunology and Infectious Diseases, Murdoch University, Perth, Australia
- Center for Translational Immunology and Infectious Diseases, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Paul U. Cameron
- The Peter Doherty Institute for Infection and Immunity, University of Melbourne and Royal Melbourne Hospital, Melbourne, Australia
| | - Steven G. Deeks
- Division of HIV, Infectious Diseases and Global Medicine, Department of Medicine, Zuckerberg San Francisco General Hospital, University of California, San Francisco, California, United States of America
| | - Joshua T. Schiffer
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Sharon R. Lewin
- The Peter Doherty Institute for Infection and Immunity, University of Melbourne and Royal Melbourne Hospital, Melbourne, Australia
| | - Marc K. Hellerstein
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, California, United States of America
| | - Joseph M. McCune
- Global Health Innovative Technology Solutions/HIV Frontiers, Bill & Melinda Gates Foundation, Seattle, Washington, United States of America
| | - Peter W. Hunt
- Division of Experimental Medicine, Department of Medicine, University of California, San Francisco, California, United States of America
- * E-mail:
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12
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Cells producing residual viremia during antiretroviral treatment appear to contribute to rebound viremia following interruption of treatment. PLoS Pathog 2020; 16:e1008791. [PMID: 32841299 PMCID: PMC7473585 DOI: 10.1371/journal.ppat.1008791] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 09/04/2020] [Accepted: 07/08/2020] [Indexed: 12/16/2022] Open
Abstract
During antiretroviral therapy (ART) that suppresses HIV replication to below the limit-of-quantification, virions produced during ART can be detected at low frequencies in the plasma, termed residual viremia (RV). We hypothesized that a reservoir of HIV-infected cells actively produce and release virions during ART that are potentially infectious, and that following ART-interruption, these virions can complete full-cycles of replication and contribute to rebound viremia. Therefore, we studied the dynamics of RV sequence variants in 3 participants who initiated ART after ~3 years of infection and were ART-suppressed for >6 years prior to self-initiated ART-interruptions. Longitudinal RV C2V5env sequences were compared to sequences from pre-ART plasma, supernatants of quantitative viral outgrowth assays (QVOA) of cells collected during ART, post-ART-interruption plasma, and ART-re-suppression plasma. Identical, “putatively clonal,” RV sequences comprised 8–84% of sequences from each timepoint. The majority of RV sequences were genetically similar to those from plasma collected just prior to ART-initiation, but as the duration of ART-suppression increased, an increasing proportion of RV variants were similar to sequences from earlier in infection. Identical sequences were detected in RV over a median of 3 years (range: 0.3–8.2) of ART-suppression. RV sequences were identical to pre-ART plasma viruses (5%), infectious viruses induced in QVOA (4%) and rebound viruses (5%) (total n = 21/154 (14%) across the 3 participants). RV sequences identical to ART-interruption “rebound” sequences were detected 0.1–7.4 years prior to ART-interruption. RV variant prevalence and persistence were not associated with detection of the variant among rebound sequences. Shortly after ART-re-suppression, variants that had been replicating during ART-interruptions were detected as RV (n = 5). These studies show a dynamic, virion-producing HIV reservoir that contributes to rekindling infection upon ART-interruption. The persistence of identical RV variants over years suggests that a subpopulation of HIV-infected clones frequently or continuously produce virions that may resist immune clearance; this suggests that cure strategies should target this active as well as latent reservoirs. HIV-infected individuals receiving effective antiretroviral treatment (ART) produce virions detected in the blood at very low levels, termed residual viremia (RV). To understand the significance of RV as related to the persistence of HIV infection, we characterized the dynamics of RV sequence variants among plasma viruses over nearly a decade of ART and assessed whether RV contributed to rekindling viremia upon ART-interruption. The HIV reservoir producing RV appeared to be “seeded” at various times before ART-initiation. Identical RV sequences likely produced by a clonal cell population, varied over time, with unique sequence variants persisting over a median of 3 years. A subset of RV variants (14%) were identical to viruses found in pre-ART plasma, infectious viruses induced from cultured CD4+ T blood lymphocytes collected during ART, or in rebound plasma during ART-interruption. The persistence of unique RV variants over years, infers that the clones of HIV-infected cells producing these virions resist immune clearance or a subset of these clones are activated on a rolling basis, and that novel treatment strategies are needed to target this active reservoir that contributes to viral rebound.
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13
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Jagarapu A, Piovoso MJ, Zurakowski R. An Integrated Spatial Dynamics-Pharmacokinetic Model Explaining Poor Penetration of Anti-retroviral Drugs in Lymph Nodes. Front Bioeng Biotechnol 2020; 8:667. [PMID: 32676500 PMCID: PMC7333380 DOI: 10.3389/fbioe.2020.00667] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 05/28/2020] [Indexed: 12/14/2022] Open
Abstract
Although combined anti-retroviral therapy (cART) suppresses plasma HIV viremia below the limit of detection in a majority of HIV patients, evidence is emerging that the distribution of the anti-retroviral drugs is heterogeneous in tissue. Clinical studies measuring antiretroviral drug concentrations in lymph nodes (LNs) revealed lower concentrations compared to peripheral blood levels suggesting poor drug penetration properties. Our current study is an attempt to understand this poor anti-retroviral drug penetration inside lymph node lobules through integrating known pharmacokinetic and pharmacodynamic (PK/PD) parameters of the anti-retroviral drugs into a spatial model of reaction and transport dynamics within a solid lymph node lobule. Simulated drug penetration values were compared against experimental results whenever available or matched with data that is available for other drugs in a similar class. Our integrated spatial dynamics pharmacokinetic model reproduced the experimentally observed exclusion of antivirals from lymphoid sites. The strongest predictor of drug exclusion from the lymphoid lobule, independent of drug class, was lobule size; large lobules (high inflammation) exhibited high levels of drug exclusion. PK/PD characteristics associated with poor lymphoid penetration include high cellular uptake rates and low intracellular half-lives. To determine whether this exclusion might lead to ongoing replication, target CD4+ T cell, infected CD4+ T cell, free virus, and intracellular IC50 values of anti-retroviral drugs were incorporated into the model. Notably, for median estimates of PK/PD parameters and lobule diameters consistent with low to moderate inflammation, the model predicts no ongoing viral replication, despite substantial exclusion of the drugs from the lymphoid site. Monte-Carlo studies drawn from the prior distributions of the PK/PD parameters predicts increases in site-specific HIV replication in a small fraction of the patient population for lobule diameters greater than 0.2 mm; this fraction increases as the site diameter/ inflammation level increases. The model shows that cART consisting of two nRTIs and one PI is the most likely treatment combination to support formation of a sanctuary site, a finding that is consistent with clinical observations.
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Affiliation(s)
- Aditya Jagarapu
- Department of Biomedical Engineering, University of Delaware, Newark, DE, United States
| | - Michael J Piovoso
- Department of Electrical and Computer Engineering, University of Delaware, Newark, DE, United States
| | - Ryan Zurakowski
- Department of Biomedical Engineering, University of Delaware, Newark, DE, United States
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14
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Thomas J, Ruggiero A, Paxton WA, Pollakis G. Measuring the Success of HIV-1 Cure Strategies. Front Cell Infect Microbiol 2020; 10:134. [PMID: 32318356 PMCID: PMC7154081 DOI: 10.3389/fcimb.2020.00134] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 03/13/2020] [Indexed: 01/10/2023] Open
Abstract
HIV-1 eradication strategies aim to achieve viral remission in the absence of antiretroviral therapy (ART). The development of an HIV-1 cure remains challenging due to the latent reservoir (LR): long-lived CD4 T cells that harbor transcriptionally silent HIV-1 provirus. The LR is stable despite years of suppressive ART and is the source of rebound viremia following therapy interruption. Cure strategies such as "shock and kill" aim to eliminate or reduce the LR by reversing latency, exposing the infected cells to clearance via the immune response or the viral cytopathic effect. Alternative strategies include therapeutic vaccination, which aims to prime the immune response to facilitate control of the virus in the absence of ART. Despite promising advances, these strategies have been unable to significantly reduce the LR or increase the time to viral rebound but have provided invaluable insight in the field of HIV-1 eradication. The development and assessment of an HIV-1 cure requires robust assays that can measure the LR with sufficient sensitivity to detect changes that may occur following treatment. The viral outgrowth assay (VOA) is considered the gold standard method for LR quantification due to its ability to distinguish intact and defective provirus. However, the VOA is time consuming and resource intensive, therefore several alternative assays have been developed to bridge the gap between practicality and accuracy. Whilst a cure for HIV-1 infection remains elusive, recent advances in our understanding of the LR and methods for its eradication have offered renewed hope regarding achieving ART free viral remission.
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Affiliation(s)
- Jordan Thomas
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
| | - Alessandra Ruggiero
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom.,Immune and Infectious Disease Division, Academic Department of Pediatrics (DPUO), Bambino Gesù Children's Hospital, Rome, Italy
| | - William A Paxton
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
| | - Georgios Pollakis
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
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15
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Abstract
PURPOSE OF REVIEW To provide a summary of the recent data examining infected CD4+ T cell dynamics during ART and implications for cure strategies. RECENT FINDINGS HIV-1 cure is a worldwide unmet medical need. Although combination antiretroviral therapies effectively suppress HIV-1 replication in vivo, viral rebound occurs shortly after therapy cessation. The major barrier to HIV-1 cure is a pool of latently infected CD4+ T cells, called the latent reservoir, which is established early during infection, has a long half-life in vivo, and is not eliminated by treatment. It was thought that the stability of the reservoir came from long-lived latently infected CD4+ T cells, but more recent data suggests that the reservoir is dynamic, such that there is an equilibrium in which proliferation of HIV-1-infected cells is offset by an equivalent loss of cells harboring HIV-1 DNA. SUMMARY We review the evidence to support this dynamic model of persistence, mechanisms by which infected cells expand and are eliminated, and discuss the impact of a dynamic reservoir on the future of HIV-1 cure studies.
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16
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Virgilio MC, Collins KL. The Impact of Cellular Proliferation on the HIV-1 Reservoir. Viruses 2020; 12:E127. [PMID: 31973022 PMCID: PMC7077244 DOI: 10.3390/v12020127] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 01/16/2020] [Accepted: 01/18/2020] [Indexed: 12/25/2022] Open
Abstract
Human immunodeficiency virus (HIV) is a chronic infection that destroys the immune system in infected individuals. Although antiretroviral therapy is effective at preventing infection of new cells, it is not curative. The inability to clear infection is due to the presence of a rare, but long-lasting latent cellular reservoir. These cells harboring silent integrated proviral genomes have the potential to become activated at any moment, making therapy necessary for life. Latently-infected cells can also proliferate and expand the viral reservoir through several methods including homeostatic proliferation and differentiation. The chromosomal location of HIV proviruses within cells influences the survival and proliferative potential of host cells. Proliferating, latently-infected cells can harbor proviruses that are both replication-competent and defective. Replication-competent proviral genomes contribute to viral rebound in an infected individual. The majority of available techniques can only assess the integration site or the proviral genome, but not both, preventing reliable evaluation of HIV reservoirs.
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Affiliation(s)
- Maria C. Virgilio
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI 48109, USA;
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Kathleen L. Collins
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI 48109, USA;
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA
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17
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Impact of Antiretroviral Therapy Duration on HIV-1 Infection of T Cells within Anatomic Sites. J Virol 2020; 94:JVI.01270-19. [PMID: 31723024 PMCID: PMC7000983 DOI: 10.1128/jvi.01270-19] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 11/02/2019] [Indexed: 12/23/2022] Open
Abstract
Understanding the impact of antiretroviral therapy (ART) duration on HIV-infected cells is critical for developing successful curative strategies. To address this issue, we conducted a cross-sectional/inter-participant genetic characterization of HIV-1 RNA from pre- and on-therapy plasmas and HIV-1 DNA from CD4+ T cell subsets derived from peripheral blood (PB), lymph node (LN), and gut tissues of 26 participants after 3 to 17.8 years of ART. Our studies revealed in four acute/early participants who had paired PB and LN samples a substantial reduction in the proportion of HIV-infected cells per year on therapy within the LN. Extrapolation to all 12 acute/early participants estimated a much smaller reduction in the proportion of HIV-1-infected cells within LNs per year on therapy that was similar to that in the participants treated during chronic infection. LN-derived effector memory T (TEM) cells contained HIV-1 DNA that was genetically identical to viral sequences derived from pre- and on-therapy plasma samples. The proportion of identical HIV-1 DNA sequences increased within PB-derived TEM cells. However, the infection frequency of TEM cells in PB was stable, indicating that cellular proliferation that compensates for T cell loss over time contributes to HIV-1 persistence. This study suggests that ART reduces HIV-infected T cells and that clonal expansion of HIV-infected cells maintains viral persistence. Importantly, LN-derived TEM cells are a probable source of HIV-1 genomes capable of producing infectious HIV-1 and should be targeted by future curative strategies.IMPORTANCE HIV-1 persists as an integrated genome in CD4+ memory T cells during effective therapy, and cessation of current treatments results in resumption of viral replication. To date, the impact of antiretroviral therapy duration on HIV-infected CD4+ T cells and the mechanisms of viral persistence in different anatomic sites is not clearly elucidated. In the current study, we found that treatment duration was associated with a reduction in HIV-infected T cells. Our genetic analyses revealed that CD4+ effector memory T (TEM) cells derived from the lymph node appeared to contain provirus that was genetically identical to plasma-derived virions. Moreover, we found that cellular proliferation counterbalanced the decay of HIV-infected cells throughout therapy. The contribution of cellular proliferation to viral persistence is particularly significant in TEM cells. Our study emphasizes the importance of HIV-1 intervention and provides new insights into the location of memory T cells infected with HIV-1 DNA, which is capable of contributing to viremia.
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18
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Falcinelli SD, Ceriani C, Margolis DM, Archin NM. New Frontiers in Measuring and Characterizing the HIV Reservoir. Front Microbiol 2019; 10:2878. [PMID: 31921056 PMCID: PMC6930150 DOI: 10.3389/fmicb.2019.02878] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 11/28/2019] [Indexed: 12/13/2022] Open
Abstract
A cure for HIV infection remains elusive due to the persistence of replication-competent HIV proviral DNA during suppressive antiretroviral therapy (ART). With the exception of rare elite or post-treatment controllers of viremia, withdrawal of ART invariably results in the rebound of viremia and progression of HIV disease. A thorough understanding of the reservoir is necessary to develop new strategies in order to reduce or eliminate the reservoir. However, there is significant heterogeneity in the sequence composition, genomic location, stability, and expression of the HIV reservoir both within and across individuals, and a majority of proviral sequences are replication-defective. These factors, and the low frequency of persistently infected cells in individuals on suppressive ART, make understanding the reservoir and its response to experimental reservoir reduction interventions challenging. Here, we review the characteristics of the HIV reservoir, state-of-the-art assays to measure and characterize the reservoir, and how these assays can be applied to accurately detect reductions in reservoir during efforts to develop a cure for HIV infection. In particular, we highlight recent advances in the development of direct measures of provirus, including intact proviral DNA assays and full-length HIV DNA sequencing with integration site analysis. We also focus on novel techniques to quantitate persistent and inducible HIV, including RNA sequencing and RNA/gag protein staining techniques, as well as modified viral outgrowth methods that seek to improve upon throughput, sensitivity and dynamic range.
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Affiliation(s)
- Shane D Falcinelli
- UNC HIV Cure Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States.,Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Cristina Ceriani
- UNC HIV Cure Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States.,Department of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - David M Margolis
- UNC HIV Cure Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States.,Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States.,Department of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Nancie M Archin
- UNC HIV Cure Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States.,Department of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
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19
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Zaikos TD, Terry VH, Sebastian Kettinger NT, Lubow J, Painter MM, Virgilio MC, Neevel A, Taschuk F, Onafuwa-Nuga A, McNamara LA, Riddell J, Bixby D, Markowitz N, Collins KL. Hematopoietic Stem and Progenitor Cells Are a Distinct HIV Reservoir that Contributes to Persistent Viremia in Suppressed Patients. Cell Rep 2019; 25:3759-3773.e9. [PMID: 30590047 DOI: 10.1016/j.celrep.2018.11.104] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 09/12/2018] [Accepted: 11/29/2018] [Indexed: 01/03/2023] Open
Abstract
Long-lived reservoirs of persistent HIV are a major barrier to a cure. CD4+ hematopoietic stem and progenitor cells (HSPCs) have the capacity for lifelong survival, self-renewal, and the generation of daughter cells. Recent evidence shows that they are also susceptible to HIV infection in vitro and in vivo. Whether HSPCs harbor infectious virus or contribute to plasma virus (PV) is unknown. Here, we provide strong evidence that clusters of identical proviruses from HSPCs and their likely progeny often match residual PV. A higher proportion of these sequences match residual PV than proviral genomes from bone marrow and peripheral blood mononuclear cells that are observed only once. Furthermore, an analysis of near-full-length genomes isolated from HSPCs provides evidence that HSPCs harbor functional HIV proviral genomes that often match residual PV. These results support the conclusion that HIV-infected HSPCs form a distinct and functionally significant reservoir of persistent HIV in infected people.
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Affiliation(s)
- Thomas D Zaikos
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Valeri H Terry
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Nadia T Sebastian Kettinger
- Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, MI, USA; Medical Scientist Training Program, University of Michigan, Ann Arbor, MI, USA
| | - Jay Lubow
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Mark M Painter
- Graduate Program in Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Maria C Virgilio
- Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, MI, USA
| | - Andrew Neevel
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Frances Taschuk
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | | | - Lucy A McNamara
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - James Riddell
- Division of Infectious Disease, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Dale Bixby
- Division of Oncology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Norman Markowitz
- Division of Infectious Diseases, Henry Ford Hospital, Detroit, MI, USA
| | - Kathleen L Collins
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA; Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA; Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, MI, USA; Medical Scientist Training Program, University of Michigan, Ann Arbor, MI, USA; Division of Infectious Disease, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA; Graduate Program in Immunology, University of Michigan, Ann Arbor, MI, USA.
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20
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Lee E, Bacchetti P, Milush J, Shao W, Boritz E, Douek D, Fromentin R, Liegler T, Hoh R, Deeks SG, Hecht FM, Chomont N, Palmer S. Memory CD4 + T-Cells Expressing HLA-DR Contribute to HIV Persistence During Prolonged Antiretroviral Therapy. Front Microbiol 2019; 10:2214. [PMID: 31611857 PMCID: PMC6775493 DOI: 10.3389/fmicb.2019.02214] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Accepted: 09/10/2019] [Indexed: 11/13/2022] Open
Abstract
To date, most assays for measuring the human immunodeficiency virus (HIV-1) reservoir do not include memory CD4+ T-cells expressing the activation marker, human leukocyte antigen-antigen D related (HLA-DR). However, little is known concerning the role these cells play in maintaining persistent HIV-1 during effective antiretroviral therapy (ART). To address this issue, we examined, cellular activation/exhaustion markers (Ki67, CCR5, PD-1, Lag-3 and Tim-3) and viral gag-pol DNA sequences within HLA-DR− and HLA-DR+ memory CD4+ T-cell subsets longitudinally from the peripheral blood of six participants over 3 to ≥15 years of effective therapy. HLA-DR expression was readily detected during the study period in all participants. The average expression levels of CCR5, PD-1 and Tim-3 were higher on the HLA-DR+ T-cell subset whereas the average of LAG-3 expression was higher on their HLA-DR− counterpart. The proportion of HIV-infected cells increased within the HLA-DR+ subset by an average of 18% per year of ART whereas the frequency of infected HLA-DR− T-cells slightly decreased over time (5% per year). We observed that 20–33% of HIV-DNA sequences from the early time points were genetically identical to viral sequences from the last time point within the same cell subset during ART. This indicates that a fraction of proviruses persists within HLA-DR+ and HLA-DR− T-cell subsets during prolonged ART. Our HIV-DNA sequence analyses also revealed that cells transitioned between the HLA-DR+ and HLA-DR− phenotypes. The Ki67 expression, a marker for cellular proliferation, and the combined markers of Ki67/PD-1 averaged 19-fold and 22-fold higher on the HLA-DR+ T-cell subset compared to their HLA-DR− counterpart. Moreover, cellular proliferation, as reflected by the proportion of genetically identical HIV-DNA sequences, increased within both T-cell subsets over the study period; however, this increase was greater within the HLA-DR+ T-cells. Our research revealed that cellular transition and proliferation contribute to the persistence of HIV in HLA-DR+ and HLA-DR− T-cell subsets during prolonged therapy. As such, the HIV reservoir expands during effective ART when both the HLA-DR+ and HLA-DR− cell subsets are included, and therapeutic interventions aimed at reducing the HIV-1 reservoir should target HLA-DR+ and HLA-DR− T-cells.
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Affiliation(s)
- Eunok Lee
- Centre for Virus Research, The Westmead Institute for Medical Research, Sydney, NSW, Australia.,Sydney Medical School, The University of Sydney, Sydney, NSW, Australia
| | - Peter Bacchetti
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, United States
| | - Jeffery Milush
- Department of Medicine, University of California, San Francisco, San Francisco, CA, United States
| | - Wei Shao
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, United States
| | - Eli Boritz
- Human Immunology Section, Vaccine Research Center, National Institutes of Allergy and Infectious Diseases, National Institute of Health, Bethesda, MD, United States
| | - Daniel Douek
- Human Immunology Section, Vaccine Research Center, National Institutes of Allergy and Infectious Diseases, National Institute of Health, Bethesda, MD, United States
| | - Remi Fromentin
- Centre de Recherche du CHUM et Département de Microbiologie, Infectiologie et Immunologie, Université de Montreal, Montreal, QC, Canada
| | - Teri Liegler
- Department of Medicine, University of California, San Francisco, San Francisco, CA, United States
| | - Rebecca Hoh
- Department of Medicine, University of California, San Francisco, San Francisco, CA, United States
| | - Steve G Deeks
- Department of Medicine, University of California, San Francisco, San Francisco, CA, United States
| | - Frederick M Hecht
- Department of Medicine, University of California, San Francisco, San Francisco, CA, United States
| | - Nicolas Chomont
- Centre de Recherche du CHUM et Département de Microbiologie, Infectiologie et Immunologie, Université de Montreal, Montreal, QC, Canada
| | - Sarah Palmer
- Centre for Virus Research, The Westmead Institute for Medical Research, Sydney, NSW, Australia.,Sydney Medical School, The University of Sydney, Sydney, NSW, Australia
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21
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Mok HP, Norton NJ, Hirst JC, Fun A, Bandara M, Wills MR, Lever AML. No evidence of ongoing evolution in replication competent latent HIV-1 in a patient followed up for two years. Sci Rep 2018; 8:2639. [PMID: 29422601 PMCID: PMC5805784 DOI: 10.1038/s41598-018-20682-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 01/22/2018] [Indexed: 12/22/2022] Open
Abstract
The persistence of infected T cells harbouring intact HIV proviruses is the barrier to the eradication of HIV. This reservoir is stable over long periods of time despite antiretroviral therapy. There has been controversy on whether low level viral replication is occurring at sanctuary sites periodically reseeding infected cells into the latent reservoir to account its durability. To study viral evolution in a physiologically relevant population of latent viruses, we repeatedly performed virus outgrowth assays on a stably treated HIV positive patient over two years and sequenced the reactivated latent viruses. We sought evidence of increasing sequence pairwise distances with time as evidence of ongoing viral replication. 64 reactivatable latent viral sequences were obtained over 103 weeks. We did not observe an increase in genetic distance of the sequences with the time elapsed between sampling. No evolution could be discerned in these reactivatable latent viruses. Thus, in this patient, the contribution of low-level replication to the maintenance of the latent reservoir detectable in the blood compartment is limited.
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Affiliation(s)
- Hoi Ping Mok
- Department of Medicine, University of Cambridge, Cambridge, UK
| | | | - Jack C Hirst
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Axel Fun
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Mikaila Bandara
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Mark R Wills
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Andrew M L Lever
- Department of Medicine, University of Cambridge, Cambridge, UK. .,Yong Loo Lin School of Medicine, Singapore, Singapore.
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22
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Rose R, Nolan DJ, Maidji E, Stoddart CA, Singer EJ, Lamers SL, McGrath MS. Eradication of HIV from Tissue Reservoirs: Challenges for the Cure. AIDS Res Hum Retroviruses 2018; 34:3-8. [PMID: 28691499 DOI: 10.1089/aid.2017.0072] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The persistence of HIV infection, even after lengthy and successful combined antiretroviral therapy (cART), has precluded an effective cure. The anatomical locations and biological mechanisms through which the viral population is maintained remain unknown. Much research has focused nearly exclusively on circulating resting T cells as the predominant source of persistent HIV, a strategy with limited success in developing an effective cure strategy. In this study, we review research supporting the importance of anatomical tissues and other immune cells for HIV maintenance and expansion, including the central nervous system, lymph nodes, and macrophages. We present accumulated research that clearly demonstrates the limitations of using blood-derived cells as a proxy for tissue reservoirs and sanctuaries throughout the body. We cite recent studies that have successfully used deep-sequencing strategies to uncover the complexity of HIV infection and the ability of the virus to evolve despite undetectable plasma viral loads. Finally, we suggest new strategies and highlight the importance of tissue banks for future research.
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Affiliation(s)
| | | | - Ekaterina Maidji
- Division of Experimental Medicine, Department of Medicine, Zuckerberg San Francisco General Hospital, University of California, San Francisco, San Francisco, California
| | - Cheryl A. Stoddart
- Division of Experimental Medicine, Department of Medicine, Zuckerberg San Francisco General Hospital, University of California, San Francisco, San Francisco, California
| | - Elyse J. Singer
- The National Neurological AIDS Bank at David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine and Olive View-UCLA Medical Center, Los Angeles, California
| | | | - Michael S. McGrath
- The AIDS and Cancer Specimen Resource, San Francisco, California
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California
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23
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Fleury H, Tumiotto C, Bellecave P, Recordon-Pinson P. Therapeutic Vaccine Against HIV, Viral Variability, Cytotoxic T Lymphocyte Epitopes, and Genetics of Patients. AIDS Res Hum Retroviruses 2018; 34:27-30. [PMID: 28899104 DOI: 10.1089/aid.2017.0175] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The scientific and medical community is seeking to cure HIV. Several pathways have been or are being explored including therapeutic vaccination. Viroimmunological studies on primary infection as well as on elite controllers have demonstrated the importance of the cytotoxic CD8 response and have mainly oriented research on vaccine constructs toward this type of response. The results of these trials are clearly not commensurate with the hope placed in them. Might there be one or more uncontrolled variables? The genetics of patients need to be taken into consideration, especially their human lymphocyte antigen (HLA) alleles. There is a need to find a balance between the conservation of cytotoxic T lymphocyte (CTL) epitopes and presentation by HLA alleles. The pathway is a narrow one between adaptation of the virus to HLA I restriction and the definition of conserved proviral CTL epitopes presentable by HLA I alleles. It is likely that the genetics of patients will need to be considered for HIV-1 vaccine studies and that multidisciplinary collaboration will be essential in this field of infectious diseases.
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Affiliation(s)
- Herve Fleury
- Laboratoire de Virologie, CHU de Bordeaux et CNRS UMR 5234, Université de Bordeaux, Bordeaux, France
| | - Camille Tumiotto
- Laboratoire de Virologie, CHU de Bordeaux et CNRS UMR 5234, Université de Bordeaux, Bordeaux, France
| | - Pantxika Bellecave
- Laboratoire de Virologie, CHU de Bordeaux et CNRS UMR 5234, Université de Bordeaux, Bordeaux, France
| | - Patricia Recordon-Pinson
- Laboratoire de Virologie, CHU de Bordeaux et CNRS UMR 5234, Université de Bordeaux, Bordeaux, France
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24
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Norton NJ, Fun A, Bandara M, Wills MR, Mok HP, Lever AML. Innovations in the quantitative virus outgrowth assay and its use in clinical trials. Retrovirology 2017; 14:58. [PMID: 29268753 PMCID: PMC5740843 DOI: 10.1186/s12977-017-0381-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 12/12/2017] [Indexed: 01/09/2023] Open
Abstract
A robust measure of the size of the latent HIV reservoir is essential to quantifying the effect of interventions designed to deplete the pool of reactivatable, replication competent proviruses. In addition to the ability to measure a biologically relevant parameter, any assay designed to be used in a clinical trial needs to be reproducible and scalable. The need to quantify the number of resting CD4+ T cells capable of releasing infectious virus has led to the development of the quantitative viral outgrowth assay (VOA). The assay as originally described has a number of features that limit its scalability for use in clinical trials; however recent developments reducing the time and manpower requirements of the assay, while importantly improving reproducibility mean that it is becoming much more practical for it to enter into more widespread use. This review describes the background to VOA development and the practical issues that they present in utilising them in clinical trials. It describes the innovations that have made their usage more practical and the limitations that still exist.
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Affiliation(s)
| | - Axel Fun
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Mikaila Bandara
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Mark R Wills
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Hoi Ping Mok
- Department of Medicine, University of Cambridge, Cambridge, UK.
| | - Andrew M L Lever
- Department of Medicine, University of Cambridge, Cambridge, UK. .,Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
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25
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Hua CK, Ackerman ME. Increasing the Clinical Potential and Applications of Anti-HIV Antibodies. Front Immunol 2017; 8:1655. [PMID: 29234320 PMCID: PMC5712301 DOI: 10.3389/fimmu.2017.01655] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 11/13/2017] [Indexed: 01/03/2023] Open
Abstract
Preclinical and early human clinical studies of broadly neutralizing antibodies (bNAbs) to prevent and treat HIV infection support the clinical utility and potential of bNAbs for prevention, postexposure prophylaxis, and treatment of acute and chronic infection. Observed and potential limitations of bNAbs from these recent studies include the selection of resistant viral populations, immunogenicity resulting in the development of antidrug (Ab) responses, and the potentially toxic elimination of reservoir cells in regeneration-limited tissues. Here, we review opportunities to improve the clinical utility of HIV Abs to address these challenges and further accomplish functional targets for anti-HIV Ab therapy at various stages of exposure/infection. Before exposure, bNAbs' ability to serve as prophylaxis by neutralization may be improved by increasing serum half-life to necessitate less frequent administration, delivering genes for durable in vivo expression, and targeting bNAbs to sites of exposure. After exposure and/or in the setting of acute infection, bNAb use to prevent/reduce viral reservoir establishment and spread may be enhanced by increasing the potency with which autologous adaptive immune responses are stimulated, clearing acutely infected cells, and preventing cell-cell transmission of virus. In the setting of chronic infection, bNAbs may better mediate viral remission or "cure" in combination with antiretroviral therapy and/or latency reversing agents, by targeting additional markers of tissue reservoirs or infected cell types, or by serving as targeting moieties in engineered cell therapy. While the clinical use of HIV Abs has never been closer, remaining studies to precisely define, model, and understand the complex roles and dynamics of HIV Abs and viral evolution in the context of the human immune system and anatomical compartmentalization will be critical to both optimize their clinical use in combination with existing agents and define further strategies with which to enhance their clinical safety and efficacy.
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Affiliation(s)
- Casey K. Hua
- Department of Microbiology and Immunology, Geisel School of Medicine, Lebanon, NH, United States
| | - Margaret E. Ackerman
- Department of Microbiology and Immunology, Geisel School of Medicine, Lebanon, NH, United States
- Thayer School of Engineering, Dartmouth College, Hanover, NH, United States
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26
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Abstract
PURPOSE OF REVIEW The persistence of HIV within long-lived HIV-infected CD4 T cells is the primary obstacle towards HIV eradication and numerous strategies are currently being evaluated to target and kill HIV-infected cells to ultimately find a cure. HIV reservoirs are classically quantified by standard methods such as integrated HIV DNA (Alu PCR) and/or quantitative viral outgrowth assay; however, recent technical advances may offer new opportunities to comprehensively assess the impact of clinical interventions. RECENT FINDINGS Digital droplet PCR, tat/rev-induced limiting dilution analysis, enhanced quantitative viral outgrowth assay, and whole genome sequencing technologies offer increased precision and/or higher sensitivity to quantify and characterize HIV reservoirs in antiretroviral therapy-treated HIV-infected patients. SUMMARY The objective of this review is to highlight the characteristics and limits of recent technical advances that may help to monitor the impact of clinical interventions in antiretroviral therapy-treated patients.
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27
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Abstract
The bar is high to improve on current combination antiretroviral therapy (ART), now highly effective, safe, and simple. However, antibodies that bind the HIV envelope are able to uniquely target the virus as it seeks to enter new target cells, or as it is expressed from previously infected cells. Furthermore, the use of antibodies against HIV as a therapeutic may offer advantages. Antibodies can have long half-lives, and are being considered as partners for long-acting antiretrovirals for use in therapy or prevention of HIV infection. Early studies in animal models and in clinical trials suggest that such antibodies can have antiviral activity but, as with small-molecule antiretrovirals, the issues of viral escape and resistance will have to be addressed. Most promising, however, are the unique properties of anti-HIV antibodies: the potential ability to opsonize viral particles, to direct antibody-dependent cellular cytotoxicity (ADCC) against actively infected cells, and ultimately the ability to direct the clearance of HIV-infected cells by effector cells of the immune system. These distinctive activities suggest that HIV antibodies and their derivatives may play an important role in the next frontier of HIV therapeutics, the effort to develop treatments that could lead to an HIV cure.
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Affiliation(s)
- David M Margolis
- UNC HIV Cure Center, Departments of Medicine, Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Richard A Koup
- Immunology Laboratory, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Guido Ferrari
- Duke Human Vaccine Institute and Department of Surgery, Duke University Medical Center, Durham, NC, USA
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28
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Murray AJ, Kwon KJ, Farber DL, Siliciano RF. The Latent Reservoir for HIV-1: How Immunologic Memory and Clonal Expansion Contribute to HIV-1 Persistence. THE JOURNAL OF IMMUNOLOGY 2017; 197:407-17. [PMID: 27382129 DOI: 10.4049/jimmunol.1600343] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 04/12/2016] [Indexed: 12/15/2022]
Abstract
Combination antiretroviral therapy (ART) for HIV-1 infection reduces plasma virus levels to below the limit of detection of clinical assays. However, even with prolonged suppression of viral replication with ART, viremia rebounds rapidly after treatment interruption. Thus, ART is not curative. The principal barrier to cure is a remarkably stable reservoir of latent HIV-1 in resting memory CD4(+) T cells. In this review, we consider explanations for the remarkable stability of the latent reservoir. Stability does not appear to reflect replenishment from new infection events but rather normal physiologic processes that provide for immunologic memory. Of particular importance are proliferative processes that drive clonal expansion of infected cells. Recent evidence suggests that in some infected cells, proliferation is a consequence of proviral integration into host genes associated with cell growth. Efforts to cure HIV-1 infection by targeting the latent reservoir may need to consider the potential of latently infected cells to proliferate.
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Affiliation(s)
- Alexandra J Murray
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Kyungyoon J Kwon
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Donna L Farber
- Columbia Center for Translational Immunology, Columbia University Medical Center, New York, NY 10032; Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY 10032; Department of Surgery, Columbia University Medical Center, New York, NY 10032; and
| | - Robert F Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205; Howard Hughes Medical Institute, Baltimore MD 21250
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29
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Longitudinal sequencing of HIV-1 infected patients with low-level viremia for years while on ART shows no indications for genetic evolution of the virus. Virology 2017; 510:185-193. [PMID: 28750322 DOI: 10.1016/j.virol.2017.07.010] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 07/04/2017] [Accepted: 07/06/2017] [Indexed: 12/22/2022]
Abstract
HIV-infected patients on antiretroviral therapy (ART) may present low-level viremia (LLV) above the detection level of current viral load assays. In many cases LLV is persistent but does not result in overt treatment failure or selection of drug resistant viral variants. To elucidate whether LLV reflects active virus replication, we extensively sequenced pol and env genes of the viral populations present before and during LLV in 18 patients and searched for indications of genetic evolution. Maximum likelihood phylogenetic trees were inspected for temporal structure both visually and by linear regression analysis of root-to-tip and pairwise distances. Viral coreceptor tropism was assessed at different time points before and during LLV. In none of the patients consistent indications for genetic evolution were found over a median period of 4.8 years of LLV. As such these findings could not provide evidence that active virus replication is the main driver of LLV.
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30
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Mullins JI, Frenkel LM. Clonal Expansion of Human Immunodeficiency Virus-Infected Cells and Human Immunodeficiency Virus Persistence During Antiretroviral Therapy. J Infect Dis 2017; 215:S119-S127. [PMID: 28520966 DOI: 10.1093/infdis/jiw636] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The latent HIV-1 reservoir in blood decays very slowly, even during prolonged suppression of viral replication by antiretroviral therapy (ART). Mechanisms for reservoir persistence include replenishment through low-level viral replication, longevity and homeostatic proliferation of memory T cells, and most recently appreciated, clonal expansion of HIV-infected cells. Clonally expanded cells make up a large and increasing fraction of the residual infected cell population on ART, and insertion of HIV proviruses into certain host cellular genes has been associated with this proliferation. That the vast majority of proviruses are defective clouds our assessment of the degree to which clonally expanded cells harbor infectious viruses, and thus the extent to which they contribute to reservoirs relevant to curing infection. This review summarizes past studies that have defined our current understanding and the gaps in our knowledge of the mechanisms by which proviral integration and clonal expansion sustain the HIV reservoir.
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Affiliation(s)
- James I Mullins
- Departments of Microbiology, Medicine, Global Health and Laboratory Medicine, University of Washington, Seattle, WA, US
| | - Lisa M Frenkel
- Departments of Pediatrics, Medicine, Global Health and Laboratory Medicine, University of Washington, Seattle, WA, US.,Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, US
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31
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Nolan DJ, Lamers SL, Rose R, Dollar JJ, Salemi M, McGrath MS. Single Genome Sequencing of Expressed and Proviral HIV-1 Envelope Glycoprotein 120 ( gp120) and nef Genes. Bio Protoc 2017; 7:e2334. [PMID: 34541092 PMCID: PMC8410429 DOI: 10.21769/bioprotoc.2334] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 05/01/2017] [Accepted: 05/09/2017] [Indexed: 01/02/2023] Open
Abstract
The current study provides detailed protocols utilized to amplify the complete HIV-1 gp120 and nef genes from single copies of expressed or integrated HIV present in fresh-frozen autopsy tissues of patients who died while on combined antiretroviral therapy (cART) with no detectable plasma viral load (pVL) at death ( Lamers et al., 2016a and 2016b; Rose et al., 2016 ). This method optimizes protocols from previous publications ( Palmer et al., 2005 ; Norström et al., 2012 ; Lamers et al., 2015 ; 2016a and 2016b; Rife et al., 2016 ) to produce single distinct PCR products that can be directly sequenced and includes several cost-saving and time-efficient modifications.
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Affiliation(s)
- David J. Nolan
- Bioinfoexperts, LLC, Thibodaux, Louisiana, USA
- Department of Pathology, Immunology and Laboratory Medicine, Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA
| | | | | | - James J. Dollar
- Bioinfoexperts, LLC, Thibodaux, Louisiana, USA
- Department of Pathology, Immunology and Laboratory Medicine, Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA
| | - Marco Salemi
- Department of Pathology, Immunology and Laboratory Medicine, Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA
| | - Michael S. McGrath
- Departments of Laboratory Medicine, Pathology, and Medicine, University of California at San Francisco, San Francisco, California, USA
- The AIDS and Cancer Specimen Resource, University of California at San Francisco, San Francisco, California, USA
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32
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Maggiolo F, Di Filippo E, Comi L, Callegaro A, Colombo GL, Di Matteo S, Valsecchi D, Rizzi M. Reduced adherence to antiretroviral therapy is associated with residual low-level viremia. Pragmat Obs Res 2017; 8:91-97. [PMID: 28603436 PMCID: PMC5457149 DOI: 10.2147/por.s127974] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The source and significance of residual low-level viremia (LLV) during combinational antiretroviral therapy (cART) remain a matter of controversy. It is unclear whether residual viremia depends on ongoing release of HIV from the latent reservoir or if viral replication contributes to LLV. We examined the relationship between adherence and LLV. Adherence was estimated by pharmacy refill and dichotomized as ≥95% or <95%. Plasma HIV-RNA was determined, with an ultrasensitive test having a limit of detection of 3 copies/mL at least 2 times over the follow-up period. Patients were grouped according to HIV-RNA over time as K<3: constantly <3 copies/mL; V<3: sometimes below or above the cutoff limit but always <50 copies/mL; K>3: constantly between 3 and 50 copies/mL; and V>50: a measure of >50 copies/mL minimum. Overall, 2789 patients were included. At each time point approximately 92% of the patients presented an HIV-RNA <50 copies/mL and two-thirds of those <3 copies/mL, 34.6% of patients had <3 copies/mL constantly, 32.7% sometimes below or above the cutoff limit but always <50 copies/mL, 9.5% constantly between 3 and 50 copies/mL, and 23.2% a measure of >50 copies/mL minimum. The mean adherence rate was 92.1% (95% confidence interval [CI] from 91.1% to 93.1%) in K<3 patients, similar in V<3 patients (91.9%), but lowered to 88.8% in K>3 patients and to 88.4% in V>50 patients (P<0.0001). Approximately 55% of patients in groups K<3 and V<3 showed an adherence rate ≥95%; this proportion lowered to ~51% in K>3 and to 48% in V>50. Moreover, 34% of patients with a steady adherence <95% were categorized as K>3, whereas 21.7% of those with a drug holiday (21.7%) were observed in the V>50 group (P=0.002). A steady viral suppression can occur despite moderate cART non-adherence, but reduced adherence is associated with low-level residual viremia, which could reflect new rounds of HIV replication. However, a detectable HIV-RNA could also be detected in patients with optimal cART adherence, indicating additional mechanisms favoring HIV persistence.
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Affiliation(s)
| | | | | | | | - Giorgio L Colombo
- Department of Drug Sciences, University of Pavia.,S.A.V.E. Studi - Health Economics & Outcomes Research, Milan
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33
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Ferrari G, Haynes BF, Koenig S, Nordstrom JL, Margolis DM, Tomaras GD. Envelope-specific antibodies and antibody-derived molecules for treating and curing HIV infection. Nat Rev Drug Discov 2016; 15:823-834. [PMID: 27725635 PMCID: PMC5549020 DOI: 10.1038/nrd.2016.173] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
HIV-1 is a retrovirus that integrates into host chromatin and can remain transcriptionally quiescent in a pool of immune cells. This characteristic enables HIV-1 to evade both host immune responses and antiretroviral drugs, leading to persistent infection. Upon reactivation of proviral gene expression, HIV-1 envelope (HIV-1 Env) glycoproteins are expressed on the cell surface, transforming latently infected cells into targets for HIV-1 Env-specific monoclonal antibodies (mAbs), which can engage immune effector cells to kill productively infected CD4+ T cells and thus limit the spread of progeny virus. Recent innovations in antibody engineering have resulted in novel immunotherapeutics such as bispecific dual-affinity re-targeting (DART) molecules and other bi- and trispecific antibody designs that can recognize HIV-1 Env and recruit cytotoxic effector cells to kill CD4+ T cells latently infected with HIV-1. Here, we review these immunotherapies, which are designed with the goal of curing HIV-1 infection.
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Affiliation(s)
- Guido Ferrari
- Department of Surgery, Duke University, Durham, North Carolina 27710, USA
- Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina 27710, USA
- Duke Human Vaccine Institute, Duke University, Durham, North Carolina 27710, USA
| | - Barton F Haynes
- Duke Human Vaccine Institute, Duke University, Durham, North Carolina 27710, USA
- Department of Medicine, Duke University, Durham, North Carolina 27710, USA
- Department of Immunology, Duke University, Durham, North Carolina 27710, USA
| | | | | | - David M Margolis
- University of North Carolina at Chapel Hill HIV Cure Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Georgia D Tomaras
- Department of Surgery, Duke University, Durham, North Carolina 27710, USA
- Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina 27710, USA
- Duke Human Vaccine Institute, Duke University, Durham, North Carolina 27710, USA
- Department of Immunology, Duke University, Durham, North Carolina 27710, USA
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Paired quantitative and qualitative assessment of the replication-competent HIV-1 reservoir and comparison with integrated proviral DNA. Proc Natl Acad Sci U S A 2016; 113:E7908-E7916. [PMID: 27872306 DOI: 10.1073/pnas.1617789113] [Citation(s) in RCA: 147] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
HIV-1-infected individuals harbor a latent reservoir of infected CD4+ T cells that is not eradicated by antiretroviral therapy (ART). This reservoir presents the greatest barrier to an HIV-1 cure and has remained difficult to characterize, in part, because the vast majority of integrated sequences are defective and incapable of reactivation. To characterize the replication-competent reservoir, we have combined two techniques, quantitative viral outgrowth and qualitative sequence analysis of clonal outgrowth viruses. Leukapheresis samples from four fully ART-suppressed, chronically infected individuals were assayed at two time points separated by a 4- to 6-mo interval. Overall, 54% of the viruses emerging from the latent reservoir showed gp160 env sequences that were identical to at least one other virus. Moreover, 43% of the env sequences from viruses emerging from the reservoir were part of identical groups at the two time points. Groups of identical expanded sequences made up 54% of proviral DNA, and, as might be expected, the sequences of replication-competent viruses in the active reservoir showed limited overlap with integrated proviral DNA, most of which is known to represent defective viruses. Finally, there was an inverse correlation between proviral DNA clone size and the probability of reactivation, suggesting that replication-competent viruses are less likely to be found among highly expanded provirus-containing cell clones.
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HIV Maintains an Evolving and Dispersed Population in Multiple Tissues during Suppressive Combined Antiretroviral Therapy in Individuals with Cancer. J Virol 2016; 90:8984-93. [PMID: 27466425 DOI: 10.1128/jvi.00684-16] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 07/13/2016] [Indexed: 12/30/2022] Open
Abstract
UNLABELLED While combined antiretroviral therapy (cART) can result in undetectable plasma viral loads, it does not eradicate HIV infection. Furthermore, HIV-infected individuals while on cART remain at an increased risk of developing serious comorbidities, such as cancer, neurological disease, and atherosclerosis, suggesting that during cART, tissue-based HIV may contribute to such pathologies. We obtained DNA and RNA env, nef, and pol sequences using single-genome sequencing from postmortem tissues of three HIV(+) cART-treated (cART(+)) individuals with undetectable viral load and metastatic cancer at death and performed time-scaled Bayesian evolutionary analyses. We used a sensitive in situ hybridization technique to visualize HIV gag-pol mRNA transcripts in cerebellum and lymph node tissues from one patient. Tissue-associated virus evolved at similar rates in cART(+) and cART-naive (cART(-)) patients. Phylogenetic trees were characterized by two distinct features: (i) branching patterns consistent with constant viral evolution and dispersal among tissues and (ii) very recently derived clades containing both DNA and RNA sequences from multiple tissues. Rapid expansion of virus near death corresponded to wide-spread metastasis. HIV RNA(+) cells clustered in cerebellum tissue but were dispersed in lymph node tissue, mirroring the evolutionary patterns observed for that patient. Activated, infiltrating macrophages were associated with HIV RNA. Our data provide evidence that tissues serve as a sanctuary for wild-type HIV during cART and suggest the importance of macrophages as an alternative reservoir and mechanism of virus spread. IMPORTANCE Combined antiretroviral therapy (cART) reduces plasma HIV to undetectable levels; however, removal of cART results in plasma HIV rebound, thus highlighting its inability to entirely rid the body of infection. Additionally, HIV-infected individuals on cART remain at high risk of serious diseases, which suggests a contribution from residual HIV. In this study, we isolated and sequenced HIV from postmortem tissues from three HIV(+) cART(+) individuals who died with metastatic cancer and had no detectable plasma viral load. Using high-resolution evolutionary analyses, we found that tissue-based HIV continues to replicate, evolve, and migrate among tissues during cART. Furthermore, cancer onset and metastasis coincided with increased HIV expansion, suggesting a linked mechanism. HIV-expressing cells were associated with tissue macrophages, a target of HIV infection. Our results suggest the importance of tissues, and macrophages in particular, as a target for novel anti-HIV therapies.
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Puertas MC, Noguera-Julian M, Massanella M, Pou C, Buzon MJ, Clotet B, Stevenson M, Paredes R, Blanco J, Martinez-Picado J. Lack of concordance between residual viremia and viral variants driving de novo infection of CD4(+) T cells on ART. Retrovirology 2016; 13:51. [PMID: 27484989 PMCID: PMC4970251 DOI: 10.1186/s12977-016-0282-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 07/13/2016] [Indexed: 12/20/2022] Open
Abstract
Background In most patients, current antiretroviral therapy (ART) regimens can rapidly reduce plasma viral load. However, even after years of effective treatment, a significant proportion of patients show residual plasma viremia below the clinical detection limit. Although residual viremia might be associated with increased chronic immune activation and morbidity, its origin and its potential role in the replenishment of the viral reservoir during suppressive ART is not completely understood. We performed an in-depth genetic analysis of the total and episomal cell-associated viral DNA (vDNA) repertoire in purified CD4+ T cell subsets of three HIV-infected individuals, and used phylogenetic analysis to explore its relationship with plasma viruses. Results The predominant proviral reservoir was established in naïve or memory (central and transitional) CD4+ T cell subsets in patients harboring X4- or R5-tropic viruses, respectively. Regardless of the viral tropism, most plasma viruses detected under suppressive ART resembled the proviral reservoir identified in effector and transitional memory CD4+ T-cell subsets in blood, suggesting that residual viremia originates from these cells in either blood or lymphoid tissue. Most importantly, sequences in episomal vDNA in CD4+ T-cells were not well represented in residual viremia. Conclusions Viral tropism determines the differential distribution of viral reservoir among CD4+ T-cell subsets. In spite of viral tropism, the effector and transitional memory CD4+ T-cells subsets are the main source of residual viremia during suppressive ART, even though their contribution to the total proviral pool is small. However, the lack of concordance between residual viremia and viral variants driving de novo infection of CD4+ T cells on ART may reflect the predominance of defective plasma HIV RNA genomes. These findings highlight the need for monitoring the multiple viral RNA/DNA persistence markers, based on their differential contribution to viral persistence. Electronic supplementary material The online version of this article (doi:10.1186/s12977-016-0282-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Maria C Puertas
- AIDS Research Institute IrsiCaixa, Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Marc Noguera-Julian
- AIDS Research Institute IrsiCaixa, Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain.,Universitat de Vic - Universitat Central de Catalunya (UVic-UCC), Vic, Spain
| | - Marta Massanella
- AIDS Research Institute IrsiCaixa, Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain.,Département de Microbiologie, Infectiologie et Immunologie, Centre de Recherche du CHUM et Université de Montréal, Montreal, Canada
| | - Christian Pou
- AIDS Research Institute IrsiCaixa, Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain.,Department of Cell and Molecular Biology, Karolinska Institutet, Solna, Stockholm, Sweden
| | - Maria J Buzon
- AIDS Research Institute IrsiCaixa, Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain.,Infectious Diseases Department, Hospital Universitari Vall d'Hebron, Barcelona, Spain
| | - Bonaventura Clotet
- AIDS Research Institute IrsiCaixa, Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain.,"Lluita Contra la Sida" Foundation, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain.,Universitat de Vic - Universitat Central de Catalunya (UVic-UCC), Vic, Spain
| | - Mario Stevenson
- Division of Infectious Diseases, Department of Medicine, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Roger Paredes
- AIDS Research Institute IrsiCaixa, Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain.,"Lluita Contra la Sida" Foundation, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain.,Universitat de Vic - Universitat Central de Catalunya (UVic-UCC), Vic, Spain
| | - Julià Blanco
- AIDS Research Institute IrsiCaixa, Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain.,Universitat de Vic - Universitat Central de Catalunya (UVic-UCC), Vic, Spain
| | - Javier Martinez-Picado
- AIDS Research Institute IrsiCaixa, Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain. .,Universitat de Vic - Universitat Central de Catalunya (UVic-UCC), Vic, Spain. .,Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain.
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Castley A, Williams L, James I, Guelfi G, Berry C, Nolan D. Plasma CXCL10, sCD163 and sCD14 Levels Have Distinct Associations with Antiretroviral Treatment and Cardiovascular Disease Risk Factors. PLoS One 2016; 11:e0158169. [PMID: 27355513 PMCID: PMC4927121 DOI: 10.1371/journal.pone.0158169] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 06/10/2016] [Indexed: 01/17/2023] Open
Abstract
We investigate the associations of three established plasma biomarkers in the context of HIV and treatment-related variables including a comprehensive cardiovascular disease risk assessment, within a large ambulatory HIV cohort. Patients were recruited in 2010 to form the Royal Perth Hospital HIV/CVD risk cohort. Plasma sCD14, sCD163 and CXCL10 levels were measured in 475 consecutive patients with documented CVD risk (age, ethnicity, gender, smoking, blood pressure, BMI, fasting metabolic profile) and HIV treatment history including immunological/virological outcomes. The biomarkers assessed showed distinct associations with virological response: CXCL10 strongly correlated with HIV-1 RNA (p<0.001), sCD163 was significantly reduced among 'aviraemic' patients only (p = 0.02), while sCD14 was unaffected by virological status under 10,000 copies/mL (p>0.2). Associations between higher sCD163 and protease inhibitor therapy (p = 0.05) and lower sCD14 with integrase inhibitor therapy (p = 0.02) were observed. Levels of sCD163 were also associated with CVD risk factors (age, ethnicity, HDL, BMI), with a favourable influence of Framingham score <10% (p = 0.04). Soluble CD14 levels were higher among smokers (p = 0.002), with no effect of other CVD risk factors, except age (p = 0.045). Our findings confirm CXCL10, sCD163 and sCD14 have distinct associations with different aspects of HIV infection and treatment. Levels of CXCL10 correlated with routinely monitored variables, sCD163 levels reflect a deeper level of virological suppression and influence of CVD risk factors, while sCD14 levels were not associated with routinely monitored variables, with evidence of specific effects of smoking and integrase inhibitor therapy warranting further investigation.
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Affiliation(s)
- Alison Castley
- PathWest Laboratory Medicine, Department of Clinical Immunology: Royal Perth Hospital, Perth, Western Australia, Australia
- School of Veterinary and Life Sciences, Murdoch University, Perth, Western Australia, Australia
| | - Leah Williams
- PathWest Laboratory Medicine, Department of Clinical Immunology: Royal Perth Hospital, Perth, Western Australia, Australia
| | - Ian James
- Institute for Immunology and Infectious Diseases (IIID), Murdoch University, Perth, Western Australia, Australia
| | - George Guelfi
- PathWest Laboratory Medicine, Department of Clinical Immunology: Royal Perth Hospital, Perth, Western Australia, Australia
| | - Cassandra Berry
- School of Veterinary and Life Sciences, Murdoch University, Perth, Western Australia, Australia
| | - David Nolan
- PathWest Laboratory Medicine, Department of Clinical Immunology: Royal Perth Hospital, Perth, Western Australia, Australia
- Institute for Immunology and Infectious Diseases (IIID), Murdoch University, Perth, Western Australia, Australia
- * E-mail:
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Maldarelli F. The role of HIV integration in viral persistence: no more whistling past the proviral graveyard. J Clin Invest 2016; 126:438-47. [PMID: 26829624 DOI: 10.1172/jci80564] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
A substantial research effort has been directed to identifying strategies to eradicate or control HIV infection without a requirement for combination antiretroviral therapy (cART). A number of obstacles prevent HIV eradication, including low-level viral persistence during cART, long-term persistence of HIV-infected cells, and latent infection of resting CD4+ T cells. Mechanisms of persistence remain uncertain, but integration of the provirus into the host genome represents a central event in replication and pathogenesis of all retroviruses, including HIV. Analysis of HIV proviruses in CD4+ lymphocytes from individuals after prolonged cART revealed that a substantial proportion of the infected cells that persist have undergone clonal expansion and frequently have proviruses integrated in genes associated with regulation of cell growth. These data suggest that integration may influence persistence and clonal expansion of HIV-infected cells after cART is introduced, and these processes may represent key mechanisms for HIV persistence. Determining the diversity of host genes with integrants in HIV-infected cells that persist for prolonged periods may yield useful information regarding pathways by which infected cells persist for prolonged periods. Moreover, many integrants are defective, and new studies are required to characterize the role of clonal expansion in the persistence of replication-competent HIV.
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39
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Persistent HIV-1 replication maintains the tissue reservoir during therapy. Nature 2016; 530:51-56. [PMID: 26814962 PMCID: PMC4865637 DOI: 10.1038/nature16933] [Citation(s) in RCA: 497] [Impact Index Per Article: 62.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 12/18/2015] [Indexed: 12/11/2022]
Abstract
Lymphoid tissue is a key reservoir established by HIV-1 during acute infection. It is a site associated with viral production, storage of viral particles in immune complexes, and viral persistence. Although combinations of antiretroviral drugs usually suppress viral replication and reduce viral RNA to undetectable levels in blood, it is unclear whether treatment fully suppresses viral replication in lymphoid tissue reservoirs. Here we show that virus evolution and trafficking between tissue compartments continues in patients with undetectable levels of virus in their bloodstream. We present a spatial and dynamic model of persistent viral replication and spread that indicates why the development of drug resistance is not a foregone conclusion under conditions in which drug concentrations are insufficient to completely block virus replication. These data provide new insights into the evolutionary and infection dynamics of the virus population within the host, revealing that HIV-1 can continue to replicate and replenish the viral reservoir despite potent antiretroviral therapy.
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40
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Conway JM, Perelson AS. Residual Viremia in Treated HIV+ Individuals. PLoS Comput Biol 2016; 12:e1004677. [PMID: 26735135 PMCID: PMC4703306 DOI: 10.1371/journal.pcbi.1004677] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 11/26/2015] [Indexed: 12/20/2022] Open
Abstract
Antiretroviral therapy (ART) effectively controls HIV infection, suppressing HIV viral loads. However, some residual virus remains, below the level of detection, in HIV-infected patients on ART. The source of this viremia is an area of debate: does it derive primarily from activation of infected cells in the latent reservoir, or from ongoing viral replication? Observations seem to be contradictory: there is evidence of short term evolution, implying that there must be ongoing viral replication, and viral strains should thus evolve. However, phylogenetic analyses, and rare emergent drug resistance, suggest no long-term viral evolution, implying that virus derived from activated latent cells must dominate. We use simple deterministic and stochastic models to gain insight into residual viremia dynamics in HIV-infected patients. Our modeling relies on two underlying assumptions for patients on suppressive ART: that latent cell activation drives viral dynamics and that the reproductive ratio of treated infection is less than 1. Nonetheless, the contribution of viral replication to residual viremia in patients on ART may be non-negligible. However, even if the portion of viremia attributable to viral replication is significant, our model predicts (1) that latent reservoir re-seeding remains negligible, and (2) some short-term viral evolution is permitted, but long-term evolution can still be limited: stochastic analysis of our model shows that de novo emergence of drug resistance is rare. Thus, our simple models reconcile the seemingly contradictory observations on residual viremia and, with relatively few parameters, recapitulates HIV viral dynamics observed in patients on suppressive therapy. In HIV+ individuals, antiretroviral therapy (ART) effectively controls HIV viral loads to below levels detectable by routine tests. However, more sensitive tests can detect some residual viremia. The source of this virus is a matter of debate: does it derive from ongoing viral replication, or from viral production following activation of latently infected cells? Experimental observations support both sides of the argument: in patients on therapy, HIV shows no long-term evolution, and emergence of drug-resistant mutants is rare, implying no ongoing viral replication, but there remains short-term evolution, implying the opposite. To reconcile these observations, we propose a mathematical model of latently and productively infected cells and virus. Using our models we predict that, in patients on suppressive ART, the contribution of viral replication to residual virus, while small, yields short term-evolution. But even if the contribution is large, for example if adherence to therapy is poor, long-term evolution can still be limited, and de novo emergence of drug resistance is rare. Thus, our simple models reconcile the seemingly contradictory observations on residual viremia.
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Affiliation(s)
- Jessica M. Conway
- Department of Mathematics and Center for Infectious Disease Dynamics (CIDD), The Pennsylvania State University, University Park, Pennsylvania, United States of America
- * E-mail:
| | - Alan S. Perelson
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
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41
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McKinnon E, Castley A, Payne L, Pummer S, Nolan D. Determinants of residual viraemia during combination HIV treatment: Impacts of baseline HIV RNA levels and treatment choice. HIV Med 2015; 17:495-504. [PMID: 26537660 DOI: 10.1111/hiv.12323] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/16/2015] [Indexed: 01/12/2023]
Abstract
OBJECTIVES Effective HIV therapy reflects suppression of plasma HIV RNA levels below assay detection thresholds, although lower levels of "residual viraemia" have also been demonstrated over extended periods of effective antiretroviral treatment. Here we examine the determinants of HIV RNA suppression below the standard assay threshold (40 HIV-1 RNA copies/mL) as well as factors associated with detectable HIV RNA below this reported detection limit. METHODS Between 2007 and 2010, 11 575 consecutive viral load (VL) tests were obtained from 1540 patients, including 356 on effective antiretroviral therapy followed since initiation (1996-2001: n = 165; 2002-2009: n = 191). Analyses modelled the probability of an undetectable VL given successful suppression to < 200 copies/mL, and the probability of residual viraemia given an undetectable result. RESULTS Detectable HIV RNA amplification was demonstrated in 20% of samples with a VL result < 40 copies/mL. Longitudinal analyses from 356 patients revealed that the likelihood of achieving results < 40 copies/mL was increased with current nonnucleoside reverse transcriptase inhibitor (NNRTI) therapy [odds ratio (OR) 2.0; P < 0.05] and reduced with prior virological rebound (OR 0.5; P < 0.05). In contrast, the presence of detectable HIV RNA < 40 copies/mL was strongly associated with pretreatment HIV RNA levels among those on current protease inhibitor (PI) treatment (OR 1.5 per log10 copies/mL increase; P = 0.02) as well as those on NNRTIs (OR 1.7; P = 0.002). CONCLUSIONS While HIV treatment history was associated with plasma HIV RNA levels below the detection limit, residual viraemia results were dominantly determined by pretreatment VL. These findings support the concept of a stable, long-lived reservoir of latently infected cells as a source of residual viraemia despite effective HIV treatment.
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Affiliation(s)
- E McKinnon
- Institute for Immunology and Infectious Diseases, Murdoch University, Perth, WA, Australia
| | - A Castley
- PathWest Laboratory Medicine, Department of Clinical Immunology, Royal Perth Hospital, Perth, WA, Australia.,School of Veterinary and Life Sciences, Murdoch University, Perth, WA, Australia
| | - L Payne
- PathWest Laboratory Medicine, Department of Clinical Immunology, Royal Perth Hospital, Perth, WA, Australia
| | - S Pummer
- PathWest Laboratory Medicine, Department of Clinical Immunology, Royal Perth Hospital, Perth, WA, Australia
| | - D Nolan
- Institute for Immunology and Infectious Diseases, Murdoch University, Perth, WA, Australia.,PathWest Laboratory Medicine, Department of Clinical Immunology, Royal Perth Hospital, Perth, WA, Australia
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42
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Thornhill J, Frater J, Fidler S. Post-treatment control: a functional cure for HIV. Future Virol 2015. [DOI: 10.2217/fvl.15.92] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Controlled plasma viral load to levels below limits of detection off antiretroviral therapy (ART), referred to as a functional cure, or remission, is an aspiration for people living with HIV avoiding the need for daily ART while preserving immunological function. For the majority of people, stopping suppressive ART is associated with virological rebound. Spontaneous viral control is reported among rare individuals in the absence of ART. More recently, strategic use of transient ART, initiated close to the time of HIV acquisition, has been associated with a phenotype of viral control after stopping therapy termed post-treatment control. We explore the phenotype of post-treatment viral control, potential underlying mechanisms, and how this area of research can inform HIV cure research.
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Affiliation(s)
- John Thornhill
- Winston Churchill Wing, St Marys Hospital Imperial College London, Praed St, London, W2 1NY, UK
| | - John Frater
- Winston Churchill Wing, St Marys Hospital Imperial College London, Praed St, London, W2 1NY, UK
- Peter Medwar Building, University of Oxford, S Parks Rd, Oxford OX1 3SY, UK
| | - Sarah Fidler
- Winston Churchill Wing, St Marys Hospital Imperial College London, Praed St, London, W2 1NY, UK
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43
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Pegu A, Asokan M, Wu L, Wang K, Hataye J, Casazza JP, Guo X, Shi W, Georgiev I, Zhou T, Chen X, O'Dell S, Todd JP, Kwong PD, Rao SS, Yang ZY, Koup RA, Mascola JR, Nabel GJ. Activation and lysis of human CD4 cells latently infected with HIV-1. Nat Commun 2015; 6:8447. [PMID: 26485194 PMCID: PMC4633990 DOI: 10.1038/ncomms9447] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Accepted: 08/21/2015] [Indexed: 12/18/2022] Open
Abstract
The treatment of AIDS with combination antiretroviral therapy (cART) remains lifelong largely because the virus persists in latent reservoirs. Elimination of latently infected cells could therefore reduce treatment duration and facilitate immune reconstitution. Here we report an approach to reduce the viral reservoir by activating dormant viral gene expression and directing T lymphocytes to lyse previously latent, HIV-1-infected cells. An immunomodulatory protein was created that combines the specificity of a HIV-1 broadly neutralizing antibody with that of an antibody to the CD3 component of the T-cell receptor. CD3 engagement by the protein can stimulate T-cell activation that induces proviral gene expression in latently infected T cells. It further stimulates CD8 T-cell effector function and redirects T cells to lyse these previously latent-infected cells through recognition of newly expressed Env. This immunomodulatory protein could potentially help to eliminate latently infected cells and deplete the viral reservoir in HIV-1-infected individuals. The elimination of latently infected cells is a sought after goal in the treatment of HIV-1 infections. Here the authors develop an approach to eliminate latently HIV-1 infected cells by using an immunomodulatory protein, which can activate viral gene expression in these cells and direct T lymphocytes to lyse them in vitro.
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Affiliation(s)
- Amarendra Pegu
- Vaccine Research Center National Institute for Allergy and Infectious Diseases, National Institutes of Health, Building 40, Room 4502, MSC-3005 40 Convent Drive, Bethesda, Maryland 20892-3005, USA
| | - Mangaiarkarasi Asokan
- Vaccine Research Center National Institute for Allergy and Infectious Diseases, National Institutes of Health, Building 40, Room 4502, MSC-3005 40 Convent Drive, Bethesda, Maryland 20892-3005, USA
| | - Lan Wu
- Vaccine Research Center National Institute for Allergy and Infectious Diseases, National Institutes of Health, Building 40, Room 4502, MSC-3005 40 Convent Drive, Bethesda, Maryland 20892-3005, USA
| | - Keyun Wang
- Vaccine Research Center National Institute for Allergy and Infectious Diseases, National Institutes of Health, Building 40, Room 4502, MSC-3005 40 Convent Drive, Bethesda, Maryland 20892-3005, USA
| | - Jason Hataye
- Vaccine Research Center National Institute for Allergy and Infectious Diseases, National Institutes of Health, Building 40, Room 4502, MSC-3005 40 Convent Drive, Bethesda, Maryland 20892-3005, USA
| | - Joseph P Casazza
- Vaccine Research Center National Institute for Allergy and Infectious Diseases, National Institutes of Health, Building 40, Room 4502, MSC-3005 40 Convent Drive, Bethesda, Maryland 20892-3005, USA
| | - Xiaoti Guo
- Vaccine Research Center National Institute for Allergy and Infectious Diseases, National Institutes of Health, Building 40, Room 4502, MSC-3005 40 Convent Drive, Bethesda, Maryland 20892-3005, USA
| | - Wei Shi
- Vaccine Research Center National Institute for Allergy and Infectious Diseases, National Institutes of Health, Building 40, Room 4502, MSC-3005 40 Convent Drive, Bethesda, Maryland 20892-3005, USA
| | - Ivelin Georgiev
- Vaccine Research Center National Institute for Allergy and Infectious Diseases, National Institutes of Health, Building 40, Room 4502, MSC-3005 40 Convent Drive, Bethesda, Maryland 20892-3005, USA
| | - Tongqing Zhou
- Vaccine Research Center National Institute for Allergy and Infectious Diseases, National Institutes of Health, Building 40, Room 4502, MSC-3005 40 Convent Drive, Bethesda, Maryland 20892-3005, USA
| | - Xuejun Chen
- Vaccine Research Center National Institute for Allergy and Infectious Diseases, National Institutes of Health, Building 40, Room 4502, MSC-3005 40 Convent Drive, Bethesda, Maryland 20892-3005, USA
| | - Sijy O'Dell
- Vaccine Research Center National Institute for Allergy and Infectious Diseases, National Institutes of Health, Building 40, Room 4502, MSC-3005 40 Convent Drive, Bethesda, Maryland 20892-3005, USA
| | - John-Paul Todd
- Vaccine Research Center National Institute for Allergy and Infectious Diseases, National Institutes of Health, Building 40, Room 4502, MSC-3005 40 Convent Drive, Bethesda, Maryland 20892-3005, USA
| | - Peter D Kwong
- Vaccine Research Center National Institute for Allergy and Infectious Diseases, National Institutes of Health, Building 40, Room 4502, MSC-3005 40 Convent Drive, Bethesda, Maryland 20892-3005, USA
| | - Srinivas S Rao
- Vaccine Research Center National Institute for Allergy and Infectious Diseases, National Institutes of Health, Building 40, Room 4502, MSC-3005 40 Convent Drive, Bethesda, Maryland 20892-3005, USA
| | - Zhi-yong Yang
- Vaccine Research Center National Institute for Allergy and Infectious Diseases, National Institutes of Health, Building 40, Room 4502, MSC-3005 40 Convent Drive, Bethesda, Maryland 20892-3005, USA
| | - Richard A Koup
- Vaccine Research Center National Institute for Allergy and Infectious Diseases, National Institutes of Health, Building 40, Room 4502, MSC-3005 40 Convent Drive, Bethesda, Maryland 20892-3005, USA
| | - John R Mascola
- Vaccine Research Center National Institute for Allergy and Infectious Diseases, National Institutes of Health, Building 40, Room 4502, MSC-3005 40 Convent Drive, Bethesda, Maryland 20892-3005, USA
| | - Gary J Nabel
- Vaccine Research Center National Institute for Allergy and Infectious Diseases, National Institutes of Health, Building 40, Room 4502, MSC-3005 40 Convent Drive, Bethesda, Maryland 20892-3005, USA
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Calcagno A, Motta I, Ghisetti V, Lo Re S, Allice T, Marinaro L, Milia MG, Tettoni MC, Trentini L, Orofino G, Salassa B, Di Perri G, Bonora S. HIV-1 Very Low Level Viremia Is Associated with Virological Failure in Highly Active Antiretroviral Treatment-Treated Patients. AIDS Res Hum Retroviruses 2015; 31:999-1008. [PMID: 26165150 DOI: 10.1089/aid.2015.0102] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The aim of this study was to evaluate the impact of HIV-1 very low-level viremia (<50 copies/ml) on the 2-year risk of virological failure. A retrospective analysis including HIV-positive patients presenting two consecutive HIV RNA below 50 copies/ml (outpatient clinic in Italy, first semester of 2010) was performed. HIV RNA was measured through real time polymerase chain reaction (PCR) assay CAP/CTM HIV-1 version 2.0 (detection limit: 20 copies/ml) and stratified as undetectable RNA ("Target Not Detected", TND), <20 copies/ml, 20-50 copies/ml. After 96 weeks virological failure was defined as two consecutive viral loads above 50 copies/ml. Log-rank tests and a multivariate Cox proportional hazard model were used for univariate and multivariate analysis. A total of 1,055 patients (71.4% male, 87.4% white, aged 46.7 years) were included: nadir and current CD4 cell counts were 203 cells/mm(3) (106-292) and 554 cells/mm(3) (413-713.5). HIV RNA was undetectable in 781 patients (74%), <20 copies/ml in 190 patients (18%) and 20-50 copies/ml in 84 patients (8%). Virological failure was observed in 81 patients (7.7%); at multivariate analysis detectable RNA at baseline (p=0.017), HCV infection (p=0.020), more than three pills in the regimen (p=0.003), and duration of HIV RNA <50 copies/ml below 2 years (p<0.001) were independently associated with virological failure. In 14 patients newly selected resistance-associated mutations were observed. Undetectable HIV RNA by real-time PCR is significantly associated with a lower 2-year risk of virological failure along with Ab HCV negativity, longer viral control, and lower pill burden. Studies investigating the management of residual viremia under antiretroviral treatment are warranted.
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Affiliation(s)
- Andrea Calcagno
- Unit of Infectious Diseases, Department of Medical Sciences, University of Torino, Torino, Italy
| | - Ilaria Motta
- Unit of Infectious Diseases, Department of Medical Sciences, University of Torino, Torino, Italy
| | - Valeria Ghisetti
- Laboratory of Microbiology and Molecular Biology, Ospedale Amedeo di Savoia, Torino, Italy
| | - Salvatore Lo Re
- Unit of Infectious Diseases, Department of Medical Sciences, University of Torino, Torino, Italy
| | - Tiziano Allice
- Laboratory of Microbiology and Molecular Biology, Ospedale Amedeo di Savoia, Torino, Italy
| | - Letizia Marinaro
- Unit of Infectious Diseases, Department of Medical Sciences, University of Torino, Torino, Italy
| | - Maria Grazia Milia
- Laboratory of Microbiology and Molecular Biology, Ospedale Amedeo di Savoia, Torino, Italy
| | - Maria C. Tettoni
- Unit of Infectious Diseases, Department of Medical Sciences, University of Torino, Torino, Italy
| | - Laura Trentini
- Unit of Infectious Diseases, Department of Medical Sciences, University of Torino, Torino, Italy
| | - Giancarlo Orofino
- Unit of Infectious Diseases, “Divisione A,” Ospedale Amedeo di Savoia, Torino, Italy
| | - Bernardino Salassa
- Unit of Infectious Diseases, Department of Medical Sciences, University of Torino, Torino, Italy
| | - Giovanni Di Perri
- Unit of Infectious Diseases, Department of Medical Sciences, University of Torino, Torino, Italy
| | - Stefano Bonora
- Unit of Infectious Diseases, Department of Medical Sciences, University of Torino, Torino, Italy
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Bruner KM, Hosmane NN, Siliciano RF. Towards an HIV-1 cure: measuring the latent reservoir. Trends Microbiol 2015; 23:192-203. [PMID: 25747663 PMCID: PMC4386620 DOI: 10.1016/j.tim.2015.01.013] [Citation(s) in RCA: 163] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Revised: 01/23/2015] [Accepted: 01/28/2015] [Indexed: 02/07/2023]
Abstract
The latent reservoir (LR) of HIV-1 in resting memory CD4(+) T cells serves as a major barrier to curing HIV-1 infection. While many PCR- and culture-based assays have been used to measure the size of the LR, correlation between results of different assays is poor and recent studies indicate that no available assay provides an accurate measurement of reservoir size. The discrepancies between assays are a hurdle to clinical trials that aim to measure the efficacy of HIV-1 eradication strategies. Here we describe the advantages and disadvantages of various approaches to measuring the LR.
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Affiliation(s)
- Katherine M Bruner
- Department of Medicine, Johns Hopkins University School of Medicine, 733 North Broadway, Baltimore, MD 21205, USA
| | - Nina N Hosmane
- Department of Medicine, Johns Hopkins University School of Medicine, 733 North Broadway, Baltimore, MD 21205, USA
| | - Robert F Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, 733 North Broadway, Baltimore, MD 21205, USA; Howard Hughes Medical Institute, 733 North Broadway, Baltimore, MD 21205, USA.
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Dynamics of HIV DNA and Residual Viremia in Patients Treated With a Raltegravir-Containing Regimen. J Acquir Immune Defic Syndr 2015; 68:e18-20. [DOI: 10.1097/qai.0000000000000414] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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Sahu GK. Potential implication of residual viremia in patients on effective antiretroviral therapy. AIDS Res Hum Retroviruses 2015; 31:25-35. [PMID: 25428885 DOI: 10.1089/aid.2014.0194] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The current antiretroviral therapy (ART) has suppressed viremia to below the limit of detection of clinical viral load assays; however, it cannot eliminate viremia completely in the body even after prolonged treatment. Plasma HIV-1 loads persist at extremely low levels below the clinical detection limit. This low-level viremia (termed "residual viremia") cannot be abolished in most patients, even after the addition of a new class of drug, i.e., viral integrase inhibitor, to the combined antiretroviral regimens. Neither the cellular source nor the clinical significance of this residual viremia in patients on ART remains fully clear at present. Since residual plasma viruses generally do not evolve with time in the presence of effective ART, one prediction is that these viruses are persistently released at low levels from one or more stable but yet unknown HIV-1 reservoirs in the body during therapy. This review attempts to emphasize the source of residual viremia as another important reservoir (namely, "active reservoir") distinct from the well-known latent HIV-1 reservoir in the body, and why its elimination should be a priority in the effort for HIV-1 eradication.
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Affiliation(s)
- Gautam K. Sahu
- HIV Biology and Persistence Laboratory, Department of Medicine, Roger Williams Medical Center, Providence, Rhode Island
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Archin NM, Sung JM, Garrido C, Soriano-Sarabia N, Margolis DM. Eradicating HIV-1 infection: seeking to clear a persistent pathogen. Nat Rev Microbiol 2014; 12:750-64. [PMID: 25402363 PMCID: PMC4383747 DOI: 10.1038/nrmicro3352] [Citation(s) in RCA: 219] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Effective antiretroviral therapy (ART) blunts viraemia, which enables HIV-1-infected individuals to control infection and live long, productive lives. However, HIV-1 infection remains incurable owing to the persistence of a viral reservoir that harbours integrated provirus within host cellular DNA. This latent infection is unaffected by ART and hidden from the immune system. Recent studies have focused on the development of therapies to disrupt latency. These efforts unmasked residual viral genomes and highlighted the need to enable the clearance of latently infected cells, perhaps via old and new strategies that improve the HIV-1-specific immune response. In this Review, we explore new approaches to eradicate established HIV-1 infection and avoid the burden of lifelong ART.
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Affiliation(s)
- Nancie M Archin
- Department of Medicine, University of North Carolina at Chapel Hill
| | - Julia Marsh Sung
- Department of Medicine, University of North Carolina at Chapel Hill
| | - Carolina Garrido
- Department of Medicine, University of North Carolina at Chapel Hill
| | | | - David M Margolis
- 1] Department of Medicine, University of North Carolina at Chapel Hill. [2] Department of Microbiology and Immunology, University of North Carolina at Chapel Hill. [3] Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
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Sebastian NT, Collins KL. Targeting HIV latency: resting memory T cells, hematopoietic progenitor cells and future directions. Expert Rev Anti Infect Ther 2014; 12:1187-201. [PMID: 25189526 DOI: 10.1586/14787210.2014.956094] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Current therapy for HIV effectively suppresses viral replication and prolongs life, but the infection persists due, at least in part, to latent infection of long-lived cells. One favored strategy toward a cure targets latent virus in resting memory CD4(+) T cells by stimulating viral production. However, the existence of an additional reservoir in bone marrow hematopoietic progenitor cells has been detected in some treated HIV-infected people. This review describes approaches investigators have used to reactivate latent proviral genomes in resting CD4(+) T cells and hematopoietic progenitor cells. In addition, the authors review approaches for clearance of these reservoirs along with other important topics related to HIV eradication.
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Affiliation(s)
- Nadia T Sebastian
- Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, MI 48109, USA
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Improved single-copy assays for quantification of persistent HIV-1 viremia in patients on suppressive antiretroviral therapy. J Clin Microbiol 2014; 52:3944-51. [PMID: 25187636 DOI: 10.1128/jcm.02060-14] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
A quantitative real-time PCR (qRT-PCR) assay with single-copy sensitivity targeting HIV-1 gag RNA (the gag single-copy assay [gSCA]) has been used widely to quantify plasma viremia below the limit of detection of clinical assays in patients on effective antiretroviral therapy (ART), but viral RNA in 15 to 30% of samples amplifies inefficiently because of primer/probe mismatches. We sought to develop improved single-copy assays with increased sensitivity by improving nucleic acid recovery, designing qRT-PCR primers and a probe for a highly conserved region of integrase in the HIV-1 pol gene (the integrase single-copy assay [iSCA]), and increasing the plasma volume tested (Mega-iSCA). We evaluated gSCA versus iSCA in paired plasma samples from 10 consecutive patients with viremia of >1,000 copies/ml and 25 consecutive patients on suppressive ART. Three of 10 viremic samples amplified inefficiently with gSCA compared to the Roche Cobas Ampliprep/TaqMan 2.0, whereas all 10 samples amplified efficiently with iSCA. Among 25 samples from patients on suppressive ART, 8 of 12 samples that were negative for HIV-1 RNA by gSCA had detectable HIV-1 RNA by iSCA, and iSCA detected 3-fold or higher HIV-1 RNA levels compared to gSCA in 10 of 25 samples. Large-volume plasma samples (>20 ml) from 7 patients were assayed using Mega-iSCA, and HIV-1 RNA was quantifiable in 6, including 4 of 5 that were negative by standard-volume iSCA. These improved assays with superior sensitivity will be useful for evaluating whether in vivo interventions can reduce plasma viremia and for assessing relationships between residual viremia and other virologic parameters, including the inducible proviral reservoir.
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