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Johnson MM, Jones CE, Clark DN. The Effect of Treatment-Associated Mutations on HIV Replication and Transmission Cycles. Viruses 2022; 15:107. [PMID: 36680147 PMCID: PMC9861436 DOI: 10.3390/v15010107] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 12/21/2022] [Accepted: 12/28/2022] [Indexed: 12/31/2022] Open
Abstract
HIV/AIDS mortality has been decreasing over the last decade. While promising, this decrease correlated directly with increased use of antiretroviral drugs. As a natural consequence of its high mutation rate, treatments provide selection pressure that promotes the natural selection of escape mutants. Individuals may acquire drug-naive strains, or those that have already mutated due to treatment. Even within a host, mutation affects HIV tropism, where initial infection begins with R5-tropic virus, but the clinical transition to AIDS correlates with mutations that lead to an X4-tropic switch. Furthermore, the high mutation rate of HIV has spelled failure for all attempts at an effective vaccine. Pre-exposure drugs are currently the most effective drug-based preventatives, but their effectiveness is also threatened by viral mutation. From attachment and entry to assembly and release, the steps in the replication cycle are also discussed to describe the drug mechanisms and mutations that arise due to those drugs. Revealing the patterns of HIV-1 mutations, their effects, and the coordinated attempt to understand and control them will lead to effective use of current preventative measures and treatment options, as well as the development of new ones.
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Affiliation(s)
- Madison M. Johnson
- Department of Microbiology, Weber State University, Ogden, UT 84408, USA
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2
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Connell BJ, Hermans LE, Wensing AMJ, Schellens I, Schipper PJ, van Ham PM, de Jong DTCM, Otto S, Mathe T, Moraba R, Borghans JAM, Papathanasopoulos MA, Kruize Z, Venter FWD, Kootstra NA, Tempelman H, Tesselaar K, Nijhuis M. Immune activation correlates with and predicts CXCR4 co-receptor tropism switch in HIV-1 infection. Sci Rep 2020; 10:15866. [PMID: 32985522 PMCID: PMC7522993 DOI: 10.1038/s41598-020-71699-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 08/10/2020] [Indexed: 12/31/2022] Open
Abstract
HIV-1 cell entry is mediated by binding to the CD4-receptor and chemokine co-receptors CCR5 (R5) or CXCR4 (X4). R5-tropic viruses are predominantly detected during early infection. A switch to X4-tropism often occurs during the course of infection. X4-tropism switching is strongly associated with accelerated disease progression and jeopardizes CCR5-based HIV-1 cure strategies. It is unclear whether host immunological factors play a causative role in tropism switching. We investigated the relationship between immunological factors and X4-tropism in a cross-sectional study in HIV-1 subtype C (HIV-1C)-infected patients and in a longitudinal HIV-1 subtype B (HIV-1B) seroconverter cohort. Principal component analysis identified a cluster of immunological markers (%HLA-DR+ CD4+ T-cells, %CD38+HLA-DR+ CD4+ T-cells, %CD38+HLA-DR+ CD8+ T-cells, %CD70+ CD4+ T-cells, %CD169+ monocytes, and absolute CD4+ T-cell count) in HIV-1C patients that was independently associated with X4-tropism (aOR 1.044, 95% CI 1.003–1.087, p = 0.0392). Analysis of individual cluster contributors revealed strong correlations of two markers of T-cell activation (%HLA-DR+ CD4+ T-cells, %HLA-DR+CD38+ CD4+ T-cells) with X4-tropism, both in HIV-1C patients (p = 0.01;p = 0.03) and HIV-1B patients (p = 0.0003;p = 0.0001). Follow-up data from HIV-1B patients subsequently revealed that T-cell activation precedes and independently predicts X4-tropism switching (aHR 1.186, 95% CI 1.065–1.321, p = 0.002), providing novel insights into HIV-1 pathogenesis and CCR5-based curative strategies.
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Affiliation(s)
- Bridgette J Connell
- Department of Medical Microbiology, Virology, University Medical Center Utrecht (UMCU), Utrecht, The Netherlands
| | - Lucas E Hermans
- Department of Medical Microbiology, Virology, University Medical Center Utrecht (UMCU), Utrecht, The Netherlands.,Ezintsha, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Ndlovu Research Consortium, Elandsdoorn, Limpopo Province, South Africa
| | - Annemarie M J Wensing
- Department of Medical Microbiology, Virology, University Medical Center Utrecht (UMCU), Utrecht, The Netherlands.,Ezintsha, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Ndlovu Research Consortium, Elandsdoorn, Limpopo Province, South Africa
| | - Ingrid Schellens
- Center for Translational Immunology, UMCU, Utrecht, The Netherlands
| | - Pauline J Schipper
- Department of Medical Microbiology, Virology, University Medical Center Utrecht (UMCU), Utrecht, The Netherlands
| | - Petra M van Ham
- Department of Medical Microbiology, Virology, University Medical Center Utrecht (UMCU), Utrecht, The Netherlands
| | - Dorien T C M de Jong
- Department of Medical Microbiology, Virology, University Medical Center Utrecht (UMCU), Utrecht, The Netherlands
| | - Sigrid Otto
- Center for Translational Immunology, UMCU, Utrecht, The Netherlands
| | - Tholakele Mathe
- Ndlovu Research Consortium, Elandsdoorn, Limpopo Province, South Africa
| | - Robert Moraba
- Ndlovu Research Consortium, Elandsdoorn, Limpopo Province, South Africa
| | | | - Maria A Papathanasopoulos
- HIV Pathogenesis Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Zita Kruize
- Amsterdam University Medical Center, Amsterdam Infection and Immunity Institute, Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Francois W D Venter
- Ezintsha, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Neeltje A Kootstra
- Amsterdam University Medical Center, Amsterdam Infection and Immunity Institute, Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Hugo Tempelman
- Ndlovu Research Consortium, Elandsdoorn, Limpopo Province, South Africa
| | - Kiki Tesselaar
- Center for Translational Immunology, UMCU, Utrecht, The Netherlands
| | - Monique Nijhuis
- Department of Medical Microbiology, Virology, University Medical Center Utrecht (UMCU), Utrecht, The Netherlands. .,Ndlovu Research Consortium, Elandsdoorn, Limpopo Province, South Africa. .,HIV Pathogenesis Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
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van Lelyveld SFL, Symons J, van Ham P, Connell BJ, Nijhuis M, Wensing AMJ, Hoepelman AIM. Clinical outcome of maraviroc-containing therapy in heavily pre-treated HIV-1-infected patients. Int J Antimicrob Agents 2015; 47:84-90. [PMID: 26585497 DOI: 10.1016/j.ijantimicag.2015.09.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Revised: 09/10/2015] [Accepted: 09/10/2015] [Indexed: 12/13/2022]
Abstract
Available data on the use of maraviroc (MVC) in clinical settings are limited. In this cohort study, the clinical outcomes of HIV-1-infected patients treated with MVC were analysed and the predictive values of different tropism assays were compared. Baseline viral tropism was assessed and compared by phenotypic (Trofile and MT-2) and genotypic assays. Virological and immunological responses were evaluated. In total, 62 predominantly extensively pre-treated patients started MVC [median GSS 2.0 (IQR 2.0-2.5)]. Tropism assays were performed on baseline samples of 58 patients (93.5%). Thirty-two samples (80.0%) were classified as R5 by Trofile, 41 (80.4%) by genotypic tropism test (GTT) and 17 (81.0%) by MT-2. At least two types of tropism assay were performed on samples from 39 patients, whereas in 15 patients all three assays were performed (concordance 84.8-94.1%). Plasma HIV-RNA was <50 copies/mL in 82.1%, 85.0% and 68.8% of patients after 12, 24 and 36 months, respectively; median CD4 cell increase was 199 (IQR 108-283), 291 (IQR 187-413) and 234 (IQR 106-444)cells/μL. The predictive values of different tropism assays were comparably high: at Month 24, 92.9% (Trofile and GTT) and 100.0% (MT-2) of patients had plasma HIV-RNA <50 copies/mL. Three patients stopped MVC treatment because of suspected side effects. Five patients died during follow-up. In this heavily pre-treated cohort, treatment with MVC was well tolerated and resulted in good immunological and virological responses. Results generated by the different tropism assays correlated well with each other and had a high predictive value.
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Affiliation(s)
- S F L van Lelyveld
- Department of Internal Medicine & Gastroenterology, Spaarne Gasthuis, Haarlem, The Netherlands; Department of Internal Medicine & Infectious Diseases, University Medical Center Utrecht, Utrecht, The Netherlands.
| | - J Symons
- Department of Medical Microbiology & Virology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - P van Ham
- Department of Medical Microbiology & Virology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - B J Connell
- Department of Medical Microbiology & Virology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - M Nijhuis
- Department of Medical Microbiology & Virology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - A M J Wensing
- Department of Medical Microbiology & Virology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - A I M Hoepelman
- Department of Internal Medicine & Infectious Diseases, University Medical Center Utrecht, Utrecht, The Netherlands
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Cavarelli M, Mainetti L, Pignataro AR, Bigoloni A, Tolazzi M, Galli A, Nozza S, Castagna A, Sampaolo M, Boeri E, Scarlatti G. Complexity and dynamics of HIV-1 chemokine receptor usage in a multidrug-resistant adolescent. AIDS Res Hum Retroviruses 2014; 30:1243-50. [PMID: 25275490 DOI: 10.1089/aid.2014.0124] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Maraviroc (MVC) is licensed in clinical practice for patients with R5 virus and virological failure; however, in anecdotal reports, dual/mixed viruses were also inhibited. We retrospectively evaluated the evolution of HIV-1 coreceptor tropism in plasma and peripheral blood mononuclear cells (PBMCs) of an infected adolescent with a CCR5/CXCR4 Trofile profile who experienced an important but temporary immunological and virological response during a 16-month period of MVC-based therapy. Coreceptor usage of biological viral clones isolated from PBMCs was investigated in U87.CD4 cells expressing wild-type or chimeric CCR5 and CXCR4. Plasma and PBMC-derived viral clones were sequenced to predict coreceptor tropism using the geno2pheno algorithm from the V3 envelope sequence and pol gene-resistant mutations. From start to 8.5 months of MVC treatment only R5X4 viral clones were observed, whereas at 16 months the phenotype enlarged to also include R5 and X4 clones. Chimeric receptor usage suggested the preferential usage of the CXCR4 coreceptor by the R5X4 biological clones. According to phenotypic data, R5 viruses were susceptible, whereas R5X4 and X4 viruses were resistant to RANTES and MVC in vitro. Clones at 16 months, but not at baseline, showed an amino acidic resistance pattern in protease and reverse transcription genes, which, however, did not drive their tropisms. The geno2pheno algorithm predicted at baseline R5 viruses in plasma, and from 5.5 months throughout follow-up only CXCR4-using viruses. An extended methodological approach is needed to unravel the complexity of the phenotype and variation of viruses resident in the different compartments of an infected individual. The accurate evaluation of the proportion of residual R5 viruses may guide therapeutic intervention in highly experienced patients with limited therapeutic options.
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Affiliation(s)
- Mariangela Cavarelli
- Viral Evolution and Transmission Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Lara Mainetti
- Viral Evolution and Transmission Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Angela Rosa Pignataro
- Laboratory of Microbiology and Virology, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Università Vita Salute San Raffaele, Milan, Italy
| | - Alba Bigoloni
- Vaccine and Immunotherapy Research Center, Department of Infectious and Tropical Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Monica Tolazzi
- Viral Evolution and Transmission Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Andrea Galli
- Vaccine and Immunotherapy Research Center, Department of Infectious and Tropical Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Silvia Nozza
- Vaccine and Immunotherapy Research Center, Department of Infectious and Tropical Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Antonella Castagna
- Vaccine and Immunotherapy Research Center, Department of Infectious and Tropical Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Michela Sampaolo
- Laboratory of Microbiology and Virology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Enzo Boeri
- Laboratory of Microbiology and Virology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Gabriella Scarlatti
- Viral Evolution and Transmission Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
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Armenia D, Soulie C, Di Carlo D, Fabeni L, Gori C, Forbici F, Svicher V, Bertoli A, Sarmati L, Giuliani M, Latini A, Boumis E, Zaccarelli M, Bellagamba R, Andreoni M, Marcelin AG, Calvez V, Antinori A, Ceccherini-Silberstein F, Perno CF, Santoro MM. A very low geno2pheno false positive rate is associated with poor viro-immunological response in drug-naïve patients starting a first-line HAART. PLoS One 2014; 9:e105853. [PMID: 25153969 PMCID: PMC4143365 DOI: 10.1371/journal.pone.0105853] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Accepted: 07/27/2014] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND We previously found that a very low geno2pheno false positive rate (FPR ≤ 2%) defines a viral population associated with low CD4 cell count and the highest amount of X4-quasispecies. In this study, we aimed at evaluating whether FPR ≤ 2% might impact on the viro-immunological response in HIV-1 infected patients starting a first-line HAART. METHODS The analysis was performed on 305 HIV-1 B subtype infected drug-naïve patients who started their first-line HAART. Baseline FPR (%) values were stratified according to the following ranges: ≤ 2; 2-5; 5-10; 10-20; 20-60; >60. The impact of genotypically-inferred tropism on the time to achieve immunological reconstitution (a CD4 cell count gain from HAART initiation ≥ 150 cells/mm(3)) and on the time to achieve virological success (the first HIV-RNA measurement <50 copies/mL from HAART initiation) was evaluated by survival analyses. RESULTS Overall, at therapy start, 27% of patients had FPR ≤ 10 (6%, FPR ≤ 2; 7%, FPR 2-5; 14%, FPR 5-10). By 12 months of therapy the rate of immunological reconstitution was overall 75.5%, and it was significantly lower for FPR ≤ 2 (54.1%) in comparison to other FPR ranks (78.8%, FPR 2-5; 77.5%, FPR 5-10; 71.7%, FPR 10-20; 81.8%, FPR 20-60; 75.1%, FPR >60; p = 0.008). The overall proportion of patients achieving virological success was 95.5% by 12 months of therapy. Multivariable Cox analyses showed that patients having pre-HAART FPR ≤ 2% had a significant lower relative adjusted hazard [95% C.I.] both to achieve immunological reconstitution (0.37 [0.20-0.71], p = 0.003) and to achieve virological success (0.50 [0.26-0.94], p = 0.031) than those with pre-HAART FPR >60%. CONCLUSIONS Beyond the genotypically-inferred tropism determination, FPR ≤ 2% predicts both a poor immunological reconstitution and a lower virological response in drug-naïve patients who started their first-line therapy. This parameter could be useful to identify patients potentially with less chance of achieving adequate immunological reconstitution and virological undetectability.
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Affiliation(s)
- Daniele Armenia
- Department of Experimental Medicine and Surgery, University of Rome Tor Vergata, Rome, Italy
| | - Cathia Soulie
- Unité Mixte de Recherche en Santé (UMR_S) 1136 Pierre Louis Institute of Epidemiology and Public Health, Université Pierre et Marie Curie (UPMC) University Paris 06, Paris, France
- UMR_S 1136 Pierre Louis Institute of Epidemiology and Public Health, Institut National de la Santé et de la Recherche Médicale (INSERM), Paris, France
- Laboratoire de Virologie, Assistance Publique-Hôpitaux de Paris (AP-HP), Groupe hospitalier Pitié Salpêtrière, Paris, France
| | - Domenico Di Carlo
- Department of Experimental Medicine and Surgery, University of Rome Tor Vergata, Rome, Italy
| | - Lavinia Fabeni
- Antiviral Drug Monitoring Unit, Istituto Nazionale delle Malattie Infettive (INMI) Lazzaro Spallanzani, Rome, Italy
| | - Caterina Gori
- Antiviral Drug Monitoring Unit, Istituto Nazionale delle Malattie Infettive (INMI) Lazzaro Spallanzani, Rome, Italy
| | - Federica Forbici
- Antiviral Drug Monitoring Unit, Istituto Nazionale delle Malattie Infettive (INMI) Lazzaro Spallanzani, Rome, Italy
| | - Valentina Svicher
- Department of Experimental Medicine and Surgery, University of Rome Tor Vergata, Rome, Italy
| | - Ada Bertoli
- Department of Experimental Medicine and Surgery, University of Rome Tor Vergata, Rome, Italy
- Molecular Virology, University Hospital Tor Vergata, Rome, Italy
| | - Loredana Sarmati
- Infectious Disease Unit, University Hospital Tor Vergata, Rome, Italy
| | - Massimo Giuliani
- Department of Infectious Dermatology, San Gallicano Hospital, Rome, Italy
| | - Alessandra Latini
- Department of Infectious Dermatology, San Gallicano Hospital, Rome, Italy
| | - Evangelo Boumis
- Infectious Diseases Division, Istituto Nazionale delle Malattie Infettive (INMI) Lazzaro Spallanzani, Rome, Italy
| | - Mauro Zaccarelli
- Infectious Diseases Division, Istituto Nazionale delle Malattie Infettive (INMI) Lazzaro Spallanzani, Rome, Italy
| | - Rita Bellagamba
- Infectious Diseases Division, Istituto Nazionale delle Malattie Infettive (INMI) Lazzaro Spallanzani, Rome, Italy
| | - Massimo Andreoni
- Infectious Disease Unit, University Hospital Tor Vergata, Rome, Italy
| | - Anne-Geneviève Marcelin
- Unité Mixte de Recherche en Santé (UMR_S) 1136 Pierre Louis Institute of Epidemiology and Public Health, Université Pierre et Marie Curie (UPMC) University Paris 06, Paris, France
- UMR_S 1136 Pierre Louis Institute of Epidemiology and Public Health, Institut National de la Santé et de la Recherche Médicale (INSERM), Paris, France
- Laboratoire de Virologie, Assistance Publique-Hôpitaux de Paris (AP-HP), Groupe hospitalier Pitié Salpêtrière, Paris, France
| | - Vincent Calvez
- Unité Mixte de Recherche en Santé (UMR_S) 1136 Pierre Louis Institute of Epidemiology and Public Health, Université Pierre et Marie Curie (UPMC) University Paris 06, Paris, France
- UMR_S 1136 Pierre Louis Institute of Epidemiology and Public Health, Institut National de la Santé et de la Recherche Médicale (INSERM), Paris, France
- Laboratoire de Virologie, Assistance Publique-Hôpitaux de Paris (AP-HP), Groupe hospitalier Pitié Salpêtrière, Paris, France
| | - Andrea Antinori
- Infectious Diseases Division, Istituto Nazionale delle Malattie Infettive (INMI) Lazzaro Spallanzani, Rome, Italy
| | | | - Carlo-Federico Perno
- Department of Experimental Medicine and Surgery, University of Rome Tor Vergata, Rome, Italy
- Antiviral Drug Monitoring Unit, Istituto Nazionale delle Malattie Infettive (INMI) Lazzaro Spallanzani, Rome, Italy
- Molecular Virology, University Hospital Tor Vergata, Rome, Italy
| | - Maria Mercedes Santoro
- Department of Experimental Medicine and Surgery, University of Rome Tor Vergata, Rome, Italy
- * E-mail:
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Pérez-Olmeda M, Alcami J. Determination of HIV tropism and its use in the clinical practice. Expert Rev Anti Infect Ther 2014; 11:1291-302. [DOI: 10.1586/14787210.2013.852469] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Genotypic analysis of the V3 region of HIV from virologic nonresponders to maraviroc-containing regimens reveals distinct patterns of failure. Antimicrob Agents Chemother 2013; 57:6122-30. [PMID: 24080655 DOI: 10.1128/aac.01534-13] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Changes in HIV tropism from R5 to non-R5 or development of drug resistance is often associated with virologic failure in patients treated with maraviroc, a CCR5 antagonist. We sought to examine changes in HIV envelope sequences and inferred tropism in patients who did not respond to maraviroc-based regimens. We selected 181 patients who experienced early virologic failure on maraviroc-containing therapy in the MOTIVATE trials. All patients had R5 HIV by the original Trofile assay before entry. We used population-based sequencing methods and the geno2pheno algorithm to examine changes in tropism and V3 sequences at the time of failure. Using deep sequencing, we assessed whether V3 sequences observed at failure emerged from preexisting subpopulations. From population genotyping data at failure, 90 patients had R5 results, and 91 had non-R5 results. Of the latter group, the geno2pheno false-positive rate (FPR) value fell from a median of 20 at screening to 1.1 at failure. By deep sequencing, the median percentage of non-R5 variants in these patients rose from 1.4% to 99.5% after a median of 4 weeks on maraviroc. In 70% of cases, deep sequencing could detect a pretreatment CXCR4-using subpopulation, which emerged at failure. Overall, there were two distinct patterns of failure of maraviroc. Patients failing with R5 generally had few V3 substitutions and low non-R5 prevalence by deep sequencing. Patients with non-R5 HIV who were failing developed very-high-prevalence non-R5 HIV (median, 99%) and had very low geno2pheno values.
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