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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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2
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Dimeglio C, Raymond S, Jeanne N, Reynes C, Carcenac R, Lefebvre C, Cazabat M, Nicot F, Delobel P, Izopet J. THETA: a new genotypic approach for predicting HIV-1 CRF02-AG coreceptor usage. Bioinformatics 2020; 36:416-421. [PMID: 31350559 DOI: 10.1093/bioinformatics/btz585] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 06/28/2019] [Accepted: 07/19/2019] [Indexed: 02/07/2023] Open
Abstract
MOTIVATION The circulating recombinant form of HIV-1 CRF02-AG is the most frequent non-B subtype in Europe. Anti-HIV therapy and pathophysiological studies on the impact of HIV-1 tropism require genotypic determination of HIV-1 tropism for non-B subtypes. But genotypic approaches based on analysis of the V3 envelope region perform poorly when used to determine the tropism of CRF02-AG. We, therefore, designed an algorithm based on information from the gp120 and gp41 ectodomain that better predicts the tropism of HIV-1 subtype CRF02-AG. RESULTS We used a bio-statistical method to identify the genotypic determinants of CRF02-AG coreceptor use. Toulouse HIV Extended Tropism Algorithm (THETA), based on a Least Absolute Shrinkage and Selection Operator method, uses HIV envelope sequence from phenotypically characterized clones. Prediction of R5X4/X4 viruses was 86% sensitive and that of R5 viruses was 89% specific with our model. The overall accuracy of THETA was 88%, making it sufficiently reliable for predicting the tropism of subtype CRF02-AG sequences. AVAILABILITY AND IMPLEMENTATION Binaries are freely available for download at https://github.com/viro-tls/THETA. It was implemented in Matlab and supported on MS Windows platform. The sequence data used in this work are available from GenBank under the accession numbers MK618182-MK618417.
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Affiliation(s)
- Chloé Dimeglio
- CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie
| | - Stéphanie Raymond
- CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie.,INSERM U1043-CNRS UMR 5282-Toulouse University Paul Sabatier, CPTP, Toulouse F-31300, France
| | - Nicolas Jeanne
- CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie
| | - Christelle Reynes
- Institut de Génomique Fonctionnelle, 34090 Montpellier, France.,UM-Université de Montpellier, 34090 Montpellier, France.,Faculté de Pharmacie, 34090 Montpellier, France
| | | | | | | | - Florence Nicot
- CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie
| | - Pierre Delobel
- CHU de Toulouse, Service de Maladies Infectieuses et Tropicales, 31059 Toulouse, France
| | - Jacques Izopet
- CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie.,INSERM U1043-CNRS UMR 5282-Toulouse University Paul Sabatier, CPTP, Toulouse F-31300, France
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3
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Abstract
OBJECTIVE To study the long-term evolution of the transmitted CXCR4-using viruses. CCR5-using viruses (R5 viruses) predominate during primary HIV-1 infections (PHI) while CXCR4-using viruses are isolated in less than 10% of PHI. DESIGN Six patients infected with an R5X4 virus, detected by a sensitive phenotypic assay during PHI, were matched with six patients infected with a pure R5 virus for sex, Fiebig stage, time of antiretroviral initiation and duration of follow-up. METHODS We used MiSeq ultra-deep sequencing to determine the composition of the virus quasispecies during PHI and at the end of follow-up (median time of follow-up: 12.5 years). RESULTS X4 viruses were detected by genetic analysis in three of six samples from the R5X4 group, accounting for 1.3-100% of the virus quasispecies, during PHI, and in four of six samples (accounting for 6.7-100%) at the end of follow-up. No X4 virus was detected in the R5 group during PHI and in only one patient (accounting for 1.2%) at the end of follow-up. The complexity of the virus quasispecies at the stage of PHI was higher in the R5X4 group than in the R5 group. Complexity increased from PHI to the end of follow-up in the R5 group but remained stable in the R5X4 group. CONCLUSION CXCR4-using viruses persisted in the peripheral blood mononuclear cells of several patients on suppressive antiretroviral therapy for a median duration of 12.5 years after PHI. The genetic complexity of HIV-1 evolved differently post-PHI in patients infected with R5X4 viruses from those infected with R5 viruses.
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4
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Zhang J, Gao X, Martin J, Rosa B, Chen Z, Mitreva M, Henrich T, Kuritzkes D, Ratner L. Evolution of coreceptor utilization to escape CCR5 antagonist therapy. Virology 2016; 494:198-214. [PMID: 27128349 PMCID: PMC4913893 DOI: 10.1016/j.virol.2016.04.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 04/04/2016] [Accepted: 04/07/2016] [Indexed: 01/05/2023]
Abstract
The HIV-1 envelope interacts with coreceptors CCR5 and CXCR4 in a dynamic, multi-step process, its molecular details not clearly delineated. Use of CCR5 antagonists results in tropism shift and therapeutic failure. Here we describe a novel approach using full-length patient-derived gp160 quasispecies libraries cloned into HIV-1 molecular clones, their separation based on phenotypic tropism in vitro, and deep sequencing of the resultant variants for structure-function analyses. Analysis of functionally validated envelope sequences from patients who failed CCR5 antagonist therapy revealed determinants strongly associated with coreceptor specificity, especially at the gp120-gp41 and gp41-gp41 interaction surfaces that invite future research on the roles of subunit interaction and envelope trimer stability in coreceptor usage. This study identifies important structure-function relationships in HIV-1 envelope, and demonstrates proof of concept for a new integrated analysis method that facilitates laboratory discovery of resistant mutants to aid in development of other therapeutic agents.
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Affiliation(s)
- Jie Zhang
- Division of Molecular Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Xiang Gao
- Division of Molecular Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - John Martin
- The McDonnelle Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Bruce Rosa
- The McDonnelle Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Zheng Chen
- Department of Computer Science and Engineering, Washington University in St. Louis, St. Louis, MO, USA
| | - Makedonka Mitreva
- The McDonnelle Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Timothy Henrich
- Division of Infectious Diseases, Brigham and Women׳s Hospital, Harvard Medical School, MA, USA
| | - Daniel Kuritzkes
- Division of Infectious Diseases, Brigham and Women׳s Hospital, Harvard Medical School, MA, USA
| | - Lee Ratner
- Division of Molecular Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA.
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5
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Danaviah S, de Oliveira T, Gordon M, Govender S, Chelule P, Pillay S, Naicker T, Cassol S, Ndung'u T. Analysis of Dominant HIV Quasispecies Suggests Independent Viral Evolution Within Spinal Granulomas Coinfected with Mycobacterium tuberculosis and HIV-1 Subtype C. AIDS Res Hum Retroviruses 2016; 32:262-70. [PMID: 26564424 DOI: 10.1089/aid.2015.0189] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Extrapulmonary tuberculosis (TB) is a significant public health challenge in South Africa and worldwide, largely fuelled by the HIV epidemic. In spinal TB, Mycobacteria infect the spinal column without dissemination to the spinal cord. The immune microenvironment, target cell characteristics, and other evolutionary forces within granulomas during HIV/TB coinfection are poorly characterized. We investigated whether spinal TB granulomas represent a sequestered anatomical site where independent HIV evolution occurs, and assessed the role of macrophages as a target cell for both HIV and mycobacteria. RNA was extracted from plasma and granulomatous tissue from six antiretroviral-naive HIV-1/spinal TB-coinfected patients, RT-PCR amplified, and the C2-V5 env segment was cloned and sequenced. Analysis of genetic diversity, phylogeny and coalescence patterns was performed on clonal sequences. To investigate their role in HIV sequestration, macrophages and the HIV-1 p24 protein were immune localized and ultrastructural features were studied. Intercompartment diversity measurements and phylogenetic reconstruction revealed anatomically distinct monophyletic HIV-1 clusters in four of six patients. Genotypic CCR5-tropic variants were predominant (98.9%) with conservation of putative N-linked glycosylation sites in both compartments. CD68(+) reactivity was associated with higher tissue viral load (r = 1.0; p < 0.01) but not greater intrapatient diversity (r = 0.60; p > 0.05). Ultrastructural imaging revealed the presence of bacterial and virus-like particles within membrane-bound intracellular compartments of macrophages. Spinal tuberculosis granulomas may form anatomically discreet sites of divergent viral evolution. Macrophages in these granulomas harbored both pathogens, suggesting that they may facilitate the process of viral sequestration within this compartment.
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Affiliation(s)
- Sivapragashini Danaviah
- Africa Centre for Health and Population Studies, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal (UKZN), Durban, South Africa
| | - Tulio de Oliveira
- Africa Centre for Health and Population Studies, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal (UKZN), Durban, South Africa
| | - Michelle Gordon
- Department of Virology, Nelson R. Mandela School of Medicine, UKZN, Durban, South Africa
- KwaZulu-Natal Research Institute for Tuberculosis and HIV (K-RITH), UKZN, Durban, South Africa
| | - Shunmugam Govender
- Department of Orthopedics, Nelson R. Mandela School of Medicine, UKZN, Durban, South Africa
| | - Paul Chelule
- School of Public Health, Sefako Makgatho Health Sciences University, Medunsa, South Africa
| | - Sureshnee Pillay
- Africa Centre for Health and Population Studies, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal (UKZN), Durban, South Africa
| | - Thajasvarie Naicker
- Optics and Imaging Centre, Nelson R. Mandela School of Medicine, UKZN, Durban, South Africa
| | - Sharon Cassol
- MRC Inflammation and Immunity Unit, Department of Immunology, University of Pretoria, Pretoria, South Africa
| | - Thumbi Ndung'u
- KwaZulu-Natal Research Institute for Tuberculosis and HIV (K-RITH), UKZN, Durban, South Africa
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, UKZN, Durban, South Africa
- Max Planck Institute for Infection Biology, Chariteplatz, Berlin, Germany
- The Ragon Institute of MGH, MIT and Harvard University, Cambridge, Massachusetts
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6
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Pacheco-Martínez E, Figueroa-Medina E, Villarreal C, Cocho G, Medina-Franco JL, Méndez-Lucio O, Huerta L. Statistical correlation of nonconservative substitutions of HIV gp41 variable amino acid residues with the R5X4 HIV-1 phenotype. Virol J 2016; 13:28. [PMID: 26879054 PMCID: PMC4754869 DOI: 10.1186/s12985-016-0486-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 02/09/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The interaction of the envelope glycoprotein of HIV-1 (gp120/gp41) with coreceptor molecules has important implications for specific cellular targeting and pathogenesis. Experimental and theoretical evidences have shown a role for gp41 in coreceptor tropism, although there is no consensus about the positions involved. Here we analyze the association of physicochemical properties of gp41 amino acid residues with viral tropism (X4, R5, and R5X4) using a large set of HIV-1 sequences. Under the assumption that conserved regions define the complex structural features essential for protein function, we focused our search only on amino acids in the gp41 variable regions. METHODS Gp41 amino acid sequences of 2823 HIV-1 strains from all clades with known coreceptor tropism were retrieved from Los Alamos HIV Database. Consensus sequences were constructed for homologous sequences (those obtained from the same patient and having the same tropism) in order to avoid bias due to sequence overrepresentation, and the variability (entropy) per site was determined. Comparisons of hydropathy index (HI) and charge (Q) of amino acid residues at highly variable positions between coreceptor groups were performed using two non-parametrical tests and Benjamini-Hochberg correction. Pearson's correlation analysis was performed to determine covariance of HI and Q values. RESULTS Calculation of variability per site rendered 58 highly variable amino acid positions. Of these, statistical analysis rendered significantly different HI or Q only for the R5 vs. R5X4 comparison at twelve positions: 535, 602, 619, 636, 640, 641, 658, 662, 667, 723, 756 and 841. The largest differences in particular amino acid frequencies between coreceptor groups were found at 619, 636, 640, 641, 662, 723 and 756. A hydrophobic tendency of residues 619, 640, 641, 723 and 756, along with a hydrophilic/charged tendency at residues 636 and 662 was observed in R5X4 with respect to R5 sequences. HI of position 640 covariated with that of 602, 619, 636, 662, and 756. CONCLUSIONS Variability and significant correlations of physicochemical properties with viral phenotype suggest that substitutions at residues in the loop (602 and 619), the HR2 (636, 640, 641, 662), and the C-terminal tail (723, 756) of gp41 may contribute to phenotype of R5X4 strains.
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Affiliation(s)
- Elena Pacheco-Martínez
- Programa de Maestría y Doctorado en Ciencias Bioquímicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Distrito Federal, 04510, México
| | - Evangelina Figueroa-Medina
- Unidad de Radio Oncología, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Secretaría de Salud, Avenida Vasco de Quiroga No.15, ᅟDistrito Federal, 14080, México
| | - Carlos Villarreal
- Departmento de Física Teórica, Instituto de Física, Universidad Nacional Autónoma de México, Ciudad Universitaria, ᅟDistrito Federal, 04510, México.,Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Ciudad Univesitaria, ᅟDistrito Federal, 04510, México
| | - Germinal Cocho
- Departmento de Sistemas Complejos, Instituto de Física, Universidad Nacional Autónoma de México, Ciudad Universitaria, ᅟDistrito Federal, 04510, México.,Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Ciudad Univesitaria, ᅟDistrito Federal, 04510, México
| | - José L Medina-Franco
- Departmento de Farmacia, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad Universitaria, ᅟDistrito Federal, 04510, México
| | - Oscar Méndez-Lucio
- Departmento de Farmacia, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad Universitaria, ᅟDistrito Federal, 04510, México
| | - Leonor Huerta
- Departmento de Immunología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Distrito Federal, México.
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7
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Lombardi F, Nakamura KJ, Chen T, Sobrera ER, Tobin NH, Aldrovandi GM. A Conserved Glycan in the C2 Domain of HIV-1 Envelope Acts as a Molecular Switch to Control X4 Utilization by Clonal Variants with Identical V3 Loops. PLoS One 2015; 10:e0128116. [PMID: 26083631 PMCID: PMC4471078 DOI: 10.1371/journal.pone.0128116] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 04/23/2015] [Indexed: 11/18/2022] Open
Abstract
Nearly all persons newly infected with HIV-1 harbor exclusively CCR5-using virus. CXCR4-using variants eventually arise in up to 50% of patients infected with subtypes B or D. This transition to efficient CXCR4 utilization is often co-incident with progression to AIDS. The basis for HIV-1's initial dependence on CCR5, the selective force(s) that drive CXCR4-utilization, and the evolutionary pathways by which it occurs are incompletely understood. Greater knowledge of these processes will inform interventions at all stages, from vaccination to cure. The determinants of co-receptor use map primarily, though not exclusively, to the V3 loop of gp120. In this study, we describe five clonal variants with identical V3 loops but divergent CXCR4 use. Mutagenesis revealed two residues controlling this phenotypic switch: a rare polymorphism in C1 and a highly conserved N-glycan in C2. To our knowledge, this is the first description of co-receptor usage regulated by the N-glycan at position 262.
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Affiliation(s)
- Francesca Lombardi
- Department of Pediatrics, Children’s Hospital Los Angeles, Los Angeles, CA, United States of America
| | - Kyle J. Nakamura
- Department of Pediatrics, Children’s Hospital Los Angeles, Los Angeles, CA, United States of America
| | - Thomas Chen
- Department of Pediatrics, Children’s Hospital Los Angeles, Los Angeles, CA, United States of America
| | - Edwin R. Sobrera
- Department of Pediatrics, Children’s Hospital Los Angeles, Los Angeles, CA, United States of America
| | - Nicole H. Tobin
- Department of Pediatrics, Children’s Hospital Los Angeles, Los Angeles, CA, United States of America
| | - Grace M. Aldrovandi
- Department of Pediatrics, Children’s Hospital Los Angeles, Los Angeles, CA, United States of America
- * E-mail:
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8
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Cashin K, Sterjovski J, Harvey KL, Ramsland PA, Churchill MJ, Gorry PR. Covariance of charged amino acids at positions 322 and 440 of HIV-1 Env contributes to coreceptor specificity of subtype B viruses, and can be used to improve the performance of V3 sequence-based coreceptor usage prediction algorithms. PLoS One 2014; 9:e109771. [PMID: 25313689 PMCID: PMC4196930 DOI: 10.1371/journal.pone.0109771] [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: 06/26/2014] [Accepted: 09/05/2014] [Indexed: 11/18/2022] Open
Abstract
The ability to determine coreceptor usage of patient-derived human immunodeficiency virus type 1 (HIV-1) strains is clinically important, particularly for the administration of the CCR5 antagonist maraviroc. The envelope glycoprotein (Env) determinants of coreceptor specificity lie primarily within the gp120 V3 loop region, although other Env determinants have been shown to influence gp120-coreceptor interactions. Here, we determined whether conserved amino acid alterations outside the V3 loop that contribute to coreceptor usage exist, and whether these alterations improve the performance of V3 sequence-based coreceptor usage prediction algorithms. We demonstrate a significant covariant association between charged amino acids at position 322 in V3 and position 440 in the C4 Env region that contributes to the specificity of HIV-1 subtype B strains for CCR5 or CXCR4. Specifically, positively charged Lys/Arg at position 322 and negatively charged Asp/Glu at position 440 occurred more frequently in CXCR4-using viruses, whereas negatively charged Asp/Glu at position 322 and positively charged Arg at position 440 occurred more frequently in R5 strains. In the context of CD4-bound gp120, structural models suggest that covariation of amino acids at Env positions 322 and 440 has the potential to alter electrostatic interactions that are formed between gp120 and charged amino acids in the CCR5 N-terminus. We further demonstrate that inclusion of a "440 rule" can improve the sensitivity of several V3 sequence-based genotypic algorithms for predicting coreceptor usage of subtype B HIV-1 strains, without compromising specificity, and significantly improves the AUROC of the geno2pheno algorithm when set to its recommended false positive rate of 5.75%. Together, our results provide further mechanistic insights into the intra-molecular interactions within Env that contribute to coreceptor specificity of subtype B HIV-1 strains, and demonstrate that incorporation of Env determinants outside V3 can improve the reliability of coreceptor usage prediction algorithms.
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Affiliation(s)
- Kieran Cashin
- Center for Biomedical Research, Burnet Institute, Melbourne, Australia
- Department of Microbiology and Immunology, University of Melbourne, Melbourne, Australia
| | | | - Katherine L. Harvey
- Center for Biomedical Research, Burnet Institute, Melbourne, Australia
- Department of Microbiology and Immunology, University of Melbourne, Melbourne, Australia
| | - Paul A. Ramsland
- Center for Biomedical Research, Burnet Institute, Melbourne, Australia
- Department of Surgery (Austin Health), University of Melbourne, Melbourne, Australia
- Department of Immunology, Monash University, Melbourne, Australia
- School of Biomedical Sciences, CHIRI Biosciences, Faculty of Health Sciences, Curtin University, Perth, Australia
| | - Melissa J. Churchill
- Center for Biomedical Research, Burnet Institute, Melbourne, Australia
- Department of Microbiology, Monash University, Melbourne, Australia
- Department of Medicine, Monash University, Melbourne, Australia
| | - Paul R. Gorry
- Center for Biomedical Research, Burnet Institute, Melbourne, Australia
- Department of Microbiology and Immunology, University of Melbourne, Melbourne, Australia
- Department of Infectious Diseases, Monash University, Melbourne, Australia
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9
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Coelho LPO, Ferreira JLDP, Cabral GB, Guimarães PMDS, Brigido LFDM. Genotypic tropism prediction from paired cell and plasma using single and replicate sequences. AIDS Res Hum Retroviruses 2014; 30:711-6. [PMID: 24673579 DOI: 10.1089/aid.2013.0258] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
HIV-1 tropism determination is necessary prior to CCR5 antagonist use as antiretroviral therapy. Genotypic prediction of coreceptor use is a practical alternative to phenotypic tests. Cell DNA and plasma RNA-based prediction has shown discordance in many studies. We evaluate paired cell and plasma either as single or replicate V3 sequences to assess prediction comparability. The HIV-1 partial env region was sequenced and tropism was predicted using geno2pheno and position-specific scoring matrices (PSSM). Nucleotide ambiguities at V3 were quantified and genetic distance (Protdist) was determined using BioEdit. Wilcoxon signed-rank test, t tests, and Spearman correlation were performed with Prism GraphPad5.0. Results are expressed as medians, with a level of significance of p<0.05, two tailed. Single (n=28) or replicate (n=26) paired cell/plasma sequences were obtained from 54 patients. Although the clonalfalse-positive rate (FPR) value from both compartments strongly correlated (r=0.86 p<0.0001), discordance in tropism prediction was observed in both singles and replicates using geno2pheno or PSSM. Applying clonalFPR(10%) 46% (25/54) were X4 tropic, with a plasma/cell discordance of 11% in singles and 23% in replicates. Genetic distance (p<0.0001) and clonalFPR value dispersion (p=0.003) were significantly higher among replicate sequences from cells. Discordance of viral tropism prediction is not uncommon and the use of replicates does not decrease its occurrence, but improves X4 sensitivity. Sequences from provirus had greater genetic distance and dispersion of clonalFPR values. This may suggest that DNA replicate assays may better represent the diversity of HIV-1 variants, but the clinical significance of these findings needs further evaluation.
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10
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HIV-1 tropism testing and clinical management of CCR5 antagonists: Quebec review and recommendations. CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY 2014; 24:202-8. [PMID: 24489562 DOI: 10.1155/2013/982759] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
HIV-1 tropism assays play a crucial role in determining the response to CCR5 receptor antagonists. Initially, phenotypic tests were used, but limited access to these tests prompted the development of alternative strategies. Recently, genotyping tropism has been validated using a Canadian technology in clinical trials investigating the use of maraviroc in both experienced and treatment-naive patients. The present guidelines review the evidence supporting the use of genotypic assays and provide recommendations regarding tropism testing in daily clinical management.
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Aiamkitsumrit B, Dampier W, Antell G, Rivera N, Martin-Garcia J, Pirrone V, Nonnemacher MR, Wigdahl B. Bioinformatic analysis of HIV-1 entry and pathogenesis. Curr HIV Res 2014; 12:132-61. [PMID: 24862329 PMCID: PMC4382797 DOI: 10.2174/1570162x12666140526121746] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Revised: 03/18/2014] [Accepted: 05/06/2014] [Indexed: 02/07/2023]
Abstract
The evolution of human immunodeficiency virus type 1 (HIV-1) with respect to co-receptor utilization has been shown to be relevant to HIV-1 pathogenesis and disease. The CCR5-utilizing (R5) virus has been shown to be important in the very early stages of transmission and highly prevalent during asymptomatic infection and chronic disease. In addition, the R5 virus has been proposed to be involved in neuroinvasion and central nervous system (CNS) disease. In contrast, the CXCR4-utilizing (X4) virus is more prevalent during the course of disease progression and concurrent with the loss of CD4(+) T cells. The dual-tropic virus is able to utilize both co-receptors (CXCR4 and CCR5) and has been thought to represent an intermediate transitional virus that possesses properties of both X4 and R5 viruses that can be encountered at many stages of disease. The use of computational tools and bioinformatic approaches in the prediction of HIV-1 co-receptor usage has been growing in importance with respect to understanding HIV-1 pathogenesis and disease, developing diagnostic tools, and improving the efficacy of therapeutic strategies focused on blocking viral entry. Current strategies have enhanced the sensitivity, specificity, and reproducibility relative to the prediction of co-receptor use; however, these technologies need to be improved with respect to their efficient and accurate use across the HIV-1 subtypes. The most effective approach may center on the combined use of different algorithms involving sequences within and outside of the env-V3 loop. This review focuses on the HIV-1 entry process and on co-receptor utilization, including bioinformatic tools utilized in the prediction of co-receptor usage. It also provides novel preliminary analyses for enabling identification of linkages between amino acids in V3 with other components of the HIV-1 genome and demonstrates that these linkages are different between X4 and R5 viruses.
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Affiliation(s)
| | | | | | | | | | | | | | - Brian Wigdahl
- Department of Microbiology and Immunology, Drexel University College of Medicine, 245 N. 15th Street, Philadelphia, PA 19102.
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Dobrowsky TM, Rabi SA, Nedellec R, Daniels BR, Mullins JI, Mosier DE, Siliciano RF, Wirtz D. Adhesion and fusion efficiencies of human immunodeficiency virus type 1 (HIV-1) surface proteins. Sci Rep 2013; 3:3014. [PMID: 24145278 PMCID: PMC3804852 DOI: 10.1038/srep03014] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Accepted: 09/30/2013] [Indexed: 12/20/2022] Open
Abstract
In about half of patients infected with HIV-1 subtype B, viral populations shift from utilizing the transmembrane protein CCR5 to CXCR4, as well as or instead of CCR5, during late stage progression of the disease. How the relative adhesion efficiency and fusion competency of the viral Env proteins relate to infection during this transition is not well understood. Using a virus-cell fusion assay and live-cell single-molecule force spectroscopy, we compare the entry competency of viral clones to tensile strengths of the individual Env-receptor bonds of Env proteins obtained from a HIV-1 infected patient prior to and during coreceptor switching. The results suggest that the genetic determinants of viral entry were predominantly enriched in the C3, HR1 and CD regions rather than V3. Env proteins can better mediate entry into cells after coreceptor switch; this effective entry capacity does not correlate with the bond strengths between viral Env and cellular receptors.
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Affiliation(s)
- Terrence M Dobrowsky
- 1] Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, USA [2]
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13
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Pou C, Codoñer FM, Thielen A, Bellido R, Pérez-Álvarez S, Cabrera C, Dalmau J, Curriu M, Lie Y, Noguera-Julian M, Puig J, Martínez-Picado J, Blanco J, Coakley E, Däumer M, Clotet B, Paredes R. HIV-1 tropism testing in subjects achieving undetectable HIV-1 RNA: diagnostic accuracy, viral evolution and compartmentalization. PLoS One 2013; 8:e67085. [PMID: 23936293 PMCID: PMC3731261 DOI: 10.1371/journal.pone.0067085] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Accepted: 05/15/2013] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Technically, HIV-1 tropism can be evaluated in plasma or peripheral blood mononuclear cells (PBMCs). However, only tropism testing of plasma HIV-1 has been validated as a tool to predict virological response to CCR5 antagonists in clinical trials. The preferable tropism testing strategy in subjects with undetectable HIV-1 viremia, in whom plasma tropism testing is not feasible, remains uncertain. METHODS & RESULTS We designed a proof-of-concept study including 30 chronically HIV-1-infected individuals who achieved HIV-1 RNA <50 copies/mL during at least 2 years after first-line ART initiation. First, we determined the diagnostic accuracy of 454 and population sequencing of gp120 V3-loops in plasma and PBMCs, as well as of MT-2 assays before ART initiation. The Enhanced Sensitivity Trofile Assay (ESTA) was used as the technical reference standard. 454 sequencing of plasma viruses provided the highest agreement with ESTA. The accuracy of 454 sequencing decreased in PBMCs due to reduced specificity. Population sequencing in plasma and PBMCs was slightly less accurate than plasma 454 sequencing, being less sensitive but more specific. MT-2 assays had low sensitivity but 100% specificity. Then, we used optimized 454 sequence data to investigate viral evolution in PBMCs during viremia suppression and only found evolution of R5 viruses in one subject. No de novo CXCR4-using HIV-1 production was observed over time. Finally, Slatkin-Maddison tests suggested that plasma and cell-associated V3 forms were sometimes compartmentalized. CONCLUSIONS The absence of tropism shifts during viremia suppression suggests that, when available, testing of stored plasma samples is generally safe and informative, provided that HIV-1 suppression is maintained. Tropism testing in PBMCs may not necessarily produce equivalent biological results to plasma, because the structure of viral populations and the diagnostic performance of tropism assays may sometimes vary between compartments. Thereby, proviral DNA tropism testing should be specifically validated in clinical trials before it can be applied to routine clinical decision-making.
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Affiliation(s)
- Christian Pou
- Institut de Recerca de la SIDA irsiCaixa – HIVACAT, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, Catalonia, Spain
- * E-mail: (CP); (RP)
| | - Francisco M. Codoñer
- Institut de Recerca de la SIDA irsiCaixa – HIVACAT, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, Catalonia, Spain
| | | | - Rocío Bellido
- Institut de Recerca de la SIDA irsiCaixa – HIVACAT, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, Catalonia, Spain
| | - Susana Pérez-Álvarez
- Institut de Recerca de la SIDA irsiCaixa – HIVACAT, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, Catalonia, Spain
| | - Cecilia Cabrera
- Institut de Recerca de la SIDA irsiCaixa – HIVACAT, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, Catalonia, Spain
| | - Judith Dalmau
- Institut de Recerca de la SIDA irsiCaixa – HIVACAT, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, Catalonia, Spain
| | - Marta Curriu
- Institut de Recerca de la SIDA irsiCaixa – HIVACAT, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, Catalonia, Spain
| | - Yolanda Lie
- Monogram Biosciences Inc., South San Francisco, California, United States of America
| | - Marc Noguera-Julian
- Institut de Recerca de la SIDA irsiCaixa – HIVACAT, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, Catalonia, Spain
| | - Jordi Puig
- HIV Unit-Fundació Lluita contra la SIDA, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, Catalonia, Spain
| | - Javier Martínez-Picado
- Institut de Recerca de la SIDA irsiCaixa – HIVACAT, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, Catalonia, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Julià Blanco
- Institut de Recerca de la SIDA irsiCaixa – HIVACAT, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, Catalonia, Spain
| | - Eoin Coakley
- Monogram Biosciences Inc., South San Francisco, California, United States of America
| | - Martin Däumer
- Institut für Immunologie und Genetik, Kaiserlautern, Germany
| | - Bonaventura Clotet
- Institut de Recerca de la SIDA irsiCaixa – HIVACAT, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, Catalonia, Spain
- HIV Unit-Fundació Lluita contra la SIDA, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, Catalonia, Spain
| | - Roger Paredes
- Institut de Recerca de la SIDA irsiCaixa – HIVACAT, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, Catalonia, Spain
- HIV Unit-Fundació Lluita contra la SIDA, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, Catalonia, Spain
- * E-mail: (CP); (RP)
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Díez-Fuertes F, Delgado E, Vega Y, Fernández-García A, Cuevas MT, Pinilla M, García V, Pérez-Álvarez L, Thomson MM. Improvement of HIV-1 coreceptor tropism prediction by employing selected nucleotide positions of the env gene in a Bayesian network classifier. J Antimicrob Chemother 2013; 68:1471-85. [DOI: 10.1093/jac/dkt077] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
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15
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Cashin K, Gray LR, Jakobsen MR, Sterjovski J, Churchill MJ, Gorry PR. CoRSeqV3-C: a novel HIV-1 subtype C specific V3 sequence based coreceptor usage prediction algorithm. Retrovirology 2013; 10:24. [PMID: 23446039 PMCID: PMC3599735 DOI: 10.1186/1742-4690-10-24] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Accepted: 02/12/2013] [Indexed: 12/17/2022] Open
Abstract
Background The majority of HIV-1 subjects worldwide are infected with HIV-1 subtype C (C-HIV). Although C-HIV predominates in developing regions of the world such as Southern Africa and Central Asia, C-HIV is also spreading rapidly in countries with more developed economies and health care systems, whose populations are more likely to have access to wider treatment options, including the CCR5 antagonist maraviroc (MVC). The ability to reliably determine C-HIV coreceptor usage is therefore becoming increasingly more important. In silico V3 sequence based coreceptor usage prediction algorithms are a relatively rapid and cost effective method for determining HIV-1 coreceptor specificity. In this study, we elucidated the V3 sequence determinants of C-HIV coreceptor usage, and used this knowledge to develop and validate a novel, user friendly, and highly sensitive C-HIV specific coreceptor usage prediction algorithm. Results We characterized every phenotypically-verified C-HIV gp120 V3 sequence available in the Los Alamos HIV Database. Sequence analyses revealed that compared to R5 C-HIV V3 sequences, CXCR4-using C-HIV V3 sequences have significantly greater amino acid variability, increased net charge, increased amino acid length, increased frequency of insertions and substitutions within the GPGQ crown motif, and reduced frequency of glycosylation sites. Based on these findings, we developed a novel C-HIV specific coreceptor usage prediction algorithm (CoRSeqV3-C), which we show has superior sensitivity for determining CXCR4 usage by C-HIV strains compared to all other available algorithms and prediction rules, including Geno2pheno[coreceptor] and WebPSSMSINSI-C, which has been designed specifically for C-HIV. Conclusions CoRSeqV3-C is now openly available for public use at http://www.burnet.edu.au/coreceptor. Our results show that CoRSeqV3-C is the most sensitive V3 sequence based algorithm presently available for predicting CXCR4 usage of C-HIV strains, without compromising specificity. CoRSeqV3-C may be potentially useful for assisting clinicians to decide the best treatment options for patients with C-HIV infection, and will be helpful for basic studies of C-HIV pathogenesis.
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Affiliation(s)
- Kieran Cashin
- Center for Virology, Burnet Institute, 85 Commercial Rd, Melbourne 3004VIC, Australia
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Dimonte S, Babakir-Mina M, Mercurio F, Di Pinto D, Ceccherini-Silberstein F, Svicher V, Perno CF. Selected amino acid changes in HIV-1 subtype-C gp41 are associated with specific gp120(V3) signatures in the regulation of co-receptor usage. Virus Res 2012; 168:73-83. [PMID: 22732432 DOI: 10.1016/j.virusres.2012.06.019] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2012] [Revised: 06/13/2012] [Accepted: 06/15/2012] [Indexed: 11/18/2022]
Abstract
The majority of studies have characterized the tropism of HIV-1 subtype-B isolates, but little is known about the determinants of tropism in other subtypes. So, the goal of the present study was to genetically characterize the envelope of viral proteins in terms of co-receptor usage by analyzing 356 full-length env sequences derived from HIV-1 subtype-C infected individuals. The co-receptor usage of V3 sequences was inferred by using the Geno2Pheno and PSSM algorithms, and also analyzed to the "11/25 rule". All reported env sequences were also analyzed with regard to N-linked glycosylation sites, net charge and hydrophilicity, as well as the binomial correlation phi coefficient to assess covariation among gp120(V3) and gp41 signatures and the average linkage hierarchical agglomerative clustering were also performed. Among env sequences present in Los Alamos Database, 255 and 101 sequences predicted as CCR5 and CXCR4 were selected, respectively. The classical V3 signatures at positions 11 and 25, and other specific V3 and gp41 amino acid changes were found statistically associated with different co-receptor usage. Furthermore, several statistically significant associations between V3 and gp41 signatures were also observed. The dendrogram topology showed a cluster associated with CCR5-usage composed by five gp41 mutated positions, A22V, R133M, E136G, N140L, and N166Q that clustered with T2V(V3) and G24T(V3) (bootstrap=1). Conversely, a heterogeneous cluster with CXCR4-usage, involving S11GR(V3), 13-14insIG/LG(V3), P16RQ(V3), Q18KR(V3), F20ILV(V3), D25KRQ(V3), Q32KR(V3) along with A30T(gp41), S107N(gp41), D148E(gp41), A189S(gp41) was identified (bootstrap=0.86). Our results show that as observed for HIV-1 subtype-B, also in subtype-C specific and different gp41 and gp120V3 amino acid changes are associated individually or together with CXCR4 and/or CCR5 usage. These findings strengthen previous observations that determinants of tropism may also reside in the gp41 protein.
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Affiliation(s)
- Salvatore Dimonte
- University of Rome Tor Vergata, Via Montpellier 1, 00133 Rome, Italy.
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Gutiérrez F, Rodríguez JC, García F, Poveda E. [Methods for determination of HIV tropism and their clinical use]. Enferm Infecc Microbiol Clin 2012; 29 Suppl 5:45-50. [PMID: 22305669 DOI: 10.1016/s0213-005x(11)70043-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Determination of HIV-1 tropism is mandatory before using CCR5 antagonists in clinical practice. One drug of this class, maraviroc, has been approved for the treatment of HIV infection. The phenotypic assay, TrofileTM, was clinically validated in the clinical development program of maraviroc and has been widely used to select candidates for maraviroc therapy. Phenotypic tests, however, have the disadvantage of being complex, are costly and time-consuming, and their accessibility is limited, which hampers their routine use in clinical diagnosis. Genotypic assays, based on sequencing the third hypervariable (V3 loop) of the viral gene env, interpreted according to various genotypic bioinformatic tools, such as geno2pheno and PSSM, are faster and cheaper than phenotypic assays, and are also more accessible. In retrospective analyses of the maraviroc pivotal trials, genotypic methods using either conventional ("bulk") or deep-sequencing technology predicted virologic response to maraviroc similarly to phenotypic assays and are now included within several European recommendations to guide the clinical use of CCR5 antagonists.
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Affiliation(s)
- Félix Gutiérrez
- Servicio de Enfermedades Infecciosas, Hospital General Universitario de Elche, Alicante, Departamento de Medicina, Universidad Miguel Hernández, Alicante, España.
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