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Yu Y, Feng Y, Zhou Z, Li K, Hu X, Liao L, Xing H, Shao Y. Substitution of gp120 C4 region compensates for V3 loss-of-fitness mutations in HIV-1 CRF01_AE co-receptor switching. Emerg Microbes Infect 2023; 12:e2169196. [PMID: 36647730 PMCID: PMC9980400 DOI: 10.1080/22221751.2023.2169196] [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] [Indexed: 01/18/2023]
Abstract
HIV-1 infection is mediated by a viral envelope subsequently binding to CD4 receptor and two main coreceptors, CCR5 (R5) for primary infection and CXCR4 (X4) in chronic infection. Switching from R5 to X4 tropism in HIV-1 infection is associated with increased viral pathogenesis and disease progression. The coreceptor switching is mainly due to variations in the V3 loop, while the mechanism needs to be further elucidated. We systematically studied the determinant for HIV-1 coreceptor switching by substitution of the genes from one R5 and one X4 pseudoviruses. The study results in successfully constructing two panels of chimeric viruses of R5 to X4 forward and X4 to R5 reverse switching. The determinants for tropism switching are the combined substitution of the V3 loop and C4 region of the HIV-1 envelope. The possible mechanism of the tropism switching includes two components, the V3 loop to enable the viral envelope binding to the newly switched coreceptor and the C4 region, to compensate for the loss of fitness caused by deleterious V3 loop mutations to maintain the overall viral viability. The combined C4 and V3 substitution showed at least an eightfold increase in replication activity compared with the pseudovirus with only V3 loop substitution. The site-directed mutations of N425R and S440-I442 with charged amino acids could especially increase viral activity. This study could facilitate HIV-1 phenotype surveillance and select right entry inhibitor, CCR5 or CXCR4 antagonists, for antiviral therapy.
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Affiliation(s)
- Yueyang Yu
- School of Medicine, Nankai University, Tianjin, People’s Republic of China
| | - Yi Feng
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Zehua Zhou
- School of Medicine, Nankai University, Tianjin, People’s Republic of China
| | - Kang Li
- School of Medicine, Nankai University, Tianjin, People’s Republic of China
| | - Xiaoyan Hu
- School of Medicine, Nankai University, Tianjin, People’s Republic of China
| | - Lingjie Liao
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Hui Xing
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Yimig Shao
- School of Medicine, Nankai University, Tianjin, People’s Republic of China,State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China,Changping Laboratory, Beijing, People’s Republic of China, Yimig Shao State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
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2
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Mangan RJ, Stamper L, Ohashi T, Eudailey JA, Go EP, Jaeger FH, Itell HL, Watts BE, Fouda GG, Erickson HP, Alam SM, Desaire H, Permar SR. Determinants of Tenascin-C and HIV-1 envelope binding and neutralization. Mucosal Immunol 2019; 12:1004-1012. [PMID: 30976088 PMCID: PMC6599478 DOI: 10.1038/s41385-019-0164-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 03/19/2019] [Accepted: 03/21/2019] [Indexed: 02/04/2023]
Abstract
Interactions between innate antiviral factors at mucosal surfaces and HIV-1 virions contribute to the natural inefficiency of HIV-1 transmission and are a platform to inform the development of vaccine and nonvaccine strategies to block mucosal HIV-1 transmission. Tenascin-C (TNC) is a large, hexameric extracellular matrix glycoprotein identified in breast milk and genital fluids that broadly neutralizes HIV-1 via interaction with the HIV-1 Envelope (Env) variable 3 (V3) loop. In this report, we characterize the specific determinants of the interaction between TNC and the HIV-1 Env. We observed that TNC binding and neutralization of HIV-1 is dependent on the TNC fibrinogen-like globe (fbg) and fibronectin-type III (fn) domains, oligomerization, and its newly-mapped glycan structure. Moreover, we observed that TNC-mediated neutralization is also dependent on Env V3 residues 321/322 and 326/327, which surround the IGDIR motif of the V3 loop, as well the N332 glycan, which is critical to the broadly neutralizing activity of glycan-dependent V3-specific antibodies such as PGT128. Our results demonstrate a striking parallel between innate and adaptive immune mechanisms of broad HIV neutralization and provide further insight into the host protein-virus interactions responsible for the natural inefficiency of mucosal HIV-1 transmission.
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Affiliation(s)
- Riley J. Mangan
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Lisa Stamper
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Tomoo Ohashi
- Department of Cell Biology, Duke University, Durham, NC, USA
| | - Joshua A. Eudailey
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Eden P. Go
- Department of Chemistry, University of Kansas, Lawrence, Kansas, USA
| | - Frederick H. Jaeger
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Hannah L. Itell
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Brian E. Watts
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Genevieve G. Fouda
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | | | - S. Munir Alam
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Heather Desaire
- Department of Chemistry, University of Kansas, Lawrence, Kansas, USA
| | - Sallie R. Permar
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA;,Department of Pediatrics, Duke University School of Medicine, Durham, NC, USA;,Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA,Address correspondence to Sallie R. Permar, MD., Ph.D.,
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3
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Morton SP, Phillips JB, Phillips JL. The Molecular Basis of pH-Modulated HIV gp120 Binding Revealed. Evol Bioinform Online 2019; 15:1176934319831308. [PMID: 30872918 PMCID: PMC6407167 DOI: 10.1177/1176934319831308] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2018] [Accepted: 12/17/2018] [Indexed: 01/31/2023] Open
Abstract
Decades of research has yet to provide a vaccine for HIV, the virus which causes AIDS. Recent theoretical research has turned attention to mucosa pH levels over systemic pH levels. Previous research in this field developed a computational approach for determining pH sensitivity that indicated higher potential for transmission at mucosa pH levels present during intercourse. The process was extended to incorporate a principal component analysis (PCA)-based machine learning technique for classification of gp120 proteins against a known transmitted variant called Biomolecular Electro-Static Indexing (BESI). The original process has since been extended to the residue level by a process we termed Electrostatic Variance Masking (EVM) and used in conjunction with BESI to determine structural differences present among various subspecies across Clades A1 and C. Results indicate that structures outside of the core selected by EVM may be responsible for binding affinity observed in many other studies and that pH modulation of select substructures indicated by EVM may influence specific regions of the viral envelope protein (Env) involved in protein-protein interactions.
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Affiliation(s)
- Scott P Morton
- Center for Computational Science, College of Basic and Applied Sciences, Middle Tennessee State University, Murfreesboro, TN, USA
| | | | - Joshua L Phillips
- Center for Computational Science, College of Basic and Applied Sciences, Middle Tennessee State University, Murfreesboro, TN, USA.,Department of Computer Science, College of Basic and Applied Sciences, Middle Tennessee State University, Murfreesboro, TN, USA
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4
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Vicenti I, Lai A, Giannini A, Boccuto A, Dragoni F, Saladini F, Zazzi M. Performance of Geno2Pheno[coreceptor] to infer coreceptor use in human immunodeficiency virus type 1 (HIV-1) subtype A. J Clin Virol 2018; 111:12-18. [PMID: 30594700 DOI: 10.1016/j.jcv.2018.12.007] [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] [Received: 08/21/2018] [Revised: 12/03/2018] [Accepted: 12/19/2018] [Indexed: 11/29/2022]
Abstract
BACKGROUND Assessment of human immunodeficiency virus type 1 (HIV-1) coreceptor usage is required prior to treatment with the CCR5 antagonist maraviroc to exclude the presence of CXCR4-using (X4) strains. Genotype-based interpretation systems are mostly designed on subtype B and have been reported to be less accurate for subtype A/CRF02_AG. OBJECTIVES To evaluate the performance of the widely used Geno2Pheno[coreceptor] (G2P[c]) algorithm for prediction of coreceptor usage with subtype A/CRF02_AG vs. subtype B. STUDY DESIGN Co-receptor tropism of 24 subtype A/CRF02_AG and 24 subtype B viruses was measured phenotypically by a homebrew single-cycle assay and genotypically by using G2P[c]. Samples with discrepant genotype-phenotype results were analyzed by next generation sequencing (NGS) and interpreted by the NGS Geno2Pheno algorithm (G2P[454]). RESULTS At 10% false positive rate (FPR), the G2P[c]/phenotype discordance rate was 12.5% (n = 3) for subtype A/CRF02_AG and 8.3% (n = 2) for subtype B. Minority X4 species escaping detection by bulk sequencing but documented by NGS explained the two subtype B and possibly one subtype A/CRF02_AG discordant case. The other two subtype A/CRF02_AG miscalled by G2P[c] could be explained by X4 overcalling at borderline FPR and/or by algorithm failure. DISCUSSION Our study did not demonstrate relevantly higher G2P[c] inaccuracy with subtype A/CRF02_AG with respect to subtype B. Genotype/phenotype discordances can be due to different reasons, including but not limited to, algorithm inaccuracy. Very large genotype/phenotype correlation panels are required to detect and explain the reason for any consistent difference in genotypic tropism prediction for subtype A/CRF02_AG vs. subtype B.
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Affiliation(s)
- Ilaria Vicenti
- Department of Medical Biotechnologies, University of Siena, Siena, Italy.
| | - Alessia Lai
- Department of Biomedical and Clinical Sciences L. Sacco, University of Milan, Milan, Italy
| | - Alessia Giannini
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Adele Boccuto
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Filippo Dragoni
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Francesco Saladini
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Maurizio Zazzi
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
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5
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Sojane K, Kangethe RT, Chang CC, Moosa MYS, Lewin SR, French MA, Ndung'u T. Individuals with HIV-1 Subtype C Infection and Cryptococcal Meningitis Exhibit Viral Genetic Intermixing of HIV-1 Between Plasma and Cerebrospinal Fluid and a High Prevalence of CXCR4-Using Variants. AIDS Res Hum Retroviruses 2018; 34:607-620. [PMID: 29658309 PMCID: PMC6314437 DOI: 10.1089/aid.2017.0209] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The genotypic properties of human immunodeficiency virus type 1 (HIV-1) subtype C in individuals presenting with cryptococcal meningitis (CM) are not well established. Employing single-genome amplification as well as bulk PCR, cloning and sequencing strategies, we evaluated the genetic properties of HIV-1 subtype C env in 16 antiretroviral therapy-naive study participants with CM. Eleven of the 16 participants had matched blood plasma and cerebrospinal fluid (CSF) evaluated, with the rest having either a plasma or CSF sample evaluated. Before antiretroviral therapy initiation, matched plasma and CSF-derived env sequences of all 11 participants displayed genetic intermixing between the two compartments. Overall, 7 of the 16 (∼43.8%) participants harbored CXCR4-using variants in plasma and/or CSF, according to coreceptor usage prediction algorithms. This study suggests that HIV-1 subtype C genetic intermixing between peripheral blood and the central nervous system is common in individuals presenting with CM, and that CXCR4 usage is present in one or both compartments in approximately 44% of individuals.
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Affiliation(s)
- Katlego Sojane
- 1 HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R Mandela School of Medicine, University of KwaZulu-Natal , Durban, South Africa
| | - Richard T Kangethe
- 1 HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R Mandela School of Medicine, University of KwaZulu-Natal , Durban, South Africa
| | - Christina C Chang
- 2 Department of Infectious Diseases, Alfred Hospital and Monash University , Melbourne, Australia
| | - Mahomed-Yunus S Moosa
- 3 Department of Infectious Diseases, King Edward VIII Hospital, University of KwaZulu-Natal , Durban, South Africa
| | - Sharon R Lewin
- 2 Department of Infectious Diseases, Alfred Hospital and Monash University , Melbourne, Australia
- 4 The Peter Doherty Institute for Infection and Immunity, University of Melbourne and Royal Melbourne Hospital , Melbourne, Australia
| | - Martyn A French
- 5 Medical School and School of Biomedical Sciences, University of Western Australia , Perth, Australia
- 6 Department of Clinical Immunology, Royal Perth Hospital and PathWest Laboratory Medicine , Perth, Australia
| | - Thumbi Ndung'u
- 1 HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R Mandela School of Medicine, University of KwaZulu-Natal , Durban, South Africa
- 7 Africa Health Research Institute , Durban, South Africa
- 8 Ragon Institute of MGH, MIT and Harvard University , Cambridge, Massachusetts
- 9 Max Planck Institute for Infection Biology , Berlin, Germany
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6
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Maternal Binding and Neutralizing IgG Responses Targeting the C-Terminal Region of the V3 Loop Are Predictive of Reduced Peripartum HIV-1 Transmission Risk. J Virol 2017; 91:JVI.02422-16. [PMID: 28202762 DOI: 10.1128/jvi.02422-16] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Accepted: 02/08/2017] [Indexed: 01/07/2023] Open
Abstract
The development of an effective maternal HIV-1 vaccine that could synergize with antiretroviral therapy (ART) to eliminate pediatric HIV-1 infection will require the characterization of maternal immune responses capable of blocking transmission of autologous HIV to the infant. We previously determined that maternal plasma antibody binding to linear epitopes within the variable loop 3 (V3) region of HIV envelope (Env) and neutralizing responses against easy-to-neutralize tier 1 viruses were associated with reduced risk of peripartum HIV infection in the historic U.S. Woman and Infant Transmission Study (WITS) cohort. Here, we defined the fine specificity and function of the potentially protective maternal V3-specific IgG antibodies associated with reduced peripartum HIV transmission risk in this cohort. The V3-specific IgG binding that predicted low risk of mother-to-child-transmission (MTCT) was dependent on the C-terminal flank of the V3 crown and particularly on amino acid position 317, a residue that has also been associated with breakthrough transmission in the RV144 vaccine trial. Remarkably, the fine specificity of potentially protective maternal plasma V3-specific tier 1 virus-neutralizing responses was dependent on the same region in the V3 loop. Our findings suggest that MTCT risk is associated with neutralizing maternal IgG that targets amino acid residues in the C-terminal region of the V3 loop crown, suggesting the importance of the region in immunogen design for maternal vaccines to prevent MTCT.IMPORTANCE Efforts to curb HIV-1 transmission in pediatric populations by antiretroviral therapy (ART) have been highly successful in both developed and developing countries. However, more than 150,000 infants continue to be infected each year, likely due to a combination of late maternal HIV diagnosis, lack of ART access or adherence, and drug-resistant viral strains. Defining the fine specificity of maternal humoral responses that partially protect against MTCT of HIV is required to inform the development of a maternal HIV vaccine that will enhance these responses during pregnancy. In this study, we identified amino acid residues targeted by potentially protective maternal V3-specific IgG binding and neutralizing responses, localizing the potentially protective response in the C-terminal region of the V3 loop crown. Our findings have important implications for the design of maternal vaccination strategies that could synergize with ART during pregnancy to achieve the elimination of pediatric HIV infections.
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7
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Learning the Relationship between the Primary Structure of HIV Envelope Glycoproteins and Neutralization Activity of Particular Antibodies by Using Artificial Neural Networks. Int J Mol Sci 2016; 17:ijms17101710. [PMID: 27727189 PMCID: PMC5085742 DOI: 10.3390/ijms17101710] [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: 08/13/2016] [Revised: 09/26/2016] [Accepted: 10/03/2016] [Indexed: 12/02/2022] Open
Abstract
The dependency between the primary structure of HIV envelope glycoproteins (ENV) and the neutralization data for given antibodies is very complicated and depends on a large number of factors, such as the binding affinity of a given antibody for a given ENV protein, and the intrinsic infection kinetics of the viral strain. This paper presents a first approach to learning these dependencies using an artificial feedforward neural network which is trained to learn from experimental data. The results presented here demonstrate that the trained neural network is able to generalize on new viral strains and to predict reliable values of neutralizing activities of given antibodies against HIV-1.
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8
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Gasser R, Hamoudi M, Pellicciotta M, Zhou Z, Visdeloup C, Colin P, Braibant M, Lagane B, Negroni M. Buffering deleterious polymorphisms in highly constrained parts of HIV-1 envelope by flexible regions. Retrovirology 2016; 13:50. [PMID: 27473399 PMCID: PMC4967302 DOI: 10.1186/s12977-016-0285-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Accepted: 07/18/2016] [Indexed: 02/07/2023] Open
Abstract
Background Covariation is an essential process that leads to coevolution of parts of proteins and genomes. In organisms subject to strong selective pressure, coevolution is central to keep the balance between the opposite requirements of antigenic variation and retention of functionality. Being the viral component most exposed to the external environment, the HIV-1 glycoprotein gp120 constitutes the main target of the immune response. Accordingly its more external portions are characterised by extensive sequence heterogeneity fostering constant antigenic variation. Results We report that a single polymorphism, present at the level of the viral population in the conserved internal region C2, was sufficient to totally abolish Env functionality when introduced in an exogenous genetic context. The prominent defect of the non-functional protein is a block occurring after recognition of the co-receptor CCR5, likely due to an interference with the subsequent conformational changes that lead to membrane fusion. We also report that the presence of compensatory polymorphisms at the level of the external and hypervariable region V3 fully restored the functionality of the protein. The functional revertant presents different antigenic profiles and sensitivity to the entry inhibitor TAK 779. Conclusions Our data suggest that variable regions, besides harbouring intrinsic extensive antigenic diversity, can also contribute to sequence diversification in more structurally constrained parts of the gp120 by buffering the deleterious effect of polymorphisms, further increasing the genetic flexibility of the protein and the antigenic repertoire of the viral population.
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Affiliation(s)
- Romain Gasser
- Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC, 15 rue René Descartes, 67084, Strasbourg, France
| | - Meriem Hamoudi
- Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC, 15 rue René Descartes, 67084, Strasbourg, France.,U1016, UMR 8104, INSERM-CNRS, Institut Cochin, Université Paris Descartes, Paris, France
| | - Martina Pellicciotta
- Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC, 15 rue René Descartes, 67084, Strasbourg, France
| | - Zhicheng Zhou
- INSERM U1108, Viral Pathogenesis Unit, Department of Virology, Institut Pasteur, Paris, France
| | | | - Philippe Colin
- INSERM U1108, Viral Pathogenesis Unit, Department of Virology, Institut Pasteur, Paris, France
| | | | - Bernard Lagane
- INSERM U1108, Viral Pathogenesis Unit, Department of Virology, Institut Pasteur, Paris, France
| | - Matteo Negroni
- Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC, 15 rue René Descartes, 67084, Strasbourg, France.
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9
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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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10
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Cashin K, Gray LR, Harvey KL, Perez-Bercoff D, Lee GQ, Sterjovski J, Roche M, Demarest JF, Drummond F, Harrigan PR, Churchill MJ, Gorry PR. Reliable genotypic tropism tests for the major HIV-1 subtypes. Sci Rep 2015; 5:8543. [PMID: 25712827 PMCID: PMC4894445 DOI: 10.1038/srep08543] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 01/23/2015] [Indexed: 01/21/2023] Open
Abstract
Over the past decade antiretroviral drugs have dramatically improved the prognosis for HIV-1 infected individuals, yet achieving better access to vulnerable populations remains a challenge. The principal obstacle to the CCR5-antagonist, maraviroc, from being more widely used in anti-HIV-1 therapy regimens is that the pre-treatment genotypic "tropism tests" to determine virus susceptibility to maraviroc have been developed primarily for HIV-1 subtype B strains, which account for only 10% of infections worldwide. We therefore developed PhenoSeq, a suite of HIV-1 genotypic tropism assays that are highly sensitive and specific for establishing the tropism of HIV-1 subtypes A, B, C, D and circulating recombinant forms of subtypes AE and AG, which together account for 95% of HIV-1 infections worldwide. The PhenoSeq platform will inform the appropriate use of maraviroc and future CCR5 blocking drugs in regions of the world where non-B HIV-1 predominates, which are burdened the most by the HIV-1 pandemic.
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Affiliation(s)
- Kieran Cashin
- 1] Center for Biomedical Research, Burnet Institute, Melbourne, Australia 3004 [2] Department of Microbiology and Immunology, University of Melbourne, Parkville, Australia 3010
| | - Lachlan R Gray
- 1] Center for Biomedical Research, Burnet Institute, Melbourne, Australia 3004 [2] Department of Infectious Diseases, Monash University, Melbourne, Australia 3800
| | - Katherine L Harvey
- 1] Center for Biomedical Research, Burnet Institute, Melbourne, Australia 3004 [2] Department of Microbiology and Immunology, University of Melbourne, Parkville, Australia 3010
| | | | - Guinevere Q Lee
- BC Centre for Excellence in HIV/AIDS, Vancouver, Canada Y6Z 1Y6
| | - Jasminka Sterjovski
- 1] Center for Biomedical Research, Burnet Institute, Melbourne, Australia 3004 [2] Department of Infectious Diseases, Monash University, Melbourne, Australia 3800
| | - Michael Roche
- 1] Center for Biomedical Research, Burnet Institute, Melbourne, Australia 3004 [2] Department of Infectious Diseases, Monash University, Melbourne, Australia 3800
| | - James F Demarest
- ViiV Healthcare, Research Triangle Park, North Carolina, USA 27709-3398
| | | | | | - Melissa J Churchill
- 1] Center for Biomedical Research, Burnet Institute, Melbourne, Australia 3004 [2] Department of Medicine, Monash University, Melbourne, Australia 3800 [3] Department of Microbiology, Monash University, Melbourne, Australia 3800
| | - Paul R Gorry
- 1] Center for Biomedical Research, Burnet Institute, Melbourne, Australia 3004 [2] Department of Microbiology and Immunology, University of Melbourne, Parkville, Australia 3010 [3] Department of Infectious Diseases, Monash University, Melbourne, Australia 3800 [4] School of Applied Sciences, College of Science, Engineering and Health, RMIT University, Melbourne, Australia 3001
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