1
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Claireaux M, Robinot R, Kervevan J, Patgaonkar M, Staropoli I, Brelot A, Nouël A, Gellenoncourt S, Tang X, Héry M, Volant S, Perthame E, Avettand-Fenoël V, Buchrieser J, Cokelaer T, Bouchier C, Ma L, Boufassa F, Hendou S, Libri V, Hasan M, Zucman D, de Truchis P, Schwartz O, Lambotte O, Chakrabarti LA. Low CCR5 expression protects HIV-specific CD4+ T cells of elite controllers from viral entry. Nat Commun 2022; 13:521. [PMID: 35082297 PMCID: PMC8792008 DOI: 10.1038/s41467-022-28130-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 01/10/2022] [Indexed: 11/09/2022] Open
Abstract
HIV elite controllers maintain a population of CD4 + T cells endowed with high avidity for Gag antigens and potent effector functions. How these HIV-specific cells avoid infection and depletion upon encounter with the virus remains incompletely understood. Ex vivo characterization of single Gag-specific CD4 + T cells reveals an advanced Th1 differentiation pattern in controllers, except for the CCR5 marker, which is downregulated compared to specific cells of treated patients. Accordingly, controller specific CD4 + T cells show decreased susceptibility to CCR5-dependent HIV entry. Two controllers carried biallelic mutations impairing CCR5 surface expression, indicating that in rare cases CCR5 downregulation can have a direct genetic cause. Increased expression of β-chemokine ligands upon high-avidity antigen/TCR interactions contributes to autocrine CCR5 downregulation in controllers without CCR5 mutations. These findings suggest that genetic and functional regulation of the primary HIV coreceptor CCR5 play a key role in promoting natural HIV control.
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Affiliation(s)
- Mathieu Claireaux
- Virus and Immunity Unit, Institut Pasteur, Université de Paris, Paris, France.,CNRS UMR3569, Paris, France
| | - Rémy Robinot
- Virus and Immunity Unit, Institut Pasteur, Université de Paris, Paris, France.,CNRS UMR3569, Paris, France
| | - Jérôme Kervevan
- Virus and Immunity Unit, Institut Pasteur, Université de Paris, Paris, France.,CNRS UMR3569, Paris, France
| | - Mandar Patgaonkar
- Virus and Immunity Unit, Institut Pasteur, Université de Paris, Paris, France.,CNRS UMR3569, Paris, France
| | - Isabelle Staropoli
- Virus and Immunity Unit, Institut Pasteur, Université de Paris, Paris, France.,CNRS UMR3569, Paris, France
| | - Anne Brelot
- Virus and Immunity Unit, Institut Pasteur, Université de Paris, Paris, France.,CNRS UMR3569, Paris, France
| | - Alexandre Nouël
- Virus and Immunity Unit, Institut Pasteur, Université de Paris, Paris, France.,CNRS UMR3569, Paris, France
| | - Stacy Gellenoncourt
- Virus and Immunity Unit, Institut Pasteur, Université de Paris, Paris, France.,CNRS UMR3569, Paris, France
| | - Xian Tang
- Virus and Immunity Unit, Institut Pasteur, Université de Paris, Paris, France.,CNRS UMR3569, Paris, France
| | - Mélanie Héry
- Virus and Immunity Unit, Institut Pasteur, Université de Paris, Paris, France.,CNRS UMR3569, Paris, France
| | - Stevenn Volant
- Bioinformatics and Biostatistics Hub, Department of Computational Biology, Institut Pasteur, Université de Paris, Paris, France
| | - Emeline Perthame
- Bioinformatics and Biostatistics Hub, Department of Computational Biology, Institut Pasteur, Université de Paris, Paris, France
| | - Véronique Avettand-Fenoël
- AP-HP Hôpital Necker-Enfants Malades, Laboratoire de Microbiologie clinique, Paris, France.,CNRS 8104, INSERM U1016, Université Paris Descartes, Sorbonne Paris Cité, Faculté de Médecine, Paris, France
| | - Julian Buchrieser
- Virus and Immunity Unit, Institut Pasteur, Université de Paris, Paris, France.,CNRS UMR3569, Paris, France
| | - Thomas Cokelaer
- Bioinformatics and Biostatistics Hub, Department of Computational Biology, Institut Pasteur, Université de Paris, Paris, France.,Biomics Platform, C2RT, Institut Pasteur, Université de Paris, Paris, France
| | - Christiane Bouchier
- Biomics Platform, C2RT, Institut Pasteur, Université de Paris, Paris, France
| | - Laurence Ma
- Biomics Platform, C2RT, Institut Pasteur, Université de Paris, Paris, France
| | - Faroudy Boufassa
- INSERM U1018, Center for Research in Epidemiology and Population Health (CESP), Le Kremlin-Bicêtre, France
| | - Samia Hendou
- INSERM U1018, Center for Research in Epidemiology and Population Health (CESP), Le Kremlin-Bicêtre, France
| | - Valentina Libri
- Cytometry and Biomarkers (CB UTechS), Translational Research Center, Institut Pasteur, Université de Paris, Paris, France
| | - Milena Hasan
- Cytometry and Biomarkers (CB UTechS), Translational Research Center, Institut Pasteur, Université de Paris, Paris, France
| | | | - Pierre de Truchis
- AP-HP, Infectious and Tropical Diseases Department, Raymond Poincaré Hospital, Garches, France
| | - Olivier Schwartz
- Virus and Immunity Unit, Institut Pasteur, Université de Paris, Paris, France.,CNRS UMR3569, Paris, France
| | - Olivier Lambotte
- INSERM U1184, Université Paris Sud, CEA, Center for Immunology of Viral Infections and Autoimmune Diseases, Le Kremlin-Bicêtre, France.,AP-HP, Department of Internal Medicine and Clinical Immunology, University Hospital Paris Sud, Le Kremlin-Bicêtre, France
| | - Lisa A Chakrabarti
- Virus and Immunity Unit, Institut Pasteur, Université de Paris, Paris, France. .,CNRS UMR3569, Paris, France.
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Wang H, Li Y, Li Y, Li B, Zhu X, Yan D, Li M, Wu W, Sun M, Yang R. Variations in Env at amino acids 328 and 330 affect HIV-1 replicative fitness and entry inhibitor sensitivity. Virus Res 2021; 299:198424. [PMID: 33862046 DOI: 10.1016/j.virusres.2021.198424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 04/09/2021] [Accepted: 04/10/2021] [Indexed: 11/26/2022]
Abstract
While the variations in the HIV-1 Env V3 loop have been the focus of much research to explore its functional effect, how specific mutations of certain amino acids in the V3 loop affect viral fitness remains unclear. In this study, we evaluated a series of natural polymorphisms at positions 328 and 330 with different combinations of adjacent glycosylation sites in the HIV-1 subtype B backbone to address their role in replicative fitness and sensitivity to entry inhibitors based on analysis of env sequence frequency at the population level. Pairwise growth competition experiment showed that wild-type virus with major consensus amino acids obviously had higher replicative fitness (P < 0.001). A change at position 328 to a less frequently occurring amino acid, K, together with a mutated N332 glycosylation site harbored lower fitness and became more sensitive to coreceptor antagonists (AMD3100), fusion inhibitors (T20) and sCD4. A change at position 330 to a less frequently occurring amino acid, Y, together with a mutated N332 glycosylation site resulted in higher fitness and less sensitivity to entry inhibitors (T20, AMD3100, and sCD4), and viruses containing both changes showed intermediate activity. It seems that the H330Y mutation compensated for the reduced replicative capacity caused by the Q328 K mutation. Moreover, viruses that showed lower replicative fitness also exhibited slower entry kinetics, lower levels of replication intermediates and protein packaging, and a lower ability to replicate in primary peripheral blood mononuclear cells (PBMCs). The findings highlight the functional effect of variations at 328 and 330 in the V3 loop on replicative fitness and may benefit HIV-1 treatment by helping predict the sensitivity to entry inhibitors.
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Affiliation(s)
- Hongye Wang
- Institute of Medical Biology, Pecking Union Medical College and Chinese Academy of Medical Sciences, Kunming, 650118, China
| | - Yang Li
- Unit of HIV Molecular Epidemiology and Virology, State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Ya Li
- Department of Clinical Laboratory, Yunnan Key Laboratory of Laboratory Medicine, Yunnan Innovation Team of Clinical Laboratory and Diagnosis, the First Affiliated Hospital of Kunming Medical University, Kunming, 650032, China
| | - Bingxiang Li
- Institute of Medical Biology, Pecking Union Medical College and Chinese Academy of Medical Sciences, Kunming, 650118, China
| | - Xiaoyong Zhu
- Institute of Medical Biology, Pecking Union Medical College and Chinese Academy of Medical Sciences, Kunming, 650118, China
| | - Dongshan Yan
- Institute of Medical Biology, Pecking Union Medical College and Chinese Academy of Medical Sciences, Kunming, 650118, China
| | - Mingyu Li
- Department of Clinical Laboratory, Yunnan Key Laboratory of Laboratory Medicine, Yunnan Innovation Team of Clinical Laboratory and Diagnosis, the First Affiliated Hospital of Kunming Medical University, Kunming, 650032, China
| | - Wenying Wu
- Unit of HIV Molecular Epidemiology and Virology, State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Ming Sun
- Institute of Medical Biology, Pecking Union Medical College and Chinese Academy of Medical Sciences, Kunming, 650118, China.
| | - Rongge Yang
- Unit of HIV Molecular Epidemiology and Virology, State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China.
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3
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Caetano DG, Côrtes FH, Bello G, de Azevedo SSD, Hoagland B, Villela LM, Grinsztejn B, Veloso VG, Guimarães ML, Morgado MG. A case report of HIV-1 superinfection in an HIV controller leading to loss of viremia control: a retrospective of 10 years of follow-up. BMC Infect Dis 2019; 19:588. [PMID: 31277590 PMCID: PMC6612226 DOI: 10.1186/s12879-019-4229-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 06/26/2019] [Indexed: 12/03/2022] Open
Abstract
Background HIV controllers (HICs) are a rare group of HIV-1-infected individuals able to naturally control viral replication. Several studies have identified the occurrence of HIV dual infections in seropositive individuals leading to disease progression. In HICs, however, dual infections with divergent outcomes in pathogenesis have been described. Case presentation Here, we present a case report of a HIC diagnosed in late 1999 who displayed stable CD4+ T cell levels and low plasmatic viral load across 12 years of follow-up. In early 2013, the patient started to present an increase in viral load, reaching a peak of 10,000 copies/ml in early 2014, followed by an oscillation of viremia at moderate levels in the following years. The genetic diversity of env proviral quasispecies from peripheral blood mononuclear cells (PBMCs) was studied by single genome amplification (SGA) at six timepoints across 2009–2017. Phylogenetic analyses of env sequences from 2009 and 2010 samples showed the presence of a single subtype B variant (called B1). Analyses of sequences from 2011 and after revealed an additional subtype B variant (called B2) and a subsequent dominance shift in the proviral quasispecies frequencies, with the B2 variant becoming the most frequent from 2014 onwards. Latent syphilis related to unprotected sexual intercourse was diagnosed a year before the first detection of B2, evidencing risk behavior and supporting the superinfection hypothesis. Immunologic analyses revealed an increase in CD8+ and CD4+ T cell immune activation following viremia increase and minor T cell subset alterations during follow-up. HIV-specific T cell responses remained low throughout the follow-up period. Conclusions Altogether, these results show that loss of viremia control in the HIC was associated with superinfection. These data alert to the negative consequences of reinfection on HIV pathogenesis, even in patients with a long history of viremia control and an absence of disease progression, reinforcing the need for continued use of adequate prevention strategies.
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Affiliation(s)
- Diogo Gama Caetano
- Laboratório de Aids e Imunologia Molecular, Instituto Oswaldo Cruz (IOC) -FIOCRUZ, Av. Brasil 4365, Rio de Janeiro, RJ, 21045-900, Brazil
| | - Fernanda Heloise Côrtes
- Laboratório de Aids e Imunologia Molecular, Instituto Oswaldo Cruz (IOC) -FIOCRUZ, Av. Brasil 4365, Rio de Janeiro, RJ, 21045-900, Brazil.
| | - Gonzalo Bello
- Laboratório de Aids e Imunologia Molecular, Instituto Oswaldo Cruz (IOC) -FIOCRUZ, Av. Brasil 4365, Rio de Janeiro, RJ, 21045-900, Brazil
| | - Suwellen Sardinha Dias de Azevedo
- Laboratório de Aids e Imunologia Molecular, Instituto Oswaldo Cruz (IOC) -FIOCRUZ, Av. Brasil 4365, Rio de Janeiro, RJ, 21045-900, Brazil
| | - Brenda Hoagland
- Instituto Nacional de Infectologia Evandro Chagas (INI), Laboratório de Pesquisa clínica em DST e Aids, Rio de Janeiro, Brazil
| | - Larissa Melo Villela
- Instituto Nacional de Infectologia Evandro Chagas (INI), Laboratório de Pesquisa clínica em DST e Aids, Rio de Janeiro, Brazil
| | - Beatriz Grinsztejn
- Instituto Nacional de Infectologia Evandro Chagas (INI), Laboratório de Pesquisa clínica em DST e Aids, Rio de Janeiro, Brazil
| | - Valdiléa Gonçalves Veloso
- Instituto Nacional de Infectologia Evandro Chagas (INI), Laboratório de Pesquisa clínica em DST e Aids, Rio de Janeiro, Brazil
| | - Monick Lindenmeyer Guimarães
- Laboratório de Aids e Imunologia Molecular, Instituto Oswaldo Cruz (IOC) -FIOCRUZ, Av. Brasil 4365, Rio de Janeiro, RJ, 21045-900, Brazil
| | - Mariza Gonçalves Morgado
- Laboratório de Aids e Imunologia Molecular, Instituto Oswaldo Cruz (IOC) -FIOCRUZ, Av. Brasil 4365, Rio de Janeiro, RJ, 21045-900, Brazil
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4
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Ghosn J, Bayan T, Meixenberger K, Tran L, Frange P, d'Arminio Monforte A, Zangerle R, de Mendoza C, Krastinova E, Porter K, Meyer L, Chaix ML. CD4 T cell decline following HIV seroconversion in individuals with and without CXCR4-tropic virus. J Antimicrob Chemother 2018; 72:2862-2868. [PMID: 29091208 DOI: 10.1093/jac/dkx247] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 06/22/2017] [Indexed: 11/12/2022] Open
Abstract
Background The natural clinical and immunological courses following HIV seroconversion with CXCR4-tropic or dual-mixed (X4/DM) viruses are controversial. We compared spontaneous immunological outcome in patients harbouring an X4/DM virus at the time of seroconversion with those harbouring a CCR5-tropic (R5) virus. Methods Data were included from patients participating in CASCADE, a large cohort collaboration of HIV seroconverters, with ≥2 years of follow-up since seroconversion. The HIV envelope gene was sequenced from frozen plasma samples collected at enrolment, and HIV tropism was determined using Geno2Pheno (false-positive rate 10%). The spontaneous CD4 T cell evolution was compared by modelling CD4 kinetics using linear mixed-effects models with random intercept and random slope. Results A total of 1387 patients were eligible. Median time between seroconversion and enrolment was 1 month (range 0-3). At enrolment, 202 of 1387 (15%) harboured an X4/DM-tropic virus. CD4 decrease slopes were not significantly different according to HIV-1 tropism during the first 30 months after seroconversion. No marked change in these results was found after adjusting for age, year of seroconversion and baseline HIV viral load. Time to antiretroviral treatment initiation was not statistically different between patients harbouring an R5 (20.76 months) and those harbouring an X4/DM-tropic virus (22.86 months, logrank test P = 0.32). Conclusions: In this large cohort collaboration, 15% of the patients harboured an X4/DM virus close to HIV seroconversion. Patients harbouring X4/DM-tropic viruses close to seroconversion did not have an increased risk of disease progression, estimated by the decline in CD4 T cell count or time to combined ART initiation.
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Affiliation(s)
- Jade Ghosn
- Université Paris Descartes, Sorbonne Paris Cité, Paris, France.,Inserm UMR-S 1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Université Pierre et Marie Curie, Paris, France
| | - Tatiana Bayan
- Inserm, CESP Centre for Research in Epidemiology and Population Health, U1018, HIV Epidemiology, Le Kremlin-Bicêtre, F-94276, France.,Univ Paris-Sud, UMRS 1018, Faculté de Médecine Paris-Sud, Le Kremlin-Bicêtre, F-94276, France
| | | | - Laurent Tran
- Inserm, CESP Centre for Research in Epidemiology and Population Health, U1018, HIV Epidemiology, Le Kremlin-Bicêtre, F-94276, France.,Univ Paris-Sud, UMRS 1018, Faculté de Médecine Paris-Sud, Le Kremlin-Bicêtre, F-94276, France.,AP-HP, Hopital Bicêtre, Epidemiology and Public Health Service, Le Kremlin Bicêtre, F-94276, France
| | - Pierre Frange
- Université Paris Descartes, Sorbonne Paris Cité, Paris, France.,AP-HP, Laboratoire de Microbiologie Clinique, Hôpital Universitaire Necker-Enfants Malades, Paris, France
| | - Antonella d'Arminio Monforte
- Infectious Diseases, University of Milan, San Paolo Hospital, Milano, Italy and Health Sciences, University of Milan, San Paolo Hospital, Milano, Italy
| | | | - Carmen de Mendoza
- Research Institute and University Hospital Puerta de Hierro, Majahonda, Madrid, Spain
| | - Evguenia Krastinova
- AP-HP, Hopital Bicêtre, Epidemiology and Public Health Service, Le Kremlin Bicêtre, F-94276, France
| | - Kholoud Porter
- Medical Research Council Clinical Trials Unit, University College London, London, UK
| | - Laurence Meyer
- Inserm, CESP Centre for Research in Epidemiology and Population Health, U1018, HIV Epidemiology, Le Kremlin-Bicêtre, F-94276, France.,Univ Paris-Sud, UMRS 1018, Faculté de Médecine Paris-Sud, Le Kremlin-Bicêtre, F-94276, France.,AP-HP, Hopital Bicêtre, Epidemiology and Public Health Service, Le Kremlin Bicêtre, F-94276, France
| | - Marie-Laure Chaix
- INSERM U941, Université Paris Diderot, Paris, France.,APHP, Laboratoire de Virologie, Hôpital Saint Louis, Paris, France
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5
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Soulie C, Morand-Joubert L, Cottalorda J, Charpentier C, Bellecave P, Le Guen L, Yerly S, Montes B, Fafi-Kremer S, Dina J, Avettand-Fenoel V, Amiel C, Roussel C, Pallier C, Zafilaza K, Sayon S, Signori-Schmuck A, Mirand A, Trabaud MA, Berger S, Calvez V, Marcelin AG. Performance of genotypic algorithms for predicting tropism for HIV-1 CRF01_AE recombinant. J Clin Virol 2018; 99-100:57-60. [PMID: 29331843 DOI: 10.1016/j.jcv.2017.12.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Revised: 10/04/2017] [Accepted: 12/28/2017] [Indexed: 11/19/2022]
Abstract
OBJECTIVES There is no consensus about the performances of genotypic rules for predicting HIV-1 non-B subtype tropism. Three genotypic methods were compared for CRF01_AE HIV-1 tropism determination. METHODS The V3 env region of 207 HIV-1 CRF01_AE and 178 B subtypes from 17 centers in France and 1 center in Switzerland was sequenced. Tropism was determined by Geno2Pheno algorithm with false positive rate (FPR) 5% or 10%, the 11/25 rule or the combined criteria of the 11/25, net charge rule and NXT/S mutations. RESULTS Overall, 72.5%, 59.4%, 86.0%, 90.8% of the 207 HIV-1 CRF01_AE were R5-tropic viruses determined by Geno2pheno FPR5%, Geno2pheno FPR10%, the combined criteria and the 11/25 rule, respectively. A concordance of 82.6% was observed between Geno2pheno FPR5% and the combined criteria for CRF01_AE. The results were nearly similar for the comparison between Geno2pheno FPR5% and the 11/25 rule. More mismatches were observed when Geno2pheno was used with the FPR10%. Neither HIV viral load, nor current or nadir CD4 was associated with the discordance rate between the different algorithms. CONCLUSION Geno2pheno predicted more X4-tropic viruses for this set of CRF01_AE sequences than the combined criteria or the 11/25 rule alone. For a conservative approach, Geno2pheno FPR5% seems to be a good compromise to predict CRF01_AE tropism.
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Affiliation(s)
- C Soulie
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, Institut Pierre Louis d'épidémiologie et de Santé Publique (IPLESP UMRS 1136), Paris, France; AP-HP, Hôpital Pitié-Salpêtrière, Service de Virologie, Paris, France.
| | - L Morand-Joubert
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, Institut Pierre Louis d'épidémiologie et de Santé Publique (IPLESP UMRS 1136), Paris, France; AP-HP, Hôpital Saint Antoine, Service de Virologie, Paris, France
| | | | - C Charpentier
- IAME, UMR 1137-Université Paris Diderot, Sorbonne Paris Cité, INSERM, AP-HP, Hôpital Bichat, Laboratoire de Virologie, Paris, France
| | - P Bellecave
- CHU de Bordeaux, Laboratoire de Virologie, Univ. Bordeaux, CNRS UMR 5234, Bordeaux, France
| | - L Le Guen
- Laboratoire de virologie, CHU, Nantes, France
| | - S Yerly
- Laboratory of Virology, Geneva University Hospitals, Switzerland
| | - B Montes
- Laboratoire de Virologie, CHU, Montpellier, France
| | | | - J Dina
- Laboratoire de virologie, CHU, Caen, France
| | - V Avettand-Fenoel
- AP-HP, Laboratoire de Virologie, Hôpital Necker, Paris, France; Université Paris Descartes, Sorbonne Paris Cité, Faculté de Médecine, EA7327, France
| | - C Amiel
- AP-HP, Laboratoire de Virologie, Hôpital Tenon, Paris, France
| | | | | | - K Zafilaza
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, Institut Pierre Louis d'épidémiologie et de Santé Publique (IPLESP UMRS 1136), Paris, France; AP-HP, Hôpital Pitié-Salpêtrière, Service de Virologie, Paris, France
| | - S Sayon
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, Institut Pierre Louis d'épidémiologie et de Santé Publique (IPLESP UMRS 1136), Paris, France; AP-HP, Hôpital Pitié-Salpêtrière, Service de Virologie, Paris, France
| | | | | | - M A Trabaud
- Hôpital de la Croix-Rousse, Hospices Civils de Lyon, Lyon, France
| | - S Berger
- Laboratoire de Virologie, CHU de Nancy Brabois, EA 7300, Université de Lorraine, Faculté de Médecine, Vandoeuvre les Nancy, France
| | - V Calvez
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, Institut Pierre Louis d'épidémiologie et de Santé Publique (IPLESP UMRS 1136), Paris, France; AP-HP, Hôpital Pitié-Salpêtrière, Service de Virologie, Paris, France
| | - A G Marcelin
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, Institut Pierre Louis d'épidémiologie et de Santé Publique (IPLESP UMRS 1136), Paris, France; AP-HP, Hôpital Pitié-Salpêtrière, Service de Virologie, Paris, France
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6
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Soulié C, Fofana DB, Boukli N, Sayon S, Lambert-Niclot S, Wirden M, Simon A, Katlama C, Calvez V, Girard PM, Marcelin AG, Morand-Joubert L. Performance of genotypic algorithms for predicting tropism of HIV-1CRF02_AG subtype. J Clin Virol 2016; 76:51-4. [PMID: 26826578 DOI: 10.1016/j.jcv.2016.01.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Revised: 12/18/2015] [Accepted: 01/12/2016] [Indexed: 10/22/2022]
Abstract
BACKGROUND Several genotypic rules for predicting HIV-1 non-B subtypes tropism are commonly used, but there is no consensus about their performances. OBJECTIVES Three genotypic methods were compared for CRF02_AG HIV-1 tropism determination. STUDY DESIGN V3 env region of 178HIV-1 CRF02_AG from Pitié-Salpêtrière and Saint-Antoine Hospitals was sequenced from plasma HIV-1 RNA. HIV-1 tropism was determined by Geno2Pheno algorithm, false positive rate (FPR) 5% or 10%, the 11/25 rule or the combined criteria of the 11/25 and net charge rule. RESULTS A concordance of 91.6% was observed between Geno2pheno 5% and the combined criteria. The results were nearly similar for the comparison between Geno2pheno 5% and the 11/25 rule. More mismatches were observed when Geno2pheno was used with the FPR 10%. A lower nadir CD4 cell count was associated with a discordance of tropism prediction between Geno2pheno 5% and the combined criteria or the 11/25 rule (p=0.02 and p=0.03, respectively). A lower HIV-1 viral load was associated with some discordance for the comparison of Geno2pheno 10% and the combined rule (p=0.02). CONCLUSION Geno2pheno FPR 5% or 10% predicted more X4-tropic viruses for this set of CRF02_AG sequences than the combined criteria or the 11/25 rule alone. Furthermore, Geno2pheno FPR 5% was more concordant with the 11/25 rule and the combined rule than Geno2pheno 10% to predict HIV-1 tropism. Overall, Geno2pheno 5% could be used to predict CRF02_AG tropism as well as other genotypic rules.
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Affiliation(s)
- C Soulié
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, Institut Pierre Louis d'épidémiologie et de Santé Publique (IPLESP UMRS 1136), F75013 Paris, France; AP-HP, Groupe hospitalier Pitié Salpêtrière, Laboratoire de Virologie, Paris F-75013, France.
| | - D B Fofana
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, Institut Pierre Louis d'épidémiologie et de Santé Publique (IPLESP UMRS 1136), F75013 Paris, France; AP-HP, Hôpital Saint-Antoine, Service de Virologie, Paris F-75013, France
| | - N Boukli
- AP-HP, Hôpital Saint-Antoine, Service de Virologie, Paris F-75013, France
| | - S Sayon
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, Institut Pierre Louis d'épidémiologie et de Santé Publique (IPLESP UMRS 1136), F75013 Paris, France; AP-HP, Groupe hospitalier Pitié Salpêtrière, Laboratoire de Virologie, Paris F-75013, France
| | - S Lambert-Niclot
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, Institut Pierre Louis d'épidémiologie et de Santé Publique (IPLESP UMRS 1136), F75013 Paris, France; AP-HP, Groupe hospitalier Pitié Salpêtrière, Laboratoire de Virologie, Paris F-75013, France
| | - Marc Wirden
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, Institut Pierre Louis d'épidémiologie et de Santé Publique (IPLESP UMRS 1136), F75013 Paris, France; AP-HP, Groupe hospitalier Pitié Salpêtrière, Laboratoire de Virologie, Paris F-75013, France
| | - A Simon
- AP-HP, Hôpital Pitié-Salpêtrière, Service de Médecine Interne, Paris F-75013, France
| | - C Katlama
- AP-HP, Hôpital Pitié-Salpêtrière, Service de Maladies Infectieuses, Paris F-75013, France
| | - V Calvez
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, Institut Pierre Louis d'épidémiologie et de Santé Publique (IPLESP UMRS 1136), F75013 Paris, France; AP-HP, Groupe hospitalier Pitié Salpêtrière, Laboratoire de Virologie, Paris F-75013, France
| | - P M Girard
- AP-HP, Hôpital Saint Antoine, Service de Maladies Infectieuses, Paris F-75013, France
| | - A G Marcelin
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, Institut Pierre Louis d'épidémiologie et de Santé Publique (IPLESP UMRS 1136), F75013 Paris, France; AP-HP, Groupe hospitalier Pitié Salpêtrière, Laboratoire de Virologie, Paris F-75013, France
| | - L Morand-Joubert
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, Institut Pierre Louis d'épidémiologie et de Santé Publique (IPLESP UMRS 1136), F75013 Paris, France; AP-HP, Hôpital Saint-Antoine, Service de Virologie, Paris F-75013, France
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7
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Potard V, Reynes J, Ferry T, Aubin C, Finkielsztejn L, Yazdanpanah Y, Costagliola D. Durability and Effectiveness of Maraviroc-Containing Regimens in HIV-1-Infected Individuals with Virological Failure in Routine Clinical Practice. PLoS One 2015; 10:e0144746. [PMID: 26714012 PMCID: PMC4695083 DOI: 10.1371/journal.pone.0144746] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 11/22/2015] [Indexed: 01/10/2023] Open
Abstract
INTRODUCTION Limited data are available on the durability and effectiveness of maraviroc in routine clinical practice. We assessed the durability of maraviroc-containing regimens during a 30-month period, as well as their immunovirological and clinical efficacy, according to viral tropism in treatment-experienced individuals with viral load (VL) >50 copies/ml in the French Hospital Database on HIV. METHODS Virological success was defined as VL<50 copies/ml, immunological success as a confirmed increase of at least 100 CD4 cells/mm3 measured twice at least one month apart, and clinical failure as hospitalization for a non-AIDS event, an AIDS event, or death. Multivariable Cox regression models adjusted for potential confounders were used to assess the influence of viral tropism on durability, the immunovirological responses, and clinical outcome. RESULTS 356 individuals started maraviroc with VL>50 copies/ml of whom 223 harbored R5 viruses, 44 non-R5 viruses and 89 viruses of unknown tropism. Individuals with non-R5 viruses were more likely than individuals with R5 viruses to discontinue maraviroc (75% vs 34%, p<0.0001). At 30 months, the estimated rates of virological and immunological success were respectively 89% and 51% in individuals with R5 viruses and 48% and 23% in individuals with non-R5 viruses. In multivariable analysis, non-R5 viruses were associated with a lower likelihood of both virological success (hazard ratio (HR): 0.42; 95% confidence interval (CI), 0.25-0.70) and immunological success (HR: 0.37; 95% CI, 0.18-0.77). No difference in clinical outcome was found between individuals with R5 and non-R5 viruses. The effectiveness of maraviroc-containing regimens in individuals with unknown viral tropism was not significantly different from that in individuals with R5 viruses. A limitation of the study is the absence of genotypic susceptibility score. CONCLUSION In this observational study, maraviroc-containing regimens yielded high rates of viral suppression and immunological responses in individuals with R5 viruses in whom prior regimens had failed.
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Affiliation(s)
- Valérie Potard
- Sorbonne Universités, UPMC Univ Paris 06, UMR_S 1136, Paris, France
- INSERM, UMR_S 1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Paris, France
- Inserm Transfert, Paris, France
- * E-mail:
| | - Jacques Reynes
- Université Montpellier, Montpellier, France
- IRD, UMI233 TransVIHMI Montpellier, France
- Département de Maladies Infectieuses et Tropicales, CHU Montpellier, France
| | - Tristan Ferry
- Services de Maladies Infectieuses et Tropicales, Hospices Civils de Lyon; Université Claude Bernard Lyon1; CIRI, International Center for Infectiology Research, INSERM U1111, Lyon, France
| | | | | | - Yazdan Yazdanpanah
- Université Paris Diderot 7, Paris, France
- INSERM, UMR_S 1137, ATIP-Avenir Inserm: "Modélisation, Aide à la Décision, et Coût-Efficacité en Maladies Infectieuses”, Paris, France
- Service des Maladies Infectieuses et Tropicales, Hôpital Bichat, France
| | - Dominique Costagliola
- Sorbonne Universités, UPMC Univ Paris 06, UMR_S 1136, Paris, France
- INSERM, UMR_S 1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Paris, France
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8
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Genebat M, de Pablo-Bernal RS, Pulido I, Jiménez-Mejías ME, Martínez O, Pacheco YM, Raffi-El-Idrissi Benhia M, Abad MA, Ruiz-Mateos E, Leal M. Maraviroc Clinical Test (MCT) as an alternative tool to decide CCR5-antagonists prescription in naïve HIV-infected patients. Antiviral Res 2015; 121:94-6. [PMID: 26122170 DOI: 10.1016/j.antiviral.2015.06.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Revised: 06/25/2015] [Accepted: 06/26/2015] [Indexed: 11/18/2022]
Abstract
Our aim was to analyze the virological response to a combined antiretroviral therapy started after Maraviroc Clinical Test (MCT) in naïve HIV-infected patients. Forty-one patients were exposed to MCT, based on an 8-day MVC monotherapy. If undetectability or a viral load reduction >1 log10 HIV-RNA copies/ml was achieved, a MVC-containing cART was prescribed. Forty patients showed a positive MCT; undetectability after 48weeks on cART was achieved in 34/41 (82.9%) patients. The result of MCT was compared with a genotypic tropism method and with Trofile®, showing 10.7% and 18.75% discordance rates, respectively. MCT is a reliable tool to decide CCR5-antagonists prescription, also in the naïve scenario where most patients show a virological response to MVC independently the tropism result reported by genotypic or phenotypic methods.
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Affiliation(s)
- Miguel Genebat
- Laboratory of Immunovirology, Clinic Unit of Infectious Diseases, Microbiology and Preventive Medicine, Institute of Biomedicine of Seville, IBiS, Virgen del Rocío University Hospital/CSIC/University of Seville, Seville 41013, Spain
| | - Rebeca S de Pablo-Bernal
- Laboratory of Immunovirology, Clinic Unit of Infectious Diseases, Microbiology and Preventive Medicine, Institute of Biomedicine of Seville, IBiS, Virgen del Rocío University Hospital/CSIC/University of Seville, Seville 41013, Spain
| | - Ildefonso Pulido
- Laboratory of Immunovirology, Clinic Unit of Infectious Diseases, Microbiology and Preventive Medicine, Institute of Biomedicine of Seville, IBiS, Virgen del Rocío University Hospital/CSIC/University of Seville, Seville 41013, Spain
| | - Manuel E Jiménez-Mejías
- Clinic Unit of Infectious Diseases, Microbiology and Preventive Medicine, Virgen del Rocío University Hospital, Sevilla, Spain
| | - Onofre Martínez
- Hospital Santa María del Rosell-Santa Lucía, Cartagena, Spain
| | - Yolanda M Pacheco
- Laboratory of Immunovirology, Clinic Unit of Infectious Diseases, Microbiology and Preventive Medicine, Institute of Biomedicine of Seville, IBiS, Virgen del Rocío University Hospital/CSIC/University of Seville, Seville 41013, Spain
| | - Mohammed Raffi-El-Idrissi Benhia
- Laboratory of Immunovirology, Clinic Unit of Infectious Diseases, Microbiology and Preventive Medicine, Institute of Biomedicine of Seville, IBiS, Virgen del Rocío University Hospital/CSIC/University of Seville, Seville 41013, Spain; Department of Medical Biochemistry, Molecular Biology, and Immunology, School of Medicine, University of Seville, Seville 41009, Spain
| | - María Antonia Abad
- Laboratory of Immunovirology, Clinic Unit of Infectious Diseases, Microbiology and Preventive Medicine, Institute of Biomedicine of Seville, IBiS, Virgen del Rocío University Hospital/CSIC/University of Seville, Seville 41013, Spain
| | - Ezequiel Ruiz-Mateos
- Laboratory of Immunovirology, Clinic Unit of Infectious Diseases, Microbiology and Preventive Medicine, Institute of Biomedicine of Seville, IBiS, Virgen del Rocío University Hospital/CSIC/University of Seville, Seville 41013, Spain
| | - Manuel Leal
- Laboratory of Immunovirology, Clinic Unit of Infectious Diseases, Microbiology and Preventive Medicine, Institute of Biomedicine of Seville, IBiS, Virgen del Rocío University Hospital/CSIC/University of Seville, Seville 41013, Spain.
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9
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Rodriguez C, Soulié C, Marcelin AG, Calvez V, Descamps D, Charpentier C, Flandre P, Recordon-Pinson P, Bellecave P, Pawlotsky JM, Masquelier B. HIV-1 Coreceptor Usage Assessment by Ultra-Deep Pyrosequencing and Response to Maraviroc. PLoS One 2015; 10:e0127816. [PMID: 26068869 PMCID: PMC4466260 DOI: 10.1371/journal.pone.0127816] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Accepted: 04/20/2015] [Indexed: 12/15/2022] Open
Abstract
Background Maraviroc is an HIV entry inhibitor that alters the conformation of CCR5 and is poorly efficient in patients infected by viruses that use CXCR4 as an entry coreceptor. The goal of this study was to assess the capacity of ultra-deep pyrosequencing (UDPS) and different data analysis approaches to characterize HIV tropism at baseline and predict the therapeutic outcome on maraviroc treatment. Methods 113 patients with detectable HIV-1 RNA on HAART were treated with maraviroc. The virological response was assessed at months 1, 3 and 6. The sequence of the HIV V3 loop was determined at baseline and prediction of maraviroc response by different software and interpretation algorithms was analyzed. Results UDPS followed by analysis with the Pyrotrop software or geno2pheno algorithm provided better prediction of the response to maraviroc than Sanger sequencing. We also found that the H34Y/S substitution in the V3 loop was the strongest individual predictor of maraviroc response, stronger than substitutions at positions 11 or 25 classically used in interpretation algorithms. Conclusions UDPS is a powerful tool that can be used with confidence to predict maraviroc response in HIV-1-infected patients. Improvement of the predictive value of interpretation algorithms is possible and our results suggest that adding the H34S/Y substitution would substantially improve the performance of the 11/25/charge rule.
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Affiliation(s)
- Christophe Rodriguez
- National Reference Center for Viral Hepatitis B, C and delta, Department of Virology; Henri Mondor Hospital, University of Paris-Est, Créteil, France
- INSERM U955, Créteil, France
| | - Cathia Soulié
- Department of Virology, Pitié-Salpêtrière Hospital, Paris, France
| | | | - Vincent Calvez
- Department of Virology, Pitié-Salpêtrière Hospital, Paris, France
| | - Diane Descamps
- Department of Virology, Bichat-Claude Bernard Hospital, HUPNVS, Paris, France
| | | | | | - Patricia Recordon-Pinson
- Department of Virology, University Hospital of Bordeaux and UMR5234, University of Bordeaux, Bordeaux, France
| | - Pantxika Bellecave
- Department of Virology, University Hospital of Bordeaux and UMR5234, University of Bordeaux, Bordeaux, France
| | - Jean-Michel Pawlotsky
- National Reference Center for Viral Hepatitis B, C and delta, Department of Virology; Henri Mondor Hospital, University of Paris-Est, Créteil, France
- INSERM U955, Créteil, France
- * E-mail:
| | - Bernard Masquelier
- Department of Virology, University Hospital of Bordeaux and UMR5234, University of Bordeaux, Bordeaux, France
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10
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Sierra S, Dybowski JN, Pironti A, Heider D, Güney L, Thielen A, Reuter S, Esser S, Fätkenheuer G, Lengauer T, Hoffmann D, Pfister H, Jensen B, Kaiser R. Parameters Influencing Baseline HIV-1 Genotypic Tropism Testing Related to Clinical Outcome in Patients on Maraviroc. PLoS One 2015; 10:e0125502. [PMID: 25970632 PMCID: PMC4430318 DOI: 10.1371/journal.pone.0125502] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Accepted: 03/18/2015] [Indexed: 12/25/2022] Open
Abstract
OBJECTIVES We analysed the impact of different parameters on genotypic tropism testing related to clinical outcome prediction in 108 patients on maraviroc (MVC) treatment. METHODS 87 RNA and 60 DNA samples were used. The viral tropism was predicted using the geno2pheno[coreceptor] and T-CUP tools with FPR cut-offs ranging from 1%-20%. Additionally, 27 RNA and 28 DNA samples were analysed in triplicate, 43 samples with the ESTA assay and 45 with next-generation sequencing. The influence of the genotypic susceptibility score (GSS) and 16 MVC-resistance mutations on clinical outcome was also studied. RESULTS Concordance between single-amplification testing compared to ESTA and to NGS was in the order of 80%. Concordance with NGS was higher at lower FPR cut-offs. Detection of baseline R5 viruses in RNA and DNA samples by all methods significantly correlated with treatment success, even with FPR cut-offs of 3.75%-7.5%. Triple amplification did not improve the prediction value but reduced the number of patients eligible for MVC. No influence of the GSS or MVC-resistance mutations but adherence to treatment, on the clinical outcome was detected. CONCLUSIONS Proviral DNA is valid to select candidates for MVC treatment. FPR cut-offs of 5%-7.5% and single amplification from RNA or DNA would assure a safe administration of MVC without excluding many patients who could benefit from this drug. In addition, the new prediction system T-CUP produced reliable results.
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Affiliation(s)
- Saleta Sierra
- Institute of Virology, University of Cologne, Cologne, Germany
| | - J Nikolai Dybowski
- Department for Bioinformatics, University of Duisburg-Essen, Essen, Germany
| | - Alejandro Pironti
- Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarbrücken, Germany
| | - Dominik Heider
- Department for Bioinformatics, University of Duisburg-Essen, Essen, Germany
| | - Lisa Güney
- Institute of Virology, University of Cologne, Cologne, Germany
| | - Alex Thielen
- Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarbrücken, Germany
| | - Stefan Reuter
- Department of Gastroenterology, Hepatology and Infectiology, University Hospital of Düsseldorf, Düsseldorf, Germany
| | - Stefan Esser
- Department of Dermatology, University of Duisburg-Essen, Essen, Germany
| | - Gerd Fätkenheuer
- First Department of Internal Medicine, University of Cologne, Cologne, Germany
| | - Thomas Lengauer
- Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarbrücken, Germany
| | - Daniel Hoffmann
- Department for Bioinformatics, University of Duisburg-Essen, Essen, Germany
| | - Herbert Pfister
- Institute of Virology, University of Cologne, Cologne, Germany
| | - Björn Jensen
- Department of Gastroenterology, Hepatology and Infectiology, University Hospital of Düsseldorf, Düsseldorf, Germany
| | - Rolf Kaiser
- Institute of Virology, University of Cologne, Cologne, Germany
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11
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van der Ryst E, Heera J, Demarest J, Knirsch C. Development of maraviroc, a CCR5 antagonist for treatment of HIV, using a novel tropism assay. Ann N Y Acad Sci 2015; 1346:7-17. [PMID: 25962411 DOI: 10.1111/nyas.12777] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2014] [Revised: 03/27/2015] [Accepted: 03/30/2015] [Indexed: 11/29/2022]
Abstract
Assays to identify infectious organisms are critical for diagnosis and enabling the development of therapeutic agents. The demonstration that individuals with a 32-bp deletion within the CCR5 locus were resistant to human immunodeficiency virus (HIV) infection, while those heterozygous for the mutation progressed more slowly, led to the discovery of maraviroc (MVC), a CCR5 antagonist. As MVC is only active against CCR5-tropic strains of HIV, it was critical to develop a diagnostic assay to identify appropriate patients. Trofile™, a novel phenotypic tropism assay, was used to identify patients with CCR5-tropic virus for the MVC development program. Results of these clinical studies demonstrated that the assay correctly identified patients likely to respond to MVC. Over time, the performance characteristics of the phenotypic assay were enhanced, necessitating retesting of study samples. Genotypic tropism tests that have the potential to allow for local use and more rapid turnaround times are also being developed.
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Affiliation(s)
| | - Jayvant Heera
- Pfizer Worldwide Research and Development, Groton, Connecticut
| | | | - Charles Knirsch
- Pfizer Worldwide Research and Development, Pearl River, New York
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12
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Soulie C, Peytavin G, Charpentier C, Lambert-Niclot S, Sayon S, Visseaux B, Simon A, Katlama C, Yazdanpanah Y, Descamps D, Calvez V, Marcelin AG. Antiretroviral-Experienced HIV-1-Infected Patients Treated with Maraviroc: Factors Associated with Virological Response. AIDS Res Hum Retroviruses 2015; 31:475-8. [PMID: 25420695 DOI: 10.1089/aid.2014.0223] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
There are few data on the clinical and virological factors associated with the virological response (VR) of maraviroc (MVC) in clinical practice. This study aimed to identify factors associated with the VR to MVC-containing regimens in 104 treatment-experienced but CCR5 inhibitor-naive HIV-1 patients. VR was defined at month 3 (M3) as HIV-1 RNA viral load (VL) <50 copies/ml. The impact on VR of age, sex, baseline tropism, HIV subtype (B vs. non-B), nadir CD4 cell count and CD4 cell count, baseline VL, genotypic susceptibility score of treatment, once or twice daily treatment, presence of raltegravir in optimized background therapy, and MVC concentrations was investigated. Median baseline VL was 3.3 log10 copies/ml (range 1.7-6.0 log10 copies/ml) and CD4 cell count was 299 cells/mm(3) (range 7-841 cells/mm(3)). At M3, 53.8% of patients were responders. In univariate analysis, a better efficacy of the MVC-containing regimen was associated with a high CD4 cell count (p=0.0069) and there was a trend for low baseline VL, high nadir CD4 cell count, and HIV subtype (B versus non-B). Only low baseline VL remained significantly associated with better VR in the multivariate analysis. This study demonstrated a VR of an optimized antiretroviral treatment including MVC in clinical practice similar to that observed in clinical trials. The factors associated with VR were higher baseline CD4 cell count in univariate analysis and lower baseline VL in multivariate analysis.
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Affiliation(s)
- Cathia Soulie
- Sorbonne Universités, UPMC Université Paris 06-UMR_S 1136 Pierre Louis Institute of Epidemiology and Public Health, Paris, France
- INSERM-UMR_S 1136 Pierre Louis Institute of Epidemiology and Public Health, Paris, France
- AP-HP, Laboratoire de Virologie, Groupe Hospitalier Pitié Salpêtrière, Paris, France
| | - Gilles Peytavin
- AP-HP, Service de Pharmacologie Clinique, Hôpital Bichat-Claude Bernard, Paris, France
- IAME, UMR 1137-Université Paris Diderot, Sorbonne Paris Cité, Paris, France
- INSERM UMR 1137, Paris, France
| | - Charlotte Charpentier
- IAME, UMR 1137-Université Paris Diderot, Sorbonne Paris Cité, Paris, France
- INSERM UMR 1137, Paris, France
- AP-HP, Laboratoire de Virologie, Hôpital Bichat, Paris, France
| | - Sidonie Lambert-Niclot
- Sorbonne Universités, UPMC Université Paris 06-UMR_S 1136 Pierre Louis Institute of Epidemiology and Public Health, Paris, France
- INSERM-UMR_S 1136 Pierre Louis Institute of Epidemiology and Public Health, Paris, France
- AP-HP, Laboratoire de Virologie, Groupe Hospitalier Pitié Salpêtrière, Paris, France
| | - Sophie Sayon
- Sorbonne Universités, UPMC Université Paris 06-UMR_S 1136 Pierre Louis Institute of Epidemiology and Public Health, Paris, France
- INSERM-UMR_S 1136 Pierre Louis Institute of Epidemiology and Public Health, Paris, France
- AP-HP, Laboratoire de Virologie, Groupe Hospitalier Pitié Salpêtrière, Paris, France
| | - Benoit Visseaux
- IAME, UMR 1137-Université Paris Diderot, Sorbonne Paris Cité, Paris, France
- INSERM UMR 1137, Paris, France
- AP-HP, Laboratoire de Virologie, Hôpital Bichat, Paris, France
| | - Anne Simon
- AP-HP, Service de Médecine Interne, Groupe Hospitalier Pitié Salpêtrière, Paris, France
| | - Christine Katlama
- Sorbonne Universités, UPMC Université Paris 06-UMR_S 1136 Pierre Louis Institute of Epidemiology and Public Health, Paris, France
- INSERM-UMR_S 1136 Pierre Louis Institute of Epidemiology and Public Health, Paris, France
- AP-HP, Service de Maladies Infectieuses, Groupe Hospitalier Pitié Salpêtrière, Paris, France
| | - Yazdan Yazdanpanah
- IAME, UMR 1137-Université Paris Diderot, Sorbonne Paris Cité, Paris, France
- INSERM UMR 1137, Paris, France
- AP-HP, Service des Maladies Infectieuses et Tropicales, Hôpital Bichat, Paris, France
| | - Diane Descamps
- IAME, UMR 1137-Université Paris Diderot, Sorbonne Paris Cité, Paris, France
- INSERM UMR 1137, Paris, France
- AP-HP, Laboratoire de Virologie, Hôpital Bichat, Paris, France
| | - Vincent Calvez
- Sorbonne Universités, UPMC Université Paris 06-UMR_S 1136 Pierre Louis Institute of Epidemiology and Public Health, Paris, France
- INSERM-UMR_S 1136 Pierre Louis Institute of Epidemiology and Public Health, Paris, France
- AP-HP, Laboratoire de Virologie, Groupe Hospitalier Pitié Salpêtrière, Paris, France
| | - Anne-Geneviève Marcelin
- Sorbonne Universités, UPMC Université Paris 06-UMR_S 1136 Pierre Louis Institute of Epidemiology and Public Health, Paris, France
- INSERM-UMR_S 1136 Pierre Louis Institute of Epidemiology and Public Health, Paris, France
- AP-HP, Laboratoire de Virologie, Groupe Hospitalier Pitié Salpêtrière, Paris, France
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13
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Pironti A, Sierra S, Kaiser R, Lengauer T, Pfeifer N. Effects of sequence alterations on results from genotypic tropism testing. J Clin Virol 2015; 65:68-73. [DOI: 10.1016/j.jcv.2015.02.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Revised: 01/28/2015] [Accepted: 02/06/2015] [Indexed: 11/30/2022]
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14
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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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15
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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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16
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Arruda LB, Araújo MLD, Martinez ML, Gonsalez CR, Duarte AJDS, Coakley E, Lie Y, Casseb J. Determination of viral tropism by genotyping and phenotyping assays in Brazilian HIV-1-infected patients. Rev Inst Med Trop Sao Paulo 2014; 56:287-90. [PMID: 25076427 PMCID: PMC4131812 DOI: 10.1590/s0036-46652014000400003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2013] [Accepted: 01/30/2014] [Indexed: 12/03/2022] Open
Abstract
The clinical application of CCR5 antagonists involves first determining
the coreceptor usage by the infecting viral strain. Bioinformatics programs that
predict coreceptor usage could provide an alternative method to screen candidates for
treatment with CCR5 antagonists, particularly in countries with limited financial
resources. Thus, the present study aims to identify the best approach using
bioinformatics tools for determining HIV-1 coreceptor usage in clinical practice.
Proviral DNA sequences and Trofile results from 99 HIV-1-infected subjects under
clinical monitoring were analyzed in this study. Based on the Trofile results, the
viral variants present were 81.1% R5, 21.4% R5X4 and 1.8% X4. Determination of
tropism using a Geno2pheno[coreceptor] analysis with a false positive rate
of 10% gave the most suitable performance in this sampling: the R5 and X4 strains
were found at frequencies of 78.5% and 28.4%, respectively, and there was 78.6%
concordance between the phenotypic and genotypic results. Further studies are needed
to clarify how genetic diversity amongst virus strains affects bioinformatics-driven
approaches for determining tropism. Although this strategy could be useful for
screening patients in developing countries, some limitations remain that restrict the
wider application of coreceptor usage tests in clinical practice.
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Affiliation(s)
- Liã Bárbara Arruda
- Institute of Tropical Medicine of São Paulo, University of São Paulo, São Paulo, SP, Brazil
| | - Marilia Ladeira de Araújo
- Laboratory of Investigation in Dermatology and Immunodeficiencies, Department of Dermatology School of Medicine at University of São Paulo, University of São Paulo, São Paulo, SP, Brazil
| | - Maira Luccia Martinez
- Laboratory of Investigation in Dermatology and Immunodeficiencies, Department of Dermatology School of Medicine at University of São Paulo, University of São Paulo, São Paulo, SP, Brazil
| | - Claudio Roberto Gonsalez
- HIV Out-clinic, Ambulatory of Secondary Immunodeficiencies, ADEE3002, Department of Dermatology, Hospital of Clinics at School of Medicine, University of São Paulo
| | - Alberto José da Silva Duarte
- Laboratory of Investigation in Dermatology and Immunodeficiencies, Department of Dermatology School of Medicine at University of São Paulo, University of São Paulo, São Paulo, SP, Brazil
| | - Eoin Coakley
- Monogram Biosciences, Inc., South San Francisco, CA, USA
| | - Yolanda Lie
- Monogram Biosciences, Inc., South San Francisco, CA, USA
| | - Jorge Casseb
- Institute of Tropical Medicine of São Paulo, University of São Paulo, São Paulo, SP, Brazil
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17
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Asin-Milan O, Wei Y, Sylla M, Vaisheva F, Chamberland A, Tremblay CL. Performance of a clonal-based HIV-1 tropism phenotypic assay. J Virol Methods 2014; 204:53-61. [PMID: 24731927 DOI: 10.1016/j.jviromet.2014.04.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Revised: 03/31/2014] [Accepted: 04/04/2014] [Indexed: 11/29/2022]
Abstract
Adequate determination of HIV-1 tropism is important in clinical and research settings. Genotypic and phenotypic approaches to evaluate tropism have been described. Phenotypic assays are widely used to determine HIV-1 tropism because of their sensitivity to detect minor CXCR4-using variants (X4). However they cannot differentiate mixed quasi-species of R5 and X4 viruses from dual-tropic viruses. We describe here a clonal-based HIV-1 tropism phenotypic assay. Env-pseudo-typed viruses were produced by co-transfection of the env expression plasmid pcDNA3.1/V5HisTOPO and a backbone vector pNL4-3.Luc.E-R- that expresses the entire HIV-1 genome except for env and vpr in 293T cell cultures. Co-receptor use was tested by infecting U87.CD4.CCR5+ and U87.CD4.CXCR4+ cells in the presence or absence of co-receptor inhibitors, using 10 clones from each sample. The ability of the assay to detect minor variants in a viral population was assessed by mixing X4 and R5 clones using different ratios. Both R5 and X4 minority variants were detected when present at greater than 0.4% in a mixture of envelope populations. This assay can be useful in both clinical and research laboratories.
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Affiliation(s)
- Odalis Asin-Milan
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CR-CHUM), Montréal, Canada; Department of Microbiology, Infectiology and Immunology, Faculty of Medicine, University of Montreal, Canada
| | - Yi Wei
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CR-CHUM), Montréal, Canada
| | - Mohamed Sylla
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CR-CHUM), Montréal, Canada; Department of Microbiology, Infectiology and Immunology, Faculty of Medicine, University of Montreal, Canada
| | | | - Annie Chamberland
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CR-CHUM), Montréal, Canada; Department of Microbiology, Infectiology and Immunology, Faculty of Medicine, University of Montreal, Canada
| | - Cécile L Tremblay
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CR-CHUM), Montréal, Canada; Department of Microbiology, Infectiology and Immunology, Faculty of Medicine, University of Montreal, Canada; Laboratoire de Santé Publique du Québec, Institut National de Santé Publique du Québec, Canada.
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18
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Panos G, Watson DC. Effect of HIV-1 subtype and tropism on treatment with chemokine coreceptor entry inhibitors; overview of viral entry inhibition. Crit Rev Microbiol 2014; 41:473-87. [DOI: 10.3109/1040841x.2013.867829] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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19
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Kagan RM, Johnson EP, Siaw MF, Van Baelen B, Ogden R, Platt JL, Pesano RL, Lefebvre E. Comparison of genotypic and phenotypic HIV type 1 tropism assay: results from the screening samples of Cenicriviroc Study 202, a randomized phase II trial in treatment-naive subjects. AIDS Res Hum Retroviruses 2014; 30:151-9. [PMID: 23875707 DOI: 10.1089/aid.2013.0123] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Cenicriviroc is a once-daily oral CCR5/CCR2 antagonist in development for treatment of HIV infection. CVC Study 202 (652-2-202; NCT01338883) excluded treatment-naive subjects demonstrated to harbor non-R5 (CXCR4-tropic or dual-mixed) tropic HIV-1 by either genotypic or phenotypic tropism testing. Here we compare the results of genotypic and phenotypic tropism testing in Study 202. A total of 304 subjects screened had paired genotypic and phenotypic results. Genotypic tropism testing (GTT) incorporated triplicate population sequencing using the geno2pheno algorithm and the PSSM algorithm, followed by ultradeep sequencing (UDS) for samples with R5 results. All samples were further evaluated with a phenotypic test, the enhanced-sensitivity Trofile assay (ESTA). Concordance between GTT and ESTA was 80% and increased to 84% when only geno2pheno was used for triplicate population sequencing. GTT (geno2pheno) classified 18% of the samples as non-R5 compared to 16% by ESTA. Only one-third of samples with non-R5 results by either test were classified as non-R5 by both tests. Median CD4((+)) cell counts were lower in patients with concordant non-R5 results by UDS and ESTA than in subjects with an R5 result by either assay (p=0.0004). UDS detected non-R5 virus in an additional 27/304 subjects (median 15% non-R5, interquartile range: 3.7-62%) with R5 results by ESTA. In conclusion, the geno2pheno algorithm improves concordance of GTT with a clinically validated phenotypic tropism assay as does the use of UDS. These findings provide support for recent guidelines indicating that genotypic tropism testing may be considered as an alternative to phenotypic testing.
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Affiliation(s)
- Ron M. Kagan
- Quest Diagnostics Nichols Institute, San Juan Capistrano, California
| | - Erik P. Johnson
- Quest Diagnostics Nichols Institute, San Juan Capistrano, California
| | - Martin F. Siaw
- Quest Diagnostics Nichols Institute, San Juan Capistrano, California
| | | | - Richard Ogden
- Tobira Therapeutics Inc., South San Francisco, California
| | - Jamie L. Platt
- Quest Diagnostics Nichols Institute, San Juan Capistrano, California
| | - Rick L. Pesano
- Quest Diagnostics Nichols Institute, San Juan Capistrano, California
| | - Eric Lefebvre
- Tobira Therapeutics Inc., South San Francisco, California
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20
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Sensitive deep-sequencing-based HIV-1 genotyping assay to simultaneously determine susceptibility to protease, reverse transcriptase, integrase, and maturation inhibitors, as well as HIV-1 coreceptor tropism. Antimicrob Agents Chemother 2014; 58:2167-85. [PMID: 24468782 DOI: 10.1128/aac.02710-13] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
With 29 individual antiretroviral drugs available from six classes that are approved for the treatment of HIV-1 infection, a combination of different phenotypic and genotypic tests is currently needed to monitor HIV-infected individuals. In this study, we developed a novel HIV-1 genotypic assay based on deep sequencing (DeepGen HIV) to simultaneously assess HIV-1 susceptibilities to all drugs targeting the three viral enzymes and to predict HIV-1 coreceptor tropism. Patient-derived gag-p2/NCp7/p1/p6/pol-PR/RT/IN- and env-C2V3 PCR products were sequenced using the Ion Torrent Personal Genome Machine. Reads spanning the 3' end of the Gag, protease (PR), reverse transcriptase (RT), integrase (IN), and V3 regions were extracted, truncated, translated, and assembled for genotype and HIV-1 coreceptor tropism determination. DeepGen HIV consistently detected both minority drug-resistant viruses and non-R5 HIV-1 variants from clinical specimens with viral loads of ≥1,000 copies/ml and from B and non-B subtypes. Additional mutations associated with resistance to PR, RT, and IN inhibitors, previously undetected by standard (Sanger) population sequencing, were reliably identified at frequencies as low as 1%. DeepGen HIV results correlated with phenotypic (original Trofile, 92%; enhanced-sensitivity Trofile assay [ESTA], 80%; TROCAI, 81%; and VeriTrop, 80%) and genotypic (population sequencing/Geno2Pheno with a 10% false-positive rate [FPR], 84%) HIV-1 tropism test results. DeepGen HIV (83%) and Trofile (85%) showed similar concordances with the clinical response following an 8-day course of maraviroc monotherapy (MCT). In summary, this novel all-inclusive HIV-1 genotypic and coreceptor tropism assay, based on deep sequencing of the PR, RT, IN, and V3 regions, permits simultaneous multiplex detection of low-level drug-resistant and/or non-R5 viruses in up to 96 clinical samples. This comprehensive test, the first of its class, will be instrumental in the development of new antiretroviral drugs and, more importantly, will aid in the treatment and management of HIV-infected individuals.
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21
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van Lelyveld SFL, Wensing AMJ, Hoepelman AIM. The MOTIVATE trials: maraviroc therapy in antiretroviral treatment-experienced HIV-1-infected patients. Expert Rev Anti Infect Ther 2014; 10:1241-7. [DOI: 10.1586/eri.12.114] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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22
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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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23
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Meini G, Rossetti B, Bianco C, Ceccherini-Silberstein F, Di Giambenedetto S, Sighinolfi L, Monno L, Castagna A, Rozera G, D'Arminio Monforte A, Zazzi M, De Luca A. Longitudinal analysis of HIV-1 coreceptor tropism by single and triplicate HIV-1 RNA and DNA sequencing in patients undergoing successful first-line antiretroviral therapy. J Antimicrob Chemother 2013; 69:735-41. [PMID: 24155059 PMCID: PMC3954119 DOI: 10.1093/jac/dkt426] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Objectives Maraviroc has been shown to be effective in patients harbouring CCR5-tropic HIV-1. While this CCR5 antagonist has initially been used in salvage therapy, its excellent safety profile makes it ideal for antiretroviral treatment simplification strategies in patients with suppressed plasma viraemia. The aim of this study was to compare HIV-1 tropism as detected in baseline plasma RNA and peripheral blood mononuclear cell (PBMC) DNA prior to first-line therapy and to analyse tropism evolution while on successful treatment. Methods HIV-1 tropism was determined using triplicate genotypic testing combined with geno2pheno[coreceptor] analysis at a 10% false positive rate in 42 patients. Paired pre-treatment plasma RNA and PBMC DNA and two subsequent PBMC DNA samples (the first obtained after reaching undetectable plasma HIV-1 RNA and the second after at least 2 years of suppression of plasma viraemia) were evaluated. Results Coreceptor tropism was completely concordant in paired pre-treatment RNA and DNA, with 26.2% of HIV-1 sequences predicted to be non-CCR5-tropic. During follow-up, coreceptor tropism switches were detected in 4 (9.5%) patients without any preferential direction. Although false positive rate discrepancies within triplicates were common, the rate of discordance of coreceptor tropism assignment among triplicate results in this mostly CCR5-tropic dataset was only 2.1%, questioning the added value of triplicate testing compared with single testing. Conclusions HIV-1 coreceptor tropism changes during virologically successful first-line treatment are infrequent. HIV-1 DNA analysis may thus support the choice of a CCR5 antagonist in treatment switch strategies; however, maraviroc treatment outcome data are required to confirm this option.
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Affiliation(s)
- Genny Meini
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
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24
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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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Abstract
We compared the coreceptor tropism-predicting performance of a specific genotypic algorithm for HIV-1 subtype D and that of the geno2pheno algorithm with different cutoffs. The D-specific algorithm and geno2pheno with a false-positivity rate cutoff of 2.5% had the same concordance with the phenotypic determination. The geno2pheno algorithm with a false-positivity rate cutoff of 2.5%, more sensitive but slightly less specific, seems to be an appropriate alternative.
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Mulinge M, Lemaire M, Servais JY, Rybicki A, Struck D, da Silva ES, Verhofstede C, Lie Y, Seguin-Devaux C, Schmit JC, Bercoff DP. HIV-1 tropism determination using a phenotypic Env recombinant viral assay highlights overestimation of CXCR4-usage by genotypic prediction algorithms for CRF01_AE and CRF02_AG [corrected]. PLoS One 2013; 8:e60566. [PMID: 23667426 PMCID: PMC3648519 DOI: 10.1371/journal.pone.0060566] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2012] [Accepted: 02/28/2013] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Human Immunodeficiency virus type-1 (HIV) entry into target cells involves binding of the viral envelope (Env) to CD4 and a coreceptor, mainly CCR5 or CXCR4. The only currently licensed HIV entry inhibitor, maraviroc, targets CCR5, and the presence of CXCX4-using strains must be excluded prior to treatment. Co-receptor usage can be assessed by phenotypic assays or through genotypic prediction. Here we compared the performance of a phenotypic Env-Recombinant Viral Assay (RVA) to the two most widely used genotypic prediction algorithms, Geno2Pheno[coreceptor] and webPSSM. METHODS Co-receptor tropism of samples from 73 subtype B and 219 non-B infections was measured phenotypically using a luciferase-tagged, NL4-3-based, RVA targeting Env. In parallel, tropism was inferred genotypically from the corresponding V3-loop sequences using Geno2Pheno[coreceptor] (5-20% FPR) and webPSSM-R5X4. For discordant samples, phenotypic outcome was retested using co-receptor antagonists or the validated Trofile® Enhanced-Sensitivity-Tropism-Assay. RESULTS The lower detection limit of the RVA was 2.5% and 5% for X4 and R5 minority variants respectively. A phenotype/genotype result was obtained for 210 samples. Overall, concordance of phenotypic results with Geno2Pheno[coreceptor] was 85.2% and concordance with webPSSM was 79.5%. For subtype B, concordance with Geno2pheno[coreceptor] was 94.4% and concordance with webPSSM was 79.6%. High concordance of genotypic tools with phenotypic outcome was seen for subtype C (90% for both tools). Main discordances involved CRF01_AE and CRF02_AG for both algorithms (CRF01_AE: 35.9% discordances with Geno2Pheno[coreceptor] and 28.2% with webPSSM; CRF02_AG: 20.7% for both algorithms). Genotypic prediction overestimated CXCR4-usage for both CRFs. For webPSSM, 40% discordance was observed for subtype A. CONCLUSIONS Phenotypic assays remain the most accurate for most non-B subtypes and new subtype-specific rules should be developed for non-B subtypes, as research studies more and more draw conclusions from genotypically-inferred tropism, and to avoid unnecessarily precluding patients with limited treatment options from receiving maraviroc or other entry inhibitors.
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Affiliation(s)
- Martin Mulinge
- Laboratory of Retrovirology, Centre Recherche Public de la Santé, Luxembourg, Luxembourg
| | - Morgane Lemaire
- Laboratory of Retrovirology, Centre Recherche Public de la Santé, Luxembourg, Luxembourg
| | - Jean-Yves Servais
- Laboratory of Retrovirology, Centre Recherche Public de la Santé, Luxembourg, Luxembourg
| | - Arkadiusz Rybicki
- Laboratory of Retrovirology, Centre Recherche Public de la Santé, Luxembourg, Luxembourg
| | - Daniel Struck
- Laboratory of Retrovirology, Centre Recherche Public de la Santé, Luxembourg, Luxembourg
| | | | | | - Yolanda Lie
- Monogram Biosciences Inc., South San Francisco, California, United States of America
| | - Carole Seguin-Devaux
- Laboratory of Retrovirology, Centre Recherche Public de la Santé, Luxembourg, Luxembourg
| | - Jean-Claude Schmit
- Laboratory of Retrovirology, Centre Recherche Public de la Santé, Luxembourg, Luxembourg
- Service National des Maladies Infectieuses, Centre Hospitalier de Luxembourg, Luxembourg, Luxembourg
| | - Danielle Perez Bercoff
- Laboratory of Retrovirology, Centre Recherche Public de la Santé, Luxembourg, Luxembourg
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27
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Soulié C, Charpentier C, Flandre P, Nino C, Carcelain G, Simon A, Katlama C, Landman R, Brun-Vézinet F, Descamps D, Calvez V, Marcelin AG. Natural evolution of CD4+ cell count in patients with CD4 >350 or >500 cells/mm3 at the time of diagnosis according to HIV-1 coreceptor tropism. J Med Virol 2013; 84:1853-6. [PMID: 23080487 DOI: 10.1002/jmv.23362] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The HIV-1 coreceptor usage may play a critical role in AIDS pathogenesis and the X4-using viruses are considered to be more pathogenic than the R5-tropic viruses. These observations may influence the therapeutic decisions by asking for an earlier antiretroviral (ARV) treatment for the patients infected by the X4-tropic viruses compared with those infected by the R5-tropic viruses. The natural evolution of CD4+ cell count for 109 non-treated patients infected by the R5- or X4-tropic HIV-1 viruses with CD4+ >350 and >500 cells/mm(3) at time of diagnosis was compared until the initiation of an ARV regimen. The coreceptor usage was determined from the V3 env region sequence by Geno2Pheno (false positive rate 10%). A mixed linear regression model to analyse the CD4+ data with tropism as fixed effect in the model was used. Overall, 93 (85.3%) and 16 (14.7%) were infected by R5- and X4-tropic viruses, respectively. The median age, baseline CD4+ cell count, and viral load were 34 years (IQR: 30-42), 523 cells/mm(3) (IQR: 420-604), and 4.5 log(10) copies/ml (IQR: 3.9-5.0), respectively. There was no statistical difference in time to progression between the patients harboring R5- or X4-tropic viruses. The same results were observed for the sub-group of patients with CD4+ cell count >500 cells/mm(3). The virus tropism has no impact on the CD4+ cell count evolution in these HIV-1 patients diagnosed with CD4+ >350 or >500 cells/mm(3) suggesting that the tropism determination at time of diagnosis does not seem to be a useful tool to predict the clinical progression.
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Affiliation(s)
- Cathia Soulié
- UMR S-943, Pierre et Marie Curie University, Paris, France.
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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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Sensitive cell-based assay for determination of human immunodeficiency virus type 1 coreceptor tropism. J Clin Microbiol 2013; 51:1517-27. [PMID: 23486708 DOI: 10.1128/jcm.00092-13] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
CCR5 antagonists are a powerful new class of antiretroviral drugs that require a companion assay to evaluate the presence of CXCR4-tropic (non-R5) viruses prior to use in human immunodeficiency virus (HIV)-infected individuals. In this study, we have developed, characterized, verified, and prevalidated a novel phenotypic test to determine HIV-1 coreceptor tropism (VERITROP) based on a sensitive cell-to-cell fusion assay. A proprietary vector was constructed containing a near-full-length HIV-1 genome with the yeast uracil biosynthesis (URA3) gene replacing the HIV-1 env coding sequence. Patient-derived HIV-1 PCR products were introduced by homologous recombination using an innovative yeast-based cloning strategy. The env-expressing vectors were then used in a cell-to-cell fusion assay to determine the presence of R5 and/or non-R5 HIV-1 variants within the viral population. Results were compared with (i) the original version of Trofile (Monogram Biosciences, San Francisco, CA), (ii) population sequencing, and (iii) 454 pyrosequencing, with the genotypic data analyzed using several bioinformatics tools, i.e., the 11/24/25 rule, Geno2Pheno (2% to 5.75%, 3.5%, or 10% false-positive rate [FPR]), and webPSSM. VERITROP consistently detected minority non-R5 variants from clinical specimens, with an analytical sensitivity of 0.3%, with viral loads of ≥1,000 copies/ml, and from B and non-B subtypes. In a pilot study, a 73.7% (56/76) concordance was observed with the original Trofile assay, with 19 of the 20 discordant results corresponding to non-R5 variants detected using VERITROP and not by the original Trofile assay. The degree of concordance of VERITROP and Trofile with population and deep sequencing results depended on the algorithm used to determine HIV-1 coreceptor tropism. Overall, VERITROP showed better concordance with deep sequencing/Geno2Pheno at a 0.3% detection threshold (67%), whereas Trofile matched better with population sequencing (79%). However, 454 sequencing using Geno2Pheno at a 10% FPR and 0.3% threshold and VERITROP more accurately predicted the success of a maraviroc-based regimen. In conclusion, VERITROP may promote the development of new HIV coreceptor antagonists and aid in the treatment and management of HIV-infected individuals prior to and/or during treatment with this class of drugs.
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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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Ma D, Jasinska A, Kristoff J, Grobler JP, Turner T, Jung Y, Schmitt C, Raehtz K, Feyertag F, Martinez Sosa N, Wijewardana V, Burke DS, Robertson DL, Tracy R, Pandrea I, Freimer N, Apetrei C. SIVagm infection in wild African green monkeys from South Africa: epidemiology, natural history, and evolutionary considerations. PLoS Pathog 2013; 9:e1003011. [PMID: 23349627 PMCID: PMC3547836 DOI: 10.1371/journal.ppat.1003011] [Citation(s) in RCA: 93] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2012] [Accepted: 09/20/2012] [Indexed: 11/18/2022] Open
Abstract
Pathogenesis studies of SIV infection have not been performed to date in wild monkeys due to difficulty in collecting and storing samples on site and the lack of analytical reagents covering the extensive SIV diversity. We performed a large scale study of molecular epidemiology and natural history of SIVagm infection in 225 free-ranging AGMs from multiple locations in South Africa. SIV prevalence (established by sequencing pol, env, and gag) varied dramatically between infant/juvenile (7%) and adult animals (68%) (p<0.0001), and between adult females (78%) and males (57%). Phylogenetic analyses revealed an extensive genetic diversity, including frequent recombination events. Some AGMs harbored epidemiologically linked viruses. Viruses infecting AGMs in the Free State, which are separated from those on the coastal side by the Drakensberg Mountains, formed a separate cluster in the phylogenetic trees; this observation supports a long standing presence of SIV in AGMs, at least from the time of their speciation to their Plio-Pleistocene migration. Specific primers/probes were synthesized based on the pol sequence data and viral loads (VLs) were quantified. VLs were of 10(4)-10(6) RNA copies/ml, in the range of those observed in experimentally-infected monkeys, validating the experimental approaches in natural hosts. VLs were significantly higher (10(7)-10(8) RNA copies/ml) in 10 AGMs diagnosed as acutely infected based on SIV seronegativity (Fiebig II), which suggests a very active transmission of SIVagm in the wild. Neither cytokine levels (as biomarkers of immune activation) nor sCD14 levels (a biomarker of microbial translocation) were different between SIV-infected and SIV-uninfected monkeys. This complex algorithm combining sequencing and phylogeny, VL quantification, serology, and testing of surrogate markers of microbial translocation and immune activation permits a systematic investigation of the epidemiology, viral diversity and natural history of SIV infection in wild African natural hosts.
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Affiliation(s)
- Dongzhu Ma
- Center for Vaccine Research, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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Abstract
HIV-1 subtype CRF01-AE predominates in south Asia and has spread throughout the world. The virus tropism must be determined before using CCR5 antagonists. Genotypic methods could be used, but the prediction algorithms may be inaccurate for non-B subtypes like CRF01-AE and the correlation with the phenotypic approach has not been assessed. We analyzed 61 CRF01-AE V3 clonal sequences of known phenotype from the GenBank database. The sensitivity of the Geno2pheno10 genotypic algorithm was 91%, but its specificity was poor (54%). In contrast, the combined 11/25 and net charge rule was highly specific (98%) but rather insensitive (64%). We thus identified subtype CRF01-AE determinants in the V3 region that are associated with CXCR4 use and developed a new simple rule for optimizing the genotypic prediction of CRF01-AE tropism. The concordance between the predicted CRF01-AE genotype and the phenotype was 95% for the clonal data set. We then validated this algorithm by analyzing the data from 44 patients infected with subtype CRF01-AE, whose tropism was determined using a recombinant phenotypic entry assay and V3-loop bulk sequencing. The CRF01-AE genotypic tool was 70% sensitive and 96% specific for predicting CXCR4 use, and the concordance between genotype and phenotype was 84%, approaching the concordance obtained for predicting the tropism of HIV-1 subtype B. Genotypic predictions that use a subtype CRF01-AE-specific algorithm appear to be preferable for characterizing coreceptor usage both in pathophysiological studies and for ensuring the appropriate use of CCR5 antagonists.
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HIV-1 dynamics and coreceptor usage in Maraviroc-treated patients with ongoing replication. Antimicrob Agents Chemother 2012. [PMID: 23208718 DOI: 10.1128/aac.02159-12] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
There is evidence that HIV-1 evolution under maraviroc (MVC) pressure can lead to the selection of either X4-tropic variants and/or R5-tropic, MVC-resistant isolates. However, the viral dynamics of HIV-1 variants in patients with virological failure (VF) on MVC-containing regimens remain poorly studied. Here, we investigated the V3 loop evolution of HIV-1 on MVC in relation to coreceptor usage and the nature of HIV-1 quasispecies before MVC therapy using bulk population sequences and ultradeep sequencing. The majority of patients had no detectable minority X4 variant at baseline. The evolution of tropism was followed up until VF and showed three possibilities for viral evolution in these patients: emergence of preexisting X4 variants, de novo selection of R5 variants presenting V3 loop mutations, or replication of R5 variants without selection of known mutations.
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Abravanel F, Raymond S, Pambrun E, Winnock M, Bonnard P, Sogni P, Trimoulet P, Dabis F, Salmon-Ceron D, Izopet J. HIV-1 tropism and liver fibrosis in HIV-HCV co-infected patients. PLoS One 2012; 7:e50289. [PMID: 23226258 PMCID: PMC3511493 DOI: 10.1371/journal.pone.0050289] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2012] [Accepted: 10/22/2012] [Indexed: 12/18/2022] Open
Abstract
Background and Aims Hepatic stellate cells, the major producers of extracellular matrix in the liver, and hepatocytes bear CXCR4 and CCR5, the two main co-receptors for entry of the human immunodeficiency virus (HIV). In vitro studies suggest that HIV-envelope proteins can modulate the replication of hepatitis C virus (HCV) and fibrogenesis. We investigated the influence of HIV tropism on liver fibrosis and the concentration of HCV RNA in HIV–HCV co-infected patients. Methods We used a phenotypic assay to assess HIV tropism in 172 HCV–HIV co-infected patients: one group (75 patients) had mild fibrosis (score ≤F2) and the other (97 patients) had severe fibrosis (score >F2). We also assessed the relationship between HIV tropism and HCV RNA concentration in all these patients. We also followed 34 of these patients for 3 years to determine the evolution of HIV tropism and liver fibrosis, estimated by liver stiffness. Results Initially, most patients (91.8%) received a potent antiretroviral therapy. CXCR4-using viruses were found in 29% of patients. The only factor associated with a CXCR4-using virus infection in multivariate analysis was the nadir of CD4 cells: <200/mm3 (OR: 3.94, 95%CI: 1.39–11.14). The median HCV RNA concentrations in patients infected with R5 viruses, those with dual-mixed viruses and those with X4 viruses, were all similar. The prevalence of CXCR4-using viruses in patients with mild fibrosis (≤F2) (31%) and those with severe fibrosis (F3–F4) (28%, p = 0.6) was similar. Longitudinal analyses showed that the presence of CXCR4-using viruses did not increase the likelihood of fibrosis progression, evaluated by measuring liver stiffness. Conclusions The presence of CXCR4-using viruses in patients receiving a potent antiretroviral therapy does not influence HCV RNA concentration or liver fibrosis.
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Affiliation(s)
- Florence Abravanel
- INSERM, U1043, Centre de Physiopathologie de Toulouse Purpan, Toulouse, France.
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Use of four next-generation sequencing platforms to determine HIV-1 coreceptor tropism. PLoS One 2012; 7:e49602. [PMID: 23166726 PMCID: PMC3498215 DOI: 10.1371/journal.pone.0049602] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2012] [Accepted: 09/27/2012] [Indexed: 12/17/2022] Open
Abstract
HIV-1 coreceptor tropism assays are required to rule out the presence of CXCR4-tropic (non-R5) viruses prior treatment with CCR5 antagonists. Phenotypic (e.g., Trofile™, Monogram Biosciences) and genotypic (e.g., population sequencing linked to bioinformatic algorithms) assays are the most widely used. Although several next-generation sequencing (NGS) platforms are available, to date all published deep sequencing HIV-1 tropism studies have used the 454™ Life Sciences/Roche platform. In this study, HIV-1 co-receptor usage was predicted for twelve patients scheduled to start a maraviroc-based antiretroviral regimen. The V3 region of the HIV-1 env gene was sequenced using four NGS platforms: 454™, PacBio® RS (Pacific Biosciences), Illumina®, and Ion Torrent™ (Life Technologies). Cross-platform variation was evaluated, including number of reads, read length and error rates. HIV-1 tropism was inferred using Geno2Pheno, Web PSSM, and the 11/24/25 rule and compared with Trofile™ and virologic response to antiretroviral therapy. Error rates related to insertions/deletions (indels) and nucleotide substitutions introduced by the four NGS platforms were low compared to the actual HIV-1 sequence variation. Each platform detected all major virus variants within the HIV-1 population with similar frequencies. Identification of non-R5 viruses was comparable among the four platforms, with minor differences attributable to the algorithms used to infer HIV-1 tropism. All NGS platforms showed similar concordance with virologic response to the maraviroc-based regimen (75% to 80% range depending on the algorithm used), compared to Trofile (80%) and population sequencing (70%). In conclusion, all four NGS platforms were able to detect minority non-R5 variants at comparable levels suggesting that any NGS-based method can be used to predict HIV-1 coreceptor usage.
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A genotypic test for HIV-1 tropism combining Sanger sequencing with ultradeep sequencing predicts virologic response in treatment-experienced patients. PLoS One 2012; 7:e46334. [PMID: 23029482 PMCID: PMC3459909 DOI: 10.1371/journal.pone.0046334] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2012] [Accepted: 08/31/2012] [Indexed: 12/27/2022] Open
Abstract
A tropism test is required prior to initiation of CCR5 antagonist therapy in HIV-1 infected individuals, as these agents are not effective in patients harboring CXCR4 (X4) coreceptor-using viral variants. We developed a clinical laboratory-based genotypic tropism test for detection of CCR5-using (R5) or X4 variants that utilizes triplicate population sequencing (TPS) followed by ultradeep sequencing (UDS) for samples classified as R5. Tropism was inferred using the bioinformatic algorithms geno2pheno[coreceptor] and PSSMx4r5. Virologic response as a function of tropism readout was retrospectively assessed using blinded samples from treatment-experienced subjects who received maraviroc (N = 327) in the MOTIVATE and A4001029 clinical trials. MOTIVATE patients were classified as R5 and A4001029 patients were classified as non-R5 by the original Trofile test. Virologic response was compared between the R5 and non-R5 groups determined by TPS, UDS alone, the reflex strategy and the Trofile Enhanced Sensitivity (TF-ES) test. UDS had greater sensitivity than TPS to detect minority non-R5 variants. The median log10 viral load change at week 8 was −2.4 for R5 subjects, regardless of the method used for classification; for subjects with non-R5 virus, median changes were −1.2 for TF-ES or the Reflex Test and −1.0 for UDS. The differences between R5 and non-R5 groups were highly significant in all 3 cases (p<0.0001). At week 8, the positive predictive value was 66% for TF-ES and 65% for both the Reflex test and UDS. Negative predictive values were 59% for TF-ES, 58% for the Reflex Test and 61% for UDS. In conclusion, genotypic tropism testing using UDS alone or a reflex strategy separated maraviroc responders and non-responders as well as a sensitive phenotypic test, and both assays showed improved performance compared to TPS alone. Genotypic tropism tests may provide an alternative to phenotypic testing with similar discriminating ability.
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Genebat M, Pulido I, Romero-Sánchez MC, González-Serna A, Ferrando-Martínez S, Machmach K, Pacheco YM, Muñoz-Fernández MÁ, Ruiz-Mateos E, Leal M. Patients on a combined antiretroviral therapy after maraviroc clinical test show no immunovirological impairment. Antiviral Res 2012; 95:207-11. [DOI: 10.1016/j.antiviral.2012.06.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2012] [Revised: 06/19/2012] [Accepted: 06/19/2012] [Indexed: 10/28/2022]
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Tang YW, Ou CY. Past, present and future molecular diagnosis and characterization of human immunodeficiency virus infections. Emerg Microbes Infect 2012; 1:e19. [PMID: 26038427 PMCID: PMC3630918 DOI: 10.1038/emi.2012.15] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2012] [Revised: 05/08/2012] [Accepted: 05/21/2012] [Indexed: 12/31/2022]
Abstract
Substantive and significant advances have been made in the last two decades in the characterization of human immunodeficiency virus (HIV) infections using molecular techniques. These advances include the use of real-time measurements, isothermal amplification, the inclusion of internal quality assurance protocols, device miniaturization and the automation of specimen processing. The result has been a significant increase in the availability of results to a high level of accuracy and quality. Molecular assays are currently widely used for diagnostics, antiretroviral monitoring and drug resistance characterization in developed countries. Simple and cost-effective point-of-care versions are also being vigorously developed with the eventual goal of providing timely healthcare services to patients residing in remote areas and those in resource-constrained countries. In this review, we discuss the evolution of these molecular technologies, not only in the context of the virus, but also in the context of tests focused on human genomics and transcriptomics.
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Affiliation(s)
- Yi-Wei Tang
- Memorial Sloan-Kettering Cancer Center , New York, NY 10065, USA
| | - Chin-Yih Ou
- Centers for Disease Control and Prevention , Atlanta, GA 30333, USA
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Svärd J, Sönnerborg A. Optimizing background therapy in treatment-experienced HIV-1 patients by rules-based algorithms and bioinformatics. Future Virol 2012. [DOI: 10.2217/fvl.12.66] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In HIV-1-infected patients with extensive drug resistance, the optimization of background antiretroviral therapy is essential when changing drugs after treatment failure. The genotypic sensitivity score (GSS) and phenotypic sensitivity score (PSS), determined by rules-based algorithms, are employed to predict which drugs to select in a background therapy in order to receive the best treatment response when a new drug will be used, both in investigational trials of new agents and in clinical care. However, the outcome of the GSS/PSS approach for the purpose of assessing antiretroviral efficacy in patients with multiresistance has become more problematic, despite improvements such as drug potency weighting and adding information on treatment history. Bioinformatics-based methods are more recent attractive alternatives that have demonstrated equal or better precision compared with rules-based algorithms. This review aims to discuss the usefulness of GSS/PSS and bioinformatics, respectively, for the optimization of anti-HIV background therapy in heavily treatment-experienced patients.
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Affiliation(s)
- Jenny Svärd
- Unit of Infectious Diseases, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Anders Sönnerborg
- Unit of Infectious Diseases, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
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Bozek K, Eckhardt M, Sierra S, Anders M, Kaiser R, Kräusslich HG, Müller B, Lengauer T. An expanded model of HIV cell entry phenotype based on multi-parameter single-cell data. Retrovirology 2012; 9:60. [PMID: 22830600 PMCID: PMC3464718 DOI: 10.1186/1742-4690-9-60] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2012] [Accepted: 06/07/2012] [Indexed: 11/29/2022] Open
Abstract
Background Entry of human immunodeficiency virus type 1 (HIV-1) into the host cell involves interactions between the viral envelope glycoproteins (Env) and the cellular receptor CD4 as well as a coreceptor molecule (most importantly CCR5 or CXCR4). Viral preference for a specific coreceptor (tropism) is in particular determined by the third variable loop (V3) of the Env glycoprotein gp120. The approval and use of a coreceptor antagonist for antiretroviral therapy make detailed understanding of tropism and its accurate prediction from patient derived virus isolates essential. The aim of the present study is the development of an extended description of the HIV entry phenotype reflecting its co-dependence on several key determinants as the basis for a more accurate prediction of HIV-1 entry phenotype from genotypic data. Results Here, we established a new protocol of quantitation and computational analysis of the dependence of HIV entry efficiency on receptor and coreceptor cell surface levels as well as viral V3 loop sequence and the presence of two prototypic coreceptor antagonists in varying concentrations. Based on data collected at the single-cell level, we constructed regression models of the HIV-1 entry phenotype integrating the measured determinants. We developed a multivariate phenotype descriptor, termed phenotype vector, which facilitates a more detailed characterization of HIV entry phenotypes than currently used binary tropism classifications. For some of the tested virus variants, the multivariant phenotype vector revealed substantial divergences from existing tropism predictions. We also developed methods for computational prediction of the entry phenotypes based on the V3 sequence and performed an extrapolating calculation of the effectiveness of this computational procedure. Conclusions Our study of the HIV cell entry phenotype and the novel multivariate representation developed here contributes to a more detailed understanding of this phenotype and offers potential for future application in the effective administration of entry inhibitors in antiretroviral therapies.
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Affiliation(s)
- Katarzyna Bozek
- Department of Computational Biology and Applied Algorithmics, Max Planck for Computer Sciences, Campus E1 4 66123, Saarbrücken, Germany
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Jiao Y, Song Y, Kou B, Wang R, Liu Z, Huang X, Chen D, Zhang T, Wu H. Primary CXCR4 co-receptor use in acute HIV infection leads to rapid disease progression in the AE subtype. Viral Immunol 2012; 25:262-7. [PMID: 22783935 DOI: 10.1089/vim.2012.0035] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
This is a comparative study of HIV co-receptor usage in the early stages of HIV infection between two distinct patient groups, one with a low CD4 count (group 1), and the other with a high CD4 count (group 2). Group 1 progressed to a CD4 count below 200 cells/μL within 2 y, while group 2 had a CD4 count above 500 cells/μL within 2 y. Viral RNA was extracted from the plasma of these patients, and the C2-V5 region of the HIV-1 env genes were cloned and sequenced. The co-receptor usage was predicated based on V3 loop amino acid sequences using Geno2pheno and PSSM programs. Our results indicate that in acute HIV infection of rapid progressors (low CD4 count; group 1), the primary co-receptor usage is CXCR4, while in the high CD4 count group (group 2), the co-receptor usage is predominantly CCR5. One-year follow-up data from these patients showed no obvious change in HIV co-receptor usage in either group. Sequence analysis of patients from both study groups showed prevalence of the AE subtype, and therefore we can speculate that the CXCR4 co-receptor may be the primary HIV-1 co-receptor used in the HIV-1 AE subtype, and may be responsible for rapid HIV-1 disease progression in the MSM cohort.
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Affiliation(s)
- Yanmei Jiao
- Center for Infectious Diseases, Beijing You-An Hospital, Capital Medical University, Beijing, China
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Besse B, Coste-Burel M, Bourgeois N, Feray C, Imbert-Marcille BM, André-Garnier E. Genotyping and resistance profile of hepatitis C (HCV) genotypes 1-6 by sequencing the NS3 protease region using a single optimized sensitive method. J Virol Methods 2012; 185:94-100. [PMID: 22728274 DOI: 10.1016/j.jviromet.2012.06.011] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2011] [Revised: 06/04/2012] [Accepted: 06/13/2012] [Indexed: 12/21/2022]
Abstract
The objective was to develop a method of NS3 gene sequencing that allowed simultaneous genotyping and protease inhibitor (PI) resistance profiling of HCV genotypes 1-6. To validate the use of a unique RT-PCR for genotypes 1-6 and evaluate its sensitivity, the NS3 protease region was amplified from 140 plasma samples from patients infected with HCV without previous PI therapy. In parallel, NS5b sequences were obtained. Amplification of NS3 was successful in 139/140 samples (99%). For the 135 samples with both NS5b and NS3 sequencing results, phylogenetic analysis showed concordance of genotypes with a bootstrap >90% for each cluster. PI resistance mutations were analyzed using the Geno2pheno [hcv] v1.0 tool. For the 63 genotype 1 (G1) Nantes clinical strains, 12 (19%) presented a natural resistance mutation. This proportion was higher (p<0.05) than that observed in a sample of 374 G1 reference sequences. This significant difference was observed only in subtype 1b (n=7; 25% against n=19; 8%). In conclusion, this tool allows determination of both HCV genotype and identification of PI-resistance mutations. It can be used to detect pre-existing resistance mutations in NS3 before treatment and follow the emergence of resistant viruses during therapy.
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Affiliation(s)
- Bernard Besse
- Laboratoire de Virologie, CHU Hôtel Dieu Nantes, UNAM, EA4271, Nantes, France
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Trabaud MA, Icard V, Scholtes C, Perpoint T, Koffi J, Cotte L, Makhloufi D, Tardy JC, André P. Discordance in HIV-1 co-receptor use prediction by different genotypic algorithms and phenotype assay: intermediate profile in relation to concordant predictions. J Med Virol 2012; 84:402-13. [PMID: 22246825 DOI: 10.1002/jmv.23209] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Concordant and discordant genotypic predictions of HIV-1 co-receptor tropism were analyzed. V3 region was sequenced from plasma samples of patients screened for R5 tropism by the Trofile® assay, before CCR5 antagonist prescription. Ten tools including geno2pheno, PSSM, an "11/25" and "net charge" rule, and other published algorithms were used. Patients were grouped according to concordance or discordance between tools and Trofile® result. Trofile® tropism reports from 50 patient samples were R5 in 38 and Dual/Mixed (DM) in 12. Prediction with the genotypic tools were concordant for 23 R5 samples, and discordant for the 15 other ones. From Trofile® DM strains were concordant in 6 and discordant in 6. V3 sequences were not clearly distinct between R5 and DM strains, except a greater diversity in the later. Discordances were found with any tool or combination of them, so that no one can be proposed as better than the others. Predictive values of each algorithm were similar and rather good (efficacy ranged from 74% to 84%), but the rate of non-confirmed prediction is greater when compelling the results of all tools with each individual sample. The mean of quantitative values obtained with one tool when another tool give the opposite prediction were different from those obtained when all tools agree with that prediction. The two discordant groups were often not distinguishable from each other. These results suggest that viruses giving discordant prediction with bioinformatic tools could be functionally distinct and/or in a different evolutionary state compared to those with concordant prediction.
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Affiliation(s)
- Mary-Anne Trabaud
- Laboratory of Virology, Hôpital de la Croix Rousse, Hospices Civils de Lyon, Lyon, France.
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Symons J, Vandekerckhove L, Paredes R, Verhofstede C, Bellido R, Demecheleer E, van Ham PM, van Lelyveld SFL, Stam AJ, van Versendaal D, Nijhuis M, Wensing AMJ. Impact of triplicate testing on HIV genotypic tropism prediction in routine clinical practice. Clin Microbiol Infect 2012; 18:606-12. [PMID: 21906210 DOI: 10.1111/j.1469-0691.2011.03631.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- J Symons
- Department of Virology, Medical Microbiology, University Medical Centre Utrecht, The Netherlands
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Baroncelli S, Galluzzo CM, Weimer LE, Pirillo MF, Volpe A, Mercuri A, Cavalli A, Fragola V, Monno L, Degli Antoni A, Ladisa N, Francisci D, Bucciardini R, Floridia M. Evolution of proviral DNA HIV-1 tropism under selective pressure of maraviroc-based therapy. J Antimicrob Chemother 2012; 67:1479-85. [PMID: 22361986 DOI: 10.1093/jac/dks055] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
OBJECTIVES To evaluate the evolution of HIV-1 coreceptor tropism in proviral DNA of patients during maraviroc-based therapy. METHODS Fourteen heavily high active antiretroviral therapy (HAART)-treated patients with a CCR5 Trofile profile were monitored over a 24 month period from the start of maraviroc therapy. Whole-blood samples were obtained at different timepoints, and coreceptor tropism was determined for proviral DNA from the V3-loop region sequence using the Geno2Pheno algorithm [false positive rate (FPR): 20%]. RESULTS At the start of maraviroc treatment, 13/14 patients were viraemic (median: 4.33 log copies/mL). Concordance in R5 tropism (R5/R5) was observed between circulating HIV-RNA (Trofile) and HIV-DNA provirus in 10/14 patients (median FPR = 54.0%), while 4 patients showed a CXCR4-tropic R5/X4 variant in their provirus (FPR: 5.8%, 5.7%, 16.6% and 1.1%, respectively). All R5/R5 patients showed a stable HIV-1 DNA coreceptor usage. Two out of four R5/X4 patients showed a tropism shift in their archived provirus and, after 6 months a prevalence of R5-tropic virus was detected in DNA. The other two R5/X4 patients harboured the 11/25 genotype, and maintained X4 tropism in provirus during the study. Virological response did not reveal differences in RNA decay and CD4+ cell recovery in patients with discordant tropism. CONCLUSIONS A relatively good correlation between RNA and DNA tropism was observed at baseline. Proviral DNA tropism remained stable over 24 months of maraviroc-based therapy, indicating that determination of proviral DNA V3 sequence could be used in tropism prediction in clinical practice. The data also confirm the importance of the 11/25 rule in predicting viral tropism.
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Affiliation(s)
- Silvia Baroncelli
- Department of Therapeutic Research and Medicines Evaluation, Istituto Superiore di Sanità, Rome, Italy.
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Correlation of the virological response to short-term maraviroc monotherapy with standard and deep-sequencing-based genotypic tropism prediction methods. Antimicrob Agents Chemother 2011; 56:1202-7. [PMID: 22143533 DOI: 10.1128/aac.05857-11] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Genotypic tropism testing methods are emerging as the first step before prescription of the CCR5 antagonist maraviroc (MVC) to HIV-infected patients in Europe. Studies validating genotypic tests have included other active drugs that could have potentially convoluted the effects of MVC. The maraviroc clinical test (MCT) is an in vivo drug sensitivity test based on the virological response to a short-term exposure to MVC monotherapy. Thus, our aim was to compare the results of genotypic tropism testing methods with the short-term virological response to MVC monotherapy. A virological response in the MCT was defined as a ≥ 1-log(10) decrease in HIV RNA or undetectability after 8 days of drug exposure. Seventy-three patients undergoing the MCT were included in this study. We used both standard genotypic methods (n = 73) and deep sequencing (n = 27) on MCT samples at baseline. For the standard methods, the most widely used genotypic algorithms for analyzing the V3 loop sequence, geno2pheno and PSSM, were used. For deep sequencing, the geno2pheno algorithm was used with a false-positive rate cutoff of 3.5. The discordance rates between the standard genotypic methods and the virological response were approximately 20% (including mostly patients without a virological response). Interestingly, these discordance rates were similar to that obtained from deep sequencing (18.5%). The discordance rates between the genotypic methods (tropism assays predictive of the use of the CCR5 coreceptor) and the MCT (in vivo MVC sensitivity assay) indicate that the algorithms used by genotypic methods are still not sufficiently optimized.
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Visseaux B, Hurtado-Nedelec M, Charpentier C, Collin G, Storto A, Matheron S, Larrouy L, Damond F, Brun-Vézinet F, Descamps D. Molecular determinants of HIV-2 R5-X4 tropism in the V3 loop: development of a new genotypic tool. J Infect Dis 2011; 205:111-20. [PMID: 22140264 DOI: 10.1093/infdis/jir698] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
OBJECTIVE The use of CCR5 inhibitors requires a tool to predict human immunodeficiency virus type 2 (HIV-2) tropism, as established in HIV-1. The aim of our study was to identify genotypic determinants of HIV-2 tropism located in the gp105 V3 loop. METHODS HIV-2 tropism phenotypic assays were performed on 53 HIV-2 clinical isolates using GFP expressing human osteosarcoma T4 [GHOST(3)] cell lines expressing CD4 and CCR5 or CXCR4 coreceptors. The gp105 V3 loop was sequenced and analyzed. RESULTS Thirty-four HIV-2 isolates were classified as R5, 7 as X4, and 12 as X4/R5 (dual). Substitution at residue 18 was always associated with a dual/X4 tropism (P < .00001). The following determinants were associated with dual/X4 tropism: a global net charge of more than +6 (P < .00001), V19K/R mutation (P < .00001), S22A/F/Y mutation (P < .002), Q23R mutation (P < .00001), and insertions at residue 24 (P < .00001), I25L/Y (P < .0004), R28K (P < .0004), and R30K (P < .014). These mutations were not found in R5 isolates, except R28K and R30K, which were detected in 4 and 5 R5 isolates, respectively. The 4 major genotypic determinants of dual/X4 tropism were mutation at residue 18, V19 K/R mutation, insertions at residue 24, and V3 global net charge. CONCLUSIONS We established a strong association between HIV-2 phenotypic tropism and V3-loop sequences, allowing for the prediction of R5- and/or X4-tropic viruses in HIV-2 infection.
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Affiliation(s)
- Benoit Visseaux
- Laboratoire de Virologie, Assistance Publique-Hôpitaux de Paris, Hôpital Bichat-Claude Bernard, France
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Sierra S, Kaiser R, Lübke N, Thielen A, Schuelter E, Heger E, Däumer M, Reuter S, Esser S, Fätkenheuer G, Pfister H, Oette M, Lengauer T. Prediction of HIV-1 coreceptor usage (tropism) by sequence analysis using a genotypic approach. J Vis Exp 2011:3264. [PMID: 22157596 PMCID: PMC3369655 DOI: 10.3791/3264] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Maraviroc (MVC) is the first licensed antiretroviral drug from the class of coreceptor antagonists. It binds to the host coreceptor CCR5, which is used by the majority of HIV strains in order to infect the human immune cells (Fig. 1). Other HIV isolates use a different coreceptor, the CXCR4. Which receptor is used, is determined in the virus by the Env protein (Fig. 2). Depending on the coreceptor used, the viruses are classified as R5 or X4, respectively. MVC binds to the CCR5 receptor inhibiting the entry of R5 viruses into the target cell. During the course of disease, X4 viruses may emerge and outgrow the R5 viruses. Determination of coreceptor usage (also called tropism) is therefore mandatory prior to administration of MVC, as demanded by EMA and FDA. The studies for MVC efficiency MOTIVATE, MERIT and 1029 have been performed with the Trofile assay from Monogram, San Francisco, U.S.A. This is a high quality assay based on sophisticated recombinant tests. The acceptance for this test for daily routine is rather low outside of the U.S.A., since the European physicians rather tend to work with decentralized expert laboratories, which also provide concomitant resistance testing. These laboratories have undergone several quality assurance evaluations, the last one being presented in 2011. For several years now, we have performed tropism determinations based on sequence analysis from the HIV env-V3 gene region (V3). This region carries enough information to perform a reliable prediction. The genotypic determination of coreceptor usage presents advantages such as: shorter turnover time (equivalent to resistance testing), lower costs, possibility to adapt the results to the patients' needs and possibility of analysing clinical samples with very low or even undetectable viral load (VL), particularly since the number of samples analysed with VL < 1000 copies/μl roughly increased in the last years (Fig. 3). The main steps for tropism testing (Fig. 4) demonstrated in this video: Collection of a blood sample Isolation of the HIV RNA from the plasma and/or HIV proviral DNA from blood mononuclear cells Amplification of the env region Amplification of the V3 region Sequence reaction of the V3 amplicon Purification of the sequencing samples Sequencing the purified samples Sequence editing Sequencing data interpretation and tropism prediction.
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MESH Headings
- DNA, Viral/blood
- DNA, Viral/chemistry
- DNA, Viral/genetics
- DNA, Viral/isolation & purification
- Genotyping Techniques/methods
- HIV Envelope Protein gp120/chemistry
- HIV Envelope Protein gp120/genetics
- HIV Infections/blood
- HIV Infections/virology
- HIV-1/genetics
- HIV-1/metabolism
- HIV-1/physiology
- Humans
- Oligonucleotide Array Sequence Analysis
- Peptide Fragments/chemistry
- Peptide Fragments/genetics
- Polymerase Chain Reaction/methods
- RNA, Viral/blood
- RNA, Viral/chemistry
- RNA, Viral/genetics
- RNA, Viral/isolation & purification
- Receptors, CCR5/metabolism
- Receptors, CXCR4/metabolism
- Tropism/genetics
- Tropism/physiology
- env Gene Products, Human Immunodeficiency Virus/chemistry
- env Gene Products, Human Immunodeficiency Virus/genetics
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Delgado E, Fernández-García A, Vega Y, Cuevas T, Pinilla M, García V, Sánchez M, González M, Sánchez AM, Thomson MM, Pérez-Álvarez L. Evaluation of genotypic tropism prediction tests compared with in vitro co-receptor usage in HIV-1 primary isolates of diverse subtypes. J Antimicrob Chemother 2011; 67:25-31. [PMID: 22010208 DOI: 10.1093/jac/dkr438] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
OBJECTIVES To evaluate the sensitivity and specificity of genotypic methods for predicting the co-receptor usage of subtypes B and non-B HIV-1 primary isolates, using as gold standard the infectivity of each primary isolate in GHOST cells stably expressing HIV-1 co-receptors. METHODS Primary isolates were obtained by co-culturing either patient's peripheral blood mononuclear cells (PBMCs) or ultracentrifuged plasma with donor-activated PBMCs. In vitro co-receptor usage was determined by infecting GHOST cells. Tropism prediction, based on V3 sequences, was determined with simple rules and bioinformatic tools (Geno2pheno[coreceptor] and WebPSSM). RESULTS This study includes 102 HIV-1 primary isolates; 23 (22.5%) subtype B and 79 (77.5%) non-B genetic forms. V3 sequences were classified into six subtypes (A-G), although 32 (31.4%) were circulating recombinant forms and 21 (20.6%) were unique recombinant forms. Sixty-nine isolates were R5, 27 R5X4 and 6 X4. The highest levels of sensitivity and specificity for the detection of X4 strains among V3 sequences, between 91% and 100%, were obtained by using PSSM(x4r5), PSSM(si/nsi) and the 11/25 rule for sequences of subtypes A, B and G, but not for subtype F. Establishing the recommended cut-off for clinical settings of a 10% false positive rate for Geno2pheno, we obtained 93% specificity and 97% sensitivity. CONCLUSIONS Comparing genotypic assays for HIV-1 co-receptor use with a cell-culture phenotypic assay could provide more reliable results of sensitivity and specificity for the detection of X4 strains than comparing them with recombinant assays, considered as gold standard. In general, except for subtype F isolates, there is a good correlation for tropism prediction.
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Affiliation(s)
- Elena Delgado
- HIV Biology and Variability Department, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
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