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Bratosiewicz-Wąsik J, Wąsik TJ. Genetic variants of IL-10 promoter influence susceptibility to HIV-1 infection and disease progression in the Polish population: IL-10 polymorphisms and HIV-1. Hum Immunol 2024; 85:111086. [PMID: 39153369 DOI: 10.1016/j.humimm.2024.111086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Revised: 07/23/2024] [Accepted: 08/04/2024] [Indexed: 08/19/2024]
Abstract
The risk of HIV-1 infection and the rate of disease progression vary considerably among individuals and the genetic makeup of the host may be one of the possible reasons for this. We aimed to determine association of functional single nucleotide polymorphism (SNPs), -1082A/G (rs1800896), -819C/T (rs1800871), and -592C/A (rs1800872) in IL-10 gene, with the susceptibility to HIV-1 infection and clinical parameters expressed as a baseline CD4+ T cell count, CD8+ T cell count, and viral load. Therapy naïve HIV-1 infected individuals and HIV-1 seronegative controls from Poland were recruited for this study. Genotyping results revealed significantly higher frequency of -1082G/G genotype (28.1 % vs 16.1 %; p = 0.0019, OR=0.49) and -1082G allele (47.6 % vs 38.8 %; p = 0.0028, OR = 0.70) as well as lower frequency of -592 and -819 heterozygosity (45.0 % vs 34.4 %; p = 0.0266, OR = 1.47) in controls compared to seropositive subjects. High producing haplotype GCC was associated with increased risk of HIV-1 infection (p = 0.0018, OR = 1.52). Individuals possessing -592 and -819 minor allele had significantly higher CD8+ T cell count compared to the wild type allele carriers (p = 0.0303). Moreover, presence of -1082G allele was related with lower viral load as well as CD4+ and CD8+ T cells counts among patients infected with R5 HIV-1 variant. Thus, IL-10 gene promoter variants may be a risk factor for HIV-1 transmission and may modulate disease progression in the Polish population.
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Affiliation(s)
- Jolanta Bratosiewicz-Wąsik
- Department of Microbiology and Virology, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia in Katowice, 41-200 Sosnowiec, ul. Jagiellońska 4, Poland.
| | - Tomasz J Wąsik
- Department of Medical Microbiology, Faculty of Medical Sciences in Katowice, Medical University of Silesia in Katowice, 40-752 Katowice, ul. Medyków 18, Poland.
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2
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Folgosi VÂ, Komninakis SV, Lopes L, Monteiro MA, Assone T, Fonseca LAM, Domingues W, Leite PD, Victor JR, Casseb J. Unraveling clinical outcomes of long-term cART treatment in HIV-1 patients with or without the Brazilian GWGR motif in the V3 loop. Rev Inst Med Trop Sao Paulo 2024; 66:e38. [PMID: 39052025 PMCID: PMC11251515 DOI: 10.1590/s1678-9946202466038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 05/06/2024] [Indexed: 07/27/2024] Open
Abstract
The presence of genetic mutations in HIV poses a significant challenge, potentially leading to antiretroviral resistance and hampering therapeutic development. The Brazilian population has presented variations in the HIV envelope V3 loop gene, especially the GWGR motif. This motif has been linked to reduced transmission potential and slower CD4+ T cell decline. This study aimed to assess clinical outcomes in patients with HIV-1 infected with strains containing the GWGR motif compared with those without it during long-term cART. A cohort of 295 patients with HIV was examined for the GWGR motif presence in the V3 loop. A total of 58 samples showed the GWGR signature, while 237 had other signatures. Multifactorial analyses showed no significant differences in demographic characteristics, CD4+ cell count, AIDS progression, or mortality between GWGR carriers and others. However, the mean interval between the first positive HIV test and the initial AIDS-defining event was more than two times longer for women carrying the GWGR signature (p = 0.0231). We emphasize the positive impact of cART on HIV/AIDS treatment, including viral suppression, CD4+ cell preservation, and immune function maintenance. Although no significant differences were found during cART, residual outcomes reflecting adherence challenges were observed between diagnosis and the first AIDS-defining event. The previously described outcomes, highlighting statistically significant differences between individuals carrying the GPGR motif compared with those with the Brazilian GWGR motif, may be directly linked to the natural progression of infection before advancements in cART. Presently, these physicochemical aspects may no longer hold the same relevance.
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Affiliation(s)
- Victor Ângelo Folgosi
- Universidade de São Paulo, Faculdade de Medicina, Instituto de
Medicina Tropical de São Paulo, Laboratório de Investigação Médica (LIM-56), São
Paulo, São Paulo, Brazil
| | - Shirley Vasconcelos Komninakis
- Universidade de São Paulo, Faculdade de Medicina, Instituto de
Medicina Tropical de São Paulo, Laboratório de Investigação Médica (LIM-56), São
Paulo, São Paulo, Brazil
- Universidade Federal de São Paulo, Laboratório de Retrovirologia,
São Paulo, São Paulo, Brazil
| | - Luciano Lopes
- Universidade Federal de São Paulo, Departamento de Informática em
Saúde, Divisão de Bioinformática e Ciência de Dados em Biologia, São Paulo, São
Paulo, Brazil
| | - Mariana Amélia Monteiro
- Universidade de São Paulo, Faculdade de Medicina, Instituto de
Medicina Tropical de São Paulo, Laboratório de Investigação Médica (LIM-56), São
Paulo, São Paulo, Brazil
| | - Tatiane Assone
- Universidade de São Paulo, Faculdade de Medicina, Instituto de
Medicina Tropical de São Paulo, Laboratório de Investigação Médica (LIM-56), São
Paulo, São Paulo, Brazil
| | - Luiz Augusto Marcondes Fonseca
- Universidade de São Paulo, Faculdade de Medicina, Instituto de
Medicina Tropical de São Paulo, Laboratório de Investigação Médica (LIM-56), São
Paulo, São Paulo, Brazil
| | - Wilson Domingues
- Universidade de São Paulo, Faculdade de Medicina, Instituto de
Medicina Tropical de São Paulo, Laboratório de Investigação Médica (LIM-56), São
Paulo, São Paulo, Brazil
| | - Pedro Domingos Leite
- Universidade de São Paulo, Faculdade de Medicina, Instituto de
Medicina Tropical de São Paulo, Laboratório de Investigação Médica (LIM-56), São
Paulo, São Paulo, Brazil
| | - Jefferson Russo Victor
- Universidade de São Paulo, Faculdade de Medicina, Instituto de
Medicina Tropical de São Paulo, Laboratório de Investigação Médica (LIM-56), São
Paulo, São Paulo, Brazil
- Universidade Santo Amaro, Programa de Pós-Graduação em Ciências da
Saúde, São Paulo, São Paulo, Brazil
| | - Jorge Casseb
- Universidade de São Paulo, Faculdade de Medicina, Instituto de
Medicina Tropical de São Paulo, Laboratório de Investigação Médica (LIM-56), São
Paulo, São Paulo, Brazil
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Singh K, Mehta D, Dumka S, Chauhan AS, Kumar S. Quasispecies Nature of RNA Viruses: Lessons from the Past. Vaccines (Basel) 2023; 11:308. [PMID: 36851186 PMCID: PMC9963406 DOI: 10.3390/vaccines11020308] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 01/22/2023] [Accepted: 01/23/2023] [Indexed: 01/31/2023] Open
Abstract
Viral quasispecies are distinct but closely related mutants formed by the disparity in viral genomes due to recombination, mutations, competition, and selection pressure. Theoretical derivation for the origin of a quasispecies is owed to the error-prone replication by polymerase and mutants of RNA replicators. Here, we briefly addressed the theoretical and mathematical origin of quasispecies and their dynamics. The impact of quasispecies for major salient human pathogens is reviewed. In the current global scenario, rapid changes in geographical landscapes favor the origin and selection of mutants. It comes as no surprise that a cauldron of mutants poses a significant risk to public health, capable of causing pandemics. Mutation rates in RNA viruses are magnitudes higher than in DNA organisms, explaining their enhanced virulence and evolvability. RNA viruses cause the most devastating pandemics; for example, members of the Orthomyxoviridae family caused the great influenza pandemic (1918 flu or Spanish flu), the SARS (severe acute respiratory syndrome) and MERS (Middle East respiratory syndrome) outbreak, and the human immunodeficiency viruses (HIV), lentiviruses of the Retroviridae family, caused worldwide devastation. Rapidly evolving RNA virus populations are a daunting challenge for the designing of effective control measures like vaccines. Developing awareness of the evolutionary dispositions of RNA viral mutant spectra and what influences their adaptation and virulence will help curtail outbreaks of past and future pathogens.
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Affiliation(s)
| | | | | | | | - Sachin Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, India
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Weiser B, Shi B, Kemal K, Burger H, Minkoff H, Shi Q, Gao W, Robison E, Holman S, Schroeder T, Gormley A, Anastos K, Ramirez C. Long-term antiretroviral therapy mitigates mortality and morbidity independent of HIV tropism: 18 years follow-up in a women's cohort. AIDS 2022; 36:1979-1986. [PMID: 35848576 PMCID: PMC9617757 DOI: 10.1097/qad.0000000000003337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
OBJECTIVE CXCR4 (X4)-tropic HIV-1 was found previously to herald CD4 + cell depletion and disease progression in individuals who were antiretroviral-naive or took combination antiretroviral therapy (cART) for less than 5 years. We updated this finding by investigating whether the deleterious effect of X4-tropic strains is mitigated by long-term cART. DESIGN We examined morbidity and mortality in relation to HIV-1 tropism and cART in 529 participants followed up to 18 years in the Women's Interagency HIV Study; 91% were women of color. METHODS Plasma-derived HIV-1 tropism was determined genotypically. RESULTS We categorized participants according to the number of visits reported on cART after initiation. Group 1: three or less visits, 74% of these participants reporting no cART; group 2: at least four visits and less than 70% of visits on cART; group 3: at least 70% of visits on cART. AIDS mortality rates for participants in each group with X4 virus compared with those with R5 virus exclusively were, respectively: 62 vs. 40% ( P = 0.0088); 23% vs. 22% [nonsignificant (NS)]; 7% vs. 14% (NS). Kaplan-Meier curves showed accelerated progression to AIDS death or AIDS-defining illness in participants with three or less cART visits and X4 viruses ( P = 0.0028) but no difference in progression rates stratified by tropism in other groups. Logistic regression found that HIV-1 suppression for at least 10 semiannual visits (≥5 years total) mitigated X4 tropism's deleterious effect on mortality, controlling for maximal viral load, and CD4 + nadir. CONCLUSION Long-term cART markedly mitigated the deleterious effect of X4 viruses on AIDS morbidity and mortality. Mitigation was correlated with duration of viral suppression, supporting HIV-1 suppression as a crucial goal.
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Affiliation(s)
- Barbara Weiser
- Department of Medicine, University of California, Davis School of Medicine, Sacramento
- Department of Medicine, Veterans Affairs Northern California Healthcare System, Sacramento Medical Center, Mather, CA
| | - Binshan Shi
- Department of Basic and Clinical Sciences, Albany College of Pharmacy and Health Sciences
| | - Kimdar Kemal
- Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - Harold Burger
- Department of Medicine, University of California, Davis School of Medicine, Sacramento
- Department of Medicine, Veterans Affairs Northern California Healthcare System, Sacramento Medical Center, Mather, CA
| | - Howard Minkoff
- Department of Obstetrics/Gynecology, State University of New York Health Science Center at Brooklyn
| | - Qiuhu Shi
- Department of Statistics, School of Health Sciences and Practice, New York Medical College, Valhalla
| | - Wei Gao
- Department of Medicine, Albert Einstein College of Medicine and Montefiore Health Systems, Bronx
| | - Esther Robison
- Department of Medicine, Albert Einstein College of Medicine and Montefiore Health Systems, Bronx
| | - Susan Holman
- Department of Medicine, State University of New York Health Science Center at Brooklyn, NY
| | - Tamara Schroeder
- Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - Alissa Gormley
- Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - Kathryn Anastos
- Department of Medicine, Albert Einstein College of Medicine and Montefiore Health Systems, Bronx
| | - Christina Ramirez
- Department of Biostatistics, University of California, Los Angeles, Fielding School of Public Health, Los Angeles, CA, USA
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Mohamed H, Gurrola T, Berman R, Collins M, Sariyer IK, Nonnemacher MR, Wigdahl B. Targeting CCR5 as a Component of an HIV-1 Therapeutic Strategy. Front Immunol 2022; 12:816515. [PMID: 35126374 PMCID: PMC8811197 DOI: 10.3389/fimmu.2021.816515] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 12/13/2021] [Indexed: 12/26/2022] Open
Abstract
Globally, human immunodeficiency virus type 1 (HIV-1) infection is a major health burden for which successful therapeutic options are still being investigated. Challenges facing current drugs that are part of the established life-long antiretroviral therapy (ART) include toxicity, development of drug resistant HIV-1 strains, the cost of treatment, and the inability to eradicate the provirus from infected cells. For these reasons, novel anti-HIV-1 therapeutics that can prevent or eliminate disease progression including the onset of the acquired immunodeficiency syndrome (AIDS) are needed. While development of HIV-1 vaccination has also been challenging, recent advancements demonstrate that infection of HIV-1-susceptible cells can be prevented in individuals living with HIV-1, by targeting C-C chemokine receptor type 5 (CCR5). CCR5 serves many functions in the human immune response and is a co-receptor utilized by HIV-1 for entry into immune cells. Therapeutics targeting CCR5 generally involve gene editing techniques including CRISPR, CCR5 blockade using antibodies or antagonists, or combinations of both. Here we review the efficacy of these approaches and discuss the potential of their use in the clinic as novel ART-independent therapies for HIV-1 infection.
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Affiliation(s)
- Hager Mohamed
- Department of Microbiology and Immunology, Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United States
| | - Theodore Gurrola
- Department of Microbiology and Immunology, Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United States
| | - Rachel Berman
- Department of Microbiology and Immunology, Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United States
| | - Mackenzie Collins
- Department of Microbiology and Immunology, Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United States
| | - Ilker K. Sariyer
- Department of Microbiology, Immunology, and Inflammation, Center for Neurovirology and Gene Editing, School of Medicine, Temple University, Philadelphia, PA, United States
| | - Michael R. Nonnemacher
- Department of Microbiology and Immunology, Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United States
| | - Brian Wigdahl
- Department of Microbiology and Immunology, Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, United States
- *Correspondence: Brian Wigdahl,
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Mengoli C, Basso M, Andreis S, Scaggiante R, Cruciani M, Ferretto R, Panese S, Manfrin V, Francisci D, Schiaroli E, Maffongelli G, Sarmati L, Andreoni M, Baldelli F, Palu' G, Parisi SG. Role of pretreatment variables on plasma HIV RNA value at the sixth month of antiretroviral therapy including all first line drugs in HIV naïve patients: A path analysis approach. PLoS One 2019; 14:e0213160. [PMID: 30856186 PMCID: PMC6411145 DOI: 10.1371/journal.pone.0213160] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 02/15/2019] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND AND AIMS We investigated the conditioning roles of viral tropism and other variables on plasma HIV RNA levels after 6 months of combination antiretroviral therapy (cART) in an HIV-infected Italian naïve population using regression tree, random forest regression, and path analysis (PA). Patients in this multicenter observational study were treated with all antiviral drugs that are currently recommended as first-line therapies. METHODS Adult patients with chronic HIV infection were enrolled at the beginning of first-line cART (T0). The main variables were age, gender, tropism, "lcd4_0" and "lcd4_6" (log10 CD4+counts at T0 and after 6 months of cART, respectively), and "lrna0" (log10 HIV RNA at T0). Regression tree and random forest analyses were applied. The predictive effect on lrna6 (log10-transformed plasma HIV RNA after 6 months of cART) was also investigated via PA (x4->lcd4_0->lrna0->lrna6) with a treatment selection step included as a dependent (mediator) variable for each third drug and, as predictive covariates, age, female, x4_10, x4_5, lcd4_0, and lrna0. Tropism was assessed in plasma using the Geno2pheno algorithm with 2 false positive rate (FPR) cut-offs: 5% (x4_5) and 10% (x4_10). RESULTS The study included 571 subjects (21% x4_10 and 10.7% x4_5). The only important predictor of lrna6 was lrna0, and a positive indirect effect of bearing X4 virus in plasma was suggested. A significant direct positive effect of protease inhibitors on lrna6 was found (p = 0.022), and a significant negative effect of integrase strand transfer inhibitor (INSTI) was also detected (p = 0.003 for FPR ≤ 5% and p = 0.01 for FPR < 10%). PA predicted mean residual viremias of 40 copies/mL without INSTI and 3 copies/mL with INSTI. CONCLUSIONS PA indicated a possible indirect role of HIV tropism on lrna6 with both FPR < 10% and ≤ 5%. Patients treated with INSTI had a predicted residual viremia of 3 copies/mL.
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Affiliation(s)
- Carlo Mengoli
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Monica Basso
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Samantha Andreis
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Renzo Scaggiante
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | | | - Roberto Ferretto
- Clinical Infectious Diseases, Santorso Hospital, Santorso (VI), Italy
| | - Sandro Panese
- Clinical Infectious Diseases, Mestre Hospital, Venezia, Italy
| | - Vinicio Manfrin
- Clinical Infectious Diseases, Vicenza Hospital, Vicenza, Italy
| | | | | | | | - Loredana Sarmati
- Clinical Infectious Diseases, Tor Vergata University, Roma, Italy
| | - Massimo Andreoni
- Clinical Infectious Diseases, Tor Vergata University, Roma, Italy
| | - Franco Baldelli
- Clinical Infectious Diseases, University of Perugia, Perugia, Italy
| | - Giorgio Palu'
- Department of Molecular Medicine, University of Padova, Padova, Italy
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HIV-1 coreceptor tropism: A syllogistic connection with The Veterans Aging Cohort Study Index and the CD4/CD8 ratio. PLoS One 2019; 14:e0212882. [PMID: 30818365 PMCID: PMC6394994 DOI: 10.1371/journal.pone.0212882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 02/11/2019] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The association between X4 virus and an increased risk of non-AIDS-events has been reported. Morbidity/mortality due to non-AIDS events, which are properly predicted by the CD4/CD8 ratio and VACS index, have become particularly remarkable in HIV-infected patients receiving effective combined antiretroviral therapy (cART). METHODS We verified the validity of the syllogism: as HIV-tropism (CRT) contributes to the onset of non-AIDS events which are successfully predicted by the CD4/CD8 ratio and VACS index, then CRT correlates with these two variables. The CD4/CD8 ratio and VACS index at baseline and overtime were analyzed according to CRT tested before the first successful cART regimen in newly-diagnosed patients. RESULTS Patients with R5 variants had a significantly lower baseline VACS percentage risk [mean (95%CI):18.2%(16.1-20.3) vs 24.3%(18.2-22.5), p = 0.002] and higher baseline CD4/CD8 ratio [mean (95%CI):0.43 (0.38-0.47) vs 0.28 (0.19-0.36), p = 0.002] than non-R5 patients. After an initial drop, VACS increased again in R5 and non-R5 patients and the two trend curves almost overlapped. The CD4/CD8 ratio had an increasing trend in both R5 and non-R5 patients; however, even though non-R5 patients had a greater gain of CD4+, they maintained a lower CD4/CD8 ratio at any time point. CONCLUSION Our study confirms an association between pre-therapy CRT, CD4/CD8 ratio and VACS. A successful cART regimen positively affects the CD4/CD8 ratio; however, the disadvantage conferred by a non-R5 CRT is maintained overtime. The restoration of VACS in all patients could be directly due to variables included in the VACS calculation and to factors that adversely influence these variables.
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Casadellà M, Cozzi-Lepri A, Phillips A, Noguera-Julian M, Bickel M, Sedlacek D, Zilmer K, Clotet B, Lundgren JD, Paredes R. Plasma HIV-1 Tropism and the Risk of Short-Term Clinical Progression to AIDS or Death. PLoS One 2017; 12:e0166613. [PMID: 28129343 PMCID: PMC5271314 DOI: 10.1371/journal.pone.0166613] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2016] [Accepted: 11/01/2016] [Indexed: 12/15/2022] Open
Abstract
OBJECTIVE To investigate if plasma HIV-1 tropism testing could identify subjects at higher risk for clinical progression and death in routine clinical management. DESIGN Nested case-control study within the EuroSIDA cohort. METHODS Cases were subjects with AIDS or who died from any cause, with a plasma sample with HIV-1 RNA >1000 copies/mL available for tropism testing 3 to 12 months prior to the event. At least 1 control matched for age, HIV-1 RNA and HCV status at the time of sampling were selected per each case. Conditional logistic regression was used to investigate exposures associated with clinical progression to AIDS or death. A linear mixed model with random intercept was used to compare CD4+T-cell slopes by HIV tropism over the 12 months following the date of sampling. RESULTS The study included 266 subjects, 100 cases and 166 controls; one quarter had X4 HIV; 26% were ART-naïve. Baseline factors independently associated with clinical progression or death were female gender (OR = 2.13 vs. male, 95CI = 1.04, 4.36), p = 0.038), CD4+T-cell count (OR = 0.90 (95CI = 0.80, 1.00) per 100 cells/mm3 higher, p = 0.058), being on ART (OR = 2.72 vs. being off-ART (95CI = 1.15, 6.41), p = 0.022) and calendar year of sample [OR = 0.84 (95CI = 0.77, 0.91) per more recent year, p<0.001). Baseline tropism was not associated with the risk of clinical progression or death. CD4+T-cell slopes did not differ within or between tropism groups. CONCLUSIONS The predictive role of plasma tropism determined using 454 sequencing in the context of people receiving cART with detectable VL is not helpful to identify subjects at higher risk for clinical progression to AIDS or death.
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Affiliation(s)
- Maria Casadellà
- IrsiCaixa AIDS Research Institute, Badalona, Catalonia, Spain
- Universitat Autònoma de Barcelona, Catalonia, Spain
| | | | | | - Marc Noguera-Julian
- IrsiCaixa AIDS Research Institute, Badalona, Catalonia, Spain
- Universitat Autònoma de Barcelona, Catalonia, Spain
- Universitat de Vic-Universitat Central de Catalunya, Vic, Catalonia, Spain
| | | | | | - Kai Zilmer
- West-Tallinn Central Hospital, Tallinn, Estonia
| | - Bonaventura Clotet
- IrsiCaixa AIDS Research Institute, Badalona, Catalonia, Spain
- Universitat Autònoma de Barcelona, Catalonia, Spain
- Universitat de Vic-Universitat Central de Catalunya, Vic, Catalonia, Spain
- HIV Unit, Hospital Universitari Germans Trias i Pujol, Badalona, Catalonia, Spain
| | - Jens D Lundgren
- CHIP, Department of Infectious Diseases, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Roger Paredes
- IrsiCaixa AIDS Research Institute, Badalona, Catalonia, Spain
- Universitat Autònoma de Barcelona, Catalonia, Spain
- Universitat de Vic-Universitat Central de Catalunya, Vic, Catalonia, Spain
- HIV Unit, Hospital Universitari Germans Trias i Pujol, Badalona, Catalonia, Spain
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9
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Scarpelini B, Zanoni M, Sucupira MCA, Truong HHM, Janini LMR, Segurado IDC, Diaz RS. Plasma Metabolomics Biosignature According to HIV Stage of Infection, Pace of Disease Progression, Viremia Level and Immunological Response to Treatment. PLoS One 2016; 11:e0161920. [PMID: 27941971 PMCID: PMC5152829 DOI: 10.1371/journal.pone.0161920] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 08/15/2016] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND We evaluated plasma samples HIV-infected individuals with different phenotypic profile among five HIV-infected elite controllers and five rapid progressors after recent HIV infection and one year later and from 10 individuals subjected to antiretroviral therapy, five of whom were immunological non-responders (INR), before and after one year of antiretroviral treatment compared to 175 samples from HIV-negative patients. A targeted quantitative tandem mass spectrometry metabolomics approach was used in order to determine plasma metabolomics biosignature that may relate to HIV infection, pace of HIV disease progression, and immunological response to treatment. RESULTS Twenty-five unique metabolites were identified, including five metabolites that could distinguish rapid progressors and INRs at baseline. Severe deregulation in acylcarnitine and sphingomyelin metabolism compatible with mitochondrial deficiencies was observed. β-oxidation and sphingosine-1-phosphate-phosphatase-1 activity were down-regulated, whereas acyl-alkyl-containing phosphatidylcholines and alkylglyceronephosphate synthase levels were elevated in INRs. Evidence that elite controllers harbor an inborn error of metabolism (late-onset multiple acyl-coenzyme A dehydrogenase deficiency [MADD]) was detected. CONCLUSIONS Blood-based markers from metabolomics show a very high accuracy of discriminating HIV infection between varieties of controls and have the ability to predict rapid disease progression or poor antiretroviral immunological response. These metabolites can be used as biomarkers of HIV natural evolution or treatment response and provide insight into the mechanisms of the disease.
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Affiliation(s)
- Bruno Scarpelini
- Federal University of Sao Paulo, Department of Medicine, Sao Paulo—SP, Brazil
| | - Michelle Zanoni
- Federal University of Sao Paulo, Department of Medicine, Sao Paulo—SP, Brazil
| | | | - Hong-Ha M. Truong
- University of California at San Francisco, Department of Medicine, San Francisco, CA, United States of America
| | - Luiz Mario Ramos Janini
- Federal University of Sao Paulo, Department of Medicine, Sao Paulo—SP, Brazil
- Federal University of Sao Paulo, Department of Microbiology, Sao Paulo—SP, Brazil
| | | | - Ricardo Sobhie Diaz
- Federal University of Sao Paulo, Department of Medicine, Sao Paulo—SP, Brazil
- * E-mail:
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10
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Castagna A, Monno L, Carta S, Galli L, Carrara S, Fedele V, Punzi G, Fanti I, Caramello P, Lepri AC, De Luca A, Ceccherini-Silberstein F, Monforte AD. Switch of predicted HIV-1 tropism in treated subjects and its association with disease progression. Medicine (Baltimore) 2016; 95:e5222. [PMID: 27858869 PMCID: PMC5591117 DOI: 10.1097/md.0000000000005222] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Dynamics of human immunodeficiency virus type 1 (HIV-1) tropism after antiretroviral therapy (ART) initiation and their association with disease progression are poorly investigated.This was a cohort study on subjects from the ICONA cohort receiving ART with persistently detectable (PD) or persistently undetectable (PU) viral load (VL) and with stored plasma or peripheral blood mononuclear cell (PBMC) samples at 2 time-points (T1, T2) after ART initiation. HIV-1 co-receptor tropism was determined by V3-loop sequencing and the geno2pheno algorithm. A switch in viral tropism was defined if the tropism classification at T2 differed from that observed at T1. Time to disease progression, defined as the occurrence of a new acquired immune deficiency syndrome (AIDS)-defining event/death from T2, was also evaluated.One hundred ninety-five patients were analyzed (124 PD, 71 PU). Over a median follow-up of 22.6 (19.8-28.1) months, PD and PU patients showed similar rates (95% confidence interval) of switch to a non-R5 virus [PD: 6.9 (3.7-11.2)/100-person-years of follow-up (PYFU); PU: 8.0 (3.4-14.5)/100-PYFU; P = 0.63] and of switch to a R5 virus [PD: 15.4 (7.3-26.4)/100-PYFU; PU: 8.1 (2.5-16.7)/100-PYFU; P = 0.38]. Switch to non-R5 virus was predicted by nadir CD4+ before T1.Twenty-two (18%) PD and 4 (6%) PU subjects experienced disease progression (P = 0.02). The risk of disease progression was independently associated with a switch in co-receptor tropism (adjusted hazard ratio = 4.06, 95% CI: 1.20-13.80, P = 0.03) as well as age, AIDS diagnosis, nadir CD4+ before T2, current CD4+, and VL.Switch of HIV-1 tropism under ART occurs in both directions, with similar rates in subjects with PD or PU VL and it might be predictive of future unfavorable clinical outcome.
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Affiliation(s)
- Antonella Castagna
- San Raffaele Scientific Institute
- Vita-Salute San Raffaele University, Milan
- Correspondence: Antonella Castagna, Department of Infectious Diseases, Vita-Salute San Raffaele University, San Raffaele Scientific Institute, Via Stamira d’Ancona 20, 20127 Milan, Italy (e-mail: )
| | | | - Stefania Carta
- National Institute of Infectious Diseases, L Spallanzani
| | | | | | | | | | - Iuri Fanti
- Catholic University of Sacred Heart, Rome
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Gordon K, Omar S, Nofemela A, Bandawe G, Williamson C, Woodman Z. Short Communication: A Recombinant Variant with Increased Envelope Entry Efficiency Emerged During Early Infection of an HIV-1 Subtype C Dual Infected Rapid Progressor. AIDS Res Hum Retroviruses 2016; 32:303-10. [PMID: 25905681 DOI: 10.1089/aid.2014.0100] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Mutations in functionally constrained sites of the HIV envelope (Env) can affect entry efficiency and are potential targets for vaccine and drug design. We investigated Du151, a dual-infected individual with rapid disease progression. At her death 19 months postinfection (mpi), she was infected with a recombinant variant, which outgrew both parental viruses. We aimed to determine whether the recombinant virus had enhanced Env entry efficiency compared to the parental viruses and to identify the functional determinant. We generated 15 env clones at 1, 2, 8, and 19 mpi. Pseudovirus carrying a recombinant Env clone (PSV clone), C18 (19 mpi), had significantly higher entry efficiency compared to the parents, suggesting that the recombinant virus had enhanced fitness. To identify the functional determinant, we compared two recombinant PSV clones (C18 and C63)-differing in entry efficiency (2-fold) and by four and three amino acids in gp120 and gp41, respectively. The increased entry efficiency of a C18-gp41 PSV chimera indicated that the three amino acids in the C18 gp41 region were involved (K658, G671, and F717). Site-directed mutagenesis of the three amino acids of C63 showed that a single amino acid mutation, R658K, increased pseudovirion entry efficiency. The introduction of R658 into two PSV clones (C1 and C18) decreased their entry efficiency, suggesting that R658 carries a fitness cost. Thus, our data suggest that a recombinant virus emerged at 19 mpi with enhanced Env entry efficiency. Therefore, K658 in gp41 could in part be a contributing factor to the increased viral load and rapid disease progression of Du151.
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Affiliation(s)
- Kerry Gordon
- Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
| | - Shatha Omar
- Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
| | - Andile Nofemela
- Division of Medical Virology and the Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Gama Bandawe
- Division of Medical Virology and the Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Carolyn Williamson
- Division of Medical Virology and the Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- National Health Laboratory Services, Groote Schuur Hospital, Cape Town, South Africa
| | - Zenda Woodman
- Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
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Cuevas JM, Geller R, Garijo R, López-Aldeguer J, Sanjuán R. Extremely High Mutation Rate of HIV-1 In Vivo. PLoS Biol 2015; 13:e1002251. [PMID: 26375597 PMCID: PMC4574155 DOI: 10.1371/journal.pbio.1002251] [Citation(s) in RCA: 233] [Impact Index Per Article: 25.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Accepted: 08/10/2015] [Indexed: 11/18/2022] Open
Abstract
Rates of spontaneous mutation critically determine the genetic diversity and evolution of RNA viruses. Although these rates have been characterized in vitro and in cell culture models, they have seldom been determined in vivo for human viruses. Here, we use the intrapatient frequency of premature stop codons to quantify the HIV-1 genome-wide rate of spontaneous mutation in DNA sequences from peripheral blood mononuclear cells. This reveals an extremely high mutation rate of (4.1 ± 1.7) × 10−3 per base per cell, the highest reported for any biological entity. Sequencing of plasma-derived sequences yielded a mutation frequency 44 times lower, indicating that a large fraction of viral genomes are lethally mutated and fail to reach plasma. We show that the HIV-1 reverse transcriptase contributes only 2% of mutations, whereas 98% result from editing by host cytidine deaminases of the A3 family. Hypermutated viral sequences are less abundant in patients showing rapid disease progression compared to normal progressors, highlighting the antiviral role of A3 proteins. However, the amount of A3-mediated editing varies broadly, and we find that low-edited sequences are more abundant among rapid progressors, suggesting that suboptimal A3 activity might enhance HIV-1 genetic diversity and pathogenesis. The rate of spontaneous mutation of the HIV-1 genome within its human host is exceptionally high, is mostly driven by host cytidine deaminases, and probably plays a role in disease progression. The high levels of genetic diversity of the HIV-1 virus grant it the ability to escape the immune system, to rapidly evolve drug resistance, and to circumvent vaccination strategies. However, our knowledge of HIV-1 mutation rates has been largely restricted to in vitro and cell culture studies because of the inherent complexity of measuring these rates in vivo. Here, by analyzing the frequency of premature stop codons, we show that the HIV-1 mutation rate in vivo is two orders of magnitude higher than that predicted by in vitro studies, making it the highest reported mutation rate for any biological system. A large component of this rate is from host cellular cytidine deaminases, which induce mutations in the viral DNA as a defense mechanism. While the HIV-1 genome is hypermutated in blood cells, only a very small fraction of these mutations reach the plasma, indicating that many viruses are defective as a result of the extremely high mutation load. In addition, we find that the HIV-1 mutation rate tends to be higher in patients showing normal disease progression than in those undergoing rapid progression, emphasizing the negative impact on viral fitness of hypermutation by host cytidine deaminases. However, we also observe subpopulations of weakly-mutated viral genomes whose sequence diversity may influence viral pathogenesis. Our work highlights the fine balance for HIV-1 between enough mutation to evade host responses and too much mutation that can inactivate the virus.
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Affiliation(s)
- José M. Cuevas
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Valencia, Spain
| | - Ron Geller
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Valencia, Spain
| | - Raquel Garijo
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Valencia, Spain
| | - José López-Aldeguer
- Hospital Universitario La Fe, Valencia, Spain
- CoRIS and HIV Biobank, Spanish AIDS Research Network, Spain
| | - Rafael Sanjuán
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Valencia, Spain
- Departament de Genètica, Universitat de València, Valencia, Spain
- * E-mail:
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Foster C, Kaye S, Smith C, Mackie NE. HIV-1 co-receptor tropism and disease progression in children and young adults with perinatally acquired HIV-1 infection. The HICCUP Study. J Virus Erad 2015; 1:173-8. [PMID: 27482409 PMCID: PMC4946736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
OBJECTIVES Retrospective analysis of evolution of HIV tropism and association with disease progression in perinatal HIV-1 infection (PaHIV). METHODOLOGY Eligible patients with PaHIV were grouped as slow, rapid or long-term non-progressors (LTNP). The V3 region of gp120 was sequenced from stored plasma samples and tropism determined by geno2pheno algorithm (FPR 5.75%). Logistic regression with generalised estimating equations assessed factors associated with R5 virus. Time to tropism change was assessed using standard survival methods. RESULTS At baseline (n=48) median age was 12 years (IQR 9.3-14.8), 52% were female, 79% were Black African, 96% were non-B subtypes and 81% (39/48) had R5-using virus. Median follow-up was 7.7 years (308.6 person-years), with a median of five (range 1-14) samples per subject (total 252). Analysing all samples, R5 virus was associated with higher current CD4 cell count (median 520 cells/mm(3) R5 vs 202 for X4, P=0.0005), LTNP (35% vs 11%, P=0.05), non-Black ethnicity (74% vs 89%, P=0.05) and female gender (55% vs 28%, P=0.005). Twelve of 38 (31%) with R5 virus at baseline switched to X4/dual-using virus, with an estimated 5-year risk of switch of 24.4% (95% CI 9.7-39.2%) predicted by lower current CD4 cell count (unadjusted HR 0.62/50 cells higher, 95% CI 0.47-0.81, P=0.0006). Eleven of 19 (58%) with X4/dual-using virus subsequently had R5 virus at one or more time points. CONCLUSION Maraviroc was a treatment option for 81% at 12 years, falling to 56% at 18 years, with lower CD4 cell count predictive of co-receptor switching. Paediatric studies of CCR5 antagonists should be expedited to ensure they are an early treatment option before tropism switching occurs.
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Affiliation(s)
- C Foster
- Department of GU Medicine,
Imperial College Healthcare NHS Trust,
London,
UK,Corresponding author: Caroline Foster,
Department of GU MedicineImperial College Healthcare NHS Trust,
Praed StreetLondonW2 1NY,
UK
| | - S Kaye
- Department of Retrovirology,
Imperial College London,
UK
| | - C Smith
- Research Department of Infection and Population Health,
University College London,
UK
| | - NE Mackie
- Department of GU Medicine,
Imperial College Healthcare NHS Trust,
London,
UK
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14
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Foster C, Kaye S, Smith C, Mackie N. HIV-1 co-receptor tropism and disease progression in children and young adults with perinatally acquired HIV-1 infection. The HICCUP Study. J Virus Erad 2015. [DOI: 10.1016/s2055-6640(20)30505-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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15
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Sechet M, Roussel C, Schmit JL, Saroufim C, Ghomari K, Merrien D, Cordier F, Pik JJ, Landgraf N, Douadi Y, Liné D, Duverlie G, Castelain S. X4 Tropic Virus Prediction Is Associated with a Nadir CD4 T-Cell Count below 100 Cells/mm. Intervirology 2015; 58:155-9. [PMID: 25997386 DOI: 10.1159/000398798] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Accepted: 04/09/2015] [Indexed: 11/19/2022] Open
Abstract
OBJECTIVE The aim of this study was to evaluate tropism prediction performances of three algorithms [geno2pheno false-positive rate 10% (G2P10), position-specific scoring matrix (PSSM) and a combination of the 11/25 and net charge rules] and to investigate the viral and host factors potentially involved in the X4 or R5 prediction in human immunodeficiency virus-1 (HIV-1) patients. METHODS Viral tropism was determined in 179 HIV-1-infected patients eligible for CCR5 antagonist therapy. HIV-1 RNA or DNA was extracted and amplified for env gp120 sequencing. In parallel, demographic, viral, immunological and clinical determinants were analyzed. RESULTS According to the G2P10 algorithm, 48 patients harbored X4 or X4R5 virus. The tropism prediction was concordant for 87.7 and 88.2% of samples when comparing G2P10 with PSSM or with a combination of the 11/25 and net charge rules, respectively. X4 prediction was significantly associated with more than 35 amino acids in the V3 domain (p < 0.0001) and loss of an N-linked glycosylation site (p < 0.0001). Of the factors studied, only the nadir CD4 T-cell count was significantly associated with X4 tropism (p = 0.01). CONCLUSION We determined that the X4 virus detection is closely linked to the nadir CD4 T-cell count below 100 cells/mm(3) that must be taken into account when considering a CCR5 antagonist therapy switch.
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Affiliation(s)
- Matthieu Sechet
- EA4294 Unité de Virologie Clinique et Fondamentale, UPJV et Centre Hospitalo-Universitaire, Amiens, France
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16
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Sironi F, Malnati M, Mongelli N, Cozzi P, Guzzo C, Ghezzi S, Martínez-Romero C, García-Sastre A, Lusso P, Jabes D, Biswas P. Characterization of HIV-1 entry inhibitors with broad activity against R5 and X4 viral strains. J Transl Med 2015; 13:107. [PMID: 25888743 PMCID: PMC4399250 DOI: 10.1186/s12967-015-0461-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 03/11/2015] [Indexed: 12/04/2022] Open
Abstract
Background Combined antiretroviral therapy has drastically reduced mortality and morbidity of HIV-infected individuals. Nevertheless long-term toxicity and appearance of viral resistance hampers the prolonged effectiveness of combination therapy, requiring a continuous input of drugs to replace those utilized in combination regimens. We here investigated the anti-HIV activity of novel derivatives of the suradista chemical class. Methods Compounds were tested on acute HIV-1 infection of activated peripheral blood mononuclear cells. HIV production was monitored by enzyme-linked immunosorbent assay measuring the protein p24 released in culture supernatants. Fusion assays were carried out to study the mechanism of action of these compounds. A modified version of a previously established recombinant vaccinia virus-based assay was used measuring activation of a reporter gene upon fusion of two distinct cell populations. Flow cytometry was performed in competition assays for the binding of several antibodies targeting different sites of the viral envelope glycoprotein gp120, or the receptor CD4, or the coreceptors CXCR4 and CCR5. Results Four compounds inhibited replication of a prototypic R5 (BaL) and X4 (IIIB) laboratory-adapted HIV-1 strain at low micromolar concentrations, in the absence of cytotoxicity. Approximately a ten fold greater activity was achieved against the X4 as compared to the R5 strain. The compounds blocked X4 and R5 HIV-1 fusion, a step of viral entry. This activity appeared specific for HIV-1, as entry of human herpesvirus 6 (HHV-6) and influenza virus was not substantially affected. Further investigation of the inhibitory mechanism revealed that these new molecules target the viral envelope, rather than the coreceptors, as previously shown for a congener of the same class characterized by a long plasmatic half-life. Indeed ND-4043, the most active compound, specifically competed with binding of monoclonal antibodies against the CD4-binding site (CD4-BS) and coreceptor-binding site (CoR-BS) of gp120. These compounds displayed broad anti-HIV activity, as they inhibited various primary R5, X4 and, importantly, dualtropic R5X4 HIV-1 isolates. Of the four derivatives tested, the dimeric compounds were consistently more potent than the monomeric ones. Conclusions Given their unique features, these molecules represent promising candidates for further development and exploitation as anti-HIV therapeutics. Electronic supplementary material The online version of this article (doi:10.1186/s12967-015-0461-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Francesca Sironi
- Unit of Human Virology, Division of Immunology, Transplantation and Infectious Diseases, San Raffaele Hospital, Via Olgettina 60, 20132, Milan, Italy.
| | - Mauro Malnati
- Unit of Human Virology, Division of Immunology, Transplantation and Infectious Diseases, San Raffaele Hospital, Via Olgettina 60, 20132, Milan, Italy.
| | | | | | - Christina Guzzo
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, 20892, USA.
| | - Silvia Ghezzi
- Unit of Viral Pathogens and Biosafety, Division of Immunology, Transplantation and Infectious Diseases, San Raffaele Hospital, Via Olgettina 60, 20132, Milan, Italy.
| | - Carles Martínez-Romero
- Department of Microbiology, New York, NY, 10029, USA. .,Global Health and Emerging Pathogens Institute, New York, NY, 10029, USA.
| | - Adolfo García-Sastre
- Department of Microbiology, New York, NY, 10029, USA. .,Global Health and Emerging Pathogens Institute, New York, NY, 10029, USA. .,Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
| | - Paolo Lusso
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, 20892, USA.
| | - Daniela Jabes
- NeED Pharmaceuticals srl, Viale Ortles 22/4, 20139, Milan, Italy.
| | - Priscilla Biswas
- Unit of Molecular Immunology, Division of Genetics and Cell Biology, San Raffaele Hospital, Via Olgettina 60, 20132, Milan, Italy.
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Armenia D, Soulie C, Di Carlo D, Fabeni L, Gori C, Forbici F, Svicher V, Bertoli A, Sarmati L, Giuliani M, Latini A, Boumis E, Zaccarelli M, Bellagamba R, Andreoni M, Marcelin AG, Calvez V, Antinori A, Ceccherini-Silberstein F, Perno CF, Santoro MM. A very low geno2pheno false positive rate is associated with poor viro-immunological response in drug-naïve patients starting a first-line HAART. PLoS One 2014; 9:e105853. [PMID: 25153969 PMCID: PMC4143365 DOI: 10.1371/journal.pone.0105853] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Accepted: 07/27/2014] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND We previously found that a very low geno2pheno false positive rate (FPR ≤ 2%) defines a viral population associated with low CD4 cell count and the highest amount of X4-quasispecies. In this study, we aimed at evaluating whether FPR ≤ 2% might impact on the viro-immunological response in HIV-1 infected patients starting a first-line HAART. METHODS The analysis was performed on 305 HIV-1 B subtype infected drug-naïve patients who started their first-line HAART. Baseline FPR (%) values were stratified according to the following ranges: ≤ 2; 2-5; 5-10; 10-20; 20-60; >60. The impact of genotypically-inferred tropism on the time to achieve immunological reconstitution (a CD4 cell count gain from HAART initiation ≥ 150 cells/mm(3)) and on the time to achieve virological success (the first HIV-RNA measurement <50 copies/mL from HAART initiation) was evaluated by survival analyses. RESULTS Overall, at therapy start, 27% of patients had FPR ≤ 10 (6%, FPR ≤ 2; 7%, FPR 2-5; 14%, FPR 5-10). By 12 months of therapy the rate of immunological reconstitution was overall 75.5%, and it was significantly lower for FPR ≤ 2 (54.1%) in comparison to other FPR ranks (78.8%, FPR 2-5; 77.5%, FPR 5-10; 71.7%, FPR 10-20; 81.8%, FPR 20-60; 75.1%, FPR >60; p = 0.008). The overall proportion of patients achieving virological success was 95.5% by 12 months of therapy. Multivariable Cox analyses showed that patients having pre-HAART FPR ≤ 2% had a significant lower relative adjusted hazard [95% C.I.] both to achieve immunological reconstitution (0.37 [0.20-0.71], p = 0.003) and to achieve virological success (0.50 [0.26-0.94], p = 0.031) than those with pre-HAART FPR >60%. CONCLUSIONS Beyond the genotypically-inferred tropism determination, FPR ≤ 2% predicts both a poor immunological reconstitution and a lower virological response in drug-naïve patients who started their first-line therapy. This parameter could be useful to identify patients potentially with less chance of achieving adequate immunological reconstitution and virological undetectability.
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Affiliation(s)
- Daniele Armenia
- Department of Experimental Medicine and Surgery, University of Rome Tor Vergata, Rome, Italy
| | - Cathia Soulie
- Unité Mixte de Recherche en Santé (UMR_S) 1136 Pierre Louis Institute of Epidemiology and Public Health, Université Pierre et Marie Curie (UPMC) University Paris 06, Paris, France
- UMR_S 1136 Pierre Louis Institute of Epidemiology and Public Health, Institut National de la Santé et de la Recherche Médicale (INSERM), Paris, France
- Laboratoire de Virologie, Assistance Publique-Hôpitaux de Paris (AP-HP), Groupe hospitalier Pitié Salpêtrière, Paris, France
| | - Domenico Di Carlo
- Department of Experimental Medicine and Surgery, University of Rome Tor Vergata, Rome, Italy
| | - Lavinia Fabeni
- Antiviral Drug Monitoring Unit, Istituto Nazionale delle Malattie Infettive (INMI) Lazzaro Spallanzani, Rome, Italy
| | - Caterina Gori
- Antiviral Drug Monitoring Unit, Istituto Nazionale delle Malattie Infettive (INMI) Lazzaro Spallanzani, Rome, Italy
| | - Federica Forbici
- Antiviral Drug Monitoring Unit, Istituto Nazionale delle Malattie Infettive (INMI) Lazzaro Spallanzani, Rome, Italy
| | - Valentina Svicher
- Department of Experimental Medicine and Surgery, University of Rome Tor Vergata, Rome, Italy
| | - Ada Bertoli
- Department of Experimental Medicine and Surgery, University of Rome Tor Vergata, Rome, Italy
- Molecular Virology, University Hospital Tor Vergata, Rome, Italy
| | - Loredana Sarmati
- Infectious Disease Unit, University Hospital Tor Vergata, Rome, Italy
| | - Massimo Giuliani
- Department of Infectious Dermatology, San Gallicano Hospital, Rome, Italy
| | - Alessandra Latini
- Department of Infectious Dermatology, San Gallicano Hospital, Rome, Italy
| | - Evangelo Boumis
- Infectious Diseases Division, Istituto Nazionale delle Malattie Infettive (INMI) Lazzaro Spallanzani, Rome, Italy
| | - Mauro Zaccarelli
- Infectious Diseases Division, Istituto Nazionale delle Malattie Infettive (INMI) Lazzaro Spallanzani, Rome, Italy
| | - Rita Bellagamba
- Infectious Diseases Division, Istituto Nazionale delle Malattie Infettive (INMI) Lazzaro Spallanzani, Rome, Italy
| | - Massimo Andreoni
- Infectious Disease Unit, University Hospital Tor Vergata, Rome, Italy
| | - Anne-Geneviève Marcelin
- Unité Mixte de Recherche en Santé (UMR_S) 1136 Pierre Louis Institute of Epidemiology and Public Health, Université Pierre et Marie Curie (UPMC) University Paris 06, Paris, France
- UMR_S 1136 Pierre Louis Institute of Epidemiology and Public Health, Institut National de la Santé et de la Recherche Médicale (INSERM), Paris, France
- Laboratoire de Virologie, Assistance Publique-Hôpitaux de Paris (AP-HP), Groupe hospitalier Pitié Salpêtrière, Paris, France
| | - Vincent Calvez
- Unité Mixte de Recherche en Santé (UMR_S) 1136 Pierre Louis Institute of Epidemiology and Public Health, Université Pierre et Marie Curie (UPMC) University Paris 06, Paris, France
- UMR_S 1136 Pierre Louis Institute of Epidemiology and Public Health, Institut National de la Santé et de la Recherche Médicale (INSERM), Paris, France
- Laboratoire de Virologie, Assistance Publique-Hôpitaux de Paris (AP-HP), Groupe hospitalier Pitié Salpêtrière, Paris, France
| | - Andrea Antinori
- Infectious Diseases Division, Istituto Nazionale delle Malattie Infettive (INMI) Lazzaro Spallanzani, Rome, Italy
| | | | - Carlo-Federico Perno
- Department of Experimental Medicine and Surgery, University of Rome Tor Vergata, Rome, Italy
- Antiviral Drug Monitoring Unit, Istituto Nazionale delle Malattie Infettive (INMI) Lazzaro Spallanzani, Rome, Italy
- Molecular Virology, University Hospital Tor Vergata, Rome, Italy
| | - Maria Mercedes Santoro
- Department of Experimental Medicine and Surgery, University of Rome Tor Vergata, Rome, Italy
- * E-mail:
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Abstract
BACKGROUND Transmission of HIV-1 with drug resistance mutations (DRMs) in Spain remains stable around 13%. However, the profile of recent HIV-1 seroconverters has experienced significant changes. METHODS Retrospective analyses of all individuals with HIV-1 infection acquired within the past 12 months recruited at a national registry since year 1997. RESULTS A total of 1032 recent HIV-1 seroconverters were examined (92.2% men; median age 31 years; 84% homosexual men). At the moment of diagnosis, median plasma HIV-RNA and CD4 cell counts were 4.5 log copies/ml and 558 cells/μl, respectively. A total of 136 individuals (13.8%) carried non-B subtypes. Major primary DRMs were found in 13.4%, being 7.7% for nucleoside reverse transcriptase inhibitor (NRTI), 5.8% for nonnucleoside reverse transcriptase inhibitor (NNRTI) and 2.9% for protease inhibitor. NRTI DRM significantly declined from 23.7% in 1997-2000 to 5.7% in 2010-2012 (P<0.01). Overall, X4 viruses were found in 19.7% of HIV-1 seroconverters, increasing from 11.5% before 2001 to 23.3% since year 2010 (P=0.04). Interestingly, median CD4 cell counts were significantly lower in seroconverters diagnosed during the last period after adjusting for potential confounders. In multivariate analyses, X4 tropism, high HIV-RNA, foreigners and non-B subtypes were independent predictors of lower CD4 cell counts. CONCLUSION Transmission of NRTI DRM has declined significantly in recent HIV-1 seroconverters in Spain. Conversely, X4 tropic viruses are on the rise and currently account for 23.3% of new HIV-1 infections. These individuals present with lower CD4 cell counts suggesting that circulating HIV-1 strains might have gained virulence.
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Phenotypic Susceptibility Assays for Human Immunodeficiency Virus Type 1. Antiviral Res 2014. [DOI: 10.1128/9781555815493.ch16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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HIV-1 tropism testing and clinical management of CCR5 antagonists: Quebec review and recommendations. CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY 2014; 24:202-8. [PMID: 24489562 DOI: 10.1155/2013/982759] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
HIV-1 tropism assays play a crucial role in determining the response to CCR5 receptor antagonists. Initially, phenotypic tests were used, but limited access to these tests prompted the development of alternative strategies. Recently, genotyping tropism has been validated using a Canadian technology in clinical trials investigating the use of maraviroc in both experienced and treatment-naive patients. The present guidelines review the evidence supporting the use of genotypic assays and provide recommendations regarding tropism testing in daily clinical management.
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Injecting drug use is associated with a more rapid CD4 cell decline among treatment naïve HIV-positive patients in Indonesia. J Int AIDS Soc 2014; 17:18844. [PMID: 24388495 PMCID: PMC3880941 DOI: 10.7448/ias.17.1.18844] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Revised: 11/12/2013] [Accepted: 11/27/2013] [Indexed: 11/29/2022] Open
Abstract
Background It remains unclear whether the natural course of human immunodeficiency virus (HIV) differs in subjects infected through injecting drug use (IDU) and no data have been published from low- or middle-income countries. We addressed this question in an urban cohort in Indonesia, which is experiencing a rapidly growing HIV epidemic strongly driven by IDU. Methods All antiretroviral treatment (ART) naïve HIV-positive patients who had at least two subsequent CD4 cell counts available before starting ART were included in this study. We examined the association between IDU and CD4 cell decline using a linear mixed model, with adjustment for possible confounders such as HIV viral load and hepatitis C antibodies. Results Among 284 HIV-positive ART naïve patients, the majority were male (56%) with a history of IDU (79% among men). People with a history of IDU had a statistically significant faster decline in CD4 cells (p<0.001). Based on our data, patients with a history of IDU would have an average 33% decline in CD4 cells after one year without ART, compared with a 22% decline among non-users. At two years, the decline would average 66 and 40%, respectively. No other factor was significantly associated with CD4 cell decline. Conclusions We show that a history of IDU is associated with a more rapid CD4 cell natural decline among HIV-positive individuals in Indonesia. These findings have implications for monitoring ART naïve patients with a history of IDU and for starting ART in this group.
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Abstract
Research has undergone considerable development in understanding a small subset of human immunodeficiency virus type 1 (HIV-1)-infected, therapy-naive individuals who maintain a favorable course of infection surviving for longer periods of time. Although, viral, host genetic, and immunological factors have been analyzed in many previous studies in order to delineate mechanisms that contribute to non-progressive HIV disease, there appears to be a no clear cut winner and the non-progressive HIV disease in <1% of HIV-infected individuals appears to be a complex interplay between viral and host factors. Therefore, it is important to review them separately to signify their potential contribution to non-progressive HIV disease. With respect to virological features, genomic sequencing of HIV-1 strains derived from long-term non-progressors has shown that some individuals are infected with attenuated strains of HIV-1 and harbor mutations from single nucleotide polymorphisms to large deletions in HIV-1 structure, regulatory, and accessory genes. The elucidation of functional attributes of defective/attenuated HIV strains may provide better understanding of viral pathogenesis and the discovery of new therapeutic strategies against HIV. This review mainly focuses on the defects in viral genes that possibly guide non-progressive HIV disease.
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Affiliation(s)
- Bin Wang
- Sydney Medical School, University of Sydney , Sydney, NSW , Australia
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Wood NT, Fadda E, Davis R, Grant OC, Martin JC, Woods RJ, Travers SA. The influence of N-linked glycans on the molecular dynamics of the HIV-1 gp120 V3 loop. PLoS One 2013; 8:e80301. [PMID: 24303005 PMCID: PMC3841175 DOI: 10.1371/journal.pone.0080301] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Accepted: 10/11/2013] [Indexed: 02/07/2023] Open
Abstract
N-linked glycans attached to specific amino acids of the gp120 envelope trimer of a HIV virion can modulate the binding affinity of gp120 to CD4, influence coreceptor tropism, and play an important role in neutralising antibody responses. Because of the challenges associated with crystallising fully glycosylated proteins, most structural investigations have focused on describing the features of a non-glycosylated HIV-1 gp120 protein. Here, we use a computational approach to determine the influence of N-linked glycans on the dynamics of the HIV-1 gp120 protein and, in particular, the V3 loop. We compare the conformational dynamics of a non-glycosylated gp120 structure to that of two glycosylated gp120 structures, one with a single, and a second with five, covalently linked high-mannose glycans. Our findings provide a clear illustration of the significant effect that N-linked glycosylation has on the temporal and spatial properties of the underlying protein structure. We find that glycans surrounding the V3 loop modulate its dynamics, conferring to the loop a marked propensity towards a more narrow conformation relative to its non-glycosylated counterpart. The conformational effect on the V3 loop provides further support for the suggestion that N-linked glycosylation plays a role in determining HIV-1 coreceptor tropism.
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Affiliation(s)
- Natasha T. Wood
- South African National Bioinformatics Institute, South African Medical Research Council Bioinformatics Unit, University of the Western Cape, Cape Town, South Africa
| | - Elisa Fadda
- Department of Chemistry, National University of Ireland, Maynooth, Maynooth, Ireland
| | - Robert Davis
- Complex Carbohydrate Research Centre, University of Georgia, Athens, Georgia, United States of America
| | - Oliver C. Grant
- School of Chemistry, National University of Ireland, Galway, Galway, Ireland
| | - Joanne C. Martin
- School of Chemistry, National University of Ireland, Galway, Galway, Ireland
| | - Robert J. Woods
- Complex Carbohydrate Research Centre, University of Georgia, Athens, Georgia, United States of America
- School of Chemistry, National University of Ireland, Galway, Galway, Ireland
| | - Simon A. Travers
- South African National Bioinformatics Institute, South African Medical Research Council Bioinformatics Unit, University of the Western Cape, Cape Town, South Africa
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[Consensus Statement by GeSIDA/National AIDS Plan Secretariat on antiretroviral treatment in adults infected by the human immunodeficiency virus (Updated January 2013)]. Enferm Infecc Microbiol Clin 2013; 31:602.e1-602.e98. [PMID: 24161378 DOI: 10.1016/j.eimc.2013.04.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2013] [Accepted: 04/08/2013] [Indexed: 02/08/2023]
Abstract
OBJECTIVE This consensus document is an update of combined antiretroviral therapy (cART) guidelines for HIV-1 infected adult patients. METHODS To formulate these recommendations a panel composed of members of the GeSIDA/National AIDS Plan Secretariat (Grupo de Estudio de Sida and the Secretaría del Plan Nacional sobre el Sida) reviewed the efficacy and safety advances in clinical trials, cohort and pharmacokinetic studies published in medical journals (PubMed and Embase) or presented in medical scientific meetings. The strength of the recommendations and the evidence which support them are based on a modification of the criteria of Infectious Diseases Society of America. RESULTS cART is recommended in patients with symptoms of HIV infection, in pregnant women, in serodiscordant couples with high risk of transmission, in hepatitisB co-infection requiring treatment, and in HIV nephropathy. cART is recommended in asymptomatic patients if CD4 is <500cells/μl. If CD4 are >500cells/μl cART should be considered in the case of chronic hepatitisC, cirrhosis, high cardiovascular risk, plasma viral load >100.000 copies/ml, proportion of CD4 cells <14%, neurocognitive deficits, and in people aged >55years. The objective of cART is to achieve an undetectable viral load. The first cART should include 2 reverse transcriptase inhibitors (RTI) nucleoside analogs and a third drug (a non-analog RTI, a ritonavir boosted protease inhibitor, or an integrase inhibitor). The panel has consensually selected some drug combinations, for the first cART and specific criteria for cART in acute HIV infection, in tuberculosis and other HIV related opportunistic infections, for the women and in pregnancy, in hepatitisB or C co-infection, in HIV-2 infection, and in post-exposure prophylaxis. CONCLUSIONS These new guidelines update previous recommendations related to first cART (when to begin and what drugs should be used), how to monitor, and what to do in case of viral failure or adverse drug reactions. cART specific criteria in comorbid patients and special situations are similarly updated.
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Gijsbers EF, van Sighem A, Harskamp AM, Welkers MRA, de Wolf F, Brinkman K, Prins JM, Schuitemaker H, van ’t Wout AB, Kootstra NA. The presence of CXCR4-using HIV-1 prior to start of antiretroviral therapy is an independent predictor of delayed viral suppression. PLoS One 2013; 8:e76255. [PMID: 24098454 PMCID: PMC3787987 DOI: 10.1371/journal.pone.0076255] [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: 05/21/2013] [Accepted: 08/22/2013] [Indexed: 12/04/2022] Open
Abstract
The emergence of CXCR4-using HIV variants (X4-HIV) is associated with accelerated disease progression in the absence of antiretroviral therapy. However, the effect of X4-HIV variants on the treatment response remains unclear. Here we determined whether the presence of X4-HIV variants influenced the time to undetectable viral load and CD4+ T cell reconstitution after initiation of cART in 732 patients. The presence of X4-HIV variants was determined by MT-2 assay prior to cART initiation and viral load and CD4+ T cell counts were analyzed every 3 to 6 months during a three year follow-up period. Kaplan-Meier and Cox proportional hazard analyses were performed to compare time to viral suppression and the absolute CD4+ T cell counts and increases in CD4+ T cell counts during follow-up were compared for patients with and without X4-HIV at start of cART. Patients harboring X4-HIV variants at baseline showed a delay in time to achieve viral suppression below the viral load detection limit. This delay in viral suppression was independently associated with high viral load and the presence of X4-HIV variants. Furthermore, the absolute CD4+ T cell counts were significantly lower in patients harboring X4-HIV variants at all time points during follow-up. However, no differences were observed in the increase in absolute CD4+ T cell numbers after treatment initiation, indicating that the reconstitution of CD4+ T cells is independent of the presence of X4-HIV variants. The emergence of X4-HIV has been associated with an accelerated CD4+ T cell decline during the natural course of infection and therefore, patients who develop X4-HIV variants may benefit from earlier treatment initiation in order to obtain faster reconstitution of the CD4+ T cell population to normal levels.
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Affiliation(s)
- Esther F. Gijsbers
- Department of Experimental Immunology, Sanquin Research, Landsteiner Laboratory and Center for Infectious Diseases and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | | | - Agnes M. Harskamp
- Department of Experimental Immunology, Sanquin Research, Landsteiner Laboratory and Center for Infectious Diseases and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Matthijs R. A. Welkers
- Department of Experimental Immunology, Sanquin Research, Landsteiner Laboratory and Center for Infectious Diseases and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Frank de Wolf
- Stichting HIV Monitoring, Amsterdam, The Netherlands
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom
| | - Kees Brinkman
- Department of Internal Medicine, Onze Lieve Vrouwe Gasthuis, Amsterdam, The Netherlands
| | - Jan M. Prins
- Department of Internal Medicine, Center for Infectious Diseases and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Hanneke Schuitemaker
- Department of Experimental Immunology, Sanquin Research, Landsteiner Laboratory and Center for Infectious Diseases and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Angélique B. van ’t Wout
- Department of Experimental Immunology, Sanquin Research, Landsteiner Laboratory and Center for Infectious Diseases and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Neeltje A. Kootstra
- Department of Experimental Immunology, Sanquin Research, Landsteiner Laboratory and Center for Infectious Diseases and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
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Pérez-Álvarez L, Delgado E, Vega Y, Montero V, Cuevas T, Fernández-García A, García-Riart B, Pérez-Castro S, Rodríguez-Real R, López-Álvarez MJ, Fernández-Rodríguez R, Lezaun MJ, Ordóñez P, Ramos C, Bereciartua E, Calleja S, Sánchez-García AM, Thomson MM. Predominance of CXCR4 tropism in HIV-1 CRF14_BG strains from newly diagnosed infections. J Antimicrob Chemother 2013; 69:246-53. [PMID: 23900735 DOI: 10.1093/jac/dkt305] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES R5-tropic viruses are associated with HIV-1 transmission and predominate during the early stages of infection. X4-tropic populations have been detected in ~50% of patients with late-stage disease infected with subtype B viruses. In this study, we compared the frequency of X4 tropism in individuals infected with HIV-1 CRF14_BG viruses, which have a V3 loop of subtype B, with a control group of individuals infected with subtype B viruses. METHODS Sixty-three individuals infected with HIV-1 CRF14_BG (n = 31) or subtype B (n = 32) were studied. Similar proportions of newly diagnosed and chronically infected individuals were included in the subtype B and CRF14_BG groups. V3 sequences were obtained and coreceptor tropism was predicted using the Geno2pheno[coreceptor] algorithm. V3 net charge and 11/25 rules were also used for coreceptor prediction. RESULTS Overall, X4 tropism was more frequent among individuals infected with CRF14_BG viruses (87.1%) than subtype B viruses (34.3%), a difference that was statistically highly significant (P = 0.00001). Importantly, the frequencies among newly diagnosed individuals were 90% and 13.3%, respectively (P = 0.0007). Characteristic amino acids in the V3 loop (T13, M14, V19 and W20) were identified at higher frequencies in CRF14_BG viruses (54%) than subtype B viruses (0%; P < 0.000001). CONCLUSIONS CRF14_BG is the genetic form with the highest proportion of X4-tropic viruses reported to date in newly diagnosed and chronic infections. This suggests high pathogenicity for CRF14_BG viruses, potentially leading to rapid disease progression. CCR5 antagonists will be ineffective in most CRF14_BG-infected patients, even at early stages of infection.
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Affiliation(s)
- Lucía Pérez-Álvarez
- HIV Biology and Variability Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
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Evans MC, Paquet AC, Huang W, Napolitano L, Frantzell A, Toma J, Stawiski EW, Goetz MB, Petropoulos CJ, Whitcomb J, Coakley E, Haddad M. A case-based reasoning system for genotypic prediction of HIV-1 co-receptor tropism. J Bioinform Comput Biol 2013; 11:1350006. [PMID: 23859270 DOI: 10.1142/s0219720013500066] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Accurate co-receptor tropism (CRT) determination is critical for making treatment decisions in HIV management. We created a genotypic tropism prediction tool by utilizing the case-based reasoning (CBR) technique that attempts to solve new problems through applying the solution from similar past problems. V3 loop sequences from 732 clinical samples with diverse characteristics were used to build a case library. Additional sequence and molecular properties of the V3 loop were examined and used for similarity assessment. A similarity metric was defined based on each attribute's frequency in the CXCR4-using viruses. We implemented three other genotype-based tropism predictors, support vector machines (SVM), position specific scoring matrices (PSSM), and the 11/25 rule, and evaluated their performance as the ability to predict CRT compared to Monogram's enhanced sensitivity Trofile(®) assay (ESTA). Overall concordance of the CBR based tropism prediction algorithm was 81%, as compared to ESTA. Sensitivity to detect CXCR4 usage was 90% and specificity was at 73%. In comparison, sensitivity of the SVM, PSSM, and the 11/25 rule were 85%, 81%, and 36% respectively while achieving a specificity of 90% by SVM, 75% by PSSM, and 97% by the 11/25 rule. When we evaluated these predictors in an unseen dataset, higher sensitivity was achieved by the CBR algorithm (87%), compared to SVM (82%), PSSM (76%), and the 11/25 rule (33%), while maintaining similar level of specificity. Overall this study suggests that CBR can be utilized as a genotypic tropism prediction tool, and can achieve improved performance in independent datasets compared to model or rule based methods.
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Affiliation(s)
- Mark C Evans
- Bioinformatics/Biostatistics, Monogram Biosciences Inc., South San Francisco, CA 94080, USA
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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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Abstract
PURPOSE OF REVIEW Primary HIV-1 infection is usually initiated by viruses with an exclusive affinity for the C-C chemokine receptor type 5 (CCR5) coreceptor. Viral variants that are also able to bind the C-X-C chemokine receptor type 4 (CXCR4) coreceptor arise during the course of the disease in about 50% of the infected individuals and their emergence is associated with a faster disease progression. In this article we provide a historical overview of the events that led to the discovery of the relationship between viral phenotype, coreceptor tropism and pathogenesis. RECENT FINDINGS The prevalence of CCR5 and CXCR4-using viruses differs from study to study, but overall percentages of CXCR4 use fluctuate between 2.0 and 63.0%. The association between coreceptor use and disease stage is recognized, with the lowest X4 prevalence in seroconverters and the highest in the final stage of the disease. Up to date there are insufficient arguments to support an impact of coreceptor tropism on response to combined antiretroviral therapy (cART) or an impact of cART on coreceptor tropism evolution. SUMMARY This review provides an overview of available data on coreceptor use in the different stages of the HIV-1 infection process. Although it is clear that CXCR4-using viruses emerge during the course of infection, the driving forces and mechanisms behind coreceptor switch remain largely unknown.
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Lanca AM, Collares JKB, Ferreira JLDP, Lima DM, Brigido LFDM, Rodrigues R, Fonseca BALD. HIV-1 tropism and CD4 T lymphocyte recovery in a prospective cohort of patients initiating HAART in Ribeirão Preto, Brazil. Mem Inst Oswaldo Cruz 2012; 107:96-101. [PMID: 22310542 DOI: 10.1590/s0074-02762012000100014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2011] [Accepted: 12/24/2011] [Indexed: 11/22/2022] Open
Abstract
While human immunodeficiency virus (HIV)-1 chemokine co-receptors 5 tropism and the GWGR motif in the envelope third variable region (V3 loop) have been associated with a slower disease progression, their influence on antiretroviral response remains unclear. The impact of baseline V3 characteristics on treatment response was evaluated in a randomised, double blind, prospective cohort study with patients initiating highly active antiretroviral therapy with lopinavir or efavirenz plus azithothymidine/3TC (1:1) over 48 weeks. Similar virological and immunological responses were observed for both treatment regimens. The 43 individuals had a mean baseline CD4 T cell count of 119 cells/mm(3) [standard deviation (SD) = 99] and a mean viral load of 5.09 log(10) copies/mL (SD = 0.49). The GWGR motif was not associated with a CD4 T cell response, but predicted R5 tropism by the geno2pheno([clinical20%]) algorithm correlated with higher CD4 T cell levels at all monitoring points (p < 0.05). Moreover, higher false-positive rates (FPR) values from this analysis revealed a strong correlation with CD4 T cell recovery (p < 0.0001). Transmitted drug resistance mutations, documented in 3/41 (7.3%) cases, were unrelated to the assigned antiretroviral regimen and had no impact on patient outcomes. In conclusion, naÏve HIV-1 R5 infected patients exhibited higher CD4 T cell counts at baseline; this difference was sustained throughout therapy. The geno2pheno([clinical]) option FPR positively correlated with CD4 T cell gain and may be useful in predicting CD4 T cell recovery.
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Affiliation(s)
- Andre Minhoto Lanca
- Laboratório de Retrovirus, Centro de Virologia, Instituto Adolfo Lutz, São Paulo, Brasil
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Santoro MM, Armenia D, Fabeni L, Santoro M, Gori C, Forbici F, Svicher V, Bertoli A, Dori L, Surdo M, Balestra E, Palamara G, Girardi E, Angarano G, Andreoni M, Narciso P, Antinori A, Ceccherini-Silberstein F, Perno CF. The lowest X4 Geno2Pheno false-positive rate is associated with greater CD4 depletion in HIV-1 infected patients. Clin Microbiol Infect 2012; 18:E289-98. [PMID: 22681969 DOI: 10.1111/j.1469-0691.2012.03905.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Through this study we evaluated whether the HIV-1 tropism determined by genotypic analysis correlates with HIV-1 markers, such as CD4 cell count and plasma HIV-RNA. The analysis was performed on 1221 HIV-1 B-subtype infected patients with an available V3 sequence (all maraviroc naive). Of them, 532 were antiretroviral therapy (ART) naive and 689 ART experienced. Tropism determination was performed by using the geno2pheno (co-receptor) algorithm set at a false-positive rate (FPR) of 10% and 2%. Potential associations of FPR with CD4 cell count and viraemia were evaluated. Association of V3 mutations with genotypic-determined tropism was also evaluated according to different FPR ranges. About 26% of patients (either ART naive or ART experienced) were infected by X4-tropic viruses (using the classical 10% FPR cut-off). However, a significantly lower proportion of ART-naive patients had FPR ≤ 2% in comparison with ART-experienced patients (4.9% vs. 12.6%, respectively, p <0.001). The risk of advanced HIV-1 infection (with CD4 cell count ≤ 200 cells/mm(3)) was significantly greater in X4-infected patients, either ART-naive (OR (95% CI)), 4.2 (1.8-9.2); p 0.0006) or ART-experienced (2.3 (1.4-3.6); p 0.0003), with FPR set at 2% (but not at 10%). This finding was confirmed by multivariable logistic analysis. No relationship was found between viraemia and FPR ≤2%. Some X4-related mutations were significantly associated with FPR ≤2% (ART-naive patients, S11R, Y21V, G24K and G24R, p ≤0.001; ART-experienced patients, Y7K, S11R, H13Y, p ≤0.002). In conclusion, these findings show that within the context of genotypically-assessed CXCR4 tropism, FPR ≤2% defines (far better than 10%-FPR) a viral population associated with low CD4 rank, with potentially greater cytopathic effect, and with more advanced disease.
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[Consensus document of Gesida and Spanish Secretariat for the National Plan on AIDS (SPNS) regarding combined antiretroviral treatment in adults infected by the human immunodeficiency virus (January 2012)]. Enferm Infecc Microbiol Clin 2012; 30:e1-89. [PMID: 22633764 DOI: 10.1016/j.eimc.2012.03.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2012] [Accepted: 03/19/2012] [Indexed: 11/20/2022]
Abstract
This consensus document has been prepared by a panel consisting of members of the AIDS Study Group (Gesida) and the Spanish Secretariat for the National Plan on AIDS (SPNS) after reviewing the efficacy and safety results of clinical trials, cohort and pharmacokinetic studies published in medical journals, or presented in medical scientific meetings. Gesida has prepared an objective and structured method to prioritise combined antiretroviral treatment (cART) in naïve patients. Recommendations strength (A, B, C) and the evidence which supports them (I, II, III) are based on a modification of the Infectious Diseases Society of America criteria. The current antiretroviral treatment (ART) of choice for chronic HIV infection is the combination of three drugs. ART is recommended in patients with symptomatic HIV infection, in pregnancy, in serodiscordant couples with high transmission risk, hepatitis B fulfilling treatment criteria, and HIV nephropathy. Guidelines on ART treatment in patients with concurrent diagnosis of HIV infection and an opportunistic type C infection are included. In asymptomatic patients ART is recommended on the basis of CD4 lymphocyte counts, plasma viral load and patient co-morbidities, as follows: 1) therapy should be started in patients with CD4 counts <350 cells/μL; 2) when CD4 counts are between 350 and 500 cells/μL, therapy will be recommended and only delayed if patient is reluctant to take it, the CD4 are stabilised, and the plasma viral load is low; 3) therapy could be deferred when CD4 counts are above 500 cells/μL, but should be considered in cases of cirrhosis, chronic hepatitis C, high cardiovascular risk, plasma viral load >10(5) copies/mL, proportion of CD4 cells <14%, and in people aged >55 years. ART should include 2 reverse transcriptase inhibitors nucleoside analogues and a third drug (non-analogue reverse transcriptase inhibitor, ritonavir boosted protease inhibitor or integrase inhibitor). The panel has consensually selected and given priority to using the Gesida score for some drug combinations, some of them co-formulated. The objective of ART is to achieve an undetectable viral load. Adherence to therapy plays an essential role in maintaining antiviral response. Therapeutic options are limited after ART failures, but an undetectable viral load may be possible nowadays. Adverse events are a fading problem of ART. Guidelines in acute HIV infection, in women, in pregnancy, and to prevent mother-to-child transmission and pre- and post-exposition prophylaxis are commented upon. Management of hepatitis B or C co-infection, other co-morbidities, and the characteristics of ART in HIV-2 infection are included.
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Redd AD, Laeyendecker O, Kong X, Kiwanuka N, Lutalo T, Huang W, Gray RH, Wawer MJ, Serwadda D, Eshleman SH, Quinn TC. Efficiency of CCR5 coreceptor utilization by the HIV quasispecies increases over time, but is not associated with disease progression. AIDS Res Hum Retroviruses 2012; 28:289-94. [PMID: 21663455 PMCID: PMC3292754 DOI: 10.1089/aid.2011.0006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
CCR5 is the primary coreceptor for HIV entry. Early after infection, the HIV viral population diversifies rapidly into a quasispecies. It is not known whether the initial efficiency of the viral quasispecies to utilize CCR5 is associated with HIV disease progression or if it changes in an infected individual over time. The CCR5 and CXCR4 utilization efficiencies (R5-UE and X4-UE) of the HIV quasispecies were examined using a pseudovirus, single-round infection assay for samples obtained from known seroconverters from Rakai district, Uganda (n=88). Initial and longitudinal R5-UE values were examined to assess the association of R5-UE with HIV disease progression using multivariate Cox proportional hazard models. Longitudinal samples were analyzed for 35 seroconverters who had samples available from multiple time points. There was no association between initial or longitudinal changes in R5-UE and the hazard of HIV disease progression (p=0.225 and p=0.942, respectively). In addition, R5-UE increased significantly over time after HIV seroconversion (p<0.001), regardless of HIV subtype or the emergence of CXCR4-tropic virus. These data demonstrate that the R5-UE of the viral quasispecies early in HIV infection is not associated with disease progression, and that R5-UE levels increase in HIV-infected individuals over time.
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Affiliation(s)
- Andrew D. Redd
- Laboratory of Immunoregulation, NIAID, NIH, Bethesda, Maryland
| | - Oliver Laeyendecker
- Laboratory of Immunoregulation, NIAID, NIH, Bethesda, Maryland
- School of Medicine, Johns Hopkins University, Baltimore, Maryland
| | - Xiangrong Kong
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland
| | - Noah Kiwanuka
- Rakai Health Sciences Program, Rakai District, Uganda
- Uganda Virus Research Institute, Entebbe, Uganda
- School of Public Health, Makerere University, Kampala, Uganda
| | - Tom Lutalo
- Rakai Health Sciences Program, Rakai District, Uganda
| | - Wei Huang
- Monogram Biosciences Inc., South San Francisco, California
| | - Ronald H. Gray
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland
| | - Maria J. Wawer
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland
| | - David Serwadda
- School of Public Health, Makerere University, Kampala, Uganda
| | | | - Thomas C. Quinn
- Laboratory of Immunoregulation, NIAID, NIH, Bethesda, Maryland
- School of Medicine, Johns Hopkins University, Baltimore, Maryland
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Nozza S, Canducci F, Galli L, Cozzi-Lepri A, Capobianchi MR, Ceresola ER, Narciso P, Libertone R, Castelli P, Moioli M, D'Arminio Monforte A, Castagna A. Viral tropism by geno2pheno as a tool for predicting CD4 decrease in HIV-1-infected naive patients with high CD4 counts. J Antimicrob Chemother 2012; 67:1224-7. [DOI: 10.1093/jac/dkr600] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
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Bártolo I, Abecasis AB, Borrego P, Barroso H, McCutchan F, Gomes P, Camacho R, Taveira N. Origin and epidemiological history of HIV-1 CRF14_BG. PLoS One 2011; 6:e24130. [PMID: 21969855 PMCID: PMC3182163 DOI: 10.1371/journal.pone.0024130] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2011] [Accepted: 08/05/2011] [Indexed: 01/03/2023] Open
Abstract
Background CRF14_BG isolates, originally found in Spain, are characterized by CXCR4 tropism and rapid disease progression. This study aimed to identify the origin of CRF14_BG and reconstruct its epidemiological history based on new isolates from Portugal. Methodology/Principal Findings C2V3C3 env gene sequences were obtained from 62 samples collected in 1993–1998 from Portuguese HIV-1 patients. Full-length genomic sequences were obtained from three patients. Viral subtypes, diversity, divergence rate and positive selection were investigated by phylogenetic analysis. The molecular structure of the genomes was determined by bootscanning. A relaxed molecular clock model was used to date the origin of CRF14_BG. Geno2pheno was used to predict viral tropism. Subtype B was the most prevalent subtype (45 sequences; 73%) followed by CRF14_BG (8; 13%), G (4; 6%), F1 (2; 3%), C (2; 3%) and CRF02_AG (1; 2%). Three CRF14_BG sequences were derived from 1993 samples. Near full-length genomic sequences were strongly related to the CRF14_BG isolates from Spain. Genetic diversity of the Portuguese isolates was significantly higher than the Spanish isolates (0.044 vs 0.014, P<0.0001). The mean date of origin of the CRF14_BG cluster was estimated to be 1992 (range, 1989 and 1996) based on the subtype G genomic region and 1989 (range, 1984–1993) based on the subtype B genomic region. Most CRF14_BG strains (78.9%) were predicted to be CXCR4. Finally, up to five amino acids were under selective pressure in subtype B V3 loop whereas only one was found in the CRF14_BG cluster. Conclusions CRF14_BG emerged in Portugal in the early 1990 s soon after the beginning of the HIV-1 epidemics, spread to Spain in late 1990 s as a consequence of IVDUs migration and then to the rest of Europe. CXCR4 tropism is a general characteristic of this CRF that may have been selected for by escape from neutralizing antibody response.
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Affiliation(s)
- Inês Bártolo
- Unidade dos Retrovírus e Infecções Associadas, Centro de Patogénese Molecular, Faculdade de Farmácia de Lisboa, Lisboa, Portugal
- Centro de Investigação Interdisciplinar Egas Moniz (CiiEM), Instituto Superior de Ciências da Saúde Egas Moniz, Caparica, Portugal
| | - Ana B. Abecasis
- Centro de Malária e Outras Doenças Tropicais, Instituto de Higiene e Medicina Tropical, Lisboa, Portugal
| | - Pedro Borrego
- Unidade dos Retrovírus e Infecções Associadas, Centro de Patogénese Molecular, Faculdade de Farmácia de Lisboa, Lisboa, Portugal
- Centro de Investigação Interdisciplinar Egas Moniz (CiiEM), Instituto Superior de Ciências da Saúde Egas Moniz, Caparica, Portugal
| | - Helena Barroso
- Unidade dos Retrovírus e Infecções Associadas, Centro de Patogénese Molecular, Faculdade de Farmácia de Lisboa, Lisboa, Portugal
- Centro de Investigação Interdisciplinar Egas Moniz (CiiEM), Instituto Superior de Ciências da Saúde Egas Moniz, Caparica, Portugal
| | - Francine McCutchan
- Bill and Melinda Gates Foundation, Seattle, Washington, United States of America
| | - Perpétua Gomes
- Centro de Investigação Interdisciplinar Egas Moniz (CiiEM), Instituto Superior de Ciências da Saúde Egas Moniz, Caparica, Portugal
- Centro de Malária e Outras Doenças Tropicais, Instituto de Higiene e Medicina Tropical, Lisboa, Portugal
- Laboratório de Biologia Molecular, Centro Hospitalar Lisboa Ocidental, Hospital Egas Moniz, Lisboa, Portugal
| | - Ricardo Camacho
- Centro de Malária e Outras Doenças Tropicais, Instituto de Higiene e Medicina Tropical, Lisboa, Portugal
- Laboratório de Biologia Molecular, Centro Hospitalar Lisboa Ocidental, Hospital Egas Moniz, Lisboa, Portugal
| | - Nuno Taveira
- Unidade dos Retrovírus e Infecções Associadas, Centro de Patogénese Molecular, Faculdade de Farmácia de Lisboa, Lisboa, Portugal
- Centro de Investigação Interdisciplinar Egas Moniz (CiiEM), Instituto Superior de Ciências da Saúde Egas Moniz, Caparica, Portugal
- * E-mail:
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Seclén E, Soriano V, González MM, Martín-Carbonero L, Gellermann H, Distel M, Kadus W, Poveda E. Impact of baseline HIV-1 tropism on viral response and CD4 cell count gains in HIV-infected patients receiving first-line antiretroviral therapy. J Infect Dis 2011; 204:139-44. [PMID: 21628668 DOI: 10.1093/infdis/jir218] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND Viral tropism influences the natural history of human immunodeficiency type 1 (HIV-1) disease: X4 viruses are associated with faster decreases in CD4 cell count. There is scarce information about the influence of viral tropism on treatment outcomes. METHODS Baseline plasma samples from patients recruited to the ArTEN (Atazanavir/ritnoavir vs. Nevirapine on a background of Tenofovir and Emtricitabine) trial were retrospectively tested for HIV-1 tropism using the genotypic tool geno2pheno(FPR=5.75%). ArTEN compared nevirapine with atazanavir-ritonavir, both along with tenofovir-emtricitabine, in drug-naïve patients. RESULTS Of 569 ArTEN patients, 428 completed 48 weeks of therapy; 282 of these received nevirapine and 146 of these received atazanavir-ritonavir. Overall, non-B subtypes of HIV-1 were recognized in 96 patients (22%) and X4 viruses were detected in 55 patients (14%). At baseline, patients with X4 viruses had higher plasma HIV RNA levels (5.4 vs 5.2 log copies/mL, respectively; P = .044) and lower CD4 cell counts (145 vs 188 cells/μL, respectively; P < .001) than those with R5 strains. At week 48, virologic responses were lower in patients with X4 viruses than in patients with R5 viruses (77% vs 92%, respectively; P = .009). Multivariate analysis confirmed HIV-1 tropism as an independent predictor of virologic response at week 24 (P = .012). This association was extended to week 48 (P = .007) in clade B viruses. Conversely, CD4 cell count recovery was not influenced by baseline HIV-1 tropism. CONCLUSIONS HIV-1 tropism is an independent predictor of virologic response to first-line antiretroviral therapy. In contrast, it does not seem to influence CD4 cell count recovery. CLINICAL TRIALS REGISTRATION NCT00389207.
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Affiliation(s)
- Eduardo Seclén
- Department of Infectious Diseases, Hospital Carlos III, Madrid, Spain
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Wilkin TJ, Goetz MB, Leduc R, Skowron G, Su Z, Chan ES, Heera J, Chapman D, Spritzler J, Reeves JD, Gulick RM, Coakley E. Reanalysis of coreceptor tropism in HIV-1-infected adults using a phenotypic assay with enhanced sensitivity. Clin Infect Dis 2011; 52:925-8. [PMID: 21427401 DOI: 10.1093/cid/cir072] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The enhanced-sensitivity Trofile assay (TF-ES; Monogram Biosciences) was used to retest coreceptor tropism samples from 4 different cohorts of HIV-1-infected patients. Nine percent to 26% of patients with CCR5-tropic virus by the original Trofile assay had CXCR4-using virus by TF-ES. Lower CD4 cell counts were associated with CXCR4-using virus in all cohorts.
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Affiliation(s)
- Timothy J Wilkin
- Division of Infectious Disease, Weill Cornell Medical College, New York, New York 10011, USA.
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Detection of quasispecies variants predicted to use CXCR4 by ultra-deep pyrosequencing during early HIV infection. AIDS 2011; 25:611-7. [PMID: 21160417 DOI: 10.1097/qad.0b013e328343489e] [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]
Abstract
OBJECTIVES HIV-1 V3 quasispecies was analyzed by ultra-deep pyrosequencing, in early HIV-infected patients, to assess possible correlations between quasispecies diversity, frequency of variants predicted to use CXCR4 and need for early antiretroviral treatment. METHODS Twenty patients were retrospectively enrolled: 10 patients (group A) required HAART within 6 months from seroconversion and 10 (group B) remained free of therapy during this period. V3 quasispecies was assessed on plasma viral RNA and in peripheral blood mononuclear cell-associated proviral DNA. Prediction of coreceptor usage was performed by position-specific score matrix analysis. RESULTS Variants predicted to use CXCR4 were detected (frequency ≥0.3%) in the plasma of 50% of early infected patients (60% from group A and 40% from group B). Intrapatient frequency of these variants was highly variable (0.3-56.3%). A positive correlation was observed between the proportion of X4 variants and intrapatient quasispecies diversity. Quasispecies diversity and absolute numbers of X4 variants were significantly higher in patients from group A. The analysis of proviral DNA quasispecies, performed in a subgroup of five patients, showed that X4 variants were not detected in patients with RNA frequency below 0.3%, and detected at 3.6% in the patient with 56.3% of X4 plasma variants. CONCLUSION Our findings show that X4 variants may be frequently found, at variable intrapatient frequency, in early infected patients, and that quasispecies diversity and absolute numbers of X4 variants are significantly higher in patients undergoing early antiretroviral treatment. Further studies are mandatory to explore the clinical relevance of X4 variants present during early infection with respect to clinical progression and possible therapeutic implications.
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Müller V, Fraser C, Herbeck JT. A strong case for viral genetic factors in HIV virulence. Viruses 2011; 3:204-216. [PMID: 21994727 PMCID: PMC3185695 DOI: 10.3390/v3030204] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2011] [Revised: 02/28/2011] [Accepted: 02/28/2011] [Indexed: 12/23/2022] Open
Abstract
HIV infections show great variation in the rate of progression to disease, and the role of viral genetic factors in this variation had remained poorly characterized until recently. Now a series of four studies [1-4] published within a year has filled this important gap and has demonstrated a robust effect of the viral genotype on HIV virulence.
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Affiliation(s)
- Viktor Müller
- Institute of Biology, Eötvös Loránd University, Pázmány P. s. 1/C, 1117 Budapest, Hungary
| | - Christophe Fraser
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London W2 1PG, UK; E-Mail:
| | - Joshua T. Herbeck
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98195, USA; E-Mail:
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Mapping and Characterization of Vicriviroc Resistance Mutations From HIV-1 Isolated from Treatment-Experienced Subjects Enrolled in a Phase II Study (VICTOR-E1). J Acquir Immune Defic Syndr 2011; 56:222-9. [DOI: 10.1097/qai.0b013e3181ff63ee] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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41
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HIV replication capacity is an independent predictor of disease progression in persons with untreated chronic HIV infection. J Acquir Immune Defic Syndr 2010; 53:472-9. [PMID: 20032783 DOI: 10.1097/qai.0b013e3181cae480] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
OBJECTIVE To assess the effect of pol replication capacity (RC) on the hazard ratio of progression to a composite endpoint of time to progression to <350 CD4+ cells per microliter, initiation of therapy, or death. METHODS pol RC assays were performed after study closure in baseline samples obtained from 316 enrollees in a prospectively monitored cohort of treatment-naive adults with >or=450 CD4+ cells per microliter and >or=1000 HIV-1 RNA copies per milliliter. RESULTS The median RC was 79%. Patients with a lower RC had a lower median viral load (4.0 vs 4.2 Log HIV-1 RNA copies/mL, P = 0.026) and a lower rate of protease inhibitor resistance 2% vs 8%, P = 0.03). Otherwise, baseline demographic and laboratory characteristics were similar. The hazard ratio of progression to the composite endpoint was 0.73 (P = 0.041) for persons with lower RC, 2.07 per 1.0 log10 higher viral load (P < 0.001), and 0.86 per 50 cells per microliter higher CD4+ cell count (P < 0.001). The effect of lower RC was also significant in a separate analysis of time to initiation of therapy (P = 0.04). CONCLUSIONS These results show that untreated patients with lower vs higher RC had a slower rate of progression as assessed by a composite outcome of time to CD4+ count <or=350 cells per microliter, treatment initiation, or death.
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Bridger GJ, Skerlj RT, Hernandez-Abad PE, Bogucki DE, Wang Z, Zhou Y, Nan S, Boehringer EM, Wilson T, Crawford J, Metz M, Hatse S, Princen K, De Clercq E, Schols D. Synthesis and structure-activity relationships of azamacrocyclic C-X-C chemokine receptor 4 antagonists: analogues containing a single azamacrocyclic ring are potent inhibitors of T-cell tropic (X4) HIV-1 replication. J Med Chem 2010; 53:1250-60. [PMID: 20043638 DOI: 10.1021/jm901530b] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Bis-tetraazamacrocycles such as the bicyclam AMD3100 (1) are a class of potent and selective anti-HIV-1 agents that inhibit virus replication by binding to the chemokine receptor CXCR4, the coreceptor for entry of X4 viruses. By sequential replacement and/or deletion of the amino groups within the azamacrocyclic ring systems, we have determined the minimum structural features required for potent antiviral activity in this class of compounds. All eight amino groups are not required for activity, the critical amino groups on a per ring basis are nonidentical, and the overall charge at physiological pH can be reduced without compromising potency. This approach led to the identification of several single ring azamacrocyclic analogues such as AMD3465 (3d), 36, and 40, which exhibit EC(50)'s against the cytopathic effects of HIV-1 of 9.0, 1.0, and 4.0 nM, respectively, antiviral potencies that are comparable to 1 (EC(50) against HIV-1 of 4.0 nM). More importantly, however, the key structural elements of 1 required for antiviral activity may facilitate the design of nonmacrocyclic CXCR4 antagonists suitable for HIV treatment via oral administration.
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Affiliation(s)
- Gary J Bridger
- AnorMED Inc. now Genzyme Corporation, 500 Kendall Street, Cambridge, Massachusetts 02142, USA.
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Jakobsen MR, Ellett A, Churchill MJ, Gorry PR. Viral tropism, fitness and pathogenicity of HIV-1 subtype C. Future Virol 2010. [DOI: 10.2217/fvl.09.77] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The majority of studies on HIV-1 pathogenesis have been conducted on subtype B HIV-1 (B-HIV) strains. However, B-HIV strains constitute the minority of HIV-1 cases worldwide, and are not common in regions that stand to benefit the most from advances in HIV-1 research such as southern Africa and Asia, where the HIV-1 pandemic is at its worst. The majority of individuals with HIV-1 are infected with subtype C HIV-1 (C-HIV) and reside in Southern Africa and Central Asia. Relatively little is known about C-HIV, but current evidence suggests the pathogenesis of C-HIV is distinct from B-HIV and other HIV-1 subtypes. This article summarizes what is currently known about the viral tropism, fitness and pathogenicity of C-HIV, and compares and contrasts these features to B-HIV. A thorough understanding of the molecular pathogenesis of C-HIV is important for a targeted approach to developing vaccines and novel drugs optimized for effectiveness in populations that are most in need.
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Affiliation(s)
- Martin R Jakobsen
- Centre for Virology, Burnet Institute, Melbourne, Victoria, Australia and Department of Infectious Diseases, Aarhus University Hospital, Skejby, Brendstrupgaardvej 100, 8200 Aarhus N, Denmark
| | - Anne Ellett
- Centre for Virology, Burnet Institute, Melbourne, Victoria, Australia
| | - Melissa J Churchill
- Centre for Virology, Burnet Institute, Melbourne, Victoria, Australia and Department of Medicine, Monash University, Melbourne, Victoria, Australia
| | - Paul R Gorry
- Centre for Virology, Burnet Institute, Melbourne, Victoria, Australia and Department of Medicine, Monash University, Melbourne, Victoria, Australia and Department of Microbiology & Immunology, University of Melbourne, Melbourne, Victoria, Australia
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de Silva UC, Warachit J, Sattagowit N, Jirapongwattana C, Panthong S, Utachee P, Yasunaga T, Ikuta K, Kameoka M, Boonsathorn N. Genotypic characterization of HIV type 1 env gp160 sequences from three regions in Thailand. AIDS Res Hum Retroviruses 2010; 26:223-7. [PMID: 20156104 DOI: 10.1089/aid.2009.0213] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We report 25 env gp160 sequences from patients in three geographically distinct districts of Thailand, i.e., Lampang in the north, Trang in the south and Rayong in the east. One of these is a CRF01_AE/subtype B recombinant and the other 24 sequences are purely CRF01_AE. Very little interpopulation diversity was observed between the sequences from the three different geographic regions and from those previously reported by our laboratory from central Thailand. Potential N-linked glycosylation sites (PNLGs) were reasonably conserved among the 25 sequences: we found 15 highly conserved PNLGs on gp120 and 4 almost fully conserved PNLGs on gp41. Analysis of coreceptor tropism revealed that six of the isolates were dual tropic and the others were R5 tropic. We also examined a rare seven amino acid deletion found in one isolate at position 847-853 on gp41. These results may enhance our understanding of HIV-1 currently circulating in Thailand.
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Affiliation(s)
- U. Chandimal de Silva
- Thailand–Japan Research Collaboration Centre on Emerging and Re-emerging Infections, Nonthaburi 11000, Thailand
- Department of Genome Informatics, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
| | - Jiranan Warachit
- National Institute of Health, Department of Medical Sciences, Ministry of Public Health, Nonthaburi 11000, Thailand
| | - Nerisa Sattagowit
- Medical Biotechnology Centre, Department of Medical Sciences, Ministry of Public Health, Nonthaburi 11000, Thailand
| | - Chanin Jirapongwattana
- Medical Biotechnology Centre, Department of Medical Sciences, Ministry of Public Health, Nonthaburi 11000, Thailand
| | - Sumolrat Panthong
- Medical Biotechnology Centre, Department of Medical Sciences, Ministry of Public Health, Nonthaburi 11000, Thailand
| | - Piraporn Utachee
- Thailand–Japan Research Collaboration Centre on Emerging and Re-emerging Infections, Nonthaburi 11000, Thailand
| | - Teruo Yasunaga
- Thailand–Japan Research Collaboration Centre on Emerging and Re-emerging Infections, Nonthaburi 11000, Thailand
- Department of Genome Informatics, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
| | - Kazuyoshi Ikuta
- Thailand–Japan Research Collaboration Centre on Emerging and Re-emerging Infections, Nonthaburi 11000, Thailand
- Department of Virology, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
| | - Masanori Kameoka
- Thailand–Japan Research Collaboration Centre on Emerging and Re-emerging Infections, Nonthaburi 11000, Thailand
- Department of Virology, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
| | - Naphatsawan Boonsathorn
- Medical Biotechnology Centre, Department of Medical Sciences, Ministry of Public Health, Nonthaburi 11000, Thailand
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Replicative capacity of human immunodeficiency virus type 1 transmitted from mother to child is associated with pediatric disease progression rate. J Virol 2010; 84:492-502. [PMID: 19828603 DOI: 10.1128/jvi.01743-09] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Human immunodeficiency virus (HIV)-infected infants in the developing world typically progress to AIDS or death within the first 2 years of life. However, a minority progress relatively slowly. This study addresses the potential contribution of viral factors to HIV disease progression in eight infants selected from a well-characterized cohort of C clade HIV-infected infants, monitored prospectively from birth in Durban, South Africa. Three infants were defined as "progressors," and five were defined as "slow progressors." We observed that slow-progressor infants carry HIV isolates with significantly lower replicative capacity compared to virus from progressors. Furthermore, our data suggest a link between the attenuated viral phenotype and HLA-B* 57/5801 epitope-specific Gag mutational patterns of the transmitted virus and not to coreceptor usage or to the presence of Nef deletions or insertions. These data underline the importance of virus-host interactions and highlight the contribution of viral attenuation through Gag-specific CD8(+) T-cell escape mutations, among other factors, in the control of pediatric HIV infection.
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Abstract
PURPOSE OF REVIEW A variety of methods are available to determine HIV-1 co-receptor usage, commonly referred to as viral tropism. This article reviews recent data on phenotypic and genotypic assays of HIV-1 tropism. RECENT FINDINGS Tropism assays are used to determine co-receptor usage of HIV-1 in patients who may be candidates for treatment with CCR5 antagonists. Phenotypic assays are used most often in the clinical trials of CCR5 antagonists, and are considered the 'gold standard' for comparison with other methods of tropism testing. Enhancements have allowed detection of a lower threshold of minor CXCR4-using species. When compared with phenotypic assays, genotypic methods have poor sensitivity but good specificity at detecting CXCR4-using HIV-1. Preliminary results from a recent comparative study suggest that some genotypic methods may perform as well as phenotypic tests in predicting virologic response to CCR5 antagonists. Several studies show that tropism testing may provide useful prognostic information regarding the risk of disease progression. SUMMARY Understanding the characteristic of different tropism assays is important for their clinical use. Although phenotypic testing currently is favored, genotypic assays may be a suitable alternative in appropriate settings.
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Affiliation(s)
- Nina H. Lin
- Infectious Diseases Unit, Massachusetts General Hospital, Boston, MA
- Harvard Medical School, Boston, MA
| | - Daniel R. Kuritzkes
- Harvard Medical School, Boston, MA
- Section of Retroviral Therapeutics, Brigham and Women's Hospital, Boston, MA
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ERRATA. J Acquir Immune Defic Syndr 2009. [DOI: 10.1097/qai.0b013e3181a6df09] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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