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Abstract
OBJECTIVE To study the long-term evolution of the transmitted CXCR4-using viruses. CCR5-using viruses (R5 viruses) predominate during primary HIV-1 infections (PHI) while CXCR4-using viruses are isolated in less than 10% of PHI. DESIGN Six patients infected with an R5X4 virus, detected by a sensitive phenotypic assay during PHI, were matched with six patients infected with a pure R5 virus for sex, Fiebig stage, time of antiretroviral initiation and duration of follow-up. METHODS We used MiSeq ultra-deep sequencing to determine the composition of the virus quasispecies during PHI and at the end of follow-up (median time of follow-up: 12.5 years). RESULTS X4 viruses were detected by genetic analysis in three of six samples from the R5X4 group, accounting for 1.3-100% of the virus quasispecies, during PHI, and in four of six samples (accounting for 6.7-100%) at the end of follow-up. No X4 virus was detected in the R5 group during PHI and in only one patient (accounting for 1.2%) at the end of follow-up. The complexity of the virus quasispecies at the stage of PHI was higher in the R5X4 group than in the R5 group. Complexity increased from PHI to the end of follow-up in the R5 group but remained stable in the R5X4 group. CONCLUSION CXCR4-using viruses persisted in the peripheral blood mononuclear cells of several patients on suppressive antiretroviral therapy for a median duration of 12.5 years after PHI. The genetic complexity of HIV-1 evolved differently post-PHI in patients infected with R5X4 viruses from those infected with R5 viruses.
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Kalu AW, Telele NF, Aralaguppe SG, Gebre-Selassie S, Fekade D, Marrone G, Sonnerborg A. Coreceptor Tropism and Maraviroc Sensitivity of Clonally Derived Ethiopian HIV-1C Strains Using an in-house Phenotypic Assay and Commonly Used Genotypic Methods. Curr HIV Res 2019; 16:113-120. [PMID: 29766813 DOI: 10.2174/1570162x16666180515124836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 04/23/2018] [Accepted: 05/07/2018] [Indexed: 11/22/2022]
Abstract
OBJECTIVES Genotypic Tropism Testing (GTT) tools are generally developed based on HIV-1 subtype B (HIV-1B) and used for HIV-1C as well but with a large discordance of prediction between different methods. We used an established phenotypic assay for comparison with GTT methods and for the determination of in vitro maraviroc sensitivity of pure R5-tropic and dual-tropic HIV-1C. METHODS Plasma was obtained from 58 HIV-1C infected Ethiopians. Envgp120 was cloned into a luciferase tagged NL4-3 plasmid. Phenotypic tropism was determined by in house method and the V3 sequences were analysed by five GTT methods. In vitro maraviroc sensitivity of R5-tropic and dual-tropic isolates were compared in the TZMbl cell-line. RESULTS The phenotypes were classified as R5 in 92.4% and dual tropic (R5X4) in 7.6% of 79 clones. The concordance between phenotype and genotype ranged from 64.7% to 84.3% depending on the GTT method. Only 46.9% of the R5 phenotypes were predicted as R5 by all GTT tools while R5X4 phenotypes were predicted as X4 by four methods, but not by Raymond's method. All six tested phenotypic R5 clones, as well as five of six of dual tropic clones, showed a dose response to maraviroc. CONCLUSION There is a high discordance between GTT methods, which underestimates the presence of R5 and overestimates X4 strains compared to a phenotypic assay. Currently available GTT algorithms should be further improved for tropism prediction in HIV-1C. Maraviroc has an in vitro activity against most HIV-1C viruses and could be considered as an alternative regimen in individuals infected with CCR5-tropic HIV-1C viruses.
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Affiliation(s)
- Amare Worku Kalu
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Stockholm, Sweden.,Department of Microbiology, Immunology and Parasitology, Addis Ababa University, Ethiopia
| | - Nigus Fikrie Telele
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Stockholm, Sweden.,Department of Microbiology, Immunology and Parasitology, Addis Ababa University, Ethiopia
| | - Shambhu G Aralaguppe
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Stockholm, Sweden
| | - Solomon Gebre-Selassie
- Department of Microbiology, Immunology and Parasitology, Addis Ababa University, Ethiopia
| | - Daniel Fekade
- Department of Internal Medicine, Addis Ababa University, Ethiopia
| | - Gaetano Marrone
- Division of Infectious Diseases, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Anders Sonnerborg
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Stockholm, Sweden.,Division of Infectious Diseases, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
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3
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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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4
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Abstract
: Next-generation sequencing is a sensitive method for determining HIV-1 tropism but there is a lack of data on the quantification of X4 variants. We evaluated MiSeq and 454 GS-Junior platforms for determining HIV-1 tropism and for quantifying X4 variants. Both platforms were 93% concordant for determining HIV-1 tropism and correlated well for determining the proportion of X4 variants (Spearman correlation, ρ = 0.748; P < 0.0001). MiSeq Illumina sequencing seems to be well adapted for characterizing X4-containing samples.
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Affiliation(s)
- Sasha A Fahme
- From the Center for Global Health, Weill Cornell Medical College, New York, NY (S.A.F., R.P.)
- Department of Internal Medicine, Weill Bugando School of Medicine, Mwanza, Tanzania (S.A.F., R.P.)
| | - Gerald S Bloomfield
- Duke Clinical Research Institute, Duke University School of Medicine, Durham, NC (G.S.B.)
| | - Robert Peck
- From the Center for Global Health, Weill Cornell Medical College, New York, NY (S.A.F., R.P.)
- Department of Internal Medicine, Weill Bugando School of Medicine, Mwanza, Tanzania (S.A.F., R.P.)
- Mwanza Interventions Trial Unit, Tanzania (R.P.)
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6
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Lombardi F, Belmonti S, Rapone L, Borghetti A, Ciccullo A, Gagliardini R, Baldin G, Montagnani F, Moschese D, Emiliozzi A, Rossetti B, De Luca A, Di Giambenedetto S. HIV-1 non-R5 tropism correlates with a larger size of the cellular viral reservoir and a detectable residual viremia in patients under suppressive ART. J Clin Virol 2018; 103:57-62. [PMID: 29656086 DOI: 10.1016/j.jcv.2018.03.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 03/29/2018] [Accepted: 03/31/2018] [Indexed: 12/15/2022]
Abstract
BACKGROUND The influence of HIV-1 co-receptor usage on the course of therapy in subjects fully responding to ART has been poorly investigated. OBJECTIVES To explore the relationship between co-receptor tropism and cellular reservoir size, residual viremia and subsequent virological outcome in ART-treated patients with HIV-1 RNA stable <50 copies/mL. STUDY DESIGN Viral co-receptor usage was predicted by viral env DNA sequencing with geno2pheno interpretation (FPR20%) and classified as R5 and non-R5. Total blood-associated HIV-1 DNA levels (log10 copies/106 leukocytes) were measured by qRT-PCR (5'LTR). Residual plasma viremia was categorized as detectable (1-49 cps/mL) or undetectable (<1 copy/mL). Virological rebounds (any HIV-1 RNA >50 copies/mL) were evaluated over 96 weeks. RESULTS The study included 116 subjects. Patients with R5 virus (n = 59) and non-R5 virus (n = 57) were homogeneous for the main characteristics except for the lower nadir CD4 cell count in the non-R5 group. Patients with non-R5 variants showed higher levels of HIV-1 DNA as compared to patients with R5 virus: mean 2.47 (95% CI 2.37-2.56) vs 2.17 (2.08-2.26) (p < 0.001). Moreover, a higher proportion of patients in the non-R5 group displayed detectable residual viremia with respect to the R5-group (54.4% vs 32.2%, p = .016). Detectable residual viremia was found to be significantly associated with viral rebounds. CONCLUSION The presence of non-R5 viral DNA variants is related to a higher probability of residual viremia and to a larger size of the cellular viral reservoir in this setting. These data highlight a potential role of viral tropism in the monitoring of HIV-1 infection in virologically controlled subject.
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Affiliation(s)
- Francesca Lombardi
- Institute of Clinical Infectious Diseases, Catholic University of the Sacred Heart, Largo Agostino Gemelli 8, 00168 Rome, Italy.
| | - Simone Belmonti
- Institute of Clinical Infectious Diseases, Catholic University of the Sacred Heart, Largo Agostino Gemelli 8, 00168 Rome, Italy
| | - Lucrezia Rapone
- Institute of Clinical Infectious Diseases, Catholic University of the Sacred Heart, Largo Agostino Gemelli 8, 00168 Rome, Italy
| | - Alberto Borghetti
- Institute of Clinical Infectious Diseases, Catholic University of the Sacred Heart, Largo Agostino Gemelli 8, 00168 Rome, Italy
| | - Arturo Ciccullo
- Institute of Clinical Infectious Diseases, Catholic University of the Sacred Heart, Largo Agostino Gemelli 8, 00168 Rome, Italy
| | - Roberta Gagliardini
- Institute of Clinical Infectious Diseases, Catholic University of the Sacred Heart, Largo Agostino Gemelli 8, 00168 Rome, Italy
| | - Gianmaria Baldin
- Institute of Clinical Infectious Diseases, Catholic University of the Sacred Heart, Largo Agostino Gemelli 8, 00168 Rome, Italy
| | - Francesca Montagnani
- University Division of Infectious Diseases, Department of Specialized and Internal Medicine, Siena University Hospital, Viale Bracci 16, 53100 Siena, Italy; Department of Medical Biotechnologies, University of Siena, Viale Bracci 16, 53100 Siena, Italy
| | - Davide Moschese
- Institute of Clinical Infectious Diseases, Catholic University of the Sacred Heart, Largo Agostino Gemelli 8, 00168 Rome, Italy
| | - Arianna Emiliozzi
- Institute of Clinical Infectious Diseases, Catholic University of the Sacred Heart, Largo Agostino Gemelli 8, 00168 Rome, Italy
| | - Barbara Rossetti
- University Division of Infectious Diseases, Department of Specialized and Internal Medicine, Siena University Hospital, Viale Bracci 16, 53100 Siena, Italy
| | - Andrea De Luca
- University Division of Infectious Diseases, Department of Specialized and Internal Medicine, Siena University Hospital, Viale Bracci 16, 53100 Siena, Italy; Department of Medical Biotechnologies, University of Siena, Viale Bracci 16, 53100 Siena, Italy
| | - Simona Di Giambenedetto
- Institute of Clinical Infectious Diseases, Catholic University of the Sacred Heart, Largo Agostino Gemelli 8, 00168 Rome, Italy
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7
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Abstract
HIV-1 was mainly CCR5 tropic in recent seroconverters. We analyzed the coreceptor use in 239 primary HIV-1 infections (PHIs) between 1996 and 2014 using a validated recombinant virus phenotypic entry assay. CXCR4-using viruses were detected in 8.3%, 3.8%, and 6.1% of PHIs from 1996 to 2004, 2005 to 2009, and 2010 to 2014, respectively. The presence of CXCR4-using viruses was associated with the virological failure of antiretroviral treatment initiated during PHI (odds ratio, 7.9; 95% confidence interval, 1.1 to 56.5). The phenotypic tropism assay data show that the prevalence of X4 tropic transmitted viruses was stable in this French cohort of PHIs between 1996 and 2014.
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8
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Kalu AW, Telele NF, Gebreselasie S, Fekade D, Abdurahman S, Marrone G, Sönnerborg A. Prediction of coreceptor usage by five bioinformatics tools in a large Ethiopian HIV-1 subtype C cohort. PLoS One 2017; 12:e0182384. [PMID: 28841646 PMCID: PMC5571954 DOI: 10.1371/journal.pone.0182384] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Accepted: 07/17/2017] [Indexed: 12/15/2022] Open
Abstract
Background Genotypic tropism testing (GTT) has been developed largely on HIV-1 subtype B. Although a few reports have analysed the utility of GTT in other subtypes, more studies using HIV-1 subtype C (HIV-1C) are needed, considering the huge contribution of HIV-1C to the global epidemic. Methods Plasma was obtained from 420 treatment-naïve HIV-1C infected Ethiopians recruited 2009–2011. The V3 region was sequenced and the coreceptor usage was predicted by five tools: Geno2Pheno clinical–and clonal–models, PhenoSeq-C, C-PSSM and Raymond’s algorithm. The impact of baseline tropism on antiretroviral treatment (ART) outcome was evaluated. Results Of 352 patients with successful baseline V3 sequences, the proportion of predicted R5 virus varied between the methods by 12.5% (78.1%-90.6%). However, only 58.2% of the predictions were concordant and only 1.7% were predicted to be X4-tropic across the five methods. Compared pairwise, the highest concordance was between C-PSSM and Geno2Pheno clonal (86.4%). In bivariate intention to treat (ITT) analysis, R5 infected patients achieved treatment success more frequently than X4 infected at month six as predicted by Geno2Pheno clinical (77.8% vs 58.7%, P = 0.004) and at month 12 by C-PSSM (61.9% vs 46.6%, P = 0.038). However, in the multivariable analysis adjusted for age, gender, baseline CD4 and viral load, only tropism as predicted by C-PSSM showed an impact on month 12 (P = 0.04, OR 2.47, 95% CI 1.06–5.79). Conclusion Each of the bioinformatics models predicted R5 tropism with comparable frequency but there was a large discordance between the methods. Baseline tropism had an impact on outcome of first line ART at month 12 in multivariable ITT analysis but only based on prediction by C-PSSM which thus possibly could be used for predicting outcome of ART in HIV-1C infected Ethiopians.
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Affiliation(s)
- Amare Worku Kalu
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Stockholm, Sweden
- Department of Microbiology, Immunology and Parasitology, Addis Ababa University, Addis Ababa, Ethiopia
- * E-mail: ,
| | - Nigus Fikrie Telele
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Stockholm, Sweden
- Department of Microbiology, Immunology and Parasitology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Solomon Gebreselasie
- Department of Microbiology, Immunology and Parasitology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Daniel Fekade
- Department of Internal Medicine, Addis Ababa University, Addis Ababa, Ethiopia
| | | | - Gaetano Marrone
- Unit of Infectious Diseases, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Anders Sönnerborg
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Stockholm, Sweden
- Unit of Infectious Diseases, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
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9
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Capetti AF, Micale M, Carenzi L, Niero F, Landonio S, Vimercati S, Dedivitiis G, Rizzardini G. Strategic use of dual regimens of boosted protease inhibitors plus maraviroc in poorly adherent subjects in view of long-acting drugs: A retrospective study. Medicine (Baltimore) 2017; 96:e5728. [PMID: 28207500 PMCID: PMC5319489 DOI: 10.1097/md.0000000000005728] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
In view of the forthcoming long-acting antiretrovirals, measures should be taken to prevent the selection of HIV drug resistance mutations. All subjects who had been switched to boosted protease inhibitors plus maraviroc (bPIs/MVC) with baseline HIV-1 RNA >50 copies/mL between June, 2014, and April, 2015, were retrospectively evaluated. HIV-1 RNA, CD4+ T-cells, serum glucose, creatinine, ALT, and adverse events were controlled every 3 to 4 months. We retrospectively analyzed 44 patients: 18 were taking darunavir/ritonavir (DRV/r) and 26 atazanavir/ritonavir (ATV/r) once daily, plus MVC 300 mg once daily. Seven subjects were in CDC stage C. All had a follow-up of at least 24 weeks, 28 exceeded 48 weeks, and 21 exceeded 72 weeks. All had experienced at least 1 viral failure and had selected at least 1 resistance-associated mutation (RAM). At baseline, 38 had plasma HIV-1 RNA 50-499 copies/mL and 6 had ≥500. At week 24, none had viremia >500 and 30 (68.2%) had suppressed HIV-1 RNA below 50 copies/mL. Of the subgroup with 48 weeks' follow-up, 23 had HIV-1 RNA 50-499 copies/mL, 5 had ≥500, and 20/28 suppressed to <50 copies/mL. Of the longest observed subgroup (72 weeks), 17 had HIV-1 RNA 50-499 copies/mL, and 4 had ≥500 copies/mL and 15/21 (71.4%) suppressed to <50 copies/mL. This combination allowed fair suppression of viral replication, with minor genotypic evolution in 6 subjects, and seems to be a feasible strategy to prevent damaging future options.
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Affiliation(s)
| | | | | | | | | | | | | | - Giuliano Rizzardini
- 1st Division of Infectious Diseases
- Whitwaterstrand University, Johannesburg, South Africa
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10
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Kalu AW, Telele NF, Gebreselasie S, Fekade D, Abdurahman S, Marrone G, Sönnerborg A. Monophylogenetic HIV-1C epidemic in Ethiopia is dominated by CCR5-tropic viruses-an analysis of a prospective country-wide cohort. BMC Infect Dis 2017; 17:37. [PMID: 28061826 PMCID: PMC5219668 DOI: 10.1186/s12879-016-2163-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 12/22/2016] [Indexed: 11/10/2022] Open
Abstract
Background CCR5 coreceptor using HIV-1 subtype C (HIV-1C) has been reported to dominate the Ethiopian epidemic. However, almost all data have been obtained from two large cities in the central and north-west regions and recent data is lacking. Methods Plasma were obtained from 420 treatment-naïve patients recruited 2009–2011 to a large country-wide Ethiopian cohort. The V3 region was sequenced and the co-receptor tropism was predicted by the clinical and clonal models of the geno2pheno tool at different false positive rates (fpr) and for subtype. In an intention to treat analysis the impact of baseline tropism on outcome of antiretroviral therapy was evaluated. Results V3 loop sequencing was successful in 352 (84%) patients. HIV-1C was found in 350 (99.4%) and HIV-1A in two (0.6%) patients. When comparing the geno2pheno fpr10% clonal and clinical models, 24.4% predictions were discordant. X4-virus was predicted in 17.0 and 19.0%, respectively, but the predictions were concordant in only 6%. At fpr5%, concordant X4-virus predictions were obtained in 3.1%. The proportion of X4-tropic virus (clonal fpr10%) increased from 5.6 to 17.3% (p < 0.001) when 387 Ethiopian V3 loop sequences dated from 1984 to 2003 were compared with ours. In an intention to treat analysis, 67.9% reached treatment success at month 6 and only 50% at month 12. Only age and not tropism predicted therapy outcome and no difference was found in CD4+ cell gain between R5-tropic and X4-tropic infected patients. At viral failure, R5 to X4 switch was rare while X4 to R5 switch occurred more frequently (month 6: p = 0.006; month 12: p = 0.078). Conclusion The HIV-1C epidemic is monophylogenetic in all regions of Ethiopia and R5-tropic virus dominates, even in patients with advanced immunodeficiency, although the proportion of X4-tropic virus seems to have increased over the last two decades. Geno2pheno clinical and clonal prediction models show a large discrepancy at fpr10%, but not at fpr5%. Hence further studies are needed to assess the utility of genotypic tropism testing in HIV-1C. In ITT analysis only age and not tropism influenced the outcome.
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Affiliation(s)
- Amare Worku Kalu
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Alfred Nobels Alle 8, F68, Huddinge, Stockholm, 14186, Sweden. .,Department of Microbiology, Immunology and Parasitology, Addis Ababa University, Addis Ababa, Ethiopia.
| | - Nigus Fikrie Telele
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Alfred Nobels Alle 8, F68, Huddinge, Stockholm, 14186, Sweden.,Department of Microbiology, Immunology and Parasitology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Solomon Gebreselasie
- Department of Microbiology, Immunology and Parasitology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Daniel Fekade
- Department of internal Medicine, Addis Ababa University, Addis Ababa, Ethiopia
| | - Samir Abdurahman
- Public Health Agency of Sweden, Solna, Sweden.,Department of Science and Technology, Örebro University, Örebro, Sweden
| | - Gaetano Marrone
- Unit of Infectious Diseases, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Anders Sönnerborg
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Alfred Nobels Alle 8, F68, Huddinge, Stockholm, 14186, Sweden.,Unit of Infectious Diseases, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
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11
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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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12
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Mengoli C, Andreis S, Scaggiante R, Cruciani M, Bosco O, Ferretto R, Leoni D, Maffongelli G, Basso M, Torti C, Sarmati L, Andreoni M, Palù G, Parisi SG. Structural equation modelling of viral tropism reveals its impact on achieving viral suppression within 6 months in treatment-naive HIV-1-infected patients after combination antiretroviral therapy. J Antimicrob Chemother 2016; 72:220-226. [PMID: 27605599 DOI: 10.1093/jac/dkw348] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 07/19/2016] [Accepted: 07/25/2016] [Indexed: 12/24/2022] Open
Abstract
OBJECTIVES To evaluate the role of pre-treatment co-receptor tropism of plasma HIV on the achievement of viral suppression (plasma HIV RNA 1.69 log10 copies/mL) at the sixth month of combination antiretroviral therapy (cART) in a cohort of naive patients using, for the first time in this context, a path analysis (PA) approach. PATIENTS AND METHODS Adult patients with chronic infection by subtype B HIV-1 were consecutively enrolled from the start of first-line cART (T0). Genotypic analysis of viral tropism was performed on plasma and interpreted using the bioinformatic tool Geno2pheno, with a false positive rate of 10%. A Bayesian network starting from the viro-immunological data at T0 and at the sixth month of treatment (T1) was set up and this model was evaluated using a PA approach. RESULTS A total of 262 patients (22.1% bearing an X4 virus) were included; 178 subjects (67.9%) achieved viral suppression. A significant positive indirect effect of bearing X4 virus in plasma at T0 on log10 HIV RNA at T1 was detected (P = 0.009), the magnitude of this effect was, however, over 10-fold lower than the direct effect of log10 HIV RNA at T0 on log10 HIV RNA at T1 (P = 0.000). Moreover, a significant positive indirect effect of bearing an X4 virus on log10 HIV RNA at T0 (P = 0.003) was apparent. CONCLUSIONS PA overcame the limitations implicit in common multiple regression analysis and showed the possible role of pre-treatment viral tropism at the recommended threshold on the outcome of plasma viraemia in naive patients after 6 months of therapy.
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Affiliation(s)
- Carlo Mengoli
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Samantha Andreis
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | | | | | | | | | - Davide Leoni
- Clinical Infectious Diseases, Tor Vergata University, Rome, Italy
| | | | - Monica Basso
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Carlo Torti
- Unit of Infectious Diseases, University 'Magna Graecia', Catanzaro, Italy
| | - Loredana Sarmati
- Clinical Infectious Diseases, Tor Vergata University, Rome, Italy
| | - Massimo Andreoni
- Clinical Infectious Diseases, Tor Vergata University, Rome, Italy
| | - Giorgio Palù
- Department of Molecular Medicine, University of Padova, Padova, Italy
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No selection of CXCR4-using variants in cell reservoirs of dual-mixed HIV-infected patients on suppressive maraviroc therapy. AIDS 2016; 30:965-8. [PMID: 26752281 DOI: 10.1097/qad.0000000000001013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
We used ultradeep sequencing to investigate the evolution of the frequency of CXCR4-using viruses in the peripheral blood mononuclear cells of 22 patients infected with both CCR5 and CXCR4-using viruses treated with the CCR5 antagonist maraviroc for 24 weeks and a stable antiviral therapy. The mean CXCR4-using virus frequency in peripheral blood mononuclear cells was 59% before maraviroc intensification and 52% after 24 weeks of effective treatment, indicating no selection by maraviroc.
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Clinical value of ultradeep HIV-1 genotyping and tropism testing in late presenters with advanced disease. AIDS 2015; 29:1493-504. [PMID: 26244389 DOI: 10.1097/qad.0000000000000748] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
OBJECTIVE This article aims to investigate if the detection of preexisting drug-resistant minority variant (DRMV) and/or X4 HIV-1 variants could improve the efficacy of first-line combined antiretroviral therapy (ART) in late presenters. DESIGN Post-hoc, combined analysis of two open-label, prospective, randomized clinical trials comparing first-line ART with efavirenz (EFV) vs. ritonavir-boosted protease inhibitor (PI/r)-based regimens in ART-naive, HIV-1-infected patients, with CD4 T-cell counts less than 100 cells/μl and wild-type HIV-1 by bulk sequencing. METHODS Pre-ART samples were reanalyzed for the presence of DRMVs and X4 HIV-1 using 454 sequencing. Kaplan-Meier curves and Cox regression were used to evaluate the association between X4 HIV and DRMVs and risk of virological failure. RESULTS From 141 evaluable patients, 57 received EFV, and 84 received PI/r, including first-line ART. Median pre-ART CD4 T-cell counts and HIV-1 RNA levels were 39 cells/μl and 257 424 copies/ml, respectively; 35.5% of patients had X4 HIV variants. Detection of DRMVs leading to an ART-specific cumulative HIVdb score of at least 10 increased the risk of virological failure in patients initiating EFV [log-rank P = 0.048, hazard ratio = 4.3 (95% confidence interval: 0.8, 25.0), P = 0.074], but not in those starting PI/r. Presence of X4 HIV did not affect virological outcomes, but was associated with impaired CD4 T-cell count recovery over 2 years (214 vs. 315 cells/μl with X4 vs. R5 HIV-1 tropism, respectively, P = 0.017). CONCLUSION Accounting for preexisting DRMVs may improve the outcomes of first-line nonnucleoside reverse transcriptase inhibitor-based ART in late presenters with advanced immune suppression. Presence of X4 HIV-1 at diagnosis predicts impaired immune restoration under ART.
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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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Sede MM, Moretti FA, Laufer NL, Jones LR, Quarleri JF. HIV-1 tropism dynamics and phylogenetic analysis from longitudinal ultra-deep sequencing data of CCR5- and CXCR4-using variants. PLoS One 2014; 9:e102857. [PMID: 25032817 PMCID: PMC4102574 DOI: 10.1371/journal.pone.0102857] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Accepted: 06/25/2014] [Indexed: 11/25/2022] Open
Abstract
OBJECTIVE Coreceptor switch from CCR5 to CXCR4 is associated with HIV disease progression. The molecular and evolutionary mechanisms underlying the CCR5 to CXCR4 switch are the focus of intense recent research. We studied the HIV-1 tropism dynamics in relation to coreceptor usage, the nature of quasispecies from ultra deep sequencing (UDPS) data and their phylogenetic relationships. METHODS Here, we characterized C2-V3-C3 sequences of HIV obtained from 19 patients followed up for 54 to 114 months using UDPS, with further genotyping and phylogenetic analysis for coreceptor usage. HIV quasispecies diversity and variability as well as HIV plasma viral load were measured longitudinally and their relationship with the HIV coreceptor usage was analyzed. The longitudinal UDPS data were submitted to phylogenetic analysis and sampling times and coreceptor usage were mapped onto the trees obtained. RESULTS Although a temporal viral genetic structuring was evident, the persistence of several viral lineages evolving independently along the infection was statistically supported, indicating a complex scenario for the evolution of viral quasispecies. HIV X4-using variants were present in most of our patients, exhibiting a dissimilar inter- and intra-patient predominance as the component of quasispecies even on antiretroviral therapy. The viral populations from some of the patients studied displayed evidences of the evolution of X4 variants through fitness valleys, whereas for other patients the data favored a gradual mode of emergence. CONCLUSIONS CXCR4 usage can emerge independently, in multiple lineages, along the course of HIV infection. The mode of emergence, i.e. gradual or through fitness valleys seems to depend on both virus and patient factors. Furthermore, our analyses suggest that, besides becoming dominant after population-level switches, minor proportions of X4 viruses might exist along the infection, perhaps even at early stages of it. The fate of these minor variants might depend on both viral and host factors.
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Affiliation(s)
- Mariano M. Sede
- Instituto de Investigaciones Biomédicas en Retrovirus y Sida (INBIRS), Universidad de Buenos Aires, CONICET, Buenos Aires, Argentina
- Consejo de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Franco A. Moretti
- Instituto de Investigaciones Biomédicas en Retrovirus y Sida (INBIRS), Universidad de Buenos Aires, CONICET, Buenos Aires, Argentina
- Consejo de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Natalia L. Laufer
- Instituto de Investigaciones Biomédicas en Retrovirus y Sida (INBIRS), Universidad de Buenos Aires, CONICET, Buenos Aires, Argentina
- Consejo de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Leandro R. Jones
- Consejo de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Laboratorio de Virología y Genética Molecular, Facultad de Ciencias Naturales, sede Trelew, Universidad Nacional de la Patagonia San Juan Bosco, Chubut, Argentina
| | - Jorge F. Quarleri
- Instituto de Investigaciones Biomédicas en Retrovirus y Sida (INBIRS), Universidad de Buenos Aires, CONICET, Buenos Aires, Argentina
- Consejo de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
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Trevino A, Soriano V, Poveda E, Parra P, Cabezas T, Caballero E, Roc L, Rodriguez C, Eiros JM, Lopez M, De Mendoza C, Rodriguez C, del Romero J, Tuset C, Marcaida G, Ocete MD, Tuset T, Caballero E, Molina I, Aguilera A, Rodriguez-Calvino JJ, Navarro D, Regueiro B, Benito R, Gil J, Borras M, Ortiz de Lejarazu R, Eiros JM, Manzardo C, Miro JM, Garcia J, Paz I, Calderon E, Leal M, Vallejo A, Abad M, Dronda F, Moreno S, Escudero D, Trigo M, Diz J, Alvarez P, Cortizo S, Garcia-Campello M, Rodriguez-Iglesias M, Hernandez-Betancor A, Martin AM, Ramos JM, Gutierrez F, Rodriguez JC, Gomez-Hernando C, Guelar A, Cilla G, Perez-Trallero E, Lopez-Aldeguer J, Sola J, Fernandez-Pereira L, Niubo J, Hernandez M, Lopez-Lirola AM, Gomez-Sirvent JL, Force L, Cifuentes C, Perez S, Morano L, Raya C, Gonzalez-Praetorius A, Perez JL, Penaranda M, Mena A, Montejo JM, Roc L, Martinez-Sapina A, Viciana I, Cabezas T, Lozano A, Fernandez JM, Garcia Bermejo I, Gaspar G, Garcia R, Gorgolas M, Miralles P, Aldamiz T, Garcia F, Suarez A, Trevino A, Parra P, de Mendoza C, Soriano V. HIV-2 viral tropism influences CD4+ T cell count regardless of viral load. J Antimicrob Chemother 2014; 69:2191-4. [DOI: 10.1093/jac/dku119] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Parczewski M, Urbańska A, Maciejewska K, Clark J, Leszczyszyn-Pynka M. Association of chemokine receptor gene variants with HIV-1 genotype predicted tropism. HIV Med 2014; 15:577-86. [PMID: 24750723 DOI: 10.1111/hiv.12155] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/26/2014] [Indexed: 11/28/2022]
Abstract
OBJECTIVES As a switch from chemokine (C-C motif) receptor 5 [CCR5 (R5)] to chemokine (C-X-C motif) receptor 4 [CXCR4 (X4)] HIV-1 tropism is associated with symptomatic and AIDS stages of infection, while chemokine receptor gene variants modify the tempo of HIV disease progression, we aimed to analyse the association between pretreatment HIV-1 tropism and chemokine polymorphisms known to restrict disease progression. METHODS V3 genotype tropism prediction was performed in a group of 221 treatment-naïve patients, with subsequent CCR5 Δ32 (rs333), CCR2 V64I (rs1799864), CCR5 promoter (-627 C/T; rs1799988) and CX3CR1 V249I (rs3732378) genotyping performed in 206 patients. Alleles with a protective effect were assigned positive values while risk alleles were assigned negative values to calculate genetic scores. χ(2) tests, Mann-Whitney U-tests and logistic and linear regression models were used for statistical analyses. RESULTS R5 tropism was found in 85.5% of patients (n = 189) using a false positive rate (FPR) of 5.75% and in 72.8% of patients (n = 161) using an FPR of 10%. A higher frequency of the 5.75% FPR predicted R5 tropism was associated with the CX3CR1 A allele (P = 0.027). Lower additive genetic scores were associated with an increased frequency of 5.75% FPR predicted R5 tropism (P = 0.0059), with the trend confirmed by logistic regression [odds ratio (OR) 0.5819; 95% confidence interval (CI) 0.3457-0.9795; P = 0.0416]. Viral load tended to increase with decreasing genetic score in the logistic regression analysis (slope = -0.127 ± 0.076; P = 0.095; r(2) = 0.161). CONCLUSIONS The CX3CR1 A allele and lower genetic scores may restrict the switch of HIV-1 tropism from R5 to X4. This effect may be associated with the amount of co-receptor on the cell surface. Chemokine receptor gene polymorphisms influence both disease progression and tropism variability.
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Affiliation(s)
- M Parczewski
- Department of Infectious Diseases, Hepatology and Immune Deficiency, Pomeranian Medical University, Szczecin, Poland
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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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Vancoillie L, Demecheleer E, Callens S, Vogelaers D, Vandekerckhove L, Mortier V, Verhofstede C. Markers associated with persisting low-level viraemia under antiretroviral therapy in HIV-1 infection. J Antimicrob Chemother 2013; 69:1098-103. [PMID: 24335486 DOI: 10.1093/jac/dkt484] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
OBJECTIVES To identify host and viral characteristics associated with long-term persisting low-level viraemia (PLLV) under antiretroviral therapy (ART). PATIENTS AND METHODS Seventy-one ART-treated patients with long-term PLLV (20-250 copies/mL) and 102 control patients with systematically undetectable viral load (VL) were selected retrospectively from ART-treated patients followed at the Ghent HIV reference centre. Host and viral characteristics were compared using univariate and multivariate analyses. RESULTS Higher plasma VL at therapy initiation (OR 3.52; 95% CI 1.86-6.65; P < 0.001), therapy re-initiation after an interruption (OR 3.94; 95% CI 1.70-9.16; P = 0.001), male gender (OR 4.28; 95% CI 1.40-13.00; P = 0.011), a protease inhibitor-based regimen (OR 2.90; 95% CI 1.20-6.97; P = 0.017) and predicted CCR5 co-receptor tropism (OR 2.53; 95% CI 1.05-6.11; P = 0.039) were independently associated with PLLV. CONCLUSIONS VL at ART initiation, therapy history, gender, ART regimen and co-receptor tropism were independently associated with PLLV. Gender, therapy history, co-receptor tropism and VL at ART initiation could be valuable predictive markers to identify patients at risk for PLLV.
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Affiliation(s)
- Leen Vancoillie
- AIDS Reference Laboratory, Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, De Pintelaan 185-Blok A, B-9000 Ghent, Belgium
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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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Cheng C, Vedananda S, Wu L, Harbeson S, Braman V, Tung R. Revealing the metabolic sites of atazanavir in human by parallel administrations of D-atazanavir analogs. JOURNAL OF MASS SPECTROMETRY : JMS 2013; 48:1019-1031. [PMID: 24078243 DOI: 10.1002/jms.3247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Revised: 05/24/2013] [Accepted: 06/03/2013] [Indexed: 06/02/2023]
Abstract
Atazanavir (Reyataz(®)) is an important member of the HIV protease inhibitor class. Because of the complexity of its chemical structure, metabolite identification and structural elucidation face serious challenges. So far, only seven non-conjugated metabolites in human plasma have been reported, and their structural elucidation is not complete, especially for the major metabolites produced by oxidations. To probe the exact sites of metabolism and to elucidate the relationship among in vivo metabolites of atazanavir, we designed and performed two sets of experiments. The first set of experiments was to determine atazanavir metabolites in human plasma by LC-MS, from which more than a dozen metabolites were discovered, including seven new ones that have not been reported. The second set involved deuterium labeling on potential metabolic sites to generate D-atazanavir analogs. D-atazanavir analogs were dosed to human in parallel with atazanavir. Metabolites of D-atazanavir were identified by the same LC-MS method, and the results were compared with those of atazanavir. A metabolite structure can be readily elucidated by comparing the results of the analogs and the pathway by which the metabolite is formed can be proposed with confidence. Experimental results demonstrated that oxidation is the most common metabolic pathway of atazanavir, resulting in the formation of six metabolites of monooxidation (M1, M2, M7, M8, M13, and M14) and four of dioxidation (M15, M16, M17, and M18). The second metabolic pathway is hydrolysis, and the third is N-dealkylation. Metabolites produced by hydrolysis include M3, M4, and M19. Metabolites formed by N-dealkylation are M5, M6a, and M6b.
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Affiliation(s)
- Changfu Cheng
- Concert Pharmaceuticals, Inc., 99 Hayden Avenue, Suite 500, Lexington, MA, 02421, USA
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Sterrantino G, Zaccarelli M, Di Giambenedetto S, De Luca A, Francisci D, Punzi G, Monno L, Bruzzone B, Antinori A, Zazzi M. HIV tropism and its relationship with transmitted resistance in naive patients. Future Virol 2013. [DOI: 10.2217/fvl.13.63] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Aim: The objective of the present study was to investigate whether patients with transmitted resistance more frequently harbor X4/DM tropic viral strains. Patients & methods: Patients were included from an Italian nationwide database if they were tested for tropism and resistance at the same time. HIV tropism was assessed by the Geno2pheno coreceptor system (false-positive rate: ≤10%) and enhanced-sensitivity Trofile assay. Overall, 299 naive patients, tested between 2009 and 2011, were included: 252 patients tested by Geno2pheno, 116 by enhanced-sensitivity Trofile assay and 80 by both methods. Results & conclusion: Using Geno2pheno, X4/DM tropic virus was detected in 55 patients (21.8%), with an overall mean false-positive rate of 42.3% (standard deviation: ±33.3). Using the enhanced-sensitivity Trofile assay, 29 patients (25.0%) carried X4/DM tropic virus. Resistance mutations were more frequently detected in patients harboring X4/DM tropic virus (mean: 1.18 ± 3.0 vs 0.41 ± 1.2 per patient; p = 0.001) and with both Geno2pheno (0.82 ± 2.6 vs 0.35 ± 0.9; p = 0.034) and enhanced-sensitivity Trofile assay (1.11 ± 1.9 vs 0.46 ± 1.1; p = 0.039). However, significant differences were found for reverse transcriptase-related mutations, but not for transmitted protease resistance, and this might be explained by the low frequency of transmitted protease resistance. Among single mutations, L33F and L90M with regards to protease and K65R, K70E, K219E and V106A/M with regards to reverse transcriptase were found to be significantly associated with X4/DM tropic virus. X4/DM tropism was also associated with lower CD4+ cell count, but not with higher HIV RNA levels. X4/DM tropic HIV strains were related to a higher frequency of transmitted reverse transcriptase resistance mutations in this unselected set of naive patients. As a consequence, if a patient harbors a non-CCR5 tropic virus and bears more reverse transcriptase resistance and less protease resistance, a boosted protease inhibitor-based first-line regimen should be preferred.
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Affiliation(s)
- Gaetana Sterrantino
- Azienda Ospedaliera Universitaria Careggi, Infectious Diseases, Largo Brambilla 3, 50134 Firenze, Italy
| | - Mauro Zaccarelli
- National Institute for Infectious Diseases ‘Lazzaro Spallanzani’, Viral Immunodeficiency Unit, Rome, Italy
| | | | | | | | - Grazia Punzi
- University of Bari, Laboratory of Virology, Bari, Italy
| | - Laura Monno
- University of Bari, Infectious Diseases, Bari, Italy
| | | | - Andrea Antinori
- National Institute for Infectious Diseases ‘Lazzaro Spallanzani’, Clinical Department, Rome, Italy
| | - Maurizio Zazzi
- University of Siena, Department of Molecular Biology, Siena, Italy, for the ARCA Data-Base Study Group
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Parisi SG, Andreis S, Mengoli C, Scaggiante R, Cruciani M, Ferretto R, Manfrin V, Panese S, Basso M, Boldrin C, Bressan S, Sarmati L, Andreoni M, Palù G. A stable CC-chemokine receptor (CCR)-5 tropic virus is correlated with the persistence of HIV RNA at less than 2.5 copies in successfully treated naïve subjects. BMC Infect Dis 2013; 13:314. [PMID: 23844927 PMCID: PMC3722123 DOI: 10.1186/1471-2334-13-314] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Accepted: 07/10/2013] [Indexed: 01/22/2023] Open
Abstract
Background To determine if tropism for CXCR4 or CCR5 correlates with cellular HIV DNA load, residual viraemia and CD4 count in 219 successfully treated naive subjects with HIV infection enrolled in five infectious diseases units in Northeastern Italy. Methods A subset of subjects, achieving plasma HIV RNA level <50 copies/ml after initiation of first-line therapy and maintaining it until follow-up time points, was retrospectively selected from a prospective cohort. Blood samples were collected before the beginning of therapy (T0), at the first follow-up time (T1) and, when available, at a second (T2) follow-up time. Results HIV DNA, CD4 count and plasma viraemia were available from all 219 patients at T0 and T1, and in 86 subjects at T2, while tropism determinations were available from 109 subjects at T0, 219 at T1, and from 86 subjects at T2. Achieving residual viraemia <2.5 copies/ml at T1 correlated with having the same condition at T2 (p = 0.0007). X4 tropism at T1 was negatively correlated with the possibility of achieving viraemia<2.5 copies/ml at T2 (p = 0.0076). T1-T2 tropism stability was significant (p <0.0001). T0 tropism correlated with T1 and T2 tropism (p < 0.001); therefore the stability of the tropism over the two follow-up periods was significant (p = 0.0003). An effective viremic suppression (viraemia<2.5 copies/ml) correlated with R5 coreceptor affinity (p= 0.047). Conclusions The tropism of archived virus was stable during an effective treatment, with 15-18% of subjects switching over time, despite a viraemia<50 copies/ml. R5 tropism and its stability were related to achieving and maintaining viraemia<2.5 copies/ml.
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Cheng C, Gallegos R, Bridson G, Wu L, Harbeson S, Zelle R, Tung R. Identification and structural elucidation of in vitro metabolites of atazanavir by HPLC and tandem mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2013; 48:640-650. [PMID: 23722954 DOI: 10.1002/jms.3201] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Revised: 02/11/2013] [Accepted: 02/12/2013] [Indexed: 06/02/2023]
Abstract
Atazanavir (marketed as Reyataz®) is an important member of the human immunodeficiency virus protease inhibitor class. LC-UV-MS(n) experiments were designed to identify metabolites of atazanavir after incubations in human hepatocytes. Five major (M1-M5) and seven minor (M7-M12) metabolites were identified. The most abundant metabolite, M1, was formed by a mono-oxidation on the t-butyl group at the non-prime side. The second most abundant metabolite, M2, was also a mono-oxidation product, which has not yet been definitively identified. Metabolites, M3 and M4, were structural isomers, which were apparently formed by oxidative carbamate hydrolysis. The structure of M5 comprises the non-prime side of atazanavir which contains a pyridinyl-benzyl group. Metabolite M6a was formed by the cleavage of the pyridinyl-benzyl side chain, as evidenced by the formation of the corresponding metabolic product, the pyridinyl-benzoic acid (M6b). Mono-oxidation also occurred on the pyridinyl-benzyl group to produce the low abundance metabolite M8. Oxidation of the terminal methyl groups produced M9 and M10, respectively, which have low chemical stability. Trace-level metabolites of di-oxidations, M11 and M12, were also detected, but the complexity of the molecule precluded identification of the second oxidation site. To our knowledge, metabolites M6b and M8 have not been reported.
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Affiliation(s)
- Changfu Cheng
- Concert Pharmaceuticals, Inc., Lexington, MA 02421, USA.
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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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Charpentier C, Joly V, Larrouy L, Fagard C, Visseaux B, de Verdiere NC, Raffi F, Yeni P, Descamps D, Aumaitre H, Medus M, Neuville S, Saada M, Abgrall S, Bentata M, Bouchaud O, Cailhol J, Cordel H, Dhote R, Gros H, Honore-Berlureau P, Huynh T, Krivitzky A, Mansouri R, Poupard M, Prendki V, Radia D, Rouges F, Touam F, Warde B, de Castro N, Colin de Verdiere N, Delgado J, Ferret S, Gallien S, Kandel T, Lafaurie M, Lagrange M, Lascoux-Combe C, Le D, Molina JM, Pavie J, Pintado C, Ponscarme D, Rachline A, Rozenbaum W, Sereni D, Taulera O, Estavoyer JM, Faucher JF, Foltzer A, Hoen B, Hustache-Mathieu L, Dupon M, Dutronc H, Neau D, Ragnaud JM, Raymond I, Boucly S, Lortholary O, Viard JP, Bechara C, Delfraissy JF, Ghosn J, Goujard C, Kamouh W, Mole M, Quertainmont Y, Bergmann JF, Boulanger E, Castillo H, Parrinello M, Rami A, Sellier P, Lepeu G, Pichancourt G, Bernard L, Berthe H, Clarissou J, Gory M, Melchior JC, Perronne C, Stegman S, de Truchis P, Derradji O, Malet M, Teicher E, Vittecoq D, Chakvetadze C, Fontaine C, Lukiana T, Pialloux G, Slama L, Bonnet D, Boucherit S, El Alami Talbi N, Fournier I, Gervais A, Joly V, Iordache L, Laurichesse JJ, Leport C, Pahlavan G, Phung BC, Yeni P, Bennamar N, Brunet A, Guillevin L, Salmon-Ceron D, Tahi T, Chesnel C, Dominguez S, Jouve P, Lelievre JD, Levy Y, Melica G, Sobel A, Ben Abdallah S, Bonmarchand M, Bricaire F, Herson S, Iguertsira M, Katlama C, Kouadio H, Schneider L, Simon A, Valantin MA, Abel S, Beaujolais V, Cabie A, Liauthaud B, Pierre Francois S, Abgueguen P, Chennebault JM, Loison J, Pichard E, Rabier V, Delaune J, Louis I, Morlat P, Pertusa MC, Brunel-Delmas F, Chiarello P, Jeanblanc F, Jourdain JJ, Livrozet JM, Makhloufi D, Touraine JL, Augustin-Normand C, Bailly F, Benmakhlouf N, Brochier C, Cotte L, Gueripel V, Koffi K, Lack P, Lebouche B, Maynard M, Miailhes P, Radenne S, Schlienger I, Thoirain V, Trepo C, Drogoul MP, Fabre G, Faucher O, Frixon-Marin V, Gastaut JA, Peyrouse E, Poizot-Martin I, Jacquet JM, Le Facher G, Merle de Boever C, Reynes J, Tramoni C, Allavena C, Billaud E, Biron C, Bonnet B, Bouchez S, Boutoille D, Brunet-Francois C, Hue H, Mounoury O, Raffi F, Reliquet V, Aubry O, Esnault JL, Leautez-Nainville S, Perre P, Suaud I, Breaud S, Ceppi C, Dellamonica P, De Salvador F, Durant J, Ferrando S, Fuzibet JG, Leplatois A, Mondain V, Perbost I, Pugliese P, Rahelinirina V, Rosenthal E, Sanderson F, Vassalo M, Arvieux C, Chapplain JM, Michelet C, Ratajczak M, Revest M, Souala F, Tattevin P, Cheneau C, Fischer P, Lang JM, Partisani M, Rey D, Bastides F, Besnier JM, Le Bret P, Choutet P, Dailloux JF, Guadagnin P, Nau P, Rivalain J, Soufflet A, Aissi E, Melliez H, Pavel S, Mouton Y, Yazdanpanah Y, Boyer L, Burty C, Letranchant L, May T, Wassoumbou S, Blum L, Danne O, Arthus MA, Dion P, Certain A, Tabuteau S, Beuscart A, Agher N, Frosch A, Couffin-Cadiergues S, Diallo A. Role and evolution of viral tropism in patients with advanced HIV disease receiving intensified initial regimen in the ANRS 130 APOLLO trial. J Antimicrob Chemother 2012; 68:690-6. [DOI: 10.1093/jac/dks455] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Monno L, Scudeller L, Saracino A, Santoro CR, Lagioia A, Ladisa N, Angarano G. Improved virological outcome in non-B patients: a possible role for baseline coreceptor tropism. Clin Infect Dis 2012; 55:165-7. [PMID: 22460957 DOI: 10.1093/cid/cis345] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Bordería AV, Stapleford KA, Vignuzzi M. RNA virus population diversity: implications for inter-species transmission. Curr Opin Virol 2011; 1:643-8. [PMID: 22440922 DOI: 10.1016/j.coviro.2011.09.012] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2011] [Revised: 09/13/2011] [Accepted: 09/30/2011] [Indexed: 01/25/2023]
Abstract
RNA viruses are notorious for rapidly generating genetically diverse populations during a single replication cycle, and the implications of this mutant population, often referred to as quasispecies, can be vast. Previous studies have linked RNA virus genetic variability to changes in viral pathogenesis, the ability to adapt to a host during infection, and to the acquisition of mechanisms required to switch hosts entirely. However, these initial studies are just the beginning. With the development of next generation technologies, groups will be able to dig deeper into the sequence space that is generated during an RNA virus infection and more clearly understand the development, role, and consequences of viral genetic diversity.
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Affiliation(s)
- Antonio V Bordería
- Institut Pasteur, Viral Populations and Pathogenesis Group and CNRS 3015, 75724 Paris Cedex 15, France
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