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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] [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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Grant HE, Roy S, Williams R, Tutill H, Ferns B, Cane PA, Carswell JW, Ssemwanga D, Kaleebu P, Breuer J, Leigh Brown AJ. A large population sample of African HIV genomes from the 1980s reveals a reduction in subtype D over time associated with propensity for CXCR4 tropism. Retrovirology 2022; 19:28. [PMID: 36514107 PMCID: PMC9746199 DOI: 10.1186/s12977-022-00612-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 11/12/2022] [Indexed: 12/15/2022] Open
Abstract
We present 109 near full-length HIV genomes amplified from blood serum samples obtained during early 1986 from across Uganda, which to our knowledge is the earliest and largest population sample from the initial phase of the HIV epidemic in Africa. Consensus sequences were made from paired-end Illumina reads with a target-capture approach to amplify HIV material following poor success with standard approaches. In comparisons with a smaller 'intermediate' genome dataset from 1998 to 1999 and a 'modern' genome dataset from 2007 to 2016, the proportion of subtype D was significantly higher initially, dropping from 67% (73/109), to 57% (26/46) to 17% (82/465) respectively (p < 0.0001). Subtype D has previously been shown to have a faster rate of disease progression than other subtypes in East African population studies, and to have a higher propensity to use the CXCR4 co-receptor ("X4 tropism"); associated with a decrease in time to AIDS. Here we find significant differences in predicted tropism between A1 and D subtypes in all three sample periods considered, which is particularly striking the 1986 sample: 66% (53/80) of subtype D env sequences were predicted to be X4 tropic compared with none of the 24 subtype A1. We also analysed the frequency of subtype in the envelope region of inter-subtype recombinants, and found that subtype A1 is over-represented in env, suggesting recombination and selection have acted to remove subtype D env from circulation. The reduction of subtype D frequency over three decades therefore appears to be a result of selective pressure against X4 tropism and its higher virulence. Lastly, we find a subtype D specific codon deletion at position 24 of the V3 loop, which may explain the higher propensity for subtype D to utilise X4 tropism.
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Affiliation(s)
- Heather E Grant
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, UK.
| | - Sunando Roy
- Division of Infection and Immunity, University College London, London, UK
| | - Rachel Williams
- UCL Great Ormond Street Institute of Child Health, London, UK
| | - Helena Tutill
- Division of Infection and Immunity, University College London, London, UK
| | - Bridget Ferns
- Department of Virology, University College London Hospitals NHS Foundation Trust, London, UK
| | | | | | - Deogratius Ssemwanga
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe, Uganda
| | - Pontiano Kaleebu
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe, Uganda
| | - Judith Breuer
- Division of Infection and Immunity, University College London, London, UK
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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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Prator CA, Donatelli J, Henrich TJ. From Berlin to London: HIV-1 Reservoir Reduction Following Stem Cell Transplantation. Curr HIV/AIDS Rep 2020; 17:385-393. [PMID: 32519184 DOI: 10.1007/s11904-020-00505-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
PURPOSE OF REVIEW Few interventional strategies lead to significant reductions in HIV-1 reservoir size or prolonged antiretroviral (ART)-free remission. Allogeneic stem cell transplantations (SCT) with or without donor cells harboring genetic mutations preventing functional expression of CCR5, an HIV coreceptor, lead to dramatic reductions in residual HIV burden. However, the mechanisms by which SCT reduces viral reservoirs and leads to a potential functional HIV cure are not well understood. RECENT FINDINGS A growing number of studies involving allogeneic SCT in people with HIV are emerging, including those with and without transplants involving CCR5Δ32/Δ32 mutations. Donor cells resistant to HIV entry are likely required in order to achieve permanent ART-free viral remission. However, dramatic reductions in the HIV reservoir secondary to beneficial graft-versus-host effects may lead to loss of HIV detection in blood and various tissues and lead to prolonged time to HIV rebound in individuals with wild-type CCR5 donors. Studies of SCT recipients and those who started very early ART during hyperacute infection suggest that dramatic reductions in reservoir size or restriction of initial reservoir seeding may lead to 8-10 months of time prior to eventual, and rapid, HIV recrudescence. Studies of allogeneic SCT in people with HIV have provided important insights into the size and nature of the HIV reservoir, and have invigorated other gene therapies to achieve HIV cure.
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Affiliation(s)
- Cecilia A Prator
- Division of Experimental Medicine, University of California San Francisco, 1001 Potrero Avenue Building 3, Room 525A, San Francisco, CA, 97706, USA
| | - Joanna Donatelli
- Division of Experimental Medicine, University of California San Francisco, 1001 Potrero Avenue Building 3, Room 525A, San Francisco, CA, 97706, USA.,California Institute of Regenerative Medicine, Bridges to Stem Cell Research Program, San Francisco State University, San Francisco, CA, USA
| | - Timothy J Henrich
- Division of Experimental Medicine, University of California San Francisco, 1001 Potrero Avenue Building 3, Room 525A, San Francisco, CA, 97706, USA.
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Intra-host dynamics and co-receptor usage of HIV-1 quasi-species in vertically infected patients with phenotypic switch. INFECTION GENETICS AND EVOLUTION 2019; 78:104066. [PMID: 31698113 DOI: 10.1016/j.meegid.2019.104066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Revised: 10/05/2019] [Accepted: 10/09/2019] [Indexed: 11/20/2022]
Abstract
HIV-1 infection through vertical transmission provides a good model to evaluate intra-host viral evolution and allows to gain insight into the dynamics of viral populations. Our aim was to assess the diversity and dynamics of X4- and R5-using HIV-1 variants in vertically infected children who presented a switch in SI/ NSI phenotype in MT-2 cell assays during chronic infection. Through molecular cloning and next generation sequencing of the C2-V5 env fragment, we investigated HIV-1 evolution and co-receptor usage based on V3 loop prediction bioinformatic tools of longitudinal samples obtained from 4 children. In all cases, the phylogenetic relationships were assessed by Maximum-Likelihood trees constructed with MEGA 6.0. In two cases, V3 loop sequences predicted exclusively R5-using and or X4-using strains, while in another two a higher degree of concordance was observed between the phenotypic and genotypic characteristics. In 3 of the 4 cases, C2-V5 env sequences from different time points were intermingled in phylogenetic trees, with no segregation neither by time or tropism. In only one case monophyletic clustering defined groups of sequences with different co-receptor usage. Comparison of amino acid frequency between isolates with SI and NSI phenotype allowed the identification of 9 possible genetic determinants in subtype F C2-V5 region of env associated to SI/ NSI phenotype in these patients, one of which had previously been reported for subtype B. Overall, we found a low degree of correlation between phenotypic and genotypic properties of HIV-1 quasispecies in patients under chronic infection. Whether HIV-1 subtype or other factors influence the evolution of HIV-1 in vivo will require further research.
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Wirden M, De Oliveira F, Bouvier-Alias M, Lambert-Niclot S, Chaix ML, Raymond S, Si-Mohammed A, Alloui C, André-Garnier E, Bellecave P, Malve B, Mirand A, Pallier C, Poveda JD, Rabenja T, Schneider V, Signori-Schmuck A, Stefic K, Calvez V, Descamps D, Plantier JC, Marcelin AG, Visseaux B. New HIV-1 circulating recombinant form 94: from phylogenetic detection of a large transmission cluster to prevention in the age of geosocial-networking apps in France, 2013 to 2017. Euro Surveill 2019; 24:1800658. [PMID: 31576801 PMCID: PMC6774227 DOI: 10.2807/1560-7917.es.2019.24.39.1800658] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
BackgroundEnding the HIV pandemic must involve new tools to rapidly identify and control local outbreaks and prevent the emergence of recombinant strains with epidemiological advantages.AimThis observational study aimed to investigate in France a cluster of HIV-1 cases related to a new circulating recombinant form (CRF). The confirmation this CRF's novelty as well as measures to control its spread are presented.MethodsPhylogenetic analyses of HIV sequences routinely generated for drug resistance genotyping before 2018 in French laboratories were employed to detect the transmission chain. The CRF involved was characterised by almost full-length viral sequencing for six cases. Cases' clinical data were reviewed. Where possible, epidemiological information was collected with a questionnaire.ResultsThe transmission cluster comprised 49 cases, mostly diagnosed in 2016-2017 (n = 37). All were infected with a new CRF, CRF94_cpx. The molecular proximity of this CRF to X4 strains and the high median viraemia, exceeding 5.0 log10 copies/mL, at diagnosis, even in chronic infection, raise concerns of enhanced virulence. Overall, 41 cases were diagnosed in the Ile-de-France region and 45 were men who have sex with men. Among 24 cases with available information, 20 reported finding partners through a geosocial networking app. Prevention activities in the area and population affected were undertaken.ConclusionWe advocate the systematic use of routinely generated HIV molecular data by a dedicated reactive network, to improve and accelerate targeted prevention interventions. Geosocial networking apps can play a role in the spread of outbreaks, but could also deliver local targeted preventive alerts.
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Affiliation(s)
- Marc Wirden
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique IPLESP, AP-HP, Hôpital Pitié Salpêtrière, Laboratoire de virologie, Paris, France
| | - Fabienne De Oliveira
- Normandie Université, UNIROUEN, EA2656 GRAM, CHU de Rouen, Laboratoire de virologie associé au CNR VIH, Rouen, France
| | | | | | - Marie-Laure Chaix
- AP-HP, Hôpital Saint-Louis, Laboratoire de virologie, INSERM U944, Paris, France
| | | | | | - Chakib Alloui
- Laboratoire de virologie, Hôpital Avicenne, Bobigny, France
| | | | | | - Brice Malve
- Laboratoire de virologie CHU de Nancy, Nancy, France
| | - Audrey Mirand
- Laboratoire de virologie CHU de Clermont-Ferrand, Clermont-Ferrand, France
| | - Coralie Pallier
- Laboratoire de virologie, Hôpital P. Brousse, Villejuif, France
| | | | - Theresa Rabenja
- Laboratoire du Grand Hôpital de l’Est Francilien, Jossigny, France
| | | | | | - Karl Stefic
- Laboratoire de virologie CHU de Tours, Tours, France
| | - Vincent Calvez
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique IPLESP, AP-HP, Hôpital Pitié Salpêtrière, Laboratoire de virologie, Paris, France
| | - Diane Descamps
- Laboratoire de virologie, AP-HP, Hopital Bichat Claude Bernard, Univ Paris-Diderot, INSERM, IAME, CNR VIH, Paris, France
| | - Jean-Christophe Plantier
- Normandie Université, UNIROUEN, EA2656 GRAM, CHU de Rouen, Laboratoire de virologie associé au CNR VIH, Rouen, France
| | - Anne-Genevieve Marcelin
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique IPLESP, AP-HP, Hôpital Pitié Salpêtrière, Laboratoire de virologie, Paris, France
| | - Benoit Visseaux
- Laboratoire de virologie, AP-HP, Hopital Bichat Claude Bernard, Univ Paris-Diderot, INSERM, IAME, CNR VIH, Paris, France
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7
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Nicolás D, Suárez A, Ambrosioni J, Manzardo C, Ligero C, Costa J, Fernández E, Marcos MÁ, Plana M, Mosquera MM, Sánchez-Palomino S, Gatell JM, Miró JM. Prevalence, clinical characteristics and outcome of severe primary HIV-1 infection: A prospective cohort study. Int J Infect Dis 2019; 88:73-79. [PMID: 31401201 DOI: 10.1016/j.ijid.2019.08.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 07/31/2019] [Accepted: 08/03/2019] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Severe cases of primary HIV infection have been described in patients presenting with neurological involvement, AIDS defining events or other life-threatening events. These severe forms have not been fully studied. OBJECTIVES To determine the prevalence and characteristics of severe PHI in a hospital-based cohort of primary HIV infection, and the response to the early initiation of antiretroviral therapy (ART) at 12 months. METHODS Every patient with PHI attending Hospital Clínic of Barcelona (1997-2015) was evaluated. Severe PHI was defined using clinical, analytical and immunological criteria. Chi-squared test was used for categorical variables and Student's t-test for quantitative variables. RESULTS 33% of 224 PHI patients (95% CI: 26.84%-39.16%) had a severe PHI. These patients had more symptoms, abnormal analytical parameters and hospital admissions. The severe PHI group had a significantly higher viral load although no differences were observed at 12 months in terms of viral suppression or CD4 count recovery. None died during PHI. CONCLUSIONS Up to one third of patients in our cohort presented with a severe PHI, which was associated with higher hospitalization rates and higher plasma HIV RNA viral load. However, severe forms were not associated to a worse clinical, immunological or virological outcome at 12 months.
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Affiliation(s)
- David Nicolás
- Infectious Diseases Service, Hospital Clinic-IDIBAPS, University of Barcelona, Barcelona, Spain.
| | - Antoni Suárez
- Infectious Diseases Service, Hospital Clinic-IDIBAPS, University of Barcelona, Barcelona, Spain.
| | - Juan Ambrosioni
- Infectious Diseases Service, Hospital Clinic-IDIBAPS, University of Barcelona, Barcelona, Spain.
| | - Christian Manzardo
- Infectious Diseases Service, Hospital Clinic-IDIBAPS, University of Barcelona, Barcelona, Spain.
| | - Carmen Ligero
- Infectious Diseases Service, Hospital Clinic-IDIBAPS, University of Barcelona, Barcelona, Spain.
| | - Josep Costa
- Microbiology Service, Hospital Clinic-IDIBAPS, University of Barcelona, Barcelona, Spain.
| | - Emma Fernández
- Infectious Diseases Service, Hospital Clinic-IDIBAPS, University of Barcelona, Barcelona, Spain.
| | - M Ángeles Marcos
- Microbiology Service, Hospital Clinic, University of Barcelona, Institute for Global Health, (ISGlobal), Barcelona, Spain.
| | - Montserrat Plana
- Retrovirology and Viral Immunopathology Laboratory, AIDS Research Group, IDIBAPS, Hospital Clínic, University of Barcelona, Spain.
| | - María Mar Mosquera
- Microbiology Service, Hospital Clinic, University of Barcelona, Institute for Global Health, (ISGlobal), Barcelona, Spain.
| | - Sonsoles Sánchez-Palomino
- Retrovirology and Viral Immunopathology Laboratory, AIDS Research Group, IDIBAPS, Hospital Clínic, University of Barcelona, Spain.
| | - Jose M Gatell
- Infectious Diseases Service, Hospital Clinic-IDIBAPS, University of Barcelona, Barcelona, Spain.
| | - José M Miró
- Infectious Diseases Service, Hospital Clinic-IDIBAPS, University of Barcelona, Barcelona, Spain.
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Bertels F, Marzel A, Leventhal G, Mitov V, Fellay J, Günthard HF, Böni J, Yerly S, Klimkait T, Aubert V, Battegay M, Rauch A, Cavassini M, Calmy A, Bernasconi E, Schmid P, Scherrer AU, Müller V, Bonhoeffer S, Kouyos R, Regoes RR. Dissecting HIV Virulence: Heritability of Setpoint Viral Load, CD4+ T-Cell Decline, and Per-Parasite Pathogenicity. Mol Biol Evol 2019; 35:27-37. [PMID: 29029206 PMCID: PMC5850767 DOI: 10.1093/molbev/msx246] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Pathogen strains may differ in virulence because they attain different loads in their hosts, or because they induce different disease-causing mechanisms independent of their load. In evolutionary ecology, the latter is referred to as “per-parasite pathogenicity”. Using viral load and CD4+ T-cell measures from 2014 HIV-1 subtype B-infected individuals enrolled in the Swiss HIV Cohort Study, we investigated if virulence—measured as the rate of decline of CD4+ T cells—and per-parasite pathogenicity are heritable from donor to recipient. We estimated heritability by donor–recipient regressions applied to 196 previously identified transmission pairs, and by phylogenetic mixed models applied to a phylogenetic tree inferred from HIV pol sequences. Regressing the CD4+ T-cell declines and per-parasite pathogenicities of the transmission pairs did not yield heritability estimates significantly different from zero. With the phylogenetic mixed model, however, our best estimate for the heritability of the CD4+ T-cell decline is 17% (5–30%), and that of the per-parasite pathogenicity is 17% (4–29%). Further, we confirm that the set-point viral load is heritable, and estimate a heritability of 29% (12–46%). Interestingly, the pattern of evolution of all these traits differs significantly from neutrality, and is most consistent with stabilizing selection for the set-point viral load, and with directional selection for the CD4+ T-cell decline and the per-parasite pathogenicity. Our analysis shows that the viral genotype affects virulence mainly by modulating the per-parasite pathogenicity, while the indirect effect via the set-point viral load is minor.
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Affiliation(s)
- Frederic Bertels
- Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
| | - Alex Marzel
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | | | - Venelin Mitov
- Department of Biosystems Science and Engineering, ETH Zurich, Zurich, Switzerland
| | - Jacques Fellay
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Huldrych F Günthard
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Jürg Böni
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Sabine Yerly
- Division of Infectious Diseases, Laboratory of Virology, Geneva University Hospital, Geneva, Switzerland
| | - Thomas Klimkait
- Molecular Virology, Department of Biomedicine - Petersplatz, University of Basel, Basel, Switzerland
| | - Vincent Aubert
- Division of Immunology and Allergy, University Hospital Lausanne, Lausanne, Switzerland
| | - Manuel Battegay
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
| | - Andri Rauch
- Department of Infectious Diseases, Berne University Hospital and University of Berne, Berne, Switzerland
| | - Matthias Cavassini
- Division of Infectious Diseases, University Hospital Lausanne, Lausanne, Switzerland
| | - Alexandra Calmy
- HIV/AIDS Unit, Infectious Disease Service, Geneva University Hospital, Geneva, Switzerland
| | - Enos Bernasconi
- Division of Infectious Diseases, Regional Hospital Lugano, Lugano, Switzerland
| | - Patrick Schmid
- Division of Infectious Diseases, Cantonal Hospital St Gallen, St Gallen, Switzerland
| | - Alexandra U Scherrer
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Viktor Müller
- Institute of Biology, Eötvös Loránd University, Budapest, Hungary.,Evolutionary Systems Research Group, MTA Centre for Ecological Research, Tihany, Hungary
| | | | - Roger Kouyos
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Roland R Regoes
- Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
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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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10
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Tsukamoto T. HIV Impacts CD34 + Progenitors Involved in T-Cell Differentiation During Coculture With Mouse Stromal OP9-DL1 Cells. Front Immunol 2019; 10:81. [PMID: 30761146 PMCID: PMC6361802 DOI: 10.3389/fimmu.2019.00081] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 01/11/2019] [Indexed: 12/21/2022] Open
Abstract
HIV-1 causes the loss of CD4+ T cells via depletion or impairment of their production. The latter involves infection of thymocytes, but the involvement of hematopoietic CD34+ cells remains unclear even though HIV-positive patients frequently manifest myelosuppression. In order to have a closer look at the impact of HIV-1 on T-lineage differentiation, this study utilized the OP9-DL1 coculture system, which supports in vitro T-lineage differentiation of human hematopoietic stem/progenitor cells. In the newly developed in vitro OP9-DL1/HIV-1 model, cord-derived CD34+ cells were infected with CXCR4-tropic HIV-1NL4−3 and cocultured. The HIV-infected cocultures exhibited reduced CD4+ T-cell growth at weeks 3–5 post infection compared to autologous uninfected cocultures. Further assays and analyses revealed that CD34+CD7+CXCR4+ cells can be quickly depleted as early as 1 week after infection of the subset, and this was accompanied by the emergence of rare CD34+CD7+CD4+ cells. A subsequent theoretical model analysis suggested potential influence of HIV-1 on the differentiation rate or death rate of lymphoid progenitor cells. These results indicate that CXCR4-tropic HIV-1 strains may impact the dynamics of CD34+CD7+ lymphoid progenitor cell pools, presumably leading to impaired T-cell production potential.
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Affiliation(s)
- Tetsuo Tsukamoto
- The Kirby Institute for Infection and Immunity in Society, University of New South Wales, Sydney, NSW, Australia.,Center for AIDS Research, Kumamoto University, Kumamoto, Japan.,Department of Immunology, Faculty of Medicine, Kindai University, Osaka, Japan
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11
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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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12
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Ghosn J, Bayan T, Meixenberger K, Tran L, Frange P, d'Arminio Monforte A, Zangerle R, de Mendoza C, Krastinova E, Porter K, Meyer L, Chaix ML. CD4 T cell decline following HIV seroconversion in individuals with and without CXCR4-tropic virus. J Antimicrob Chemother 2018; 72:2862-2868. [PMID: 29091208 DOI: 10.1093/jac/dkx247] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 06/22/2017] [Indexed: 11/12/2022] Open
Abstract
Background The natural clinical and immunological courses following HIV seroconversion with CXCR4-tropic or dual-mixed (X4/DM) viruses are controversial. We compared spontaneous immunological outcome in patients harbouring an X4/DM virus at the time of seroconversion with those harbouring a CCR5-tropic (R5) virus. Methods Data were included from patients participating in CASCADE, a large cohort collaboration of HIV seroconverters, with ≥2 years of follow-up since seroconversion. The HIV envelope gene was sequenced from frozen plasma samples collected at enrolment, and HIV tropism was determined using Geno2Pheno (false-positive rate 10%). The spontaneous CD4 T cell evolution was compared by modelling CD4 kinetics using linear mixed-effects models with random intercept and random slope. Results A total of 1387 patients were eligible. Median time between seroconversion and enrolment was 1 month (range 0-3). At enrolment, 202 of 1387 (15%) harboured an X4/DM-tropic virus. CD4 decrease slopes were not significantly different according to HIV-1 tropism during the first 30 months after seroconversion. No marked change in these results was found after adjusting for age, year of seroconversion and baseline HIV viral load. Time to antiretroviral treatment initiation was not statistically different between patients harbouring an R5 (20.76 months) and those harbouring an X4/DM-tropic virus (22.86 months, logrank test P = 0.32). Conclusions: In this large cohort collaboration, 15% of the patients harboured an X4/DM virus close to HIV seroconversion. Patients harbouring X4/DM-tropic viruses close to seroconversion did not have an increased risk of disease progression, estimated by the decline in CD4 T cell count or time to combined ART initiation.
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Affiliation(s)
- Jade Ghosn
- Université Paris Descartes, Sorbonne Paris Cité, Paris, France.,Inserm UMR-S 1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Université Pierre et Marie Curie, Paris, France
| | - Tatiana Bayan
- Inserm, CESP Centre for Research in Epidemiology and Population Health, U1018, HIV Epidemiology, Le Kremlin-Bicêtre, F-94276, France.,Univ Paris-Sud, UMRS 1018, Faculté de Médecine Paris-Sud, Le Kremlin-Bicêtre, F-94276, France
| | | | - Laurent Tran
- Inserm, CESP Centre for Research in Epidemiology and Population Health, U1018, HIV Epidemiology, Le Kremlin-Bicêtre, F-94276, France.,Univ Paris-Sud, UMRS 1018, Faculté de Médecine Paris-Sud, Le Kremlin-Bicêtre, F-94276, France.,AP-HP, Hopital Bicêtre, Epidemiology and Public Health Service, Le Kremlin Bicêtre, F-94276, France
| | - Pierre Frange
- Université Paris Descartes, Sorbonne Paris Cité, Paris, France.,AP-HP, Laboratoire de Microbiologie Clinique, Hôpital Universitaire Necker-Enfants Malades, Paris, France
| | - Antonella d'Arminio Monforte
- Infectious Diseases, University of Milan, San Paolo Hospital, Milano, Italy and Health Sciences, University of Milan, San Paolo Hospital, Milano, Italy
| | | | - Carmen de Mendoza
- Research Institute and University Hospital Puerta de Hierro, Majahonda, Madrid, Spain
| | - Evguenia Krastinova
- AP-HP, Hopital Bicêtre, Epidemiology and Public Health Service, Le Kremlin Bicêtre, F-94276, France
| | - Kholoud Porter
- Medical Research Council Clinical Trials Unit, University College London, London, UK
| | - Laurence Meyer
- Inserm, CESP Centre for Research in Epidemiology and Population Health, U1018, HIV Epidemiology, Le Kremlin-Bicêtre, F-94276, France.,Univ Paris-Sud, UMRS 1018, Faculté de Médecine Paris-Sud, Le Kremlin-Bicêtre, F-94276, France.,AP-HP, Hopital Bicêtre, Epidemiology and Public Health Service, Le Kremlin Bicêtre, F-94276, France
| | - Marie-Laure Chaix
- INSERM U941, Université Paris Diderot, Paris, France.,APHP, Laboratoire de Virologie, Hôpital Saint Louis, Paris, France
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13
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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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14
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Huyghe J, Magdalena S, Vandekerckhove L. Fight fire with fire: Gene therapy strategies to cure HIV. Expert Rev Anti Infect Ther 2017; 15:747-758. [DOI: 10.1080/14787210.2017.1353911] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Jon Huyghe
- Department of Internal Medicine, HIV Cure Research Center, Ghent University, Ghent, Belgium
| | - Sips Magdalena
- Department of Internal Medicine, HIV Cure Research Center, Ghent University, Ghent, Belgium
| | - Linos Vandekerckhove
- Department of Internal Medicine, HIV Cure Research Center, Ghent University, Ghent, Belgium
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15
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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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16
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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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17
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Kim MB, Giesler KE, Tahirovic YA, Truax VM, Liotta DC, Wilson LJ. CCR5 receptor antagonists in preclinical to phase II clinical development for treatment of HIV. Expert Opin Investig Drugs 2016; 25:1377-1392. [PMID: 27791451 PMCID: PMC5776690 DOI: 10.1080/13543784.2016.1254615] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
INTRODUCTION The chemokine receptor CCR5 has garnered significant attention in recent years as a target to treat HIV infection largely due to the approval and success of the drug Maraviroc. The side effects and inefficiencies with other first generation agents led to failed clinical trials, prompting the development of newer CCR5 antagonists. Areas covered: This review aims to survey the current status of 'next generation' CCR5 antagonists in the preclinical pipeline with an emphasis on emerging agents for the treatment of HIV infection. These efforts have culminated in the identification of advanced second-generation agents to reach the clinic and the dual CCR5/CCR2 antagonist Cenicriviroc as the most advanced currently in phase II clinical studies. Expert opinion: The clinical success of CCR5 inhibitors for treatment of HIV infection has rested largely on studies of Maraviroc and a second-generation dual CCR5/CCR2 antagonist Cenicriviroc. Although research efforts identified several promising preclinical candidates, these were dropped during early clinical studies. Despite patient access to Maraviroc, there is insufficient enthusiasm surrounding its use as front-line therapy for treatment of HIV. The non-HIV infection related development activities for Maraviroc and Cenicriviroc may help drive future interests.
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Affiliation(s)
- Michelle B Kim
- a Department of Chemistry , Emory University , Atlanta , GA , USA
| | - Kyle E Giesler
- a Department of Chemistry , Emory University , Atlanta , GA , USA
| | | | - Valarie M Truax
- a Department of Chemistry , Emory University , Atlanta , GA , USA
| | - Dennis C Liotta
- a Department of Chemistry , Emory University , Atlanta , GA , USA
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18
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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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19
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Impact of HIV-1 tropism on the emergence of non-AIDS events in HIV-infected patients receiving fully suppressive antiretroviral therapy. AIDS 2016; 30:731-41. [PMID: 26595543 PMCID: PMC4937812 DOI: 10.1097/qad.0000000000000977] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Objective: The impact of HIV-1 tropism on the emergence of non-AIDS events was evaluated in a cohort of 116 antiretroviral therapy (ART) responder patients. Methods: The patients were followed for the emergence of hypertension, renal impairment, metabolic and bone disorders (defined as non-AIDS events) each 8 weeks at standard visits. A V3 plasma sequence genotype analysis was performed at the time of ART initiation and the geno2pheno algorithm with the results that defines the false-positive rate (FPR) was used to infer HIV tropism. The associations between the non-AIDS events and the FPR at baseline were evaluated using the χ2 test for trend. A Cox-regression analysis using the counting process formulation of Andersen and Gill was performed to define whether the emergence of non-AIDS events was correlated to FPR. Results: The prevalence of at least one non-AIDS event resulted higher in patients with a FPR below 10% than in patients with a R5 virus (P = 0.033). Patients with a FPR below 5.0% most frequently developed non-AIDS events during ART (P = 0.01). A higher prevalence of patients with at least two AIDS events was found in the group of patients with a FPR below 5.0% with respect to the others (P < 0.001). At multivariate Cox-regression analysis, having an X4 virus and age were independently associated with a higher probability of non-AIDS event development. Conclusion: This study shows that an X4 virus, particularly a FPR less than 5%, is related to non-AIDS events development. Further studies are warranted to understand the mechanisms underlying this phenomenon.
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20
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Soulié C, Fofana DB, Boukli N, Sayon S, Lambert-Niclot S, Wirden M, Simon A, Katlama C, Calvez V, Girard PM, Marcelin AG, Morand-Joubert L. Performance of genotypic algorithms for predicting tropism of HIV-1CRF02_AG subtype. J Clin Virol 2016; 76:51-4. [PMID: 26826578 DOI: 10.1016/j.jcv.2016.01.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Revised: 12/18/2015] [Accepted: 01/12/2016] [Indexed: 10/22/2022]
Abstract
BACKGROUND Several genotypic rules for predicting HIV-1 non-B subtypes tropism are commonly used, but there is no consensus about their performances. OBJECTIVES Three genotypic methods were compared for CRF02_AG HIV-1 tropism determination. STUDY DESIGN V3 env region of 178HIV-1 CRF02_AG from Pitié-Salpêtrière and Saint-Antoine Hospitals was sequenced from plasma HIV-1 RNA. HIV-1 tropism was determined by Geno2Pheno algorithm, false positive rate (FPR) 5% or 10%, the 11/25 rule or the combined criteria of the 11/25 and net charge rule. RESULTS A concordance of 91.6% was observed between Geno2pheno 5% and the combined criteria. The results were nearly similar for the comparison between Geno2pheno 5% and the 11/25 rule. More mismatches were observed when Geno2pheno was used with the FPR 10%. A lower nadir CD4 cell count was associated with a discordance of tropism prediction between Geno2pheno 5% and the combined criteria or the 11/25 rule (p=0.02 and p=0.03, respectively). A lower HIV-1 viral load was associated with some discordance for the comparison of Geno2pheno 10% and the combined rule (p=0.02). CONCLUSION Geno2pheno FPR 5% or 10% predicted more X4-tropic viruses for this set of CRF02_AG sequences than the combined criteria or the 11/25 rule alone. Furthermore, Geno2pheno FPR 5% was more concordant with the 11/25 rule and the combined rule than Geno2pheno 10% to predict HIV-1 tropism. Overall, Geno2pheno 5% could be used to predict CRF02_AG tropism as well as other genotypic rules.
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Affiliation(s)
- C Soulié
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, Institut Pierre Louis d'épidémiologie et de Santé Publique (IPLESP UMRS 1136), F75013 Paris, France; AP-HP, Groupe hospitalier Pitié Salpêtrière, Laboratoire de Virologie, Paris F-75013, France.
| | - D B Fofana
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, Institut Pierre Louis d'épidémiologie et de Santé Publique (IPLESP UMRS 1136), F75013 Paris, France; AP-HP, Hôpital Saint-Antoine, Service de Virologie, Paris F-75013, France
| | - N Boukli
- AP-HP, Hôpital Saint-Antoine, Service de Virologie, Paris F-75013, France
| | - S Sayon
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, Institut Pierre Louis d'épidémiologie et de Santé Publique (IPLESP UMRS 1136), F75013 Paris, France; AP-HP, Groupe hospitalier Pitié Salpêtrière, Laboratoire de Virologie, Paris F-75013, France
| | - S Lambert-Niclot
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, Institut Pierre Louis d'épidémiologie et de Santé Publique (IPLESP UMRS 1136), F75013 Paris, France; AP-HP, Groupe hospitalier Pitié Salpêtrière, Laboratoire de Virologie, Paris F-75013, France
| | - Marc Wirden
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, Institut Pierre Louis d'épidémiologie et de Santé Publique (IPLESP UMRS 1136), F75013 Paris, France; AP-HP, Groupe hospitalier Pitié Salpêtrière, Laboratoire de Virologie, Paris F-75013, France
| | - A Simon
- AP-HP, Hôpital Pitié-Salpêtrière, Service de Médecine Interne, Paris F-75013, France
| | - C Katlama
- AP-HP, Hôpital Pitié-Salpêtrière, Service de Maladies Infectieuses, Paris F-75013, France
| | - V Calvez
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, Institut Pierre Louis d'épidémiologie et de Santé Publique (IPLESP UMRS 1136), F75013 Paris, France; AP-HP, Groupe hospitalier Pitié Salpêtrière, Laboratoire de Virologie, Paris F-75013, France
| | - P M Girard
- AP-HP, Hôpital Saint Antoine, Service de Maladies Infectieuses, Paris F-75013, France
| | - A G Marcelin
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, Institut Pierre Louis d'épidémiologie et de Santé Publique (IPLESP UMRS 1136), F75013 Paris, France; AP-HP, Groupe hospitalier Pitié Salpêtrière, Laboratoire de Virologie, Paris F-75013, France
| | - L Morand-Joubert
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, Institut Pierre Louis d'épidémiologie et de Santé Publique (IPLESP UMRS 1136), F75013 Paris, France; AP-HP, Hôpital Saint-Antoine, Service de Virologie, Paris F-75013, France
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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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Henrich TJ, Hanhauser E, Hu Z, Stellbrink HJ, Noah C, Martin JN, Deeks SG, Kuritzkes DR, Pereyra F. Viremic control and viral coreceptor usage in two HIV-1-infected persons homozygous for CCR5 Δ32. AIDS 2015; 29:867-76. [PMID: 25730507 DOI: 10.1097/qad.0000000000000629] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
OBJECTIVES To determine viral and immune factors involved in transmission and control of HIV-1 infection in persons without functional CCR5. DESIGN Understanding transmission and control of HIV-1 in persons homozygous for CCR5(Δ32) is important given efforts to develop HIV-1 curative therapies aimed at modifying or disrupting CCR5 expression. METHODS We identified two HIV-infected CCR5(Δ32/Δ32) individuals among a cohort of patients with spontaneous control of HIV-1 infection without antiretroviral therapy and determined coreceptor usage of the infecting viruses. We assessed genetic evolution of full-length HIV-1 envelope sequences by single-genome analysis from one participant and his sexual partner, and explored HIV-1 immune responses and HIV-1 mutations following virologic escape and disease progression. RESULTS Both participants experienced viremia of less than 4000 RNA copies/ml with preserved CD4(+) T-cell counts off antiretroviral therapy for at least 3.3 and 4.6 years after diagnosis, respectively. One participant had phenotypic evidence of X4 virus, had no known favorable human leukocyte antigen alleles, and appeared to be infected by minority X4 virus from a pool that predominately used CCR5 for entry. The second participant had virus that was unable to use CXCR4 for entry in phenotypic assay but was able to engage alternative viral coreceptors (e.g., CXCR6) in vitro. CONCLUSION Our study demonstrates that individuals may be infected by minority X4 viruses from a population that predominately uses CCR5 for entry, and that viruses may bypass traditional HIV-1 coreceptors (CCR5 and CXCR4) completely by engaging alternative coreceptors to establish and propagate HIV-1 infection.
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Determination of HIV-1 coreceptor tropism using proviral DNA in women before and after viral suppression. AIDS Res Ther 2015; 12:11. [PMID: 25897314 PMCID: PMC4403710 DOI: 10.1186/s12981-015-0055-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 04/12/2015] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND An HIV-1 tropism test is recommended prior to CCR5 antagonist administration to exclude patients harboring non-R5 virus from treatment with this class of antiretrovirals. HIV-1 tropism determination based on proviral DNA (pvDNA) may be useful in individuals with plasma viral RNA suppression. We developed a genotypic tropism assay for pvDNA and assessed its performance in a retrospective analysis of samples collected longitudinally. RESULTS We randomly selected paired plasma/PBMC samples from the Women's Interagency HIV Study with plasma viral load ≥5,000 cp/mL at time 1 (T1), undetectable viral load maintained for ≥1 year and CD4+ >200 cells/μL at time 2 (T2). pvDNA was isolated from cryopreserved PBMCs. Sequences were analyzed in triplicate from 49/50 women, with tropism assigned using the geno2pheno (g2p) algorithm. The median time between T1 and T2 was 4.1 years. CXCR4-using virus was detected in 24% of the RNA samples and 33% of the pvDNA samples at T1, compared to 37% of the pvDNA samples at T2. Concordance between plasma RNA and pvDNA tropism was 88% at T1 and 80% at T2. The g2p scores for RNA (T1) vs DNA (T1, T2) were strongly correlated (Spearman rho: 0.85 (T1); 0.78 (T2)). In women with evidence of tropism switch at T2 (either R5 to non-R5 or non-R5 to R5), there was a correlation between change in tropism and time. Mean pvDNA viral load decreased by 0.4 log10 copies/106 cells between T1 and T2 (p < 0.0001), but this decrease was not significantly associated with tropism status. CONCLUSIONS We demonstrated that pvDNA tropism in women with HIV-1 suppression is concordant with prior RNA tropism results, even after a median time of >4 years. pvDNA tropism testing may be useful to determine eligibility of patients with viral suppression to switch to a CCR5-antagonist based regimen as well as for research purposes.
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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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Henrich TJ, McLaren PJ, Rao SSP, Lin NH, Hanhauser E, Giguel F, Gulick RM, Ribaudo H, de Bakker PIW, Kuritzkes DR. Genome-Wide Association Study of Human Immunodeficiency Virus (HIV)-1 Coreceptor Usage in Treatment-Naive Patients from An AIDS Clinical Trials Group Study. Open Forum Infect Dis 2014; 1:ofu018. [PMID: 25734091 PMCID: PMC4324186 DOI: 10.1093/ofid/ofu018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Accepted: 04/03/2014] [Indexed: 01/17/2023] Open
Abstract
Phenotypic determination of HIV-1 coreceptor usage was performed on 593 pre-treatment plasma HIV-1 samples from treatment-naive participants in ACTG A5095. No human genetic variants were significantly associated with virus able to use CXCR4 for entry at the genome-wide level. Objectives. We conducted a genome-wide association study to explore whether common host genetic variants (>5% frequency) were associated with presence of virus able to use CXCR4 for entry. Methods. Phenotypic determination of human immunodeficiency virus (HIV)-1 coreceptor usage was performed on pretreatment plasma HIV-1 samples from treatment-naive participants in AIDS Clinical Trials Group A5095, a study of initial antiretroviral regimens. Associations between genome-wide single-nucleotide polymorphisms (SNPs), CCR5 Δ32 genotype, and human leukocyte antigen (HLA) class I alleles and viral coreceptor usage were explored. Results. Viral phenotypes were obtained from 593 patients with available genome-wide SNP data. Forty-four percent of subjects had virus capable of using CXCR4 for entry as determined by phenotyping. Overall, no associations, including those between polymorphisms in genes encoding viral coreceptors and their promoter regions or in HLA genes previously associated with HIV-1 disease progression, passed the statistical threshold for genome-wide significance (P < 5.0 × 10−8) in any comparison. However, the presence of viruses able to use CXCR4 for entry was marginally associated with the CCR5 Δ32 genotype in the nongenome-wide analysis. Conclusions. No human genetic variants were significantly associated with virus able to use CXCR4 for entry at the genome-wide level. Although the sample size had limited power to definitively exclude genetic associations, these results suggest that host genetic factors, including those that influence coreceptor expression or the immune pressures leading to viral envelope diversity, are either rare or have only modest effects in determining HIV-1 coreceptor usage.
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Affiliation(s)
- Timothy J Henrich
- Division of Infectious Diseases , Brigham and Women's Hospital , Boston, Massachusetts ; Harvard Medical School , Boston, Massachusetts
| | - Paul J McLaren
- École Polytechnique Fédérale de Lausanne and University of Lausanne , Switzerland ; University Hospital and University of Lausanne , Switzerland ; Swiss Institute of Bioinformatics , Switzerland
| | | | - Nina H Lin
- Massachusetts General Hospital , Boston, Massachusetts ; Harvard Medical School , Boston, Massachusetts
| | - Emily Hanhauser
- Division of Infectious Diseases , Brigham and Women's Hospital , Boston, Massachusetts
| | | | - Roy M Gulick
- Weill Medical College of Cornell University, New York, New York
| | - Heather Ribaudo
- Harvard Medical School , Boston, Massachusetts ; Harvard School of Public Health
| | - Paul I W de Bakker
- Harvard Medical School , Boston, Massachusetts ; Program in Medical and Population Genetics , Broad Institute of Harvard and MIT , Boston, Massachusetts ; Department of Medical Genetics and Department of Epidemiology , University Medical Center Utrecht , Utrecht , The Netherlands ; Divison of Genetics , Brigham and Women's Hospital , Boston, Massachusetts
| | - Daniel R Kuritzkes
- Division of Infectious Diseases , Brigham and Women's Hospital , Boston, Massachusetts ; Harvard Medical School , Boston, Massachusetts
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Brown J, Burger H, Weiser B, Pollard RB, Li XD, Clancy LJ, Baumann RE, Rogers AA, Hamdan HB, Pesano RL, Kagan RM. A genotypic HIV-1 proviral DNA coreceptor tropism assay: characterization in viremic subjects. AIDS Res Ther 2014; 11:14. [PMID: 24904682 PMCID: PMC4045881 DOI: 10.1186/1742-6405-11-14] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2014] [Accepted: 04/29/2014] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND HIV-1 coreceptor tropism testing is used to evaluate eligibility for CCR5 antagonist therapy. However, HIV-1 RNA-based tests are not suitable for virologically suppressed patients, therefore the use of proviral DNA tropism testing has been investigated. We describe a novel proviral DNA-based genotypic tropism assay and compare its performance to that of a sensitive HIV-1 RNA-based genotypic test. METHODS Tropism was determined using HIV-1 plasma RNA and proviral DNA from 42 paired samples from patients with plasma viral loads ≥1000 HIV-1 RNA copies/mL. Proviral DNA sample types included whole blood, separated peripheral blood mononuclear cells resuspended in phosphate-buffered saline and peripheral blood mononuclear cells resuspended in spun plasma. The HIV-1 envelope V3 region was PCR-amplified, sequenced in triplicate, and analyzed for tropism with the geno2pheno algorithm using a 10% false-positive rate (FPR). RESULTS Amplicons were obtained from proviral DNA and plasma RNA in 41/42 samples. Tropism predictions were highly concordant (93%-98%) between proviral DNA and plasma RNA, regardless of the proviral DNA isolation method. Non-R5 proviral DNA results were obtained for 100% of patients with detectable non-R5 plasma HIV-1 RNA results. Geno2pheno FPRs for proviral DNA and plasma RNA were highly correlated (Spearman rho = 0.86). CONCLUSIONS Our findings demonstrate that proviral DNA tropism determinations from whole blood or peripheral blood mononuclear cells were highly concordant with plasma HIV-1 RNA tropism determinations. This assay may be useful for screening virologically suppressed patients for CCR5-antagonist eligibility and for research purposes.
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Affiliation(s)
- Jennifer Brown
- Division of Infectious Diseases, Department of Internal Medicine, University of California, Davis Medical Center, 4150 V. Street, PSSB-G500, Sacramento, CA, USA
| | - Harold Burger
- University of California, Davis, School of Medicine, Davis, CA, USA
| | - Barbara Weiser
- University of California, Davis, School of Medicine, Davis, CA, USA
| | - Richard B Pollard
- Division of Infectious Diseases, Department of Internal Medicine, University of California, Davis Medical Center, 4150 V. Street, PSSB-G500, Sacramento, CA, USA
| | - Xiao-Dong Li
- University of California, Davis, School of Medicine, Davis, CA, USA
| | - Lynell J Clancy
- Division of Infectious Diseases, Department of Internal Medicine, University of California, Davis Medical Center, 4150 V. Street, PSSB-G500, Sacramento, CA, USA
| | - Russell E Baumann
- Department of Infectious Diseases, Quest Diagnostics Nichols Institute, San Juan Capistrano, CA, USA
| | - Amy A Rogers
- Department of Infectious Diseases, Quest Diagnostics Nichols Institute, San Juan Capistrano, CA, USA
| | - Hasnah B Hamdan
- Department of Infectious Diseases, Quest Diagnostics Nichols Institute, San Juan Capistrano, CA, USA
| | - Rick L Pesano
- Department of Infectious Diseases, Quest Diagnostics Nichols Institute, San Juan Capistrano, CA, USA
| | - Ron M Kagan
- Department of Infectious Diseases, Quest Diagnostics Nichols Institute, San Juan Capistrano, CA, USA
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Morris SR, Woods SP, Deutsch R, Little SJ, Wagner G, Morgan EE, Heaton RK, Letendre SL, Grant I, Smith DM. Dual-mixed HIV-1 coreceptor tropism and HIV-associated neurocognitive deficits. J Neurovirol 2014; 19:488-94. [PMID: 24078557 DOI: 10.1007/s13365-013-0203-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Revised: 08/14/2013] [Accepted: 08/20/2013] [Indexed: 11/30/2022]
Abstract
HIV coreceptor usage of CXCR4 (X4) is associated with decreased CD4+ T-cell counts and accelerated disease progression, but the role of X4 tropism in HIV-associated neurocognitive disorders (HAND) has not previously been described. This longitudinal study evaluated data on 197 visits from 72 recently HIV-infected persons who had undergone up to four sequential neurocognitive assessments over a median of 160 days (IQR, 138–192). Phenotypic tropism testing (Trofile ES, Monogram, Biosciences) was performed on stored blood samples. Multivariable mixed model repeated measures regression was used to determine the association between HAND and dual-mixed (DM) viral tropism, estimated duration of infection (EDI), HIV RNA, CD4 count, and problematic methamphetamine use. Six subjects (8.3 %) had DM at their first neurocognitive assessment and four converted to DM in subsequent sampling (for total of 10 DM) at a median EDI of 10.1 months (IQR, 7.2–12.2). There were 44 (61.1 %) subjects who demonstrated HAND on at least one study visit. HAND was associated with DM tropism (odds ratio, 4.4; 95 % CI, 0.9–20.5) and shorter EDI (odds ratio 1.1 per month earlier; 95 % CI, 1.0–1.2). This study found that recency of HIV-1 infection and the development of DM tropism may be associated with HAND in the relatively early stage of infection. Together, these data suggest that viral interaction with cellular receptors may play an important role in the early manifestation of HAND.
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Almeida FJ, Zaparoli MS, Moreira DH, de Souza Cavalcanti J, Rodrigues R, Berezin EN, de Paula Ferreira JL, Sáfadi MAP, de Macedo Brígido LF. Association of X4 tropism with disease progression in antiretroviral-treated children and adolescents living with HIV/AIDS in São Paulo, Brazil. Braz J Infect Dis 2014; 18:300-7. [PMID: 24275366 PMCID: PMC9427470 DOI: 10.1016/j.bjid.2013.10.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Revised: 09/20/2013] [Accepted: 10/15/2013] [Indexed: 01/28/2023] Open
Abstract
Management of children with HIV/AIDS is specially challenging. Age-related issues do not allow for direct transposition of adult observations to this population. CXCR4 tropism has been associated with disease progression in adults. The geno2pheno web-base is a friendly tool to predict viral tropism on envelope V3 sequences, generating a false positive rate for a CXCR4 prediction. We evaluated the association of HIV-1 tropism prediction with clinical and laboratory outcome of 73 children with HIV/AIDS in São Paulo, Brazil. The CXCR4 tropism was strongly associated with a lower (nadir) CD4 documented during follow-up (p < 0.0001) and with disease severity (clinical event and/or CD4 below 200 cells/mm3) at the last observation, using commonly applied clinical cutoffs, such as 10%FPRclonal (p = 0.001). When variables obtained during follow-up are included, both treatment adherence and viral tropism show a significant association with disease severity. As for viremia suppression, 30% (22/73) were undetectable at the last observation, with only adherence strongly associated with suppression after adjustment. The study brings further support to the notion that antiretroviral treatment adherence is pivotal to management of HIV disease, but suggests that tropism prediction may provide an additional prognostic marker to monitor HIV disease in children.
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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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Kagan RM, Johnson EP, Siaw MF, Van Baelen B, Ogden R, Platt JL, Pesano RL, Lefebvre E. Comparison of genotypic and phenotypic HIV type 1 tropism assay: results from the screening samples of Cenicriviroc Study 202, a randomized phase II trial in treatment-naive subjects. AIDS Res Hum Retroviruses 2014; 30:151-9. [PMID: 23875707 DOI: 10.1089/aid.2013.0123] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Cenicriviroc is a once-daily oral CCR5/CCR2 antagonist in development for treatment of HIV infection. CVC Study 202 (652-2-202; NCT01338883) excluded treatment-naive subjects demonstrated to harbor non-R5 (CXCR4-tropic or dual-mixed) tropic HIV-1 by either genotypic or phenotypic tropism testing. Here we compare the results of genotypic and phenotypic tropism testing in Study 202. A total of 304 subjects screened had paired genotypic and phenotypic results. Genotypic tropism testing (GTT) incorporated triplicate population sequencing using the geno2pheno algorithm and the PSSM algorithm, followed by ultradeep sequencing (UDS) for samples with R5 results. All samples were further evaluated with a phenotypic test, the enhanced-sensitivity Trofile assay (ESTA). Concordance between GTT and ESTA was 80% and increased to 84% when only geno2pheno was used for triplicate population sequencing. GTT (geno2pheno) classified 18% of the samples as non-R5 compared to 16% by ESTA. Only one-third of samples with non-R5 results by either test were classified as non-R5 by both tests. Median CD4((+)) cell counts were lower in patients with concordant non-R5 results by UDS and ESTA than in subjects with an R5 result by either assay (p=0.0004). UDS detected non-R5 virus in an additional 27/304 subjects (median 15% non-R5, interquartile range: 3.7-62%) with R5 results by ESTA. In conclusion, the geno2pheno algorithm improves concordance of GTT with a clinically validated phenotypic tropism assay as does the use of UDS. These findings provide support for recent guidelines indicating that genotypic tropism testing may be considered as an alternative to phenotypic testing.
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Affiliation(s)
- Ron M. Kagan
- Quest Diagnostics Nichols Institute, San Juan Capistrano, California
| | - Erik P. Johnson
- Quest Diagnostics Nichols Institute, San Juan Capistrano, California
| | - Martin F. Siaw
- Quest Diagnostics Nichols Institute, San Juan Capistrano, California
| | | | - Richard Ogden
- Tobira Therapeutics Inc., South San Francisco, California
| | - Jamie L. Platt
- Quest Diagnostics Nichols Institute, San Juan Capistrano, California
| | - Rick L. Pesano
- Quest Diagnostics Nichols Institute, San Juan Capistrano, California
| | - Eric Lefebvre
- Tobira Therapeutics Inc., South San Francisco, California
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Pérez-Olmeda M, Alcami J. Determination of HIV tropism and its use in the clinical practice. Expert Rev Anti Infect Ther 2014; 11:1291-302. [DOI: 10.1586/14787210.2013.852469] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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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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Mortier V, Dauwe K, Vancoillie L, Staelens D, Van Wanzeele F, Vogelaers D, Vandekerckhove L, Chalmet K, Verhofstede C. Frequency and predictors of HIV-1 co-receptor switch in treatment naive patients. PLoS One 2013; 8:e80259. [PMID: 24244665 PMCID: PMC3820624 DOI: 10.1371/journal.pone.0080259] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Accepted: 10/11/2013] [Indexed: 01/03/2023] Open
Abstract
Background Determination of HIV-1 co-receptor use is a necessity before initiation of a CCR5 antagonist but the longevity of a CCR5-use prediction remains unknown. Methods Genotypic co-receptor tropism determination was performed in 225 newly diagnosed individuals consulting an AIDS Reference Centre. Samples were collected at diagnosis and at initiation of antiretroviral therapy or just before closure of the study for patients who did not initiate therapy. For individuals with a discordant tropism prediction on the two longitudinal samples, analysis of intermediate samples and single genome sequencing of proviral DNA was performed to confirm the tropism switch. Deep sequencing was done to identify minor CXCR4 or CCR5-using populations in the initial sample. Results Overall, tropism switches were rare (7.6%). Only a geno2pheno false positive rate of <50% at baseline was retained as predictive for a subsequent switch from CCR5-use only to predicted CXCR4-use. Minor CXCR4-using virus populations were detected in the first sample of 9 of the 14 R5-to-X4 switchers but the subsequent outgrowth of these minor populations was documented in only 3. Conclusions With the current guidelines for treatment initiation at CD4+ T cell counts of <500 cells/mm3, co-receptor switch between diagnosis and starting antiretroviral therapy is rare. Patients with R5 viruses and a geno2pheno FPR of <50% are more prone to subsequent co-receptor switch than patients with an FPR of >50% and will need repeat tropism testing if initiation of maraviroc is considered and previous testing dates from more than a year before.
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Affiliation(s)
- Virginie Mortier
- Aids Reference Laboratory, Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, Gent, Belgium
| | - Kenny Dauwe
- Aids Reference Laboratory, Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, Gent, Belgium
| | - Leen Vancoillie
- Aids Reference Laboratory, Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, Gent, Belgium
| | - Delfien Staelens
- Aids Reference Laboratory, Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, Gent, Belgium
| | - Filip Van Wanzeele
- Aids Reference Center, Department of General Internal Medicine and Infectious Diseases, Ghent University Hospital, Gent, Belgium
| | - Dirk Vogelaers
- Aids Reference Center, Department of General Internal Medicine and Infectious Diseases, Ghent University Hospital, Gent, Belgium
| | - Linos Vandekerckhove
- Aids Reference Center, Department of General Internal Medicine and Infectious Diseases, Ghent University Hospital, Gent, Belgium
| | - Kristen Chalmet
- Aids Reference Laboratory, Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, Gent, Belgium
| | - Chris Verhofstede
- Aids Reference Laboratory, Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, Gent, Belgium
- * E-mail:
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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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Ng OT, Laeyendecker O, Redd AD, Munshaw S, Grabowski MK, Paquet AC, Evans MC, Haddad M, Huang W, Robb ML, Reynolds SJ, Gray RH, Wawer MJ, Serwadda D, Eshleman SH, Quinn TC. HIV type 1 polymerase gene polymorphisms are associated with phenotypic differences in replication capacity and disease progression. J Infect Dis 2013; 209:66-73. [PMID: 23922373 DOI: 10.1093/infdis/jit425] [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: 11/13/2022] Open
Abstract
BACKGROUND Determinants of intersubtype differences in human immunodeficiency virus type 1 (HIV-1) clinical disease progression remain unknown. METHODS HIV-1 subtype was independently determined for 5 separate genomic regions in 396 HIV-1 seroconverters from Rakai, Uganda, using a multiregion hybridization assay. Replication capacities (RC) in samples from a subset of 145 of these subjects were determined. HIV-1 genomic regions and pol RC were examined for association with disease progression. Amino acid polymorphisms were examined for association with pol RC. RESULTS In multivariate analyses, the hazard for progression to the composite end point (defined as a CD4(+) T-cell count <250 cells/mm(3), antiretroviral therapy initiation, or death) among patients with subtype D pol infection was 2.4 times the hazard for those infected with subtype A pol infection (P = .001). Compared with subtype A pol (the reference group), the hazard for progression to the composite end point for subtype D pol infection with a pol RC >67% (ie, the median pol RC) was significantly greater (HR, 4.6; 95% confidence interval [CI], 1.9-11.0; P = .001), whereas the hazard for progression to the composite end point for subtype D pol infection with a pol RC ≤67% was not significantly different (HR, 2.2; 95% CI, 1.0-4.9; P = .051). Amino acid substitutions at protease positions 62 and 64 and at reverse transcriptase position 272 were associated with significant differences in pol RC. CONCLUSIONS HIV-1 pol gene intersubtype and RC differences are associated with disease progression and may be influenced by amino acid polymorphisms.
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McNamara LA, Onafuwa-Nuga A, Sebastian NT, Riddell J, Bixby D, Collins KL. CD133+ hematopoietic progenitor cells harbor HIV genomes in a subset of optimally treated people with long-term viral suppression. J Infect Dis 2013; 207:1807-16. [PMID: 23554378 DOI: 10.1093/infdis/jit118] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Hematopoietic progenitor cells (HPCs) in the bone marrow of human immunodeficiency virus (HIV)-infected individuals have been proposed as a persistent reservoir of virus. However, some studies have suggested that HIV genomes detected in HPCs arise from T-cell contamination. METHODS CD133-sorted HPCs and CD133-depleted bone marrow cells were purified from bone marrow specimens obtained from 11 antiretroviral-treated donors in whom the HIV load had been <48 copies/mL for at least 6 months. CD133 and CD3 expression on the cells was assessed by flow cytometry. HIV DNA was quantified by real-time polymerase chain reaction analysis. RESULTS HIV genomes were detected in CD133-sorted samples from 6 donors, including 2 in whom viral loads were undetectable for >8 years. CD3(+) T cells represented <1% of cells in all CD133-sorted samples. For 5 of 6 CD133-sorted samples with detectable HIV DNA, the HIV genomes could not be explained by contaminating CD3(+) T cells. Donors with detectable HIV DNA in HPCs received their diagnosis significantly more recently than the remaining donors but had had undetectable viral loads for similar periods. CONCLUSIONS HIV genomes can be detected in CD133-sorted cells from a subset of donors with long-term viral suppression and, in most cases, cannot be explained by contamination with CD3(+) T cells.
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Affiliation(s)
- Lucy A McNamara
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, 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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A genotypic test for HIV-1 tropism combining Sanger sequencing with ultradeep sequencing predicts virologic response in treatment-experienced patients. PLoS One 2012; 7:e46334. [PMID: 23029482 PMCID: PMC3459909 DOI: 10.1371/journal.pone.0046334] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2012] [Accepted: 08/31/2012] [Indexed: 12/27/2022] Open
Abstract
A tropism test is required prior to initiation of CCR5 antagonist therapy in HIV-1 infected individuals, as these agents are not effective in patients harboring CXCR4 (X4) coreceptor-using viral variants. We developed a clinical laboratory-based genotypic tropism test for detection of CCR5-using (R5) or X4 variants that utilizes triplicate population sequencing (TPS) followed by ultradeep sequencing (UDS) for samples classified as R5. Tropism was inferred using the bioinformatic algorithms geno2pheno[coreceptor] and PSSMx4r5. Virologic response as a function of tropism readout was retrospectively assessed using blinded samples from treatment-experienced subjects who received maraviroc (N = 327) in the MOTIVATE and A4001029 clinical trials. MOTIVATE patients were classified as R5 and A4001029 patients were classified as non-R5 by the original Trofile test. Virologic response was compared between the R5 and non-R5 groups determined by TPS, UDS alone, the reflex strategy and the Trofile Enhanced Sensitivity (TF-ES) test. UDS had greater sensitivity than TPS to detect minority non-R5 variants. The median log10 viral load change at week 8 was −2.4 for R5 subjects, regardless of the method used for classification; for subjects with non-R5 virus, median changes were −1.2 for TF-ES or the Reflex Test and −1.0 for UDS. The differences between R5 and non-R5 groups were highly significant in all 3 cases (p<0.0001). At week 8, the positive predictive value was 66% for TF-ES and 65% for both the Reflex test and UDS. Negative predictive values were 59% for TF-ES, 58% for the Reflex Test and 61% for UDS. In conclusion, genotypic tropism testing using UDS alone or a reflex strategy separated maraviroc responders and non-responders as well as a sensitive phenotypic test, and both assays showed improved performance compared to TPS alone. Genotypic tropism tests may provide an alternative to phenotypic testing with similar discriminating ability.
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De Gascun CF, Waters A, Regan CM, O'Halloran J, Farrell G, Coughlan S, Bergin C, Powderly WG, Hall WW. Human immunodeficiency virus type 1 in Ireland: phylogenetic evidence for risk group-specific subepidemics. AIDS Res Hum Retroviruses 2012; 28:1073-81. [PMID: 22176216 DOI: 10.1089/aid.2011.0301] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
HIV genetic diversity may have an impact on viral pathogenesis, transmission, response to treatment, and vaccine development. Public health surveillance that monitors the frequency and variety of HIV subtypes in a particular region or patient group is vital to successfully control the pandemic. We present the first comprehensive report on HIV diversity in Ireland. This study comprised all new HIV-1 diagnoses that were confirmed in the National Virus Reference Laboratory, University College Dublin, from January 2004 to December 2008. HIV 1 protease and reverse transcriptase sequences were generated using the Siemens Trugene HIV 1 Genotyping System. Subtypes were determined using web-based genotyping tools. There were 1579 new diagnoses [615 (39%) female and 964 (61%) male], of which 1060 had HIV-1 RNA specimens available for sequencing. Of sequenced samples, HIV-1 subtype B accounted for 50% overall, decreasing from 55.1% in 2004 to 49.5% in 2008. In addition, subtype B accounted for more than 80% of Irish-born individuals and more than 90% of Irish-born injection drug users and men who have sex with men. Subtype C was the second most prevalent in the overall cohort, accounting for 25%, although it accounted for only 6.1% of Irish-born individuals, with no evidence of in country transmission. The prevalence of non-subtype B HIV-1 infection in Ireland is increasing. However, these appear primarily to be imported infections not yet circulating within traditional Irish risk groups. Enhanced HIV-1 molecular epidemiology surveillance is required to monitor the spread of HIV-1, to inform future public health policy, and to ultimately control the HIV-1 epidemic in Ireland.
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Affiliation(s)
- Cillian F. De Gascun
- National Virus Reference Laboratory, University College Dublin, Belfield, Dublin, Ireland
- School of Medicine and Medical Science, University College Dublin, Belfield, Dublin, Ireland
| | - Allison Waters
- National Virus Reference Laboratory, University College Dublin, Belfield, Dublin, Ireland
- School of Medicine and Medical Science, University College Dublin, Belfield, Dublin, Ireland
| | - Ciara M. Regan
- National Virus Reference Laboratory, University College Dublin, Belfield, Dublin, Ireland
| | - Jane O'Halloran
- Department of Infectious Diseases, Mater Misericordiae Hospital, Dublin, Ireland
| | - Gillian Farrell
- Department of GU Medicine and Infectious Diseases, St. James' Hospital, Dublin, Ireland
| | - Suzie Coughlan
- National Virus Reference Laboratory, University College Dublin, Belfield, Dublin, Ireland
| | - Colm Bergin
- Department of GU Medicine and Infectious Diseases, St. James' Hospital, Dublin, Ireland
| | - William G. Powderly
- School of Medicine and Medical Science, University College Dublin, Belfield, Dublin, Ireland
| | - William W. Hall
- National Virus Reference Laboratory, University College Dublin, Belfield, Dublin, Ireland
- School of Medicine and Medical Science, University College Dublin, Belfield, Dublin, Ireland
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Manak M, Sina S, Anekella B, Hewlett I, Sanders-Buell E, Ragupathy V, Kim J, Vermeulen M, Stramer SL, Sabino E, Grabarczyk P, Michael N, Peel S, Garrett P, Tovanabutra S, Busch MP, Schito M. Pilot studies for development of an HIV subtype panel for surveillance of global diversity. AIDS Res Hum Retroviruses 2012; 28:594-606. [PMID: 22149143 DOI: 10.1089/aid.2011.0271] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The continued global spread and evolution of HIV diversity pose significant challenges to diagnostics and vaccine strategies. NIAID partnered with the FDA, WRAIR, academia, and industry to form a Viral Panel Working Group to design and prepare a panel of well-characterized current and diverse HIV isolates. Plasma samples that had screened positive for HIV infection and had evidence of recently acquired infection were donated by blood centers in North and South America, Europe, and Africa. A total of 80 plasma samples were tested by quantitative nucleic acid tests, p24 antigen, EIA, and Western blot to assign a Fiebig stage indicative of approximate time from initial infection. Evaluation of viral load using FDA-cleared assays showed excellent concordance when subtype B virus was tested, but lower correlations for subtype C. Plasma samples were cocultivated with phytohemagglutinin (PHA)-stimulated peripheral blood mononuclear cells (PBMCs) from normal donors to generate 30 viral isolates (50-80% success rate for samples with viral load >10,000 copies/ml), which were then expanded to 10(7)-10(9) virus copies per ml. Analysis of env sequences showed that sequences derived from cultured PBMCs were not distinguishable from those obtained from the original plasma. The pilot collection includes 30 isolates representing subtypes B, C, B/F, CRF04_cpx, and CRF02_AG. These studies will serve as a basis for the development of a comprehensive panel of highly characterized viral isolates that reflects the current dynamic and complex HIV epidemic, and will be made available through the External Quality Assurance Program Oversight Laboratory (EQAPOL).
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Affiliation(s)
- Mark Manak
- SeraCare Life Sciences, Inc., Gaithersburg, Maryland
| | - Silvana Sina
- U.S. Military HIV Research Program, Henry M. Jackson Foundation for the Advancement of Military Medicine, Rockville, Maryland
| | | | - Indira Hewlett
- U.S. Food and Drug Administration, CBER, Bethesda, Maryland
| | - Eric Sanders-Buell
- U.S. Military HIV Research Program, Henry M. Jackson Foundation for the Advancement of Military Medicine, Rockville, Maryland
| | | | - Jerome Kim
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Rockville, Maryland
| | | | - Susan L. Stramer
- American Red Cross, Scientific Support Office, Gaithersburg, Maryland
| | - Ester Sabino
- Department of Infectious Disease/University of São Paulo, São Paulo, Brazil
| | - Piotr Grabarczyk
- Institute of Haematology and Blood Transfusion Medicine, Warsaw, Poland
| | - Nelson Michael
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Rockville, Maryland
| | - Sheila Peel
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Rockville, Maryland
| | | | - Sodsai Tovanabutra
- U.S. Military HIV Research Program, Henry M. Jackson Foundation for the Advancement of Military Medicine, Rockville, Maryland
| | | | - Marco Schito
- Henry M. Jackson Foundation, Contractor to the Division of AIDS, NIH, Bethesda, Maryland
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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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Thielen A, Lengauer T, Swenson LC, Dong WWY, McGovern RA, Lewis M, James I, Heera J, Valdez H, Harrigan PR. Mutations in gp41 are correlated with coreceptor tropism but do not improve prediction methods substantially. Antivir Ther 2011; 16:319-28. [PMID: 21555814 DOI: 10.3851/imp1769] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
BACKGROUND The main determinants of HIV-1 coreceptor usage are located in the V3-loop of gp120, although mutations in V2 and gp41 are also known. Incorporation of V2 is known to improve prediction algorithms; however, this has not been confirmed for gp41 mutations. METHODS Samples with V3 and gp41 genotypes and Trofile assay (Monogram Biosciences, South San Francisco, CA, USA) results were taken from the HOMER cohort (n=444) and from patients screened for the MOTIVATE studies (n=1,916; 859 with maraviroc outcome data). Correlations of mutations with tropism were assessed using Fisher's exact test and prediction models trained using support vector machines. Models were validated by cross-validation, by testing models from one dataset on the other, and by analysing virological outcome. RESULTS Several mutations within gp41 were highly significant for CXCR4 usage; most strikingly an insertion occurring in 7.7% of HOMER-R5 and 46.3% of HOMER-X4 samples (MOTIVATE 5.7% and 25.2%, respectively). Models trained on gp41 sequence alone achieved relatively high areas under the receiver-operating characteristic curve (AUCs; HOMER 0.713 and MOTIVATE 0.736) that were almost as good as V3 models (0.773 and 0.884, respectively). However, combining the two regions improved predictions only marginally (0.813 and 0.902, respectively). Similar results were found when models were trained on HOMER and validated on MOTIVATE or vice versa. The difference in median log viral load decrease at week 24 between patients with R5 and X4 virus was 1.65 (HOMER 2.45 and MOTIVATE 0.79) for V3 models, 1.59 for gp41-models (2.42 and 0.83, respectively) and 1.58 for the combined predictor (2.44 and 0.86, respectively). CONCLUSIONS Several mutations within gp41 showed strong correlation with tropism in two independent datasets. However, incorporating gp41 mutations into prediction models is not mandatory because they do not improve substantially on models trained on V3 sequences alone.
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Socías ME, Sued O, Laufer N, Lázaro ME, Mingrone H, Pryluka D, Remondegui C, Figueroa MI, Cesar C, Gun A, Turk G, Bouzas MB, Kavasery R, Krolewiecki A, Pérez H, Salomón H, Cahn P. Acute retroviral syndrome and high baseline viral load are predictors of rapid HIV progression among untreated Argentinean seroconverters. J Int AIDS Soc 2011; 14:40. [PMID: 21831310 PMCID: PMC3179691 DOI: 10.1186/1758-2652-14-40] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2011] [Accepted: 08/10/2011] [Indexed: 12/12/2022] Open
Abstract
Background Diagnosis of primary HIV infection (PHI) has important clinical and public health implications. HAART initiation at this stage remains controversial. Methods Our objective was to identify predictors of disease progression among Argentinean seroconverters during the first year of infection, within a multicentre registry of PHI-patients diagnosed between 1997 and 2008. Cox regression was used to analyze predictors of progression (LT-CD4 < 350 cells/mm3, B, C events or death) at 12 months among untreated patients. Results Among 134 subjects, 74% presented with acute retroviral syndrome (ARS). Seven opportunistic infections (one death), nine B events, and 10 non-AIDS defining serious events were observed. Among the 92 untreated patients, 24 (26%) progressed at 12 months versus three (7%) in the treated group (p = 0.01). The 12-month progression rate among untreated patients with ARS was 34% (95% CI 22.5-46.3) versus 13% (95% CI 1.1-24.7) in asymptomatic patients (p = 0.04). In univariate analysis, ARS, baseline LT-CD4 < 350 cells/mm3, and baseline and six-month viral load (VL) > 100,000 copies/mL were associated with progression. In multivariate analysis, only ARS and baseline VL > 100,000 copies/mL remained independently associated; HR: 8.44 (95% CI 0.97-73.42) and 9.44 (95% CI 1.38-64.68), respectively. Conclusions In Argentina, PHI is associated with significant morbidity. HAART should be considered in PHI patients with ARS and high baseline VL to prevent disease progression.
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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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Church JD, Huang W, Mwatha A, Musoke P, Jackson JB, Bagenda D, Omer SB, Donnell D, Nakabiito C, Eure C, Guay LA, Taylor A, Bakaki PM, Matovu F, McConnell M, Fowler MG, Eshleman SH. Analysis of HIV tropism in Ugandan infants. Curr HIV Res 2011; 8:498-503. [PMID: 21073438 DOI: 10.2174/157016210793499187] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2010] [Accepted: 10/12/2010] [Indexed: 11/22/2022]
Abstract
HIV-infected infants may have CXCR4-using (X4-tropic) HIV, CCR5-using (R5-tropic) HIV, or a mixture of R5-tropic and X4-tropic HIV (dual/mixed, DM HIV). The level of infectivity for R5 virus (R5-RLU) varies among HIV infected infants. HIV tropism and R5-RLU were measured in samples from HIV-infected Ugandan infants using a commercial assay. DM HIV was detected in 7/72 (9.7%) infants at the time of HIV diagnosis (birth or 6-8 weeks of age, 4/15 (26.7%) with subtype D, 3/57 (5.3 %) with other subtypes, P=0.013). A transition from R5-tropic to DM HIV was observed in only two (6.7%) of 30 infants over 6-12 months. Six (85.7%) of seven infants with DM HIV died, compared to 21/67 (31.3%) infants with R5-tropic HIV (p=0.09). Higher R5-RLU at 6-8 weeks was not associated with decreased survival. Infants with in utero infection had a higher median R5-RLU than infants who were HIV-uninfected at birth (p=0.025).
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Affiliation(s)
- Jessica D Church
- Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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Schlecht HP, Schellhorn S, Dezube BJ, Jacobson JM. New approaches in the treatment of HIV/AIDS - focus on maraviroc and other CCR5 antagonists. Ther Clin Risk Manag 2011; 4:473-85. [PMID: 18728830 PMCID: PMC2504054 DOI: 10.2147/tcrm.s1997] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Treatment of HIV-1 infection has produced dramatic success for many patients. Nevertheless, viral resistance continues to limit the efficacy of currently available agents in many patients. The CCR5 antagonists are a new class of antiretroviral agents that target a necessary coreceptor for viral entry of many strains of HIV-1. Recently, the first agent within this class, maraviroc, was approved by a number of regulatory agencies, including the Food and Drug Administration. Herein we review the role of the CCR5 receptor in HIV-1 infection and potential methods to target it in anti-HIV-1 therapy. We review the various categories of agents and discuss specific agents that have progressed to clinical study. We discuss in detail the recently approved, first in class CCR5 antagonist, maraviroc, and discuss aspects of resistance to CCR5 antagonism and the potential role of CCR5 antagonism in the management of HIV-1 infection.
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Affiliation(s)
- Hans P Schlecht
- Department of Medicine (Infectious Diseases), Hahnemann University Hospital, Drexel University College of Medicine Philadelphia, PA, USA
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HIV-1 utilizes the CXCR4 chemokine receptor to infect multipotent hematopoietic stem and progenitor cells. Cell Host Microbe 2011; 9:223-234. [PMID: 21402361 DOI: 10.1016/j.chom.2011.02.005] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2010] [Revised: 01/04/2011] [Accepted: 01/28/2011] [Indexed: 02/04/2023]
Abstract
HIV infection is characterized by gradual immune system collapse and hematopoietic dysfunction. We recently showed that HIV enters multipotent hematopoietic progenitor cells and establishes both active cytotoxic and latent infections that can be reactivated by myeloid differentiation. However, whether these multipotent progenitors include long-lived hematopoietic stem cells (HSCs) that could establish viral reservoirs for the life of the infected person remains unknown. Here we provide direct evidence that HIV targets long-lived HSCs and show that infected HSCs yield stable, multilineage engraftment in a xenograft model. Furthermore, we establish that the capacity to use the chemokine receptor CXCR4 for entry determines whether a virus will enter multipotent versus differentiated progenitor cells. Because HSCs live for the life span of the infected person and are crucial for hematopoietic health, these data may explain the poor prognosis associated with CXCR4-tropic HIV infection and suggest HSCs as long-lived cellular reservoirs of latent HIV.
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Isolation and partial characterization of Brazilian samples of feline immunodeficiency virus. Virus Res 2011; 160:59-65. [PMID: 21619902 DOI: 10.1016/j.virusres.2011.05.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2010] [Revised: 05/06/2011] [Accepted: 05/10/2011] [Indexed: 11/21/2022]
Abstract
Feline immunodeficiency virus (FIV) causes a slow progressive degeneration of the immune system which eventually leads to a disease comparable to acquired immune deficiency syndrome (AIDS) in humans. FIV has extensive sequence variation, a typical feature of lentiviruses. Sequence analysis showed that diversity was not evenly distributed throughout the genome, but was greatest in the envelope gene, env. The virus enters host cells via a sequential interaction, initiated by the envelope glycoprotein (env) binding the primary receptor molecule CD134 and followed by a subsequent interaction with chemokine co-receptor CXCR4. The purpose of this study was to isolate and characterize isolates of FIV from an open shelter in São Paulo, Brazil. The separated PBMC from 11 positive cats were co-cultured with MYA-1 cells. Full-length viral env glycoprotein genes were amplified and determined. Chimeric feline × human CD134 receptors were used to investigate the receptor utilization of 17 clones from Brazilian isolates of FIV. Analyses of the sequence present of molecular clones showed that all clones grouped within subtype B. In contrast to the virulent primary isolate FIV-GL8, expression of the first cysteine-rich domain (CRD1) of feline CD134 in the context of human CD134 was sufficient for optimal receptor function for all Brazilian FIV isolates tested.
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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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