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Musumali J, Julius P, Siyumbwa SN, Yalcin D, Kang G, Munsaka S, West JT, Wood C. Systematic post-mortem analysis of brain tissue from an HIV-1 subtype C viremic decedent revealed a paucity of infection and pathology. J Neurovirol 2022; 28:527-536. [PMID: 36198990 DOI: 10.1007/s13365-022-01099-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 09/01/2022] [Accepted: 09/16/2022] [Indexed: 01/13/2023]
Abstract
Whether the human brain is a robust reservoir for HIV-1 subtype C has yet to be established. We aimed to determine whether HIV-1 subtype C infection can be detected in the brain tissue of a viremic individual at post-mortem and whether the viral burden was differential between different brain regions. This study reports a 38-year-old Zambian female decedent with severe wasting who was on Atripla for antiretroviral therapy. The cause of death was determined to be HIV/AIDS end-stage disease. The QuantStudio 3 Real-Time PCR System analyzed formalin-fixed paraffin-embedded tissue DNA from a systematic sampling of the entire left-brain hemisphere. Plasma and cerebral spinal fluid HIV-1 RNA loads were 576,123 and 14,962 copies/mL, respectively. The lymph node DNA viral load was 2316 copies per 106 cells. Two hundred and six (96.3%) tissue blocks had amplifiable DNA. HIV-1 viral DNA was detected in 35.9% of the blocks, the highest in the basal ganglia (66.7%) and the frontal lobe (46%). Overall, HIV detection was random, with low viral copies detected by quantitative polymerase chain reaction (qPCR); the lowest was observed in the occipital (median, IQR, range) 0.0 [0.0-0.0], 0.0-31.3, and the highest in the basal ganglia (mean ± SD, range, 125.1149.5, 0.0-350.0). Significant differences in HIV-1 DNA distribution were observed between the occipital versus parietal (p = 0.049), occipital versus frontal (p = 0.019), occipital versus basal ganglia (p = 0.005), cerebellum versus frontal (p = 0.021), cerebellum versus basal ganglia (p = 0.007), and temporal versus frontal (p = 0.034).
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Affiliation(s)
- Jane Musumali
- Department of Pathology and Microbiology, School of Medicine, University of Zambia, Nationalist Road, Lusaka, Zambia
| | - Peter Julius
- Department of Pathology and Microbiology, School of Medicine, University of Zambia, Nationalist Road, Lusaka, Zambia
| | - Stepfanie N Siyumbwa
- Department of Pathology and Microbiology, School of Medicine, University of Zambia, Nationalist Road, Lusaka, Zambia
| | - Dicle Yalcin
- Department of Interdisciplinary Oncology, Louisiana State University Health Sciences Center, New Orleans, USA
| | - Guobin Kang
- Department of Interdisciplinary Oncology, Louisiana State University Health Sciences Center, New Orleans, USA
| | - Sody Munsaka
- Department of Biomedical Sciences, School of Health Sciences, University of Zambia, Nationalist Road, Lusaka, Zambia
| | - John T West
- Department of Interdisciplinary Oncology, Louisiana State University Health Sciences Center, New Orleans, USA
| | - Charles Wood
- Department of Interdisciplinary Oncology, Louisiana State University Health Sciences Center, New Orleans, USA.
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2
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Katsuya H, Cook LBM, Rowan AG, Melamed A, Turpin J, Ito J, Islam S, Miyazato P, Jek Yang Tan B, Matsuo M, Miyakawa T, Nakata H, Matsushita S, Taylor GP, Bangham CRM, Kimura S, Satou Y. Clonality of HIV-1- and HTLV-1-Infected Cells in Naturally Coinfected Individuals. J Infect Dis 2022; 225:317-326. [PMID: 33844021 DOI: 10.1093/infdis/jiab202] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 04/11/2021] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Coinfection with human immunodeficiency virus type 1 (HIV-1) and human T-cell leukemia virus type 1 (HTLV-1) diminishes the value of the CD4+ T-cell count in diagnosing AIDS, and increases the rate of HTLV-1-associated myelopathy. It remains elusive how HIV-1/HTLV-1 coinfection is related to such characteristics. We investigated the mutual effect of HIV-1/HTLV-1 coinfection on their integration sites (ISs) and clonal expansion. METHODS We extracted DNA from longitudinal peripheral blood samples from 7 HIV-1/HTLV-1 coinfected, and 12 HIV-1 and 13 HTLV-1 monoinfected individuals. Proviral loads (PVL) were quantified using real-time polymerase chain reaction (PCR). Viral ISs and clonality were quantified by ligation-mediated PCR followed by high-throughput sequencing. RESULTS PVL of both HIV-1 and HTLV-1 in coinfected individuals was significantly higher than that of the respective virus in monoinfected individuals. The degree of oligoclonality of both HIV-1- and HTLV-1-infected cells in coinfected individuals was also greater than in monoinfected subjects. ISs of HIV-1 in cases of coinfection were more frequently located in intergenic regions and transcriptionally silent regions, compared with HIV-1 monoinfected individuals. CONCLUSIONS HIV-1/HTLV-1 coinfection makes an impact on the distribution of viral ISs and clonality of virus-infected cells and thus may alter the risks of both HTLV-1- and HIV-1-associated disease.
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Affiliation(s)
- Hiroo Katsuya
- Division of Hematology, Respiratory Medicine and Oncology, Department of Internal Medicine, Faculty of Medicine, Saga University, Saga, Japan.,Division of Genomics and Transcriptomics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Lucy B M Cook
- Department of Infectious Diseases, Faculty of Medicine, Imperial College London, London, UK
| | - Aileen G Rowan
- Department of Infectious Diseases, Faculty of Medicine, Imperial College London, London, UK
| | - Anat Melamed
- Department of Infectious Diseases, Faculty of Medicine, Imperial College London, London, UK
| | - Jocelyn Turpin
- Department of Infectious Diseases, Faculty of Medicine, Imperial College London, London, UK
| | - Jumpei Ito
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Saiful Islam
- Division of Genomics and Transcriptomics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan.,International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Paola Miyazato
- Division of Genomics and Transcriptomics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan.,International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Benjy Jek Yang Tan
- Division of Genomics and Transcriptomics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan.,International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Misaki Matsuo
- Division of Genomics and Transcriptomics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan.,International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Toshikazu Miyakawa
- Department of Hematology, Rheumatology and Infectious Diseases, Kumamoto University of Medicine, Kumamoto, Japan
| | - Hirotomo Nakata
- Department of Hematology, Rheumatology and Infectious Diseases, Kumamoto University of Medicine, Kumamoto, Japan
| | - Shuzo Matsushita
- Clinical Retrovirology, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Graham P Taylor
- Department of Infectious Diseases, Faculty of Medicine, Imperial College London, London, UK
| | - Charles R M Bangham
- Department of Infectious Diseases, Faculty of Medicine, Imperial College London, London, UK
| | - Shinya Kimura
- Division of Hematology, Respiratory Medicine and Oncology, Department of Internal Medicine, Faculty of Medicine, Saga University, Saga, Japan
| | - Yorifumi Satou
- Division of Genomics and Transcriptomics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan.,International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
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3
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A DNA Regulatory Element Haplotype at Zinc Finger Genes Is Associated with Host Resilience to Small Ruminant Lentivirus in Two Sheep Populations. Animals (Basel) 2021; 11:ani11071907. [PMID: 34206933 PMCID: PMC8300134 DOI: 10.3390/ani11071907] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 06/22/2021] [Accepted: 06/22/2021] [Indexed: 12/13/2022] Open
Abstract
Small ruminant lentivirus (SRLV) causes Maedi-Visna or Ovine Progressive Pneumonia in sheep and creates insidious livestock production losses. This retrovirus is closely related to human immunodeficiency virus and currently has no vaccines or cure. Genetic marker assisted selection for sheep disease resiliency presents an attractive management solution. Previously, we identified a region containing a cluster of zinc finger genes that had association with ovine SRLV proviral concentration. Trait-association analysis validated a small insertion/deletion variant near ZNF389 (rs397514112) in multiple sheep breeds. In the current study, 543 sheep from two distinct populations were genotyped at 34 additional variants for fine mapping of the regulatory elements within this locus. Variants were selected based on ChIP-seq annotation data from sheep alveolar macrophages that defined active cis-regulatory elements predicted to influence zinc finger gene expression. We present a haplotype block of variants within regulatory elements that have improved associations and larger effect sizes (up to 4.7-fold genotypic difference in proviral concentration) than the previously validated ZNF389 deletion marker. Hypotheses for the underlying causal mutation or mutations are presented based on changes to in silico transcription factor binding sites. These variants offer alternative markers for selective breeding and are targets for future functional mutation assays.
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Di Sante L, Costantini A, Caucci S, Corsi A, Brescini L, Menzo S, Bagnarelli P. Quantification of the HIV-1 total reservoir in the peripheral blood of naïve and treated patients by a standardised method derived from a commercial HIV-1 RNA quantification assay. Clin Chem Lab Med 2020; 59:609-617. [PMID: 33326413 DOI: 10.1515/cclm-2020-0142] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 04/05/2020] [Indexed: 11/15/2022]
Abstract
OBJECTIVES HIV-1 DNA can persist in host cells, establishing a latent reservoir. This study was aimed to develop an extraction and amplification protocol for HIV-1 DNA quantification by modifying a quantitative commercial assay. METHODS HIV-1 DNA was extracted on an Abbott m2000sp instrument, using an open-mode protocol. Two calibrators, spiked with a plasmid containing HIV-1 genome (103 and 105 cps/mL), were extracted and amplified to generate a master calibration curve. Precision, accuracy, linear dynamic range, limit of quantification (LOQ) and limit of detection (LOD) were determined. A cohort of patients, naïve or chronically infected, was analysed. RESULTS Calibration curve was obtained from 42 replicates of standards (stds); precision was calculated (coefficients of variability [CVs] below 10%); accuracy was higher than 90%. Linearity covered the entire range tested (10-104 copies per reaction), and LOD (95%) was 12 copies per reaction. HIV-1 DNA was significantly higher (p < 0.0001) in drug-naïve (62) than in chronically treated patients (50), and proviral loads correlated with lymphocytes (p = 0.0002) and CD4+ (p < 0.0001) counts only in naïve patients. Both groups displayed a significant inverse correlation between CD4+ nadir and proviral loads. A significant correlation (p < 0.0001) between viraemia and HIV-1 reservoir was disclosed. No significant difference was obtained from the comparison between proviral loads on whole blood and peripheral blood mononuclear cells (PBMCs) from the same patient. CONCLUSIONS The novelty of our approach relies on the selection of appropriate reference standard extracted and amplified as clinical specimens avoiding any underestimation of the reservoir. Results confirm HIV-1 DNA as a marker of disease progression, supporting the relationship between the width of latent reservoir and the immunological status of the patient.
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Affiliation(s)
- Laura Di Sante
- Department of Molecular and Clinical Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Andrea Costantini
- Department of Molecular and Clinical Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Sara Caucci
- Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, Ancona, Italy
| | - Alice Corsi
- Department of Molecular and Clinical Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Lucia Brescini
- Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, Ancona, Italy
| | - Stefano Menzo
- Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, Ancona, Italy
| | - Patrizia Bagnarelli
- Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, Ancona, Italy
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Bon I, Calza L, Musumeci G, Longo S, Bertoldi A, D'Urbano V, Gibellini D, Magistrelli E, Viale PL, Re MC. Impact of Different Antiretroviral Strategies on Total HIV-DNA Level in Virologically Suppressed HIV-1 Infected Patients. Curr HIV Res 2019; 15:448-455. [PMID: 29210661 PMCID: PMC5876918 DOI: 10.2174/1570162x16666171206121026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 11/02/2017] [Accepted: 11/28/2017] [Indexed: 01/11/2023]
Abstract
Background: Total HIV-DNA load in peripheral blood cell (PBMCs) reflects the global viral reservoir that seems not to be affected by antiretroviral treatment. However, some studies report-ed a different permeability of different drugs in cellular compartments. Objective: To investigate the relation between the amount of total HIV-1 DNA and different treatment strategies. Methods: Total HIV-1 DNA was quantified by real time PCR in PBMCs collected from 161 patients with long-term undetectable HIV-RNA receiving different therapy schedules (3-drug regimens or 2-drug regimen containing Raltegravir as integrase inhibitor). Results: Overall, HIV patients who started therapy with a median pre-ART CD4+ cell count >400 cells/mm3 and HIV viral load of 3 log10 copies/ml, achieved a lower amount of HIV total DNA. No significant correlation was found in DNA size when patients were stratified on the basis of different therapeutic protocols. However, HIV DNA load analysis, when only performed in HIV patients with a median pre-ART CD4+ cell count >200 cells/mm3 and HIV viral load < 3 log10 copies/ml, showed a significative DNA decrease in Raltegravir treated group with respect to the NNRTIs-treated group. Conclusion: The data emphasize that HIV-DNA level represents a predictive factor in long-term sup-pressive therapy patients. In addition, the diminished reservoir, only observed in patients treated with the NRTI-sparing regimen RAL plus PI/r before immunological and virological derangement, sug-gests that latest generation drugs, such as integrase inhibitors, might represent an optimal chance in the management of HIV infection.
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Affiliation(s)
- Isabella Bon
- Microbiology Section of the Department of Experimental, Diagnostic and Specialty Medicine, School of Medicine, University of Bologna, Via Massarenti, 9, Bologna, Italy
| | - Leonardo Calza
- Unit of Infectious Diseases, Department of Medical and Surgical Sciences, School of Medicine, University of Bologna, Via Massarenti, 9, Bologna, Italy
| | - Giuseppina Musumeci
- Microbiology Section of the Department of Experimental, Diagnostic and Specialty Medicine, School of Medicine, University of Bologna, Via Massarenti, 9, Bologna, Italy
| | - Serena Longo
- Microbiology Section of the Department of Experimental, Diagnostic and Specialty Medicine, School of Medicine, University of Bologna, Via Massarenti, 9, Bologna, Italy
| | - Alessia Bertoldi
- Microbiology Section of the Department of Experimental, Diagnostic and Specialty Medicine, School of Medicine, University of Bologna, Via Massarenti, 9, Bologna, Italy
| | - Vanessa D'Urbano
- Microbiology Section of the Department of Experimental, Diagnostic and Specialty Medicine, School of Medicine, University of Bologna, Via Massarenti, 9, Bologna, Italy
| | - Davide Gibellini
- Unit of Microbiology Department of Diagnostic and Public Health, University of Verona, Verona, Italy
| | - Eleonora Magistrelli
- Unit of Infectious Diseases, Department of Medical and Surgical Sciences, School of Medicine, University of Bologna, Via Massarenti, 9, Bologna, Italy
| | - Pier Luigi Viale
- Unit of Infectious Diseases, Department of Medical and Surgical Sciences, School of Medicine, University of Bologna, Via Massarenti, 9, Bologna, Italy
| | - Maria Carla Re
- Microbiology Section of the Department of Experimental, Diagnostic and Specialty Medicine, School of Medicine, University of Bologna, Via Massarenti, 9, Bologna, Italy.,Interuniversity Consortium, National Institute of Biostructures and Biosystems (INBB), Rome, Italy
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6
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Mortier V, Demecheleer E, Staelens D, Schauvliege M, Dauwe K, Dinakis S, Hebberecht L, Vancoillie L, Verhofstede C. Quantification of total HIV-1 DNA in buffy coat cells, feasibility and potential added value for clinical follow-up of HIV-1 infected patients on ART. J Clin Virol 2018; 106:58-63. [PMID: 30077957 DOI: 10.1016/j.jcv.2018.07.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 07/24/2018] [Accepted: 07/25/2018] [Indexed: 12/30/2022]
Abstract
BACKGROUND Successfully treated HIV-1 infected patients have a sustained undetectable viral RNA load. In these cases the total HIV-1 DNA load may constitute a valuable tool to further follow the overall viral burden. The value of this marker outside of cure research has been rarely studied. OBJECTIVES To develop a quantitative (q)PCR for total HIV-1 DNA quantification in buffy coat cells and to evaluate the value of this parameter in clinical follow-up. STUDY DESIGN A qPCR using primers and a probe in the conserved HIV-1 LTR region was adapted for use on DNA extracted from buffy coat cells. Sensitivity, accuracy and reproducibility were evaluated using 8E5 cells and samples from naive and treatment experienced patients. The clinical value of DNA load analysis was assessed by testing 119 longitudinal samples from 9 patients before and after ART initiation and 249 cross sectional samples from therapy-experienced patients. RESULTS Inter- and intra-assay coefficients of variability were 5.56 and 5.94 (%CV). HIV-1 DNA was detected in 249 of the 263 (94.7%) patients on ART for at least 5 months (median: 53 months; IQR: 28-84 months). The HIV-1 DNA load varied between 0.60 and 3.37 copies/106 blood cells and showed significant correlation with the pre-ART CD4+ T-cell count nadir and peak viral RNA load. ART initiation resulted in a slow and limited decline of the total HIV-1 DNA concentration. CONCLUSIONS Quantification of total HIV-1 DNA from buffy coat cells is feasible, sensitive and reliable. Although determination of the on-therapy HIV-1 DNA load may be informative, regular testing has limited clinical value because of the very slow evolution.
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Affiliation(s)
- Virginie Mortier
- AIDS Reference Laboratory, Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, Corneel Heymanslaan, 10-MRB2, B-9000, Gent, Belgium(1)
| | - Els Demecheleer
- AIDS Reference Laboratory, Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, Corneel Heymanslaan, 10-MRB2, B-9000, Gent, Belgium(1)
| | - Delfien Staelens
- AIDS Reference Laboratory, Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, Corneel Heymanslaan, 10-MRB2, B-9000, Gent, Belgium(1)
| | - Marlies Schauvliege
- AIDS Reference Laboratory, Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, Corneel Heymanslaan, 10-MRB2, B-9000, Gent, Belgium(1)
| | - Kenny Dauwe
- AIDS Reference Laboratory, Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, Corneel Heymanslaan, 10-MRB2, B-9000, Gent, Belgium(1)
| | - Sylvie Dinakis
- AIDS Reference Laboratory, Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, Corneel Heymanslaan, 10-MRB2, B-9000, Gent, Belgium(1)
| | - Laura Hebberecht
- AIDS Reference Laboratory, Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, Corneel Heymanslaan, 10-MRB2, B-9000, Gent, Belgium(1)
| | - Leen Vancoillie
- AIDS Reference Laboratory, Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, Corneel Heymanslaan, 10-MRB2, B-9000, Gent, Belgium(1)
| | - Chris Verhofstede
- AIDS Reference Laboratory, Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, Corneel Heymanslaan, 10-MRB2, B-9000, Gent, Belgium(1).
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HIV Replication and Latency in a Humanized NSG Mouse Model during Suppressive Oral Combinational Antiretroviral Therapy. J Virol 2018; 92:JVI.02118-17. [PMID: 29343582 DOI: 10.1128/jvi.02118-17] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 01/08/2018] [Indexed: 11/20/2022] Open
Abstract
Although current combinatorial antiretroviral therapy (cART) is therapeutically effective in the majority of HIV patients, interruption of therapy can cause a rapid rebound in viremia, demonstrating the existence of a stable reservoir of latently infected cells. HIV latency is therefore considered a primary barrier to HIV eradication. Identifying, quantifying, and purging the HIV reservoir is crucial to effectively curing patients and relieving them from the lifelong requirement for therapy. Latently infected transformed cell models have been used to investigate HIV latency; however, these models cannot accurately represent the quiescent cellular environment of primary latently infected cells in vivo For this reason, in vivo humanized murine models have been developed for screening antiviral agents, identifying latently infected T cells, and establishing treatment approaches for HIV research. Such models include humanized bone marrow/liver/thymus mice and SCID-hu-thy/liv mice, which are repopulated with human immune cells and implanted human tissues through laborious surgical manipulation. However, no one has utilized the human hematopoietic stem cell-engrafted NOD/SCID/IL2rγnull (NSG) model (hu-NSG) for this purpose. Therefore, in the present study, we used the HIV-infected hu-NSG mouse to recapitulate the key aspects of HIV infection and pathogenesis in vivo Moreover, we evaluated the ability of HIV-infected human cells isolated from HIV-infected hu-NSG mice on suppressive cART to act as a latent HIV reservoir. Our results demonstrate that the hu-NSG model is an effective surgery-free in vivo system in which to efficiently evaluate HIV replication, antiretroviral therapy, latency and persistence, and eradication interventions.IMPORTANCE HIV can establish a stably integrated, nonproductive state of infection at the level of individual cells, known as HIV latency, which is considered a primary barrier to curing HIV. A complete understanding of the establishment and role of HIV latency in vivo would greatly enhance attempts to develop novel HIV purging strategies. An ideal animal model for this purpose should be easy to work with, should have a shortened disease course so that efficacy testing can be completed in a reasonable time, and should have immune correlates that are easily translatable to humans. We therefore describe a novel application of the hematopoietic stem cell-transplanted humanized NSG model for dynamically testing antiretroviral treatment, supporting HIV infection, establishing HIV latency in vivo The hu-NSG model could be a facile alternative to humanized bone marrow/liver/thymus or SCID-hu-thy/liv mice in which laborious surgical manipulation and time-consuming human cell reconstitution is required.
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Zhou J, Lazar D, Li H, Xia X, Satheesan S, Charlins P, O'Mealy D, Akkina R, Saayman S, Weinberg MS, Rossi JJ, Morris KV. Receptor-targeted aptamer-siRNA conjugate-directed transcriptional regulation of HIV-1. Am J Cancer Res 2018; 8:1575-1590. [PMID: 29556342 PMCID: PMC5858168 DOI: 10.7150/thno.23085] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 12/09/2017] [Indexed: 12/16/2022] Open
Abstract
Gene-based therapies represent a promising therapeutic paradigm for the treatment of HIV-1, as they have the potential to maintain sustained viral inhibition with reduced treatment interventions. Such an option may represent a long-term treatment alternative to highly active antiretroviral therapy. Methods: We previously described a therapeutic approach, referred to as transcriptional gene silencing (TGS), whereby small noncoding RNAs directly inhibit the transcriptional activity of HIV-1 by targeting sites within the viral promoter, specifically the 5' long terminal repeat (LTR). TGS differs from traditional RNA interference (RNAi) in that it is characterized by concomitant silent-state epigenetic marks on histones and DNA. To deliver TGS-inducing RNAs, we developed functional RNA conjugates based on the previously reported dual function of the gp120 (A-1) aptamer conjugated to 27-mer Dicer-substrate anti-HIV-1 siRNA (dsiRNA), LTR-362. Results: We demonstrate here that high levels of processed guide RNAs localize to the nucleus in infected T lymphoblastoid CEM cell line and primary human CD4+ T-cells. Treatment of the aptamer-siRNA conjugates induced TGS with an ~10-fold suppression of viral p24 levels as measured at day 12 post infection. To explore the silencing efficacy of aptamer-siRNA conjugates in vivo, HIV-1-infected humanized NOD/SCID/IL2 rγnull mice (hu-NSG) were treated with the aptamer-siRNA conjugates. Systemic delivery of the A-1-stick-LTR-362 27-mer siRNA conjugates suppressed HIV-1 infection and protected CD4+ T cell levels in viremia hu-NSG mice. Principle conclusions: Collectively these data suggest that the gp120 aptamer-dsiRNA conjugate design is suitable for systemic delivery of small RNAs that can be used to suppress HIV-1.
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9
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Ruhanya V, Jacobs GB, Glashoff RH, Engelbrecht S. Clinical Relevance of Total HIV DNA in Peripheral Blood Mononuclear Cell Compartments as a Biomarker of HIV-Associated Neurocognitive Disorders (HAND). Viruses 2017; 9:E324. [PMID: 29088095 PMCID: PMC5707531 DOI: 10.3390/v9110324] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 10/24/2017] [Accepted: 10/26/2017] [Indexed: 12/19/2022] Open
Abstract
The pathogenesis of HIV-associated neurocognitive disorders is complex and multifactorial. It is hypothesized that the critical events initiating this condition occur outside the brain, particularly in the peripheral blood. Diagnoses of HIV-induced neurocognitive disorders largely rely on neuropsychometric assessments, which are not precise. Total HIV DNA in the peripheral blood mononuclear cells (PBMCs), quantified by PCR, correlate with disease progression, which is a promising biomarker to predict HAND. Numerous PCR assays for HIV DNA in cell compartments are prone to variation due to the lack of standardization and, therefore, their utility in predicting HAND produced different outcomes. This review evaluates the clinical relevance of total HIV DNA in circulating mononuclear cells using different published quantitative PCR (qPCR) protocols. The rationale is to shed light on the most appropriate assays and sample types used to accurately quantify HIV DNA load, which predicts severity of neurocognitive impairment. The role of monocytes as a vehicle for trafficking HIV into the CNS makes it the most suitable sample for determining a HAND associated reservoir. Studies have also shown significant associations between monocyte HIV DNA levels with markers of neurodamage. However, qPCR assays using PBMCs are cheaper and available commercially, thus could be beneficial in clinical settings. There is need, however, to standardise DNA extraction, normalisation and limit of detection.
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Affiliation(s)
- Vurayai Ruhanya
- Division of Medical Virology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Francie van Zijl Avenue, P.O. Box 241, Cape Town 8000, South Africa.
- Department of Medical Microbiology, College of Health Sciences, University of Zimbabwe, P.O. Box A178, Avondale Harare 00263, Zimbabwe.
| | - Graeme B Jacobs
- Division of Medical Virology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Francie van Zijl Avenue, P.O. Box 241, Cape Town 8000, South Africa.
| | - Richard H Glashoff
- Division of Medical Microbiology and Immunology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Francie van Zijl Avenue, P.O. Box 241, Cape Town 8000, South Africa.
- Division of Medical Microbiology and Immunology, National Health Laboratory Service (NHLS), Tygerberg Business Unit, P.O. Box 241, Cape Town 8000, South Africa.
| | - Susan Engelbrecht
- Division of Medical Virology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Francie van Zijl Avenue, P.O. Box 241, Cape Town 8000, South Africa.
- Division of Medical Virology, National Health Laboratory Service (NHLS), Tygerberg Business Unit, P.O. Box 241, Cape Town 8000, South Africa.
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10
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Zhang H, Jiao Y, Li H, Zhu W, Li W, Huang X, Zhang Y, Zhang T, Lian S, Wu H. Longitudinal changes in total, 2-LTR circular, and integrated HIV-1 DNA during the first year of HIV-1 infection in CD4Low and CD4High patient groups with HIV-1 subtype AE. Viral Immunol 2014; 27:478-82. [PMID: 25188292 DOI: 10.1089/vim.2014.0064] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The level of viral DNA in early HIV-1 infection is an important parameter in the prediction of disease progression. Few data have been published on the dynamics of HIV-1 DNA during the first year of HIV infection. In this study, two distinct HIV-1 patient groups were enrolled. Group 1 (CD4High group) maintained their CD4 above 450 cells/μL within 1 year, while Group 2 (CD4Low group) progressed to CD4 below 300 cells/μL. The amounts of total, 2-long terminal repeat (2-LTR) circular, and integrated HIV-1 DNA were determined in the peripheral blood mononuclear cells at 1, 3, 6, and 12 months after HIV infection. Reductions in the amount of total and integrated HIV-1 DNA were detected in the CD4High group during the first year of HIV infection but not in the CD4Low group. Disease progression may be related to the body's ability to control HIV-1 DNA during early HIV-1 infection.
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Affiliation(s)
- Haihong Zhang
- 1 Infection Department, Beijing You'an Hospital, Capital Medical University, Beijing, China
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11
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Islam S, Kanbe K, Shimizu N, Ohtsuki T, Jinno-Oue A, Tanaka A, Hoshino H. CKR-L3, a deletion version CCR6-isoform shows coreceptor-activity for limited human and simian immunodeficiency viruses. BMC Infect Dis 2014; 14:354. [PMID: 24980635 PMCID: PMC4089560 DOI: 10.1186/1471-2334-14-354] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2013] [Accepted: 06/26/2014] [Indexed: 11/10/2022] Open
Abstract
Background The chemokine receptors (CKRs), mainly CCR5 and CXCR4 function as major coreceptors in infections caused by human immunodeficiency virus (HIV) and simian immunodeficiency virus (SIV). Approximately 20 G protein-coupled receptors (GPCRs) have been identified as minor coreceptors, alike CCR6 that we reported recently. Since CKR-L3 is indentified as a natural isoform of CCR6, we attempted in this study to explore the coreceptor function of CKR-L3. Methods NP-2 cells transduced with CD4-receptor (NP-2/CD4) normally remain resistant to HIV or SIV infection. However, the introduction of functional coreceptors can make these cells susceptible to these viruses. NP-2/CD4/CKR-L3 cells were produced to examine the coreceptor activity of CKR-L3. Likely, CCR6-isoform and the major coreceptors, CCR5 and CXCR4 were also examined in parallel. Presence of viral antigen in infected NP-2/CD4/coreceptor cells was detected by indirect immunofluorescence assay (IFA). The results were validated by detection of syncytia, proviral DNA and by measuring reverse transcriptase (RT) activities. Results HIV-2MIR and SIVsmE660 were found to infect NP-2/CD4/CKR-L3 cells, indicative of the coreceptor function of CKR-L3. Viral antigens appeared faster in NP-2/CD4/CKR-L3 cells than in NP-2/CD4/CCR6, indicating that CKR-L3 is a more efficient coreceptor. Moreover, syncytia formation was more rapid and RT release evidenced earlier and at higher levels with CKR-L3 than with CCR6. Sequence analysis in the C2-V3 envelope region of HIV-2MIR replicated through CKR-L3 and CCR6 coreceptor showed two and three amino acid substitutions respectively, in the C2 region compared to the CCR5-variant. The SIVsmE660-CKRL3 variant showed three amino acid substitutions in the V1 region, one change in the V2 and two changes in the C2 region. The SIVsmE660-CCR6 variant produced two changes in the V1 region, and three in the C2 region. Conclusions Isoform CKR-L3 exhibited coreceptor activity for limited primary HIV and SIV isolates with better efficiency than the parent CCR6-isoform. Amino acid substitutions in the envelope region of these viruses may confer selective pressure towards CKR-L3-use. CKR-L3 with other minor coreceptors may contribute to HIV and SIV pathogenesis including dissemination, trafficking and latency especially when major coreceptors become compromised. However, further works will be required to determine its clinical significance in HIV and SIV infection.
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Affiliation(s)
- Salequl Islam
- Department of Virology and Preventive Medicine, Gunma University Graduate School of Medicine, Maebashi, Gunma 371-8511, Japan.
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Damhorst GL, Watkins NN, Bashir R. Micro- and nanotechnology for HIV/AIDS diagnostics in resource-limited settings. IEEE Trans Biomed Eng 2013; 60:715-26. [PMID: 23512111 DOI: 10.1109/tbme.2013.2244894] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Thirty-four million people are living with HIV worldwide, a disproportionate number of whom live in resource-limited settings. Proper clinical management of AIDS, the disease caused by HIV, requires regular monitoring of both the status of the host's immune system and levels of the virus in their blood. Therefore, more accessible technologies capable of performing a CD4+ T cell count and HIV viral load measurement in settings where HIV is most prevalent are desperately needed to enable better treatment strategies and ultimately quell the spread of the virus within populations. This review discusses micro- and nanotechnology solutions to performing these key clinical measurements in resource-limited settings.
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Affiliation(s)
- Gregory L Damhorst
- Department of Bioengineering and the Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
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13
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Hayes AM, Qian S, Yu L, Boris-Lawrie K. Tat RNA silencing suppressor activity contributes to perturbation of lymphocyte miRNA by HIV-1. Retrovirology 2011; 8:36. [PMID: 21569500 PMCID: PMC3120759 DOI: 10.1186/1742-4690-8-36] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2009] [Accepted: 05/13/2011] [Indexed: 12/21/2022] Open
Abstract
Background MicroRNA (miRNA)-mediated RNA silencing is integral to virtually every cellular process including cell cycle progression and response to virus infection. The interplay between RNA silencing and HIV-1 is multifaceted, and accumulating evidence posits a strike-counterstrike interface that alters the cellular environment to favor virus replication. For instance, miRNA-mediated RNA silencing of HIV-1 translation is antagonized by HIV-1 Tat RNA silencing suppressor activity. The activity of HIV-1 accessory proteins Vpr/Vif delays cell cycle progression, which is a process prominently modulated by miRNA. The expression profile of cellular miRNA is altered by HIV-1 infection in both cultured cells and clinical samples. The open question stands of what, if any, is the contribution of Tat RNA silencing suppressor activity or Vpr/Vif activity to the perturbation of cellular miRNA by HIV-1. Results Herein, we compared the perturbation of miRNA expression profiles of lymphocytes infected with HIV-1NL4-3 or derivative strains that are deficient in Tat RNA silencing suppressor activity (Tat K51A substitution) or ablated of the vpr/vif open reading frames. Microarrays recapitulated the perturbation of the cellular miRNA profile by HIV-1 infection. The miRNA expression trends overlapped ~50% with published microarray results on clinical samples from HIV-1 infected patients. Moreover, the number of miRNA perturbed by HIV-1 was largely similar despite ablation of Tat RSS activity and Vpr/Vif; however, the Tat RSS mutation lessened HIV-1 downregulation of twenty-two miRNAs. Conclusions Our study identified miRNA expression changes attributable to Tat RSS activity in HIV-1NL4-3. The results accomplish a necessary step in the process to understand the interface of HIV-1 with host RNA silencing activity. The overlap in miRNA expression trends observed between HIV-1 infected CEMx174 lymphocytes and primary cells supports the utility of cultured lymphocytes as a tractable model to investigate interplay between HIV-1 and host RNA silencing. The subset of miRNA determined to be perturbed by Tat RSS in HIV-1 infection provides a focal point to define the gene networks that shape the cellular environment for HIV-1 replication.
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Affiliation(s)
- Amy M Hayes
- Department of Veterinary Biosciences, Center for Retrovirus Research, Ohio State University, Columbus OH, USA
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Masquelier B, Taieb A, Reigadas S, Marchou B, Cheneau C, Spire B, Charpentier C, Leport C, Raffi F, Chene G, Descamps D, Leport C, Raffi F, Chene G, Salamon R, Moatti JP, Pierret J, Spire B, Brun-Vezinet F, Fleury H, Masquelier B, Peytavin G, Garraffo R, Costagliola D, Dellamonica P, Katlama C, Meyer L, Salmon D, Sobel A, Cuzin L, Dupon M, Duval X, Le Moing V, Marchou B, May T, Morlat P, Rabaud C, Waldner-Combernoux A, Reboud P, Couffin-Cadiergues S, Marchand L, Bouteloup V, Bouhnik AD, Brunet-Francois C, Caron V, Carrieri MP, Courcoul M, Couturier F, Hardel L, Iordache L, Kurkdji P, Martiren S, Preau M, Protopopescu C, Surzyn J, Taieb A, Villes V, Schmit JL, Chennebault JM, Faller JP, Mgy-Bertrand N, Hoen B, Drobachef, Bouchaud O, Dupon M, Longy-Boursier, Morlat P, Ragnaud JM, Granier P, Garre M, Verdon R, Merrien D, Devidas A, Sobel A, Piroth L, Perronne C, Froguel E, Ceccaldi J, Peyramond D, Allard C, Reynes J, May T, Raffi F, Fuzibet JG, Dellamonica P, Arsac P, Bouvet E, Bricaire F, Bergmann P, Cabane J, Monsonego J, Girard PM, Guillevin L, Herson S, Leport C, Meyohas MC, Molina JM, Pialoux G, Salmon D, Roblot P, Jaussaud R, Michelet C, Lucht F, Debord T, Rey D, De Jaureguiberry JP, Marchou B, Bernard L. Cellular HIV-1 DNA quantification and short-term and long-term response to antiretroviral therapy. J Antimicrob Chemother 2011; 66:1582-9. [DOI: 10.1093/jac/dkr153] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
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Nicastri E, Tommasi C, Abbate I, Bonora S, Tempestilli M, Bellagamba R, Viscione M, Rozera G, Gallo AL, Ivanovic J, Amendola A, Pucillo L, Di Perri P, Capobianchi MR, Narciso P. Effect of raltegravir on the total and unintegrated proviral HIV DNA during raltegravir-based HAART. Antivir Ther 2011; 16:797-803. [DOI: 10.3851/imp1833] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Abstract
OBJECTIVE Human immunodeficiency virus (HIV)-infected people exhibit a high incidence of vascular diseases. Since in the general population the high cardiovascular risk has been associated with an impaired endothelial cell function, we investigated circulating endothelial progenitor cells in HIV-positive patients. DESIGN We evaluated circulating colony-forming unit-endothelial cell (CFU-EC) and endothelial colony-forming cell (ECFC) progenitors in 14 antiviral therapy-naive HIV-positive patients, in comparison with 15 normal controls. METHODS CFU-EC and ECFC derived from peripheral blood mononuclear cells from HIV-infected and HIV-uninfected individuals were recovered and evaluated for HIV genome presence by PCR. Vascular endothelial growth factor (VEGF) and apolipoprotein B mRNA-editing enzyme catalytic polypeptide like (APOBEC) subunits expression were evaluated in infected colonies by real-time PCR. RESULTS We found that circulating CFU-EC but not ECFC were significantly reduced in HIV-positive patients and that proviral HIV DNA was detectable only in CFU-EC but not in ECFC. Furthermore, the expression of APOBEC subunits was significantly lower in CFU-EC than in circulating monocytes. Accordingly, the CFU-EC displayed a high content of proviral DNA copies, suggesting that these cells have a high sensitivity to the HIV infection. CONCLUSIONS Although HIV does not affect the 'true endothelial progenitor' compartment, it infects and strongly depletes circulating endothelial progenitors with hematopoietic signature. We unravel a novel pathogenetic mechanism by which HIV infection might cause vascular diseases.
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Demetriou VL, van de Vijver DAMC, Kousiappa I, Balotta C, Clotet B, Grossman Z, Jørgensen LB, Lepej SZ, Levy I, Nielsen C, Paraskevis D, Poljak M, Roman F, Ruiz L, Schmidt JC, Vandamme AM, Van Laethem K, Vercauteren J, Kostrikis LG. Cellular HIV-1 DNA levels in drug sensitive strains are equivalent to those in drug resistant strains in newly-diagnosed patients in Europe. PLoS One 2010; 5:e10976. [PMID: 20544014 PMCID: PMC2882320 DOI: 10.1371/journal.pone.0010976] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2010] [Accepted: 05/13/2010] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND HIV-1 genotypic drug resistance is an important threat to the success of antiretroviral therapy and transmitted resistance has reached 9% prevalence in Europe. Studies have demonstrated that HIV-1 DNA load in peripheral blood mononuclear cells (PBMC) have a predictive value for disease progression, independently of CD4 counts and plasma viral load. METHODOLOGY/PRINCIPAL FINDINGS Molecular-beacon-based real-time PCR was used to measure HIV-1 second template switch (STS) DNA in PBMC in newly-diagnosed HIV-1 patients across Europe. These patients were representative for the HIV-1 epidemic in the participating countries and were carrying either drug-resistant or sensitive viral strains. The assay design was improved from a previous version to specifically detect M-group HIV-1 and human CCR5 alleles. The findings resulted in a median of 3.32 log(10) HIV-1 copies/10(6) PBMC and demonstrated for the first time no correlation between cellular HIV-1 DNA load and transmitted drug-resistance. A weak association between cellular HIV-1 DNA levels with plasma viral RNA load and CD4(+) T-cell counts was also reconfirmed. Co-receptor tropism for 91% of samples, whether or not they conferred resistance, was CCR5. A comparison of pol sequences derived from RNA and DNA, resulted in a high similarity between the two. CONCLUSIONS/SIGNIFICANCE An improved molecular-beacon-based real-time PCR assay is reported for the measurement of HIV-1 DNA in PBMC and has investigated the association between cellular HIV-1 DNA levels and transmitted resistance to antiretroviral therapy in newly-diagnosed patients from across Europe. The findings show no correlation between these two parameters, suggesting that transmitted resistance does not impact disease progression in HIV-1 infected individuals. The CCR5 co-receptor tropism predominance implies that both resistant and non-resistant strains behave similarly in early infection. Furthermore, a correlation found between RNA- and DNA-derived sequences in the pol region suggests that genotypic drug-resistance testing could be carried out on either template.
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Affiliation(s)
| | | | - Ioanna Kousiappa
- Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | - Claudia Balotta
- Institute of Infectious and Tropical Diseases, University of Milan, Milan, Italy
| | | | - Zehava Grossman
- National HIV Reference Lab, Central Virology, Public Health Laboratories, MOH Central Virology, Sheba Medical Centre, Ramat Gan, Israel
| | - Louise B. Jørgensen
- Retrovirus Laboratory, Division of Diagnostic Microbiology, Department of Virology, Statens Serum Institut Copenhagen, Copenhagen, Denmark
| | | | - Itzchak Levy
- Infectious Diseases Unit, Sheba Medical Centre, Ramat-Gan, Israel
| | - Claus Nielsen
- Retrovirus Laboratory, Division of Diagnostic Microbiology, Department of Virology, Statens Serum Institut Copenhagen, Copenhagen, Denmark
| | - Dimitrios Paraskevis
- National Retrovirus Reference Centre, Department of Hygiene Epidemiology and Medical Statistics, Medical School, University of Athens, Athens, Greece
| | - Mario Poljak
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Francois Roman
- Retrovirology Laboratory, Centre Hospitalier de Luxembourg, National Service of Infectious Diseases, Luxembourg, Luxembourg
| | - Lidia Ruiz
- IrsiCaixa Foundation, Hospital Germans Trias i Pujol, Barcelona, Spain
| | - Jean-Claude Schmidt
- Retrovirology Laboratory, Centre Hospitalier de Luxembourg, National Service of Infectious Diseases, Luxembourg, Luxembourg
| | - Anne-Mieke Vandamme
- Katholieke Universiteit Leuven, Rega Institute for Medical Research, Leuven, Belgium
| | - Kristel Van Laethem
- Katholieke Universiteit Leuven, Rega Institute for Medical Research, Leuven, Belgium
| | - Jurgen Vercauteren
- Katholieke Universiteit Leuven, Rega Institute for Medical Research, Leuven, Belgium
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