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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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CHANG CC, NARANBHAI V, STERN J, ROCHE M, DANTANARAYANA A, KE R, TENNAKOON S, SOLOMON A, HOH R, HARTOGENSIS W, HECHT FM, SIKARIS K, PRICE DJ, ELLIOTT JH, DEEKS SG, CHURCHILL M, CAMERON PU, HENGARTNER N, PERELSON AS, LEWIN SR. Variation in cell-associated unspliced HIV RNA on antiretroviral therapy is associated with the circadian regulator brain-and-muscle-ARNT-like-1. AIDS 2018; 32:2119-2128. [PMID: 30005017 PMCID: PMC6173794 DOI: 10.1097/qad.0000000000001937] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
OBJECTIVE(S) To determine whether variation in cell-associated unspliced (CA-US) HIV RNA in HIV-infected individuals on antiretroviral therapy (ART) has a circadian basis. METHODS Prospective observational study of HIV-infected individuals on ART. Blood was collected on three occasions and CA-US HIV RNA and mRNA of the circadian-locomotor-output-cycles-kaput (CLOCK)-associated genes quantified by real time PCR. CLOCK-associated proteins were over-expressed in a cell line stably transfected with an HIV long-terminal repeat (LTR) luciferase reporter. RESULTS Using a mixed effects model, there was a significant increase in log-CA-US RNA at the third visit compared with the first visit (effect size of 0.619 with standard error (SE) of 0.098, P < 0.001) and an independent effect of time of blood draw (effect size 0.051 (SE 0.025), P = 0.040). The CLOCK-associated gene, brain-and-muscle-ARNT-like-1 (BMAL-1) had a significant relationship with log CA-US HIV RNA (effect size 8.508 (SE 3.777), P = 0.028) and also with time (P = 0.045). Over expression of BMAL-1 and CLOCK in a cell line stably transfected with an HIV-LTR luciferase reporter resulted in an increase in luciferase expression and this was reduced following mutation of the second E-box in the HIV-LTR. CONCLUSION The basal level of HIV transcription on ART can vary significantly and is modulated by the circadian regulator BMAL-1, amongst other factors.
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Affiliation(s)
- Christina C CHANG
- Department of Infectious Diseases, Alfred Hospital and Monash University, Melbourne, Australia
| | - Vivek NARANBHAI
- Nuffield Dept. of Medicine, University of Oxford, Oxford, United Kingdom
| | - Jared STERN
- The Peter Doherty Institute for Infection and Immunity, The University of Melbourne and Royal Melbourne Hospital, Melbourne, Australia
| | - Michael ROCHE
- The Peter Doherty Institute for Infection and Immunity, The University of Melbourne and Royal Melbourne Hospital, Melbourne, Australia
- School of Health and Biomedical Sciences, RMIT University, Melbourne, Australia
| | - Ashanti DANTANARAYANA
- The Peter Doherty Institute for Infection and Immunity, The University of Melbourne and Royal Melbourne Hospital, Melbourne, Australia
| | - Ruian KE
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM
| | - Surekha TENNAKOON
- The Peter Doherty Institute for Infection and Immunity, The University of Melbourne and Royal Melbourne Hospital, Melbourne, Australia
| | - Ajantha SOLOMON
- The Peter Doherty Institute for Infection and Immunity, The University of Melbourne and Royal Melbourne Hospital, Melbourne, Australia
| | - Rebecca HOH
- School of Medicine, University of California San Francisco, San Francisco, CA
| | - Wendy HARTOGENSIS
- Division of Biostatistics, University of California San Francisco, San Francisco, CA
| | - Frederick M HECHT
- Osher Center for Integrative Medicine, University of California San Francisco, San Francisco, CA
| | | | - David J PRICE
- The Peter Doherty Institute for Infection and Immunity, The University of Melbourne and Royal Melbourne Hospital, Melbourne, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne
| | - Julian H ELLIOTT
- Department of Infectious Diseases, Alfred Hospital and Monash University, Melbourne, Australia
| | - Steven G DEEKS
- School of Medicine, University of California San Francisco, San Francisco, CA
| | - Melissa CHURCHILL
- School of Health and Biomedical Sciences, RMIT University, Melbourne, Australia
| | - Paul U CAMERON
- Department of Infectious Diseases, Alfred Hospital and Monash University, Melbourne, Australia
- The Peter Doherty Institute for Infection and Immunity, The University of Melbourne and Royal Melbourne Hospital, Melbourne, Australia
| | - Nicolas HENGARTNER
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM
| | - Alan S. PERELSON
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM
| | - Sharon R LEWIN
- Department of Infectious Diseases, Alfred Hospital and Monash University, Melbourne, Australia
- The Peter Doherty Institute for Infection and Immunity, The University of Melbourne and Royal Melbourne Hospital, Melbourne, Australia
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3
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Longitudinal changes in viral RNA concentration in patients with chronic hepatitis C and/or HIV infection in the absence of antiviral therapy. J Clin Virol 2013; 58:391-5. [DOI: 10.1016/j.jcv.2013.06.031] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Revised: 06/20/2013] [Accepted: 06/24/2013] [Indexed: 11/22/2022]
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4
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Xiao Y, Miao H, Tang S, Wu H. Modeling antiretroviral drug responses for HIV-1 infected patients using differential equation models. Adv Drug Deliv Rev 2013; 65:940-53. [PMID: 23603208 PMCID: PMC4017332 DOI: 10.1016/j.addr.2013.04.005] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2012] [Revised: 03/29/2013] [Accepted: 04/10/2013] [Indexed: 12/22/2022]
Abstract
We review mathematical modeling and related statistical issues of HIV dynamics primarily in response to antiretroviral drug therapy in this article. We start from a basic model of virus infection and then review a number of more advanced models with consideration of pharmacokinetic factors, adherence and drug resistance. Specifically, we illustrate how mathematical models can be developed and parameterized to understand the effects of long-term treatment and different treatment strategies on disease progression. In addition, we discuss a variety of parameter estimation methods for differential equation models that are applicable to either within- or between-host viral dynamics.
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Affiliation(s)
- Yanni Xiao
- School of Mathematics & Statistics, Xi’an Jiaotong University, Shaanxi, China
| | - Hongyu Miao
- School of Medicine and Dentistry, University of Rochester, New York, USA
| | - Sanyi Tang
- School of Mathematics & Information Sciences, Shaanxi Normal University, Shaanxi, China
| | - Hulin Wu
- School of Medicine and Dentistry, University of Rochester, New York, USA
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Abstract
PURPOSE OF REVIEW The CD4 lymphocyte count was identified as a key predictor of risk of AIDS defining diseases almost 20 years ago, early in the HIV epidemic. Several issues concerning its use to predict AIDS have arisen since. These include the difference between short and long-term prediction, the use of CD4 percentage compared with absolute counts, the impact of antiretroviral therapy on the predictive value of the CD4 count, the role relative to other markers such as viral load, the derivation of scores to predict AIDS diseases, the use of CD4 count as a surrogate endpoint, the role of the CD4 count nadir compared with the current value and the differential ability to predict different AIDS diseases. RECENT FINDINGS All the above issues have been clarified further and this process has continued through 2004 and 2005. These developments are briefly described in this review. SUMMARY The CD4 count remains the strongest short-term predictor of risk of AIDS so far identified in both treated and untreated patients and should continue to be a mainstay of monitoring for both untreated and treated patients.
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Korenromp EL, Williams BG, Schmid GP, Dye C. Clinical prognostic value of RNA viral load and CD4 cell counts during untreated HIV-1 infection--a quantitative review. PLoS One 2009; 4:e5950. [PMID: 19536329 PMCID: PMC2694276 DOI: 10.1371/journal.pone.0005950] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2009] [Accepted: 05/12/2009] [Indexed: 11/19/2022] Open
Abstract
Background The prognostic value of CD4 counts and RNA viral load for identifying treatment need in HIV-infected individuals depends on (a) variation within and among individuals, and (b) relative risks of clinical progression per unit CD4 or RNA difference. Methodology/Principal Findings We reviewed these measurements across (a) 30 studies, and (b) 16 cohorts of untreated seropositive adults. Median within-population interquartile ranges were 74,000 copies/mL for RNA with no significant change during the course of infection; and 330 cells/µL for CD4, with a slight proportional increase over infection. Applying measurement and physiological fluctuations observed on chronically infected patients, we estimate that 45% of population-level variation in RNA, and 25% of variation in CD4, were due to within-patient fluctuations. Comparing a patient with RNA at upper 75th centile with a patient at median RNA, 5-year relative risks were 1.4 (95% CI 1.2–1.7) for AIDS and 1.5 (1.3–1.9) for death, without change over the course of infection. In contrast, for a patient with CD4 count at the lower 75th centile, relative risks increased from 1.0 at seroconversion to maxima of 6.3 (4.4–8.9) for AIDS and 5.5 (2.7–10.1) for death by year 6, when the population median had fallen to 300 cells/µL. Below 300 cells/µL, prognostic power did not increase, due to a narrower CD4 range. Conclusions Findings support the current WHO recommendation (used with clinical criteria) to start antiretroviral treatment in low-income settings at CD4 thresholds of 200–350 cells/µL, without pre-treatment RNA monitoring – while not precluding earlier treatment based on clinical, socio-demographic or public health criteria.
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Affiliation(s)
- Eline L Korenromp
- Department of Public Health, Erasmus MC, University Medical Centre Rotterdam, Rotterdam, The Netherlands.
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7
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Fully automated quantification of human immunodeficiency virus (HIV) type 1 RNA in human plasma by the COBAS AmpliPrep/COBAS TaqMan system. J Clin Virol 2007; 38:304-12. [PMID: 17329164 DOI: 10.1016/j.jcv.2006.12.022] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2006] [Accepted: 12/22/2006] [Indexed: 11/18/2022]
Abstract
BACKGROUND HIV-1 RNA is a key parameter for reliable diagnosis and treatment of HIV-1 infection. The determination of HIV-1 RNA reduces the pre-seroconversion period in the diagnosis of HIV-1 infection and supports clinical management of HIV-1-infected patients. OBJECTIVES AND STUDY DESIGN The COBAS AmpliPrep/COBAS TaqMan HIV-1 Test combines automated extraction of total nucleic acids on the COBAS AmpliPrep Instrument with real-time PCR on the COBAS TaqMan Analyzer, thus greatly reducing hands-on time during sample preparation and amplification/detection. The test was evaluated for sensitivity, dynamic range, precision, subtype inclusivity, interfering substances, diagnostic and analytical specificity, as well as correlation with three other commercial tests for HIV-1 RNA quantification. RESULTS The COBAS AmpliPrep/COBAS TaqMan HIV-1 Test demonstrated an assay sensitivity of 40 copies/mL, a greater than 5 log(10) measuring range of 40-1.0E+07 copies/mL (1.6-7.0 log(10)) and a reliable determination of HIV-1 group M and N subtypes in EDTA plasma. Quantification results were highly correlated with those obtained by the COBAS AMPLICOR HIV-1 MONITOR Test v1.5, the COBAS AmpliPrep/COBAS AMPLICOR HIV-1 MONITOR Test v1.5 and the VERSANT HIV-1 RNA 3.0 assay. CONCLUSIONS The COBAS AmpliPrep/COBAS TaqMan HIV-1 Test excellently satisfies the requirements for reliable quantification of HIV-1 RNA in clinical specimens by a broad linear measuring range and a fully automated quantification procedure. It is highly appropriate for therapy monitoring and routine management of HIV-1 infection.
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Heffernan JM, Wahl LM. Natural variation in HIV infection: Monte Carlo estimates that include CD8 effector cells. J Theor Biol 2006; 243:191-204. [PMID: 16876200 DOI: 10.1016/j.jtbi.2006.05.032] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2005] [Revised: 03/31/2006] [Accepted: 05/25/2006] [Indexed: 11/22/2022]
Abstract
Viral load and CD4 T-cell counts in patients infected with the human immunodeficiency virus (HIV) are commonly used to guide clinical decisions regarding drug therapy or to assess therapeutic outcomes in clinical trials. However, random fluctuations in these markers of infection can obscure clinically significant change. We employ a Monte Carlo simulation to investigate contributing factors in the expected variability in CD4 T-cell count and viral load due solely to the stochastic nature of HIV infection. The simulation includes processes that contribute to the variability in HIV infection including CD4 and CD8 T-cell population dynamics as well as T-cell activation and proliferation. The simulation results may reconcile the wide range of variabilities in viral load observed in clinical studies, by quantifying correlations between viral load measurements taken days or weeks apart. The sensitivity of variability in T-cell count and viral load to changes in the lifetimes of CD4 and CD8 T-cells is investigated, as well as the effects of drug therapy.
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Affiliation(s)
- Jane M Heffernan
- Department of Applied Mathematics, University of Western Ontario, Western Rd, London, Ont., Canada N6A 5B7.
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9
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Heffernan JM, Wahl LM. Monte Carlo estimates of natural variation in HIV infection. J Theor Biol 2006; 236:137-53. [PMID: 16005307 DOI: 10.1016/j.jtbi.2005.03.002] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2004] [Revised: 02/02/2005] [Accepted: 03/01/2005] [Indexed: 11/21/2022]
Abstract
We describe a Monte Carlo simulation of the within-host dynamics of human immunodeficiency virus 1 (HIV-1). The simulation proceeds at the level of individual T-cells and virions in a small volume of plasma, thus capturing the inherent stochasticity in viral replication, mutation and T-cell infection. When cell lifetimes are distributed exponentially in the Monte Carlo approach, our simulation results are in perfect agreement with the predictions of the corresponding systems of differential equations from the literature. The Monte Carlo model, however, uniquely allows us to estimate the natural variability in important parameters such as the T-cell count, viral load, and the basic reproductive ratio, in both the presence and absence of drug therapy. The simulation also yields the probability that an infection will not become established after exposure to a viral inoculum of a given size. Finally, we extend the Monte Carlo approach to include distributions of cell lifetimes that are less-dispersed than exponential.
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Affiliation(s)
- Jane M Heffernan
- Department of Applied Mathematics, University of Western Road London, Ontario N6A 5B7, Canada.
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10
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Bonhoeffer S, Funk GA, Günthard HF, Fischer M, Müller V. Glancing behind virus load variation in HIV-1 infection. Trends Microbiol 2004; 11:499-504. [PMID: 14607066 DOI: 10.1016/j.tim.2003.09.002] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Although the steady-state virus load during HIV-1 infection is remarkably stable within a patient, it displays variation over several orders of magnitude between patients. Despite intensive research, the host and virus factors that are responsible for the observed variation remain poorly understood. Comparison of model predictions with clinical data suggests that most of the variation in steady-state virus load between patients reflects variation of the net rate at which activated CD4 cells are produced.
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Abstract
Viral load monitoring has become the standard of care in clinical practice to assess risk for disease progression and to monitor treatment response. Furthermore, viral load monitoring has contributed greatly to the understanding of HIV disease pathogenesis and response to various antiretroviral regimens, and has broadened its applications to include blood bank screening. The assays that are currently available are more sensitive, precise, and robust. There is now a better understanding of their limitations and the clinical scenarios and assay performance issues that result in variations of viral load results.
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12
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Chernoff DN. The significance of HIV viral load assay precision: a review of the package insert specifications of two commercial kits. JOURNAL OF THE INTERNATIONAL ASSOCIATION OF PHYSICIANS IN AIDS CARE (CHICAGO, ILL. : 2002) 2002; 1:134-40. [PMID: 12942672 DOI: 10.1177/154510970200100405] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Quantification of HIV-1 RNA levels is a vital tool in the medical management of individuals infected with HIV. The commercially available US Federal Drug Administration (FDA)-approved assays vary in their ability to accurately measure and detect significant changes in plasma viral load. A more precise assay can accurately distinguish true clinically significant biologic changes in viral plasma load from background noise, or systematic variation. These differences in precision between assays are profound at low, near-cutoff levels, but also occur throughout the dynamic range of the assays. This review examines the precision specifications, expressed as fold changes in test and retesting, across the dynamic ranges of the Bayer Versant bDNA assay, and the two available versions of the Roche Amplicor Monitor PCR assays. Highly validated data from their respective package inserts are analyzed to confirm each assay's performance throughout its dynamic range. The precision of a viral load assay is critical to patient management, and gives the clinician a clearer picture of the patient's true virologic status that is attributable to infection or treatment as opposed to systematic variation in assays.
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13
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Nowicki MJ, Benning L, Bremer JW, Meyer WA, Hanson C, Brambilla D, Silver S, Kovacs A. Longitudinal variability of human immunodeficiency virus type 1 RNA viral load measurements by nucleic acid sequence-based amplification and NucliSens assays in a large multicenter study. J Clin Microbiol 2001; 39:3760-3. [PMID: 11574612 PMCID: PMC88428 DOI: 10.1128/jcm.39.10.3760-3763.2001] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) RNA measurements were evaluated within an externally controlled multilaboratory program. Three external standards (1.5 x 10(3) to 1.5 x 10(6) copies/ml) were included in 814 assay runs by four laboratories. Results indicate that HIV-1 RNA levels can be measured with a precision equal to that of the pre-highly active antiretroviral therapy era (standard deviations, +/-0.16 to 0.25 log10 units).
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Affiliation(s)
- M J Nowicki
- University of Southern California, Pediatrics, Los Angeles, California 90033, USA.
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14
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Clarke JR, Galpin S, Braganza R, Ashraf A, Russell R, Churchill DR, Weber JN, McClure MO. Comparative quantification of diverse serotypes of HIV-1 in plasma from a diverse population of patients. J Med Virol 2000; 62:445-9. [PMID: 11074472 DOI: 10.1002/1096-9071(200012)62:4<445::aid-jmv8>3.0.co;2-n] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
HIV-1 is characterised by extensive genetic variability encompassing at least 10 different phylogenetically related clades within the major group of HIV-1 subtypes. Most commercially available HIV-1 RNA plasma viral load assays have been optimised with clade B viruses and may yield misleadingly low RNA levels for nonclade B viruses that are increasingly found in Europe. In this study we compare the most recent versions of the Roche Amplicor HIV Monitor and the Chiron Quantiplex for ability to detect viraemia in a population of patients infected with a range of HIV-1 subtypes. EDTA-treated plasma was obtained from 206 patients. The Amplicor and Quantiplex assays were carried out in accordance with manufacturers' instructions. Results from 53/206 (25.7%) samples differed by >0.4 log between Amplicor 1.5 and Quantiplex 3.0. A >0.5 log and 1.0 log difference was detected between Amplicor 1.5 and Quantiplex 3.0 in 37/206 (17.9%) and 7/206 (3.4%) of samples, respectively. Overall, Amplicor 1.5 gave a median value of 0.22 log higher than Quantiplex 3.0. Discordant results were detected in 53 out of 206 (25.7%) samples. Of these 22 out of 123 (17.9%) samples were of UK origin, 18 out of 43 (41.9%) African, 1 out of 8 (12.5%) South American, 1 out of 6 (16.7%) North American, 4 out of 9 (44.4%) North European, 3 out of 11 (23.7%) South European and 3 out of 7 (42.3%) Asian samples, respectively. Serotyping revealed that discordant viral load results between Amplicor 1.5 and Quantiplex 3.0 occurred within samples from all subtypes (A-E). Despite the improvements made to both the Roche Amplicor and the Chiron Quantiplex assays discordant results were detected between the two assays in 25.7% of cases. In a substantial minority of patients there were major discrepancies between the two assays that were not explained by HIV subtype differences.
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Affiliation(s)
- J R Clarke
- Department of Genitourinary Medicine and Communicable Diseases, Jefferiss Research Trust Laboratories, Division of Medicine, Imperial College School of Medicine at St. Mary's Hospital, London, United Kingdom.
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Masel J, Arnaout RA, O'Brien TR, Goedert JJ, Lloyd AL. Fluctuations in HIV-1 viral load are correlated to CD4+ T-lymphocyte count during the natural course of infection. J Acquir Immune Defic Syndr 2000; 23:375-9. [PMID: 10866229 DOI: 10.1097/00126334-200004150-00003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Viral load fluctuates during the natural course of asymptomatic HIV-1 infection. It is often assumed that these fluctuations are random around a set point or underlying growth trend. Using longitudinal data, we tested whether fluctuations in viral load can be better explained by changes in CD4+ T-cell count than by a set point or trend of exponential growth. The correspondence between viral load and CD4+ T-cell count could be described by a simple mathematical relation. Using a bootstrapping approach, the hypothesis that viral load fluctuations are random around a set point was rejected with p < .00005. The hypothesis that viral load fluctuations are random around a trend of exponential growth was rejected with p < .005. Viral load data was explained better by changes in CD4+ T-cell counts than by a set point or by a trend of exponential growth. The implications of this finding for improved prognostication are discussed.
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Affiliation(s)
- J Masel
- Wellcome Trust Centre for the Epidemiology of Infectious Disease, Department of Zoology, University of Oxford, UK
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16
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Fluctuations in HIV-1 Viral Load Are Correlated to CD4+ T-Lymphocyte Count During the Natural Course of Infection. J Acquir Immune Defic Syndr 2000. [DOI: 10.1097/00042560-200004150-00003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Manegold C, Krempe C, Jablonowski H, Kajala L, Dietrich M, Adams O. Comparative evaluation of two branched-DNA human immunodeficiency virus type 1 RNA quantification assays with lower detection limits of 50 and 500 copies per milliliter. J Clin Microbiol 2000; 38:914-7. [PMID: 10655416 PMCID: PMC86246 DOI: 10.1128/jcm.38.2.914-917.2000] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We have comparatively evaluated Quantiplex version 3.0 and version 2. 0 on 133 plasma samples and a repetitive dilution series. Version 3. 0 yielded higher human immunodeficiency virus RNA values, and the ratio of version 3.0 results to version 2.0 results decreased from 3. 47 below 1,000 copies/ml to 1.97 above 50,000 copies/ml [linear regression, log (version 3.0) = 0.915 + 0.871 x log (version 2.0); r(2) = 0.952].
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Affiliation(s)
- C Manegold
- Klinik für Gastroenterologie, Hepatologie und Infektiologie, Heinrich-Heine-Universität, Düsseldorf, Germany.
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18
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Abstract
Measurement of HIV-1 viral load is now an accepted part of clinical practice for the determination of clinical prognosis and antiretroviral effectiveness in HIV infection. Consensus guidelines have been published on the appropriate use of this testing. Furthermore, recent advances in molecular technology have improved the sensitivity and reproducibility of viral load assays, and these improved assays have provided new insight into the pathogenesis of HIV disease. This article reviews new issues affecting viral load quantification, including viral subtypes, sex, compartmental differences, and other covariables.
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Affiliation(s)
- M Holodniy
- AIDS Research Center, Veterans Affairs Palo Alto Health Care System, 3801 Miranda Avenue (132), Palo Alto, CA 94304, USA
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19
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Richman D, Crowe S, Harvey K. HIV viral load monitoring. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 1999; 458:199-212. [PMID: 10549392 DOI: 10.1007/978-1-4615-4743-3_19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/14/2023]
Affiliation(s)
- D Richman
- Department of Pathology, San Diego Veterans Affairs Medical Center, California, USA
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20
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Murphy DG, Gonin P, Fauvel M. Reproducibility and performance of the second-generation branched-DNA assay in routine quantification of human immunodeficiency virus type 1 RNA in plasma. J Clin Microbiol 1999; 37:812-4. [PMID: 9986862 PMCID: PMC84566 DOI: 10.1128/jcm.37.3.812-814.1999] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We examined the reproducibility of a second-generation branched-DNA (bDNA) assay (Quantiplex HIV RNA 2.0) for quantification of human immunodeficiency virus type 1 (HIV-1) RNA in plasma by retesting 325 specimens on separate runs and on different lots. The performance of the bDNA test was also assessed by data analysis obtained during routine testing of 15,365 specimens. Upon retesting, 96 and 86% of specimens displaying RNA levels above 5,000 and between 500 and 5, 000 copies/ml, respectively, showed less than a 0.3 log10 (twofold) difference with their initial values. Assay variability was found to increase as viral load decreased. Overall, the bDNA version 2.0 assay was found to be a reproducible and efficient test for routine quantification of HIV-1 RNA in plasma.
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Affiliation(s)
- D G Murphy
- Laboratoire de Santé Publique du Québec, Sainte-Anne-de-Bellevue, Québec, Canada.
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