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Amendola A, Sberna G, Forbici F, Abbate I, Lorenzini P, Pinnetti C, Antinori A, Capobianchi MR. The dual-target approach in viral HIV-1 viremia testing: An added value to virological monitoring? PLoS One 2020; 15:e0228192. [PMID: 32023284 PMCID: PMC7001951 DOI: 10.1371/journal.pone.0228192] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 01/10/2020] [Indexed: 12/03/2022] Open
Abstract
New methods of HIV-1 RNA quantification based on dual-target detection are increasingly used in HIV viral load monitoring, but clinical implications and impact of dual-target detection on HIV-1 infection management are not established. Aptima HIV-1 Quant Dx assay is a last generation HIV viral load method, that uses pol and LTR as simultaneous target, providing quantitative results based mainly on pol target, while LTR target is used to report the results when pol signal is absent. In our laboratory, about 6% of results of all HIV-1 viral load tests performed with this platform in one year period resulted from LTR signal. Interestingly, LTR-based viremia (sometimes exceeding 1,000 copies/mL) was observed in a small proportion (up to 1%) of patients under ART, considered for long time virologically suppressed on the basis of a single target (pol-based) assay. Male gender, >700 vs <200 CD4 cell/mL and dual therapy including NRTI plus either NNRTI, or PI/b or INSTI were independently associated with increased risk of LTR-based HIV-1 viral load detection by multivariable logistic regression. A significant linear correlation was observed between LTR-based HIV-1 RNA levels and PBMC-associated proviral DNA. Moreover, in a small group of patients with HIV-1 RNA levels >200 copies/mL, longitudinal assessments showed parallel kinetics between plasma viremia and proviral DNA. Sequencing of pol region for drug resistance assessment in patients with LTR-based viremia failed on plasma HIV-1 RNA, while it was successful on proviral DNA. The detection/quantification of HIV-1 viremia based only on LTR signal with a dual target assay in samples resulting undetectable with the more conventional target pol needs accurate evaluation; unravelling the biological basis of this phenomenon, here described for the first time, is mandatory to establish relevance and implication by both pathogenetic (i.e. infectivity of LTR-detected viruses, reservoir turnover, immune activation, etc.) and clinical standpoint.
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Affiliation(s)
- Alessandra Amendola
- Laboratory of Virology, National Institute for Infectious Diseases “Lazzaro Spallanzani” IRCCS, Rome, Italy
| | - Giuseppe Sberna
- Laboratory of Virology, National Institute for Infectious Diseases “Lazzaro Spallanzani” IRCCS, Rome, Italy
| | - Federica Forbici
- Laboratory of Virology, National Institute for Infectious Diseases “Lazzaro Spallanzani” IRCCS, Rome, Italy
| | - Isabella Abbate
- Laboratory of Virology, National Institute for Infectious Diseases “Lazzaro Spallanzani” IRCCS, Rome, Italy
| | - Patrizia Lorenzini
- Clinical Department, National Institute for Infectious Diseases “Lazzaro Spallanzani” IRCCS, Rome, Italy
| | - Carmela Pinnetti
- Clinical Department, National Institute for Infectious Diseases “Lazzaro Spallanzani” IRCCS, Rome, Italy
| | - Andrea Antinori
- Clinical Department, National Institute for Infectious Diseases “Lazzaro Spallanzani” IRCCS, Rome, Italy
| | - Maria Rosaria Capobianchi
- Laboratory of Virology, National Institute for Infectious Diseases “Lazzaro Spallanzani” IRCCS, Rome, Italy
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Ramalingam VV, Subramanian S, Fletcher GJ, Rupali P, Varghese G, Pulimood S, Jeyaseelan L, Nandagopal B, Sridharan G, Kannangai R. Interaction of human immunodeficiency virus-1 and human immunodeficiency virus-2 capsid amino acid variants with human tripartite motif 5α protein SPRY domain and its association with pathogenesis. Indian J Med Microbiol 2019; 37:574-583. [PMID: 32436883 DOI: 10.4103/ijmm.ijmm_20_109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Purpose The sequence variation of human immunodeficiency virus (HIV) capsid region may influence and alter the susceptibility to human tripartite motif 5α protein (huTRIM5α). Materials and Methods Molecular docking was carried out with huTRIM5α SPRY domain by the use of ClusPro and Hex docking program for HIV-1 and HIV-2 capsid sequences. Results The sequence analysis on HIV-1 and HIV-2 capsid gag gene identified 35 (19.7%) single-nucleotide polymorphisms (SNPs) in HIV-1 and 8 (4.5%) SNPs in HIV-2. The variations observed in the HIV-2 capsid region were significantly lower than HIV-1 (P < 0.001). The molecular docking analysis showed that HIV-1 wild type used V1 loop, while HIV-2 used V3 loop of huTRIM5α for interaction. HIV-1 with A116T SNP and HIV-2 with V81A SNP use V3 and V1 loop of huTRIM5α for interaction respectively. The reduced huTRIM5α inhibition may lead to a faster progression of disease among HIV-1-infected individuals. However, in case of HIV-2, increased inhibition by huTRIM5α slows down the disease progression. Conclusion Polymorphisms in the capsid protein with both HIV-1- and HIV-2-monoinfected individuals showed the difference in the docking energy from the wild type. This is the first study which documents the difference in the usage of loop between the two HIV types for interaction with huTRIM5α. Variations in the capsid protein result in alteration in the binding to the restriction factor huTRIM5α.
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Affiliation(s)
| | - Suganya Subramanian
- Sri Narayani Hospital and Research Centre, Sri Sakthi Amma Institute of Biomedical Research, Vellore, Tamil Nadu, India
| | - G John Fletcher
- Department of Clinical Virology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Priscilla Rupali
- Department of Infectious Diseases, Christian Medical College, Vellore, Tamil Nadu, India
| | - George Varghese
- Department of Infectious Diseases, Christian Medical College, Vellore, Tamil Nadu, India
| | - Susanne Pulimood
- Department of Dermatology, Christian Medical College, Vellore, Tamil Nadu, India
| | | | - Balaji Nandagopal
- Sri Narayani Hospital and Research Centre, Sri Sakthi Amma Institute of Biomedical Research, Vellore, Tamil Nadu, India
| | - Gopalan Sridharan
- Sri Narayani Hospital and Research Centre, Sri Sakthi Amma Institute of Biomedical Research, Vellore, Tamil Nadu, India
| | - Rajesh Kannangai
- Department of Clinical Virology, Christian Medical College, Vellore, Tamil Nadu, India
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Jagannath S, Sachithanandham J, Ramalingam VV, Demosthenes JP, Abraham AM, Zachariah A, Varghese GM, Kannangai R. BK virus characterisation among HIV-1-Infected individuals and its association with immunosuppression. Indian J Med Microbiol 2018; 36:172-177. [PMID: 30084406 DOI: 10.4103/ijmm.ijmm_18_54] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Purpose BK virus (BKV) is an opportunistic pathogen which causes significant morbidity and mortality in individuals who are immunodeficient. We aimed to quantitate and characterise BKV and to correlate with the degree of immunosuppression among human immunodeficiency virus (HIV)-1-infected individuals. Methods BKV DNA detection was carried out using an in-house quantitative real-time polymerase chain reaction on paired whole-blood and urine samples collected from 187 antiretroviral therapy (ART)-naïve HIV-1-infected individuals and 93 healthy individuals who served as controls. Sequencing was performed for a proportion of high BK viral load (VL) samples to observe non-coding control region (NCCR) rearrangements. Results BKV positivity in urine was 25.6% among HIV-infected individuals and 10.7% in control individuals (P = 0.03). The BK VL showed a significant negative correlation with CD4+ T-cell counts, a positive correlation with WHO clinical staging and no significant correlation with HIV-1 VL. Of 42 BKVs from urine samples sequenced, two showed rearrangements without clinically severe disease or high VL. Their NCCR and VP1 sequence-based genotyping revealed genotype I. In a small subset of individuals (n = 8) on ART who were being followed up, six individuals showed either decrease or complete clearance of virus with ART. Conclusion There was a higher frequency of BK viruria in HIV-1-infected individuals than among healthy controls and the positivity correlated with the degree of immunosuppression. There was no association of high VL with NCCR rearrangements in urine.
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Affiliation(s)
- Subha Jagannath
- Department of Clinical Virology, Christian Medical College, Vellore, Tamil Nadu, India
| | | | - Veena V Ramalingam
- Department of Clinical Virology, Christian Medical College, Vellore, Tamil Nadu, India
| | - John Paul Demosthenes
- Department of Clinical Virology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Asha M Abraham
- Department of Clinical Virology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Anand Zachariah
- Department of Medicine and Infectious Diseases, Christian Medical College, Vellore, Tamil Nadu, India
| | - George M Varghese
- Department of Medicine and Infectious Diseases, Christian Medical College, Vellore, Tamil Nadu, India
| | - Rajesh Kannangai
- Department of Clinical Virology, Christian Medical College, Vellore, Tamil Nadu, India
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Performance Evaluation of the New HIV-1 Quantification Assay, Xpert HIV-1 Viral Load, on a Wide Panel of HIV-1 Variants. J Acquir Immune Defic Syndr 2017; 72:521-6. [PMID: 27007866 DOI: 10.1097/qai.0000000000001003] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
OBJECTIVE To evaluate the quantification performance of the new Cepheid GeneXpert HIV-1 viral load assay, on a wide panel of HIV-1 variants. METHODS Clinical performance was evaluated relative to the Abbott RealTime HIV-1 assay on 285 HIV-1 seropositive samples selected to cover the assays quantification range (40 copies/mL-10,000,000 copies/mL), and included RNA undetectable or detected seropositive samples. The panel comprised 120 subtype B, 150 non-B, and 15 nontypable clinical samples; serial dilutions of 18 viral supernatants representative of the divergent viruses of HIV-1 groups N, O, and P were also tested. RESULTS Based on samples selected according to the Abbott assay viral loads (VL), the Cepheid assay detected or quantified 222/285 (78%) samples and the Abbott assay 240/285 (84%). Xpert yielded VLs for 162 (76%) of the 213 quantifiable samples with Abbott. This difference corresponded to 51 samples with VL >40 copies/mL by the Abbott assay (all below 200 copies/mL) but detected (n = 40) or undetectable (n = 11) by the Cepheid assay. VL of samples quantifiable by both assays (n = 162) showed very strong correlation, with a Spearman correlation coefficient of 0.985 and a Bland-Altman's mean of differences of -0.01. Performance for quantification of the non-M samples showed very good correlation, with significantly higher values with Cepheid for the group N and 2 group O samples. CONCLUSIONS Our study showed that the Xpert HIV-1 VL assay offered very good performance for detection and quantification of the current HIV-1 genetic diversity; differences reported at the threshold could be an issue and requires further evaluations. The practicability of this new assay makes it suitable for low-income countries, where it could facilitate and improve follow-up of patients, as well as for high-income regions.
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Braun P, Delgado R, Drago M, Fanti D, Fleury H, Hofmann J, Izopet J, Kühn S, Lombardi A, Mancon A, Marcos MA, Mileto D, Sauné K, O'Shea S, Pérez-Rivilla A, Ramble J, Trimoulet P, Vila J, Whittaker D, Artus A, Rhodes D. A European multicientre study on the comparison of HIV-1 viral loads between VERIS HIV-1 Assay and Roche COBAS® TAQMAN® HIV-1 test, Abbott RealTime HIV-1 Assay, and Siemens VERSANT HIV-1 Assay. J Clin Virol 2017; 92:75-82. [PMID: 28599228 DOI: 10.1016/j.jcv.2017.05.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 05/03/2017] [Accepted: 05/06/2017] [Indexed: 11/30/2022]
Abstract
BACKGROUND Viral load monitoring is essential for patients under treatment for HIV. Beckman Coulter has developed the VERIS HIV-1 Assay for use on the novel, automated DxN VERIS Molecular Diagnostics System.¥ OBJECTIVES: Evaluation of the clinical performance of the new quantitative VERIS HIV-1 Assay at multiple EU laboratories. STUDY DESIGN Method comparison with the VERIS HIV-1 Assay was performed with 415 specimens at 5 sites tested with COBAS® AmpliPrep/COBAS® TaqMan® HIV-1 Test, v2.0, 169 specimens at 3 sites tested with RealTime HIV-1 Assay, and 202 specimens from 2 sites tested with VERSANT HIV-1 Assay. Patient monitoring sample results from 4 sites were also compared. RESULTS Bland-Altman analysis showed the average bias between VERIS HIV-1 Assay and COBAS HIV-1 Test, RealTime HIV-1 Assay, and VERSANT HIV-1 Assay to be 0.28, 0.39, and 0.61 log10 cp/mL, respectively. Bias at low end levels below 1000cp/mL showed predicted bias to be <0.3 log10 cp/mL for VERIS HIV-1 Assay versus COBAS HIV-1 Test and RealTime HIV-1 Assay, and <0.5 log10cp/mL versus VERSANT HIV-1 Assay. Analysis on 174 specimens tested with the 0.175mL volume VERIS HIV-1 Assay and COBAS HIV-1 Test showed average bias of 0.39 log10cp/mL. Patient monitoring results using VERIS HIV-1 Assay demonstrated similar viral load trends over time to all comparators. CONCLUSIONS The VERIS HIV-1 Assay for use on the DxN VERIS System demonstrated comparable clinical performance to COBAS® HIV-1 Test, RealTime HIV-1 Assay, and VERSANT HIV-1 Assay.
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Affiliation(s)
- Patrick Braun
- Laboratory Dr. Knechten, Medical Center for HIV and Hepatitis, Aachen, Germany
| | - Rafael Delgado
- Microbiology Department, Hospital Universitario 12 de Octubre and Insituto de Investigation, Hospital 12 de Octubre (i+12) Madrid, Spain
| | - Monica Drago
- Clinical Chemistry and Microbiology Laboratories, Niguarda Ca' Granda Hospital, Milan, Italy
| | - Diana Fanti
- Clinical Chemistry and Microbiology Laboratories, Niguarda Ca' Granda Hospital, Milan, Italy
| | - Hervé Fleury
- Virology Department, Hôpital Pellegrin, CHU, Bordeaux, France
| | - Jörg Hofmann
- Virology Department, Labor Berlin - Charité Vivantes GmbH, Berlin, Germany
| | - Jacques Izopet
- Department of Virology, Federative Institute of Biology, CHU, Toulouse, France
| | - Sebastian Kühn
- Virology Department, Labor Berlin - Charité Vivantes GmbH, Berlin, Germany
| | - Alessandra Lombardi
- Clinical Microbiology, Virology and Bioemergence Diagnosis, L. Sacco University Hospital, Milan, Italy
| | - Alessandro Mancon
- Clinical Microbiology, Virology and Bioemergence Diagnosis, L. Sacco University Hospital, Milan, Italy
| | - Mª Angeles Marcos
- Department of Clinical Microbiology, Hospital Clinic, School of Medicine, University of Barcelona, Centre for International Health Research (CRESIB), Barcelona, Spain
| | - Davide Mileto
- Virology Department, Labor Berlin - Charité Vivantes GmbH, Berlin, Germany
| | - Karine Sauné
- Department of Virology, Federative Institute of Biology, CHU, Toulouse, France
| | - Siobhan O'Shea
- Viapath Analytics, Infection Sciences, Guy's and St. Thomas' NHS Foundation Trust, London, United Kingdom
| | - Alfredo Pérez-Rivilla
- Microbiology Department, Hospital Universitario 12 de Octubre and Insituto de Investigation, Hospital 12 de Octubre (i+12) Madrid, Spain
| | - John Ramble
- Viapath Analytics, Infection Sciences, Guy's and St. Thomas' NHS Foundation Trust, London, United Kingdom
| | | | - Jordi Vila
- Department of Clinical Microbiology, Hospital Clinic, School of Medicine, University of Barcelona, Centre for International Health Research (CRESIB), Barcelona, Spain
| | - Duncan Whittaker
- Laboratory Medicine Building, North Lane, Northern General Hospital, Sheffield, United Kingdom
| | - Alain Artus
- Beckman Coulter, Immunotech, 130 Ave Lattre de Tassigny, Marseille 13009, France
| | - Daniel Rhodes
- Beckman Coulter, Immunotech, 130 Ave Lattre de Tassigny, Marseille 13009, France.
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European Multicenter Study on Analytical Performance of Veris HIV-1 Assay. J Clin Microbiol 2017; 55:2055-2063. [PMID: 28424254 DOI: 10.1128/jcm.00078-17] [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: 01/24/2017] [Accepted: 04/12/2017] [Indexed: 11/20/2022] Open
Abstract
The analytical performance of the Veris HIV-1 assay for use on the new, fully automated Beckman Coulter DxN Veris molecular diagnostics system was evaluated at 10 European virology laboratories. The precision, analytical sensitivity, performance with negative samples, linearity, and performance with HIV-1 groups/subtypes were evaluated. The precision for the 1-ml assay showed a standard deviation (SD) of 0.14 log10 copies/ml or less and a coefficient of variation (CV) of ≤6.1% for each level tested. The 0.175-ml assay showed an SD of 0.17 log10 copies/ml or less and a CV of ≤5.2% for each level tested. The analytical sensitivities determined by probit analysis were 19.3 copies/ml for the 1-ml assay and 126 copies/ml for the 0.175-ml assay. The performance with 1,357 negative samples demonstrated 99.2% with not detected results. Linearity using patient samples was shown from 1.54 to 6.93 log10 copies/ml. The assay performed well, detecting and showing linearity with all HIV-1 genotypes tested. The Veris HIV-1 assay demonstrated analytical performance comparable to that of currently marketed HIV-1 assays. (DxN Veris products are Conformité Européenne [CE]-marked in vitro diagnostic products. The DxN Veris product line has not been submitted to the U.S. FDA and is not available in the U.S. market. The DxN Veris molecular diagnostics system is also known as the Veris MDx molecular diagnostics system and the Veris MDx system.).
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Sauné K, Raymond S, Boineau J, Pasquier C, Izopet J. Detection and quantification of HIV-1 RNA with a fully automated transcription-mediated-amplification assay. J Clin Virol 2016; 84:70-73. [PMID: 27728849 DOI: 10.1016/j.jcv.2016.09.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 08/29/2016] [Accepted: 09/01/2016] [Indexed: 02/04/2023]
Abstract
BACKGROUND Nucleic acid testing is the major method used to monitor HIV viral load. Commercial systems based on real-time PCR assays are available for high-volume centralized laboratory testing, but they are not fully automated. OBJECTIVES AND STUDY DESIGN We have compared the diagnostic performance of the Hologic Aptima HIV-1 Quant Dx assay (Aptima) (based on real-time TMA) on the Panther instrument, a fully-automated random access platform, to that of, the Roche Cobas Ampliprep Cobas TaqMan (CAP/CTM) HIV-1 version 2.0 (based on real-time PCR). RESULTS Probit analysis of replicate dilutions of NIBSC WHO International HIV-1 Standard, gave LODs of 8.6 c/ml for Aptima and 15.2 c/ml for CAP/CTM. The agreement between the assays was excellent when measuring HIV RNA in a calibrated reference (κ=0.90, p<0.001) and good when measuring clinical samples (κ=0.62, p<0.001). The correlation among the samples quantified by the two methods was very good (r=0.95, p<0.001) and the mean difference between the values obtained with the two assays was 0.02 log c/ml for B and non-B subtypes. The vast majority of results showed <0.5 log variance between the two assays (89%); only one sample showed results that differed by over 1.0 log c/ml. CONCLUSION The performance of the new fully automated Aptima assay is adequate for clinical monitoring of HIV-1 RNA during infections and treatment. The Aptima assay is well suited for routine laboratory use.
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Affiliation(s)
- K Sauné
- INSERM, U1043, Centre de Physiopathologie de Toulouse Purpan, Toulouse, France; CHU Toulouse, Hôpital Purpan, Laboratoire de Virologie, Institut Fédératif de Biologie, Toulouse, France.
| | - S Raymond
- INSERM, U1043, Centre de Physiopathologie de Toulouse Purpan, Toulouse, France; CHU Toulouse, Hôpital Purpan, Laboratoire de Virologie, Institut Fédératif de Biologie, Toulouse, France
| | - J Boineau
- CHU Toulouse, Hôpital Purpan, Laboratoire de Virologie, Institut Fédératif de Biologie, Toulouse, France
| | - C Pasquier
- INSERM, U1043, Centre de Physiopathologie de Toulouse Purpan, Toulouse, France; CHU Toulouse, Hôpital Purpan, Laboratoire de Virologie, Institut Fédératif de Biologie, Toulouse, France
| | - J Izopet
- INSERM, U1043, Centre de Physiopathologie de Toulouse Purpan, Toulouse, France; CHU Toulouse, Hôpital Purpan, Laboratoire de Virologie, Institut Fédératif de Biologie, Toulouse, France
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Discordant CSF/plasma HIV-1 RNA in patients with unexplained low-level viraemia. J Neurovirol 2016; 22:852-860. [PMID: 27194435 PMCID: PMC5127885 DOI: 10.1007/s13365-016-0448-1] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Revised: 04/04/2016] [Accepted: 04/17/2016] [Indexed: 02/03/2023]
Abstract
The central nervous system has been proposed as a sanctuary site where HIV can escape antiretroviral control and develop drug resistance. HIV-1 RNA can be at higher levels in CSF than plasma, termed CSF/plasma discordance. We aimed to examine whether discordance in CSF is associated with low level viraemia (LLV) in blood. In this MRC-funded multicentre study, we prospectively recruited patients with LLV, defined as one or more episode of unexplained plasma HIV-1 RNA within 12 months, and undertook CSF examination. Separately, we prospectively collected CSF from patients undergoing lumbar puncture for a clinical indication. Patients with durable suppression of viraemia and no evidence of CNS infection were identified as controls from this group. Factors associated with CSF/plasma HIV-1 discordance overall were examined. One hundred fifty-three patients were recruited across 13 sites; 40 with LLV and 113 undergoing clinical lumbar puncture. Seven of the 40 (18 %) patients with LLV had CSF/plasma discordance, which was significantly more than 0/43 (0 %) with durable suppression in blood from the clinical group (p = 0.005). Resistance associated mutations were shown in six CSF samples from discordant patients with LLV (one had insufficient sample for testing), which affected antiretroviral therapy at sampling in five. Overall discordance was present in 20/153 (13 %) and was associated with nadir CD4 but not antiretroviral concentrations in plasma or CSF. CSF/plasma discordance is observed in patients with LLV and is associated with antiretroviral resistance associated mutations in CSF. The implications for clinical practice require further investigation.
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Nightingale S, Michael BD, Fisher M, Winston A, Nelson M, Taylor S, Ustianowski A, Ainsworth J, Gilson R, Haddow L, Ong E, Leen C, Minton J, Post F, Beloukas A, Borrow R, Pirmohamed M, Geretti AM, Khoo S, Solomon T. CSF/plasma HIV-1 RNA discordance even at low levels is associated with up-regulation of host inflammatory mediators in CSF. Cytokine 2016; 83:139-146. [PMID: 27131579 PMCID: PMC4889775 DOI: 10.1016/j.cyto.2016.04.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Revised: 04/04/2016] [Accepted: 04/05/2016] [Indexed: 12/20/2022]
Abstract
Discordant HIV in CSF is associated with raised inflammatory mediators in CSF. CSF mediators are raised with discordance both at high and low levels. Discordance on ultrasensitive testing can also be also associated with raised mediators.
Introduction HIV-1 RNA can be found at higher levels in cerebrospinal fluid (CSF) than in plasma, termed CSF/plasma discordance. The clinical significance of CSF/plasma discordance is not known and the degree of discordance considered important varies. We aimed to determine whether a panel of CSF cytokines, chemokines and associated mediators were raised in patients with CSF/plasma discordance at different levels. Methods A nested case-control study of 40 CSF samples from the PARTITION study. We used a cytometric bead array to measure CSF mediator concentrations in 19 discordant and 21 non-discordant samples matched for plasma HIV-1 RNA. Discordant samples were subdivided into ‘high discordance’ (>1log10) and ‘low discordance’ (0.5–1log10, or ultrasensitive discordance). CSF mediators significant in univariate analysis went forward to two-way unsupervised hierarchical clustering based on the patterns of relative mediator concentrations. Results In univariate analysis 19 of 21 CSF mediators were significantly higher in discordant than non-discordant samples. There were no significant differences between samples with high versus low discordance. The samples grouped into two clusters which corresponded to CSF/plasma discordance (p < 0.0001). In cluster one all mediators had relatively high abundance; this included 18 discordant samples and three non-discordant samples. In cluster two all mediators had relatively low abundance; this included 18 non-discordant samples and one non-discordant sample with ultrasensitive discordance only. Conclusions CSF/plasma discordance is associated with potentially damaging neuroinflammatory process. Patients with discordance at lower levels (ie. 0.5–1log10) should also be investigated as mediator profiles were similar to those with discordance >1log10. Sensitive testing may have a role to determine whether ultrasensitive discordance is present in those with low level CSF escape.
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Affiliation(s)
- Sam Nightingale
- Institute of Infection and Global Health, University of Liverpool, UK; Department of Molecular and Clinical Pharmacology, University of Liverpool, Liverpool, UK; Royal Liverpool and Broadgreen University Hospitals NHS Trust, UK.
| | - Benedict D Michael
- Institute of Infection and Global Health, University of Liverpool, UK; Walton Centre for Neurology and Neurosurgery, Liverpool, UK
| | - Martin Fisher
- Brighton and Sussex University Hospitals NHS Trust, UK
| | - Alan Winston
- St Marys' Hospital, Imperial College Heathcare NHS Trust, London, UK
| | - Mark Nelson
- St Stephen's AIDS Research Trust and Chelsea and Westminster Hospital NHS Foundation Trust, UK
| | - Steven Taylor
- Birmingham Heartlands Hospital, Heart of England NHS Foundation Trust, UK
| | - Andrew Ustianowski
- North Manchester General Hospital, Pennine Acute Hospitals NHS Trust, UK
| | | | - Richard Gilson
- Research Department of Infection and Population Health, University College London, UK
| | - Lewis Haddow
- Research Department of Infection and Population Health, University College London, UK
| | - Edmund Ong
- Victoria Royal Infirmary, Newcastle upon Tyne Hospitals NHS Trust, UK
| | | | - Jane Minton
- Leeds General Infirmary, Leeds Teaching Hosptials NHS Trust, UK
| | - Frank Post
- Kings College Hospital NHS Foundation Trust, London, UK
| | | | - Ray Borrow
- Vaccine Evaluation Unit at the Health Protection Agency (HPA) North West, Manchester, UK
| | - Munir Pirmohamed
- Department of Molecular and Clinical Pharmacology, University of Liverpool, Liverpool, UK
| | | | - Saye Khoo
- Department of Molecular and Clinical Pharmacology, University of Liverpool, Liverpool, UK
| | - Tom Solomon
- Institute of Infection and Global Health, University of Liverpool, UK; Walton Centre for Neurology and Neurosurgery, Liverpool, UK
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Amendola A, Pisciotta M, Aleo L, Ferraioli V, Angeletti C, Capobianchi MR. Evaluation of the Aptima(®) HIV-1 Quant Dx assay for HIV-1 RNA viral load detection and quantitation in plasma of HIV-1-infected individuals: A comparison with Abbott RealTime HIV-1 assay. J Med Virol 2016; 88:1535-44. [PMID: 26864171 PMCID: PMC6585778 DOI: 10.1002/jmv.24493] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/28/2016] [Indexed: 11/16/2022]
Abstract
The Hologic Aptima® HIV‐1 Quant Dx assay (Aptima HIV) is a real‐time transcription‐mediated amplification method CE‐approved for use in diagnosis and monitoring of HIV‐1 infection. The analytical performance of this new assay was compared to the FDA‐approved Abbott RealTime HIV‐1 (RealTime). The evaluation was performed using 220 clinical plasma samples, the WHO 3rd HIV‐1 International Standard, and the QCMD HIV‐1 RNA EQA. Concordance on qualitative results, correlation between quantitative results, accuracy, and reproducibility of viral load data were analyzed. The ability to measure HIV‐1 subtypes was assessed on the second WHO International Reference Preparation Panel for HIV‐1 Subtypes. With clinical samples, inter‐assay agreement for qualitative results was high (91.8%) with Cohen's kappa statistic equal to 0.836. For samples with quantitative results in both assays (n = 93), Lin's concordance correlation coefficient was 0.980 (P
< 0.0001) and mean differences of measurement, conducted according to Bland–Altman method, was low (0.115 log10 copies/ml). The Aptima HIV quantified the WHO 3rd HIV‐1 International Standard diluted from 2000 to 31 cp/ml (5,700–88 IU/ml) at expected values with excellent linearity (R2 > 0.970) and showed higher sensitivity compared to RealTime being able to detect HIV‐1 RNA in 10 out of 10 replicates containing down to 7 cp/ml (20 IU/ml). Reproducibility was very high, even at low HIV‐1 RNA values. The Aptima HIV was able to detect and accurately quantify all the main HIV‐1 subtypes in both reference panels and clinical samples. Besides excellent performance, Aptima HIV shows full automation, ease of use, and improved workflow compared to RealTime. J. Med. Virol. 88:1535–1544, 2016. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Alessandra Amendola
- Laboratory of VirologyNational Institute for Infectious Diseases “Lazzaro Spallanzani,”RomeItaly
| | - Maria Pisciotta
- Laboratory of VirologyNational Institute for Infectious Diseases “Lazzaro Spallanzani,”RomeItaly
| | - Loredana Aleo
- Laboratory of VirologyNational Institute for Infectious Diseases “Lazzaro Spallanzani,”RomeItaly
| | - Valeria Ferraioli
- Laboratory of VirologyNational Institute for Infectious Diseases “Lazzaro Spallanzani,”RomeItaly
| | - Claudio Angeletti
- Department of EpidemiologyNational Institute for Infectious Diseases “Lazzaro Spallanzani,”RomeItaly
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Mani M, Ramalingam VV, Lionel J, Christina SA, Sachithanandham J, Peedicayil A, Kannangai R. Emergence of HIV-1 drug-resistant variants in women following antiretroviral prophylaxis for the prevention of mother to child transmission. Indian J Med Microbiol 2015; 33:225-30. [PMID: 25865972 DOI: 10.4103/0255-0857.154860] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
PURPOSE Emergence of drug resistance following HIV prophylaxis has an important impact on ART program. OBJECTIVE To investigate the emergence of drug resistance in HIV-1 infected pregnant women. MATERIALS AND METHODS Fifty-three HIV-1 infected pregnant women who had received 4-12 weeks of antenatal AZT followed by Nevirapine during delivery and Combivir [AZT + 3TC] for 1 week postpartum (group-1, n = 48) or who come at the time of delivery and received Nevirapine followed by Combivir for 1 week (group-2, n = 5) were recruited. Samples were collected prior to the start of the prophylaxis and 5-8 weeks postpartum. In addition, a third sample was collected between 26-65 weeks postpartum from 7 women. Amplification of HIV-1 pol gene and drug resistance analysis was done. RESULT Two (3.8%) women in group-1 showed transmitted drug resistance and they continued to show this even at 6 weeks postpartum. One (2%) woman from group-1 showed a mutation after 6-8 weeks of prophylaxis. Among the samples collected between 26-65 weeks postpartum, 3/7 (43%) showed mutations and all these women belong to group-1. Women belonging to group-2 didn't show mutation prior to or following prophylaxis. CONCLUSION In contrast to the available data among pregnant women with ART prophylaxis, our data showed reduced frequency of mutations following 5-8 weeks of postpartum but an emergence of mutation later (26-65 weeks). The addition of Combivir with the single dose Nevirapine during delivery and the early stage of the disease with higher CD4 counts could be the reasons for this.
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Affiliation(s)
| | | | | | | | | | | | - R Kannangai
- Department of Clinical Virology, Christian Medical College, Vellore, Tamil Nadu, India
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Hopkins M, Hau S, Tiernan C, Papadimitropoulos A, Chawla A, Beloukas A, Geretti AM. Comparative performance of the new Aptima HIV-1 Quant Dx assay with three commercial PCR-based HIV-1 RNA quantitation assays. J Clin Virol 2015. [PMID: 26209380 DOI: 10.1016/j.jcv.2015.05.020] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
BACKGROUND Quantitative measurement of HIV-1 RNA levels in plasma ('viral load') plays a central role in clinical management. The choice of assay platform can influence results and treatment decisions. OBJECTIVE To compare the analytical performance of the new TMA-based Hologic Aptima(®) HIV-1 Quant Dx assay with that of three PCR-based assays: Abbott RealTime HIV-1, Qiagen Artus(®) HI Virus-1 QS-RGQ, and Roche CAP/CTM HIV-1 Test v2. STUDY DESIGN Assay performance was evaluated using Acrometrix HIV-1 RNA Standard panels; the 3rd WHO HIV-1 RNA International Standard (12-500 copies/ml; 6 dilutions; 9 replicates); and plasma samples from 191 HIV-positive patients. RESULTS Aptima showed high (>0.99) precision, accuracy and concordance with the Acrometrix Standards across a wide dynamic range (2.0-6.7 log10copies/ml). Variance caused up to 2.1 (Aptima), 1.7 (RealTime), 7.5 (Artus), and 1.9 (CAP/CTM) fold changes in the International Standard quantifications at 50-500 copies/ml. HIV-1 RNA detection rates in plasma samples were 141/191 (74%), 119/191 (62%), 108/191 (57%), and 145/191 (76%) for Aptima, RealTime, Artus and CAP/CTM, respectively. For categorising samples either side of 50 copies/ml, Aptima had excellent agreement with RealTime (kappa 0.92; 95% CI 0.87-0.98); lowest agreement was with Artus (kappa 0.79; 95%CI 0.70-0.88). Aptima quantifications were mean 0.12 and 0.06 log10copies/ml higher compared with RealTime and CAP/CTM, respectively, and 0.05 log10copies/ml lower compared with Artus. Limits of agreement were narrowest when comparing Aptima to RealTime. CONCLUSIONS The new Aptima HIV assay is sensitive, precise, and accurate. HIV assays exhibit discordance at low HIV-1 RNA copy numbers.
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Affiliation(s)
- Mark Hopkins
- Liverpool Clinical Laboratories, Liverpool, United Kingdom.
| | - Sarah Hau
- Liverpool Clinical Laboratories, Liverpool, United Kingdom
| | | | | | - Anu Chawla
- Liverpool Clinical Laboratories, Liverpool, United Kingdom
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Amendola A, Marsella P, Bloisi M, Forbici F, Angeletti C, Capobianchi MR. Ability of two commercially available assays (Abbott RealTime HIV-1 and Roche Cobas AmpliPrep/Cobas TaqMan HIV-1 Version 2.0) to quantify low HIV-1 RNA Levels (<1,000 copies/milliliter): comparison with clinical samples and NIBSC working reagent for nucleic acid testing assays. J Clin Microbiol 2014; 52:2019-26. [PMID: 24671791 PMCID: PMC4042785 DOI: 10.1128/jcm.00288-14] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Accepted: 03/21/2014] [Indexed: 11/20/2022] Open
Abstract
Concordance between molecular assays may be suboptimal at low HIV-1 viremia levels (<1,000 copies/ml); therefore, it may be difficult to define and compare virologic endpoints for successful and failed therapy. We compared two commercial assays (the Abbott RealTime HIV-1 and the Roche Cobas AmpliPrep/TaqMan HIV-1 version 2.0) for their ability to detect and quantify low viral loads. A comparison was performed using 167 residual clinical samples (with values ranging from "not detected" to 1,000 copies/ml, as measured by the Abbott assay) and the National Institute and Biological Standards and Control (NIBSC) HIV-1 RNA working reagent 1 for nucleic acid amplification techniques (NAT) assays (serially diluted to a range from 1 to 1,000 copies/ml). Quantitative results were compared using Lin's concordance correlation coefficient and a Bland-Altman plot. Concordance with the qualitative results was measured by Cohen's kappa statistic. With clinical samples, the degree of interassay concordance of the qualitative results at a 40-copies/ml HIV-1 RNA threshold was substantial (κ = 0.762); the correlation among the quantified samples was suboptimal (concordance correlation coefficient, 0.728; P < 0.0001); the mean difference of the values between the Roche and Abbott assays was 0.193 log10 copies/ml. Using the HIV-1 RNA working reagent 1 for NAT assays, the results provided by the Roche assay were, on average, 3 times higher than expected, while the Abbott assay showed high accuracy. The Roche assay was highly sensitive, being able to detect a level as low as 3.5 copies/ml HIV-1 RNA with 95% probability. The performance characteristics of each molecular assay should be taken into account when HIV-1 RNA threshold values for "virologic suppression," "virologic failure," "persistent low viral loads," etc., are defined and indicated in the support of clinical decisions.
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Affiliation(s)
| | - Patrizia Marsella
- National Institute for Infectious Diseases Lazzaro Spallanzani, Rome, Italy
| | - Maria Bloisi
- National Institute for Infectious Diseases Lazzaro Spallanzani, Rome, Italy
| | - Federica Forbici
- National Institute for Infectious Diseases Lazzaro Spallanzani, Rome, Italy
| | - Claudio Angeletti
- National Institute for Infectious Diseases Lazzaro Spallanzani, Rome, Italy
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14
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Abstract
Nuclear acid testing is more and more used for the diagnosis of infectious diseases. This paper focuses on the use of molecular tools for HIV screening. The term 'screening' will be used under the meaning of first-line HIV molecular techniques performed on a routine basis, which excludes HIV molecular tests designed to confirm or infirm a newly discovered HIV-seropositive patient or other molecular tests performed for the follow-up of HIV-infected patients. The following items are developed successively: i) presentation of the variety of molecular tools used for molecular HIV screening, ii) use of HIV molecular tools for the screening of blood products, iii) use of HIV molecular tools for the screening of organs and tissue from human origin, iv) use of HIV molecular tools in medically assisted procreation and v) use of HIV molecular tools in neonates from HIV-infected mothers.
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Affiliation(s)
- Thomas Bourlet
- Groupe Immunité des Muqueuses et Agents Pathogènes (GIMAP) - EA3064, Faculty of Medicine of Saint-Etienne, 42023, University of Lyon, France
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15
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Swenson LC, Cobb B, Geretti AM, Harrigan PR, Poljak M, Seguin-Devaux C, Verhofstede C, Wirden M, Amendola A, Boni J, Bourlet T, Huder JB, Karasi JC, Zidovec Lepej S, Lunar MM, Mukabayire O, Schuurman R, Tomažič J, Van Laethem K, Vandekerckhove L, Wensing AMJ. Comparative performances of HIV-1 RNA load assays at low viral load levels: results of an international collaboration. J Clin Microbiol 2014; 52:517-23. [PMID: 24478482 PMCID: PMC3911321 DOI: 10.1128/jcm.02461-13] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Accepted: 11/26/2013] [Indexed: 11/20/2022] Open
Abstract
Low-level viremia during antiretroviral therapy and its accurate measurement are increasingly relevant. Here, we present an international collaboration of 4,221 paired blood plasma viral load (pVL) results from four commercial assays, emphasizing the data with low pVL. The assays compared were the Abbott RealTime assay, the Roche Amplicor assay, and the Roche TaqMan version 1 and version 2 assays. The correlation between the assays was 0.90 to 0.97. However, at a low pVL, the correlation fell to 0.45 to 0.85. The observed interassay concordance was higher when detectability was defined as 200 copies/ml than when it was defined as 50 copies/ml. A pVL of ∼100 to 125 copies/ml by the TaqMan version 1 and version 2 assays corresponded best to a 50-copies/ml threshold with the Amplicor assay. Correlation and concordance between the viral load assays were lower at a low pVL. Clear guidelines are needed on the clinical significance of low-level viremia.
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Affiliation(s)
- Luke C. Swenson
- BC Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Bryan Cobb
- Roche Molecular Systems, Pleasanton, California, USA
| | - Anna Maria Geretti
- Institute of Infection and Global Health, University of Liverpool, United Kingdom
| | | | - Mario Poljak
- University of Ljubljana, Institute of Microbiology and Immunology, Ljubljana, Slovenia
| | | | | | - Marc Wirden
- AP-HP, Pitié-Salpêtrière Hospital, INSERM U 943, and Pierre et Marie Curie University Paris, Paris, France
| | - Alessandra Amendola
- Laboratory of Virology, National Institute for Infectious Diseases Lazzaro Spallanzani, Rome, Italy
| | - Jurg Boni
- Institute of Medical Virology, Swiss National Center for Retroviruses, University of Zurich, Zurich, Switzerland
| | - Thomas Bourlet
- Laboratory of Virology, CHU de Saint-Etienne, Saint-Etienne, France
| | - Jon B. Huder
- Institute of Medical Virology, Swiss National Center for Retroviruses, University of Zurich, Zurich, Switzerland
| | | | | | - Maja M. Lunar
- University of Ljubljana, Institute of Microbiology and Immunology, Ljubljana, Slovenia
| | | | - Rob Schuurman
- University Medical Center Utrecht, Utrecht, Netherlands
| | - Janez Tomažič
- University of Ljubljana, Institute of Microbiology and Immunology, Ljubljana, Slovenia
| | - Kristel Van Laethem
- Clinical and Epidemiological Virology, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
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Garcia-Diaz A, Guerrero-Ramos A, McCormick A, Macartney M, Conibear T, Johnson M, Haque T, Webster D. Evaluation of the Roche prototype 454 HIV-1 ultradeep sequencing drug resistance assay in a routine diagnostic laboratory. J Clin Virol 2013; 58:468-73. [DOI: 10.1016/j.jcv.2013.07.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Revised: 07/10/2013] [Accepted: 07/12/2013] [Indexed: 11/28/2022]
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