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Vojnov L, Carmona S, Zeh C, Markby J, Boeras D, Prescott MR, Mayne ALH, Sawadogo S, Adje-Toure C, Zhang G, Perez Gonzalez M, Stevens WS, Doherty M, Yang C, Alexander H, Peter TF, Nkengasong J. The performance of using dried blood spot specimens for HIV-1 viral load testing: A systematic review and meta-analysis. PLoS Med 2022; 19:e1004076. [PMID: 35994520 PMCID: PMC9447868 DOI: 10.1371/journal.pmed.1004076] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 09/06/2022] [Accepted: 07/13/2022] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Accurate routine HIV viral load testing is essential for assessing the efficacy of antiretroviral treatment (ART) regimens and the emergence of drug resistance. While the use of plasma specimens is the standard for viral load testing, its use is restricted by the limited ambient temperature stability of viral load biomarkers in whole blood and plasma during storage and transportation and the limited cold chain available between many health care facilities in resource-limited settings. Alternative specimen types and technologies, such as dried blood spots, may address these issues and increase access to viral load testing; however, their technical performance is unclear. To address this, we conducted a meta-analysis comparing viral load results from paired dried blood spot and plasma specimens analyzed with commonly used viral load testing technologies. METHODS AND FINDINGS Standard databases, conferences, and gray literature were searched in 2013 and 2018. Nearly all studies identified (60) were conducted between 2007 and 2018. Data from 40 of the 60 studies were included in the meta-analysis, which accounted for a total of 10,871 paired dried blood spot:plasma data points. We used random effects models to determine the bias, accuracy, precision, and misclassification for each viral load technology and to account for between-study variation. Dried blood spot specimens produced consistently higher mean viral loads across all technologies when compared to plasma specimens. However, when used to identify treatment failure, each technology compared best to plasma at a threshold of 1,000 copies/ml, the present World Health Organization recommended treatment failure threshold. Some heterogeneity existed between technologies; however, 5 technologies had a sensitivity greater than 95%. Furthermore, 5 technologies had a specificity greater than 85% yet 2 technologies had a specificity less than 60% using a treatment failure threshold of 1,000 copies/ml. The study's main limitation was the direct applicability of findings as nearly all studies to date used dried blood spot samples prepared in laboratories using precision pipetting that resulted in consistent input volumes. CONCLUSIONS This analysis provides evidence to support the implementation and scale-up of dried blood spot specimens for viral load testing using the same 1,000 copies/ml treatment failure threshold as used with plasma specimens. This may support improved access to viral load testing in resource-limited settings lacking the required infrastructure and cold chain storage for testing with plasma specimens.
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Affiliation(s)
- Lara Vojnov
- Clinton Health Access Initiative, Boston, Massachusetts, United States of America
- * E-mail:
| | - Sergio Carmona
- National Health Laboratory Service, Johannesburg, South Africa
| | - Clement Zeh
- Center for Global Health, Division of Global HIV/TB, US Centers for Disease Control, Atlanta, Georgia, United States of America
| | | | - Debrah Boeras
- Center for Global Health, Division of Global HIV/TB, US Centers for Disease Control, Atlanta, Georgia, United States of America
| | - Marta R. Prescott
- Clinton Health Access Initiative, Boston, Massachusetts, United States of America
| | | | - Souleymane Sawadogo
- Center for Global Health, Division of Global HIV/TB, US Centers for Disease Control, Windhoek, Namibia
| | - Christiane Adje-Toure
- Center for Global Health, Division of Global HIV/TB, US Centers for Disease Control, Abidjan, Cote d’Ivoire
| | - Guoqing Zhang
- Center for Global Health, Division of Global HIV/TB, US Centers for Disease Control, Atlanta, Georgia, United States of America
| | | | - Wendy S. Stevens
- National Health Laboratory Service, Johannesburg, South Africa
- Department of Molecular Medicine and Haematology, University of the Witwatersrand, Johannesburg, South Africa
| | - Meg Doherty
- World Health Organization, Geneva, Switzerland
| | - Chunfu Yang
- Center for Global Health, Division of Global HIV/TB, US Centers for Disease Control, Atlanta, Georgia, United States of America
| | - Heather Alexander
- Center for Global Health, Division of Global HIV/TB, US Centers for Disease Control, Atlanta, Georgia, United States of America
| | - Trevor F. Peter
- Clinton Health Access Initiative, Boston, Massachusetts, United States of America
| | - John Nkengasong
- Center for Global Health, Division of Global HIV/TB, US Centers for Disease Control, Atlanta, Georgia, United States of America
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HIV-1 pretreatment drug resistance negatively impacts outcomes of first-line antiretroviral treatment. AIDS 2022; 36:923-931. [PMID: 35113046 DOI: 10.1097/qad.0000000000003182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
INTRODUCTION Pretreatment drug resistance (PDR) prevalence in sub-Saharan Africa is rising, but evidence of its impact on efavirenz (EFV)-based antiretroviral treatment (ART) is inconclusive. We determined the impact of PDR on outcomes of EFV-based ART in a subanalysis of a randomized clinical trial comparing different ART monitoring strategies implemented at a rural treatment facility in Limpopo, South Africa. METHODS Participants initiating EFV-based first-line ART (2015-2017) were enrolled and received 96 weeks follow-up. Resistance to nucleos(t)ide reverse transcriptase inhibitors (NRTIs) and non-NRTI's (NNRTIs) was retrospectively assessed by population-based sequencing. Virological failure was defined as a viral load of at least 1000 copies/ml after at least 24 weeks of ART. RESULTS A total of 207 participants were included, 60.4% (125/207) of whom were female. Median age was 38.8 (interquartile range: 31.4-46.7) years. Median CD4+ cell count was 191 (interquartile range: 70-355) cells/μl. PDR was detected in 12.9% (25/194) of participants with available sequencing results; 19 had NNRTI-resistance, and six had NRTI- and NNRTI-resistance. 26.0% of participants (40/154) with sequencing results and virological follow-up developed virological failure. PDR was independently associated with failure (adjusted hazard ratio: 3.7 [95% confidence interval: 1.68.5], P = 0.002). At failure, 87.5% (7/8) of participants with PDR harboured dual-class resistant virus, versus 16.7% (4/24) of participants without PDR (P = 0.0007). Virological resuppression after failure on first-line ART occurred in 57.7% (15/26) of participants without PDR versus 14.3% (1/7) of participants with PDR (P = 0.09). CONCLUSION PDR was detected in 13% of study participants. PDR significantly increased the risk of virological failure of EFV-based ART. Accumulation of resistance at failure and inability to achieve virological resuppression illustrates the profound impact of PDR on treatment outcomes.
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Development of C-TILDA: A modified TILDA method for reservoir quantification in long term treated patients infected with subtype C HIV-1. J Virol Methods 2019; 276:113778. [PMID: 31756409 DOI: 10.1016/j.jviromet.2019.113778] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 11/11/2019] [Accepted: 11/18/2019] [Indexed: 12/30/2022]
Abstract
A better characterization of the HIV reservoir is pivotal for the development of effective eradication strategies. Accurate quantification of the latent reservoir remains challenging. Starting from a regular blood draw, the Tat/Rev induced limiting dilution assay (TILDA) combines serial dilution of CD4+ T cells with a PCR-based detection of HIV-1 spliced mRNA produced upon cell stimulation. Here we adapted the original protocol for HIV-1 subtype B to detect tat/rev mRNAs transcribed from reactivated latently infected cells in long term suppressed patients infected with HIV-1 subtype C. Given the heterogeneity of global HIV epidemiology, it is pivotal to develop assays with optimal performances also in patients infected with non-B subtypes. We observed that, in these patients infected with subtype C virus, the HIV reservoir quantified by TILDA correlates with both the time of virological suppression and CD4/CD8 ratio.
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Bosman KJ, Wensing AMJ, Pijning AE, van Snippenberg WJ, van Ham PM, de Jong DMC, Hoepelman AIM, Nijhuis M. Development of sensitive ddPCR assays to reliably quantify the proviral DNA reservoir in all common circulating HIV subtypes and recombinant forms. J Int AIDS Soc 2018; 21:e25185. [PMID: 30375818 PMCID: PMC6138437 DOI: 10.1002/jia2.25185] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 08/17/2018] [Indexed: 12/21/2022] Open
Abstract
INTRODUCTION The latent reservoir is the main barrier on the road to HIV cure, and clinical approaches towards eradication are often evaluated by their effect on proviral DNA. To ensure inclusiveness and representativeness in HIV cure studies, proviral DNA quantification assays that are able to detect all common circulating HIV clades are urgently needed. Here, three HIV DNA assays targeting three different genomic regions were evaluated for their sensitivity and subtype-tolerance using digital PCR. METHODS A subtype-B-specific assay targeting gag (GAG) and two assays targeting conserved sequences in ltr and pol (LTR and JO) were assessed for their sensitivity and subtype-tolerance in digital PCR (Bio-Rad QX200), using a panel of serially diluted subtype reference plasmids as well as a panel of clinical isolates. Both panels represent subtypes A, B, C, D, F, G and circulating recombinant forms (CRFs) AE and AG, which together are responsible for 94% of HIV infections worldwide. RESULTS HIV subtype was observed to greatly affect HIV DNA quantification results. Robust regression analysis of the serially diluted plasmid panel showed that the GAG assay was only able to linearly quantify subtype B, D and G isolates (4/13 reference plasmids, average R2 = 0.99), whereas LTR and JO were able to quantify all tested isolates (13/13 reference plasmids, respective average R2 = 0.99 and 0.98). In the clinical isolates panel, isolates were considered detectable if all replicates produced a positive result. The GAG assay could detect HIV DNA in four out of five subtype B and one out of two subtype D isolates, whereas the LTR and JO assays detected HIV DNA in all twenty-nine tested isolates. LTR and JO results were found to be equally precise but more precise than GAG. CONCLUSIONS The results demonstrate the need for a careful validation of proviral reservoir quantification assays prior to investigations into non-B subtype reservoirs. The LTR and JO assays can sensitively and reliably quantify HIV DNA in a panel that represents the worldwide most prevalent subtypes and CRFs (A, B, C, D, AE, F, G and AG), justifying their application in future trials aimed at global HIV cure.
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Affiliation(s)
- Kobus J Bosman
- Department of Medical MicrobiologyUniversity Medical Center UtrechtUtrechtthe Netherlands
| | - Annemarie MJ Wensing
- Department of Medical MicrobiologyUniversity Medical Center UtrechtUtrechtthe Netherlands
| | - Aster E Pijning
- Department of Medical MicrobiologyUniversity Medical Center UtrechtUtrechtthe Netherlands
| | | | - Petra M van Ham
- Department of Medical MicrobiologyUniversity Medical Center UtrechtUtrechtthe Netherlands
| | - Dorien MC de Jong
- Department of Medical MicrobiologyUniversity Medical Center UtrechtUtrechtthe Netherlands
| | - Andy IM Hoepelman
- Department of Internal Medicine and Infectious DiseasesUniversity Medical Center UtrechtUtrechtthe Netherlands
| | - Monique Nijhuis
- Department of Medical MicrobiologyUniversity Medical Center UtrechtUtrechtthe Netherlands
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Guichet E, Aghokeng A, Eymard-Duvernay S, Vidal N, Ayouba A, Mpoudi Ngole E, Delaporte E, Ciaffi L, Peeters M. Field evaluation of an open and polyvalent universal HIV-1/SIVcpz/SIVgor quantitative RT-PCR assay for HIV-1 viral load monitoring in comparison to Abbott RealTime HIV-1 in Cameroon. J Virol Methods 2016; 237:121-126. [PMID: 27609535 DOI: 10.1016/j.jviromet.2016.09.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 09/03/2016] [Accepted: 09/04/2016] [Indexed: 11/19/2022]
Abstract
With the increasing demand of HIV viral load (VL) tests in resource-limited countries (RLCs) there is a need for assays at affordable cost and able to quantify all known HIV-1 variants. VLs obtained with a recently developed open and polyvalent universal HIV-1/SIVcpz/SIVgor RT-qPCR were compared to Abbott RealTime HIV-1 assay in Cameroon. On 474 plasma samples, characterized by a wide range of VLs and a broad HIV-1 group M genetic diversity, 97.5% concordance was observed when using the lower detection limit of each assay. When using the threshold of 3.00 log10 copies/mL, according to WHO guidelines to define virological failure (VF) in RLCs, the concordance was 94.7%, 360/474 versus 339/474 patients were identified with VF with the new assay and Abbott RealTime HIV-1, respectively. Higher VLs were measured with the new assay, +0.47 log10 copies/mL (95% CI; 0.42-0.52) as shown with Bland-Altman analysis. Eleven samples from patients on VF with drug resistance were not detected by Abbott RealTime HIV-1 versus two only with the new assay. Overall, our study showed that the new assay can be easily implemented in a laboratory in RLCs with VL experience and showed good performance on a wide diversity of HIV-1 group M variants.
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Affiliation(s)
- Emilande Guichet
- UMI233-TransVIHMI, Institut de Recherche pour le Développement (IRD), INSERM U1175, University of Montpellier, Montpellier, France
| | - Avelin Aghokeng
- UMI233-TransVIHMI, Institut de Recherche pour le Développement (IRD), INSERM U1175, University of Montpellier, Montpellier, France; Centre de Recherche sur les Maladies Emergentes et Réémergentes (CREMER), Virology laboratory IMPM-IRD, Yaoundé, Cameroon
| | - Sabrina Eymard-Duvernay
- UMI233-TransVIHMI, Institut de Recherche pour le Développement (IRD), INSERM U1175, University of Montpellier, Montpellier, France
| | - Nicole Vidal
- UMI233-TransVIHMI, Institut de Recherche pour le Développement (IRD), INSERM U1175, University of Montpellier, Montpellier, France
| | - Ahidjo Ayouba
- UMI233-TransVIHMI, Institut de Recherche pour le Développement (IRD), INSERM U1175, University of Montpellier, Montpellier, France
| | - Eitel Mpoudi Ngole
- Centre de Recherche sur les Maladies Emergentes et Réémergentes (CREMER), Virology laboratory IMPM-IRD, Yaoundé, Cameroon
| | - Eric Delaporte
- UMI233-TransVIHMI, Institut de Recherche pour le Développement (IRD), INSERM U1175, University of Montpellier, Montpellier, France
| | - Laura Ciaffi
- UMI233-TransVIHMI, Institut de Recherche pour le Développement (IRD), INSERM U1175, University of Montpellier, Montpellier, France
| | - Martine Peeters
- UMI233-TransVIHMI, Institut de Recherche pour le Développement (IRD), INSERM U1175, University of Montpellier, Montpellier, France.
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Clinical Evaluation of an Affordable Qualitative Viral Failure Assay for HIV Using Dried Blood Spots in Uganda. PLoS One 2016; 11:e0145110. [PMID: 26824465 PMCID: PMC4732948 DOI: 10.1371/journal.pone.0145110] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Accepted: 11/28/2015] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND WHO recommends regular viral load (VL) monitoring of patients on antiretroviral therapy (ART) for timely detection of virological failure, prevention of acquired HIV drug resistance (HIVDR) and avoiding unnecessary switching to second-line ART. However, the cost and complexity of routine VL testing remains prohibitive in most resource limited settings (RLS). We evaluated a simple, low-cost, qualitative viral-failure assay (VFA) on dried blood spots (DBS) in three clinical settings in Uganda. METHODS We conducted a cross-sectional diagnostic accuracy study in three HIV/AIDS treatment centres at the Joint Clinical Research Centre in Uganda. The VFA employs semi-quantitative detection of HIV-1 RNA amplified from the LTR gene. We used paired dry blood spot (DBS) and plasma with the COBASAmpliPrep/COBASTaqMan, Roche version 2 (VLref) as the reference assay. We used the VFA at two thresholds of viral load, (>5,000 or >1,000 copies/ml). RESULTS 496 paired VFA and VLref results were available for comparative analysis. Overall, VFA demonstrated 78.4% sensitivity, (95% CI: 69.7%-87.1%), 93% specificity (95% CI: 89.7%-96.4%), 89.3% accuracy (95% CI: 85%-92%) and an agreement kappa = 0.72 as compared to the VLref. The predictive values of positivity and negativity among patients on ART for >12 months were 72.7% and 99.3%, respectively. CONCLUSIONS VFA allowed 89% of correct classification of VF. Only 11% of the patients were misclassified with the potential of unnecessary or late switch to second-line ART. Our findings present an opportunity to roll out simple and affordable VL monitoring for HIV-1 treatment in RLS.
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Wu L, Sun W, Wang B, Zhao H, Li Y, Cai S, Xiang L, Zhu Y, Yao H, Song J, Cheng YC, Chen S. An integrated system for identifying the hidden assassins in traditional medicines containing aristolochic acids. Sci Rep 2015; 5:11318. [PMID: 26270958 PMCID: PMC4535178 DOI: 10.1038/srep11318] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Accepted: 04/24/2015] [Indexed: 01/08/2023] Open
Abstract
Traditional herbal medicines adulterated and contaminated with plant materials from the Aristolochiaceae family, which contain aristolochic acids (AAs), cause aristolochic acid nephropathy. Approximately 256 traditional Chinese patent medicines, containing Aristolochiaceous materials, are still being sold in Chinese markets today. In order to protect consumers from health risks due to AAs, the hidden assassins, efficient methods to differentiate Aristolochiaceous herbs from their putative substitutes need to be established. In this study, 158 Aristolochiaceous samples representing 46 species and four genera as well as 131 non-Aristolochiaceous samples representing 33 species, 20 genera and 12 families were analyzed using DNA barcodes based on the ITS2 and psbA-trnH sequences. Aristolochiaceous materials and their non-Aristolochiaceous substitutes were successfully identified using BLAST1, the nearest distance method and the neighbor-joining (NJ) tree. In addition, based on sequence information of ITS2, we developed a Real-Time PCR assay which successfully identified herbal material from the Aristolochiaceae family. Using Ultra High Performance Liquid Chromatography-Mass Spectrometer (UHPLC-HR-MS), we demonstrated that most representatives from the Aristolochiaceae family contain toxic AAs. Therefore, integrated DNA barcodes, Real-Time PCR assays using TaqMan probes and UHPLC-HR-MS system provides an efficient and reliable authentication system to protect consumers from health risks due to the hidden assassins (AAs).
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Affiliation(s)
- Lan Wu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China
| | - Wei Sun
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Bo Wang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Haiyu Zhao
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yaoli Li
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University Health Science Centre, Beijing, China
| | - Shaoqing Cai
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University Health Science Centre, Beijing, China
| | - Li Xiang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yingjie Zhu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Hui Yao
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Jingyuan Song
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Yung-Chi Cheng
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Shilin Chen
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
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HIV diversity and drug resistance from plasma and non-plasma analytes in a large treatment programme in western Kenya. J Int AIDS Soc 2014; 17:19262. [PMID: 25413893 PMCID: PMC4238965 DOI: 10.7448/ias.17.1.19262] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Revised: 09/23/2014] [Accepted: 10/10/2014] [Indexed: 12/13/2022] Open
Abstract
INTRODUCTION Antiretroviral resistance leads to treatment failure and resistance transmission. Resistance data in western Kenya are limited. Collection of non-plasma analytes may provide additional resistance information. METHODS We assessed HIV diversity using the REGA tool, transmitted resistance by the WHO mutation list and acquired resistance upon first-line failure by the IAS-USA mutation list, at the Academic Model Providing Access to Healthcare (AMPATH), a major treatment programme in western Kenya. Plasma and four non-plasma analytes, dried blood-spots (DBS), dried plasma-spots (DPS), ViveST(TM)-plasma (STP) and ViveST-blood (STB), were compared to identify diversity and evaluate sequence concordance. RESULTS Among 122 patients, 62 were treatment-naïve and 60 treatment-experienced; 61% were female, median age 35 years, median CD4 182 cells/µL, median viral-load 4.6 log10 copies/mL. One hundred and ninety-six sequences were available for 107/122 (88%) patients, 58/62 (94%) treatment-naïve and 49/60 (82%) treated; 100/122 (82%) plasma, 37/78 (47%) attempted DBS, 16/45 (36%) attempted DPS, 14/44 (32%) attempted STP from fresh plasma and 23/34 (68%) from frozen plasma, and 5/42 (12%) attempted STB. Plasma and DBS genotyping success increased at higher VL and shorter shipment-to-genotyping time. Main subtypes were A (62%), D (15%) and C (6%). Transmitted resistance was found in 1.8% of plasma sequences, and 7% combining analytes. Plasma resistance mutations were identified in 91% of treated patients, 76% NRTI, 91% NNRTI; 76% dual-class; 60% with intermediate-high predicted resistance to future treatment options; with novel mutation co-occurrence patterns. Nearly 88% of plasma mutations were identified in DBS, 89% in DPS and 94% in STP. Of 23 discordant mutations, 92% in plasma and 60% in non-plasma analytes were mixtures. Mean whole-sequence discordance from frozen plasma reference was 1.1% for plasma-DBS, 1.2% plasma-DPS, 2.0% plasma-STP and 2.3% plasma-STB. Of 23 plasma-STP discordances, one mutation was identified in plasma and 22 in STP (p<0.05). Discordance was inversely significantly related to VL for DBS. CONCLUSIONS In a large treatment programme in western Kenya, we report high HIV-1 subtype diversity; low plasma transmitted resistance, increasing when multiple analytes were combined; and high-acquired resistance with unique mutation patterns. Resistance surveillance may be augmented by using non-plasma analytes for lower-cost genotyping in resource-limited settings.
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Newman H, Breunig L, van Zyl G, Stich A, Preiser W. A qualitative PCR minipool strategy to screen for virologic failure and antiretroviral drug resistance in South African patients on first-line antiretroviral therapy. J Clin Virol 2014; 60:387-91. [DOI: 10.1016/j.jcv.2014.05.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Revised: 05/15/2014] [Accepted: 05/20/2014] [Indexed: 01/11/2023]
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Ondoa P, Shamu T, Bronze M, Wellington M, Boender TS, Manting C, Steegen K, Luethy R, Rinke de Wit T. Performance and logistical challenges of alternative HIV-1 virological monitoring options in a clinical setting of Harare, Zimbabwe. BIOMED RESEARCH INTERNATIONAL 2014; 2014:102598. [PMID: 25025031 PMCID: PMC4082876 DOI: 10.1155/2014/102598] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Revised: 04/25/2014] [Accepted: 05/18/2014] [Indexed: 11/29/2022]
Abstract
We evaluated a low-cost virological failure assay (VFA) on plasma and dried blood spot (DBS) specimens from HIV-1 infected patients attending an HIV clinic in Harare. The results were compared to the performance of the ultrasensitive heat-denatured p24 assay (p24). The COBAS AmpliPrep/COBAS TaqMan HIV-1 test, version 2.0, served as the gold standard. Using a cutoff of 5,000 copies/mL, the plasma VFA had a sensitivity of 94.5% and specificity of 92.7% and was largely superior to the VFA on DBS (sensitivity = 61.9%; specificity = 99.0%) or to the p24 (sensitivity = 54.3%; specificity = 82.3%) when tested on 302 HIV treated and untreated patients. However, among the 202 long-term ART-exposed patients, the sensitivity of the VFA decreased to 72.7% and to 35.7% using a threshold of 5,000 and 1,000 RNA copies/mL, respectively. We show that the VFA (either on plasma or on DBS) and the p24 are not reliable to monitor long-term treated, HIV-1 infected patients. Moreover, achieving acceptable assay sensitivity using DBS proved technically difficult in a less-experienced laboratory. Importantly, the high level of virological suppression (93%) indicated that quality care focused on treatment adherence limits virological failure even when PCR-based viral load monitoring is not available.
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Affiliation(s)
- Pascale Ondoa
- Amsterdam Institute for Global Health and Development (AIGHD), Department of Global Health, Academic Medical Center, P.O. Box 22700, 1100 DE Amsterdam, The Netherlands
| | - Tinei Shamu
- Newlands Clinic, 56 Enterprise Road, Newlands, Harare, Zimbabwe
| | - Michelle Bronze
- Department of Molecular Medicine and Haematology, University of the Witwatersrand 7 York Road, Parktown, Johannesburg 2193, South Africa
| | | | - Tamara Sonia Boender
- Amsterdam Institute for Global Health and Development (AIGHD), Department of Global Health, Academic Medical Center, P.O. Box 22700, 1100 DE Amsterdam, The Netherlands
| | - Corry Manting
- Amsterdam Institute for Global Health and Development (AIGHD), Department of Global Health, Academic Medical Center, P.O. Box 22700, 1100 DE Amsterdam, The Netherlands
| | - Kim Steegen
- Department of Molecular Medicine and Haematology, University of the Witwatersrand 7 York Road, Parktown, Johannesburg 2193, South Africa
| | - Rudi Luethy
- Newlands Clinic, 56 Enterprise Road, Newlands, Harare, Zimbabwe
| | - Tobias Rinke de Wit
- Amsterdam Institute for Global Health and Development (AIGHD), Department of Global Health, Academic Medical Center, P.O. Box 22700, 1100 DE Amsterdam, The Netherlands
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van der Kuyl AC, Bakker M, Jurriaans S, Back NKT, Pasternak AO, Cornelissen M, Berkhout B. Translational HIV-1 research: from routine diagnostics to new virology insights in Amsterdam, the Netherlands during 1983-2013. Retrovirology 2013; 10:93. [PMID: 23985078 PMCID: PMC3765835 DOI: 10.1186/1742-4690-10-93] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Accepted: 08/21/2013] [Indexed: 02/07/2023] Open
Abstract
An HIV-1 diagnostic laboratory was established in the Academic Medical Center (AMC) of the University of Amsterdam after the discovery of human immunodeficiency virus (HIV) as the cause of the acquired immunodeficiency syndrome (AIDS). The first AIDS patients were diagnosed here in 1981 and since 1983 we have tested the samples of 50992 patients using a variety of assays that greatly improved over the years. We will describe some of the basic results from this diagnostic laboratory and then focus on the spin-off in terms of the development of novel virus assays to detect super-infections and ultra-sensitive assays to measure the intracellular HIV-1 RNA load. We also review several original research findings in the field of HIV-1 virology that stem from initial observations made in the diagnostic unit. This includes the study of genetic defects in the HIV-1 genome and time trends of the replication fitness over 30 years of viral evolution, but also the description of novel HIV-1 variants in difficult-to-diagnose clinical specimen.
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Affiliation(s)
- Antoinette C van der Kuyl
- Laboratory of Experimental Virology, Academic Medical Center of the University of Amsterdam, Amsterdam, the Netherlands.
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Bronze M, Aitken SC, Wallis CL, Steegen K, Stuyver LJ, de Wit TFR, Stevens W. Evaluation of an affordable HIV-1 virological failure assay and antiretroviral drug resistance genotyping protocol. J Virol Methods 2013; 194:300-7. [PMID: 23994150 DOI: 10.1016/j.jviromet.2013.08.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Revised: 08/08/2013] [Accepted: 08/15/2013] [Indexed: 11/28/2022]
Abstract
HIV-1 RNA viral load is the preferred tool to monitor virological failure during antiretroviral therapy (ART) exposure. Timely detection of virological failure can reduce the prevalence and complexity of HIV-1 drug resistance. This field evaluation further characterizes a two-step approach to identify virological failure, as a measure of ART adherence, and detect HIVDR mutations in the reverse transcriptase (RT) gene of HIV-1. Two hundred and forty-eight (248) samples were tested; 225 from South African HIV-1 participants enrolled in the PharmAccess African Studies to Evaluate Resistance (PASER) cohort, forty of which had paired dried blood spot (DBS) samples and 23 HIV-1 negative samples. A newly developed virological failure assay (ARTA-VFA) was used on all samples, and those with a viral load >5000 RNA copies/ml were genotyped with a shortened RT protocol to detect HIVDR (ARTA-HIVDR(ultralight)). The ARTA-VFA showed good precision and linearity as compared to a commercial reference assay (NucliSENS EasyQ v1.2, Roche) with an R(2) of 0.99. Accuracy studies illustrated standard deviations of <1 log RNA copies/ml for plasma and DBS ARTA-VFA results compared to the reference method. The ARTA-VFA's intended use was to deliver qualitative results either < or >5000 RNA copies/ml. No significant differences in the proportion of results < or > either the 5000 RNA copies/ml or 1000 RNA copies/ml cut-off were noted for plasma indicating either cut-off to be useful. Significant differences were noted in these proportions when DBS were used (P=0.0002), where a 5000 RNA copies/ml cut-off was deemed more appropriate. The sensitivity and specificity of the ARTA-VFA with plasma were 95% and 93% and 91% and 95% for DBS using a 5000 RNA copies/ml cut-off. The ARTA HIVDR(ultralight) assay was reliable for plasma and DBS samples with a viral load >5000 RNA copies/ml, with amplification and sequencing success rates of 91% and 92% respectively for plasma, and 95% and 80% respectively for DBS. HIVDR profiles for plasma and DBS were 100% concordant with the reference assay. This study evaluated a previously described combination of two assays potentially useful in assessing HIV-1 virological failure and resistance, showing good concordance with reference assays. These assays are simple to perform and are affordable, viable options to detect virological failures in certain resource limited settings. The assays' compatibility with DBS sampling extends the access of HIV-1 virological monitoring to more remote settings.
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Affiliation(s)
- M Bronze
- Department of Molecular Medicine and Haematology, University of the Witwatersrand, Johannesburg, South Africa; Department of Molecular Medicine and Haematology, National Health Laboratory Services, Charlotte Maxeke Johannesburg Academic Hospital, South Africa.
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