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Vuchas C, Teyim P, Dang BF, Neh A, Keugni L, Che M, Che PN, Beloko H, Fondoh V, Ndi NN, Wandji IAG, Fundoh M, Manga H, Mbuli C, Creswell J, Bisso A, Donkeng V, Sander M. Implementation of large-scale pooled testing to increase rapid molecular diagnostic test coverage for tuberculosis: a retrospective evaluation. Sci Rep 2023; 13:15358. [PMID: 37717043 PMCID: PMC10505184 DOI: 10.1038/s41598-023-41904-w] [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] [Received: 03/06/2023] [Accepted: 09/01/2023] [Indexed: 09/18/2023] Open
Abstract
In 2021, only 6.4 million of the 10.6 million people with tuberculosis (TB) were diagnosed and treated for the disease. Although the World Health Organization recommends initial diagnostic testing using a rapid sensitive molecular assay, only 38% of people diagnosed with TB benefited from these, due to barriers including the high cost of available assays. Pooled testing has been used as an approach to increase testing efficiency in many resource-constrained situations, such as the COVID-19 pandemic, but it has not yet been widely adopted for TB diagnostic testing. Here we report a retrospective analysis of routine pooled testing of 10,117 sputum specimens using the Xpert MTB/RIF and Xpert MTB/RIF Ultra assays that was performed from July 2020 to February 2022. Pooled testing saved 48% of assays and enabled rapid molecular testing for 4156 additional people as compared to individual testing, with 6.6% of specimens positive for TB. From an in silico analysis, the positive percent agreement of pooled testing in pools of 3 as compared with individual testing for the Xpert MTB/RIF Ultra assay was estimated as 99.4% (95% CI, 96.6% to 100%). These results support the scale-up of pooled testing for efficient TB diagnosis.
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Affiliation(s)
- Comfort Vuchas
- Center for Health Promotion and Research, Bamenda, Northwest, Cameroon.
| | - Pride Teyim
- Tuberculosis Reference Laboratory Douala, Douala, Littoral, Cameroon
| | | | - Angela Neh
- Center for Health Promotion and Research, Bamenda, Northwest, Cameroon
| | - Liliane Keugni
- Tuberculosis Reference Laboratory Douala, Douala, Littoral, Cameroon
| | - Mercy Che
- Center for Health Promotion and Research, Bamenda, Northwest, Cameroon
| | - Pantalius Nji Che
- Center for Health Promotion and Research, Bamenda, Northwest, Cameroon
| | - Hamada Beloko
- Tuberculosis Reference Laboratory Douala, Douala, Littoral, Cameroon
| | - Victor Fondoh
- Bamenda Regional Hospital, Bamenda, Northwest, Cameroon
| | - Norah Nyah Ndi
- Baptist Convention Health Services and Baptist Institute of Health Sciences, Bamenda, Northwest, Cameroon
| | | | - Mercy Fundoh
- National TB Program- Northwest Region, Bamenda, Northwest, Cameroon
| | - Henri Manga
- National TB Program, Yaoundé, Center, Cameroon
| | - Cyrille Mbuli
- Center for Health Promotion and Research, Bamenda, Northwest, Cameroon
| | | | - Annie Bisso
- National TB Program, Yaoundé, Center, Cameroon
| | | | - Melissa Sander
- Center for Health Promotion and Research, Bamenda, Northwest, Cameroon.
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2
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Dien Bard J, Babady NE. The Successes and Challenges of SARS-CoV-2 Molecular Testing in the United States. Clin Lab Med 2022; 42:147-160. [PMID: 35636819 PMCID: PMC8901381 DOI: 10.1016/j.cll.2022.02.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Jennifer Dien Bard
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, 4650 Sunset Blvd, MS#32, Los Angeles, CA 90027, USA; Department of Pathology, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA.
| | - N Esther Babady
- Clinical Microbiology Service, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, 327 East 64th Street, CLM-522, NY 10065, USA; Infectious Disease Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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3
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Improvement of Sensitivity of Pooling Strategies for COVID-19. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2021; 2021:6636396. [PMID: 34691239 PMCID: PMC8528573 DOI: 10.1155/2021/6636396] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 07/05/2021] [Accepted: 09/17/2021] [Indexed: 12/18/2022]
Abstract
Group testing (or pool testing), for example, Dorfman's method or grid method, has been validated for COVID-19 RT-PCR tests and implemented widely by most laboratories in many countries. These methods take advantages since they reduce resources, time, and overall costs required for a large number of samples. However, these methods could have more false negative cases and lower sensitivity. In order to maintain both accuracy and efficiency for different prevalence, we provide a novel pooling strategy based on the grid method with an extra pool set and an optimized rule inspired by the idea of error-correcting codes. The mathematical analysis shows that (i) the proposed method has the best sensitivity among all the methods we compared, if the false negative rate (FNR) of an individual test is in the range [1%, 20%] and the FNR of a pool test is closed to that of an individual test, and (ii) the proposed method is efficient when the prevalence is below 10%. Numerical simulations are also performed to confirm the theoretical derivations. In summary, the proposed method is shown to be felicitous under the above conditions in the epidemic.
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4
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Brand A, May S, Hughes JP, Nakigozi G, Reynolds SJ, Gabriel EE. Prediction-driven pooled testing methods: Application to HIV treatment monitoring in Rakai, Uganda. Stat Med 2021; 40:4185-4199. [PMID: 34046930 PMCID: PMC8487918 DOI: 10.1002/sim.9022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 04/19/2021] [Accepted: 04/21/2021] [Indexed: 11/11/2022]
Abstract
Chronic medical conditions often necessitate regular testing for proper treatment. Regular testing of all afflicted individuals may not be feasible due to limited resources, as is true with HIV monitoring in resource-limited settings. Pooled testing methods have been developed in order to allow regular testing for all while reducing resource burden. However, the most commonly used methods do not make use of covariate information predictive of treatment failure, which could improve performance. We propose and evaluate four prediction-driven pooled testing methods that incorporate covariate information to improve pooled testing performance. We then compare these methods in the HIV treatment management setting to current methods with respect to testing efficiency, sensitivity, and number of testing rounds using simulated data and data collected in Rakai, Uganda. Results show that the prediction-driven methods increase efficiency by up to 20% compared with current methods while maintaining equivalent sensitivity and reducing number of testing rounds by up to 70%. When predictions were incorrect, the performance of prediction-based matrix methods remained robust. The best performing method using our motivating data from Rakai was a prediction-driven hybrid method, maintaining sensitivity over 96% and efficiency over 75% in likely scenarios. If these methods perform similarly in the field, they may contribute to improving mortality and reducing transmission in resource-limited settings. Although we evaluate our proposed pooling methods in the HIV treatment setting, they can be applied to any setting that necessitates testing of a quantitative biomarker for a threshold-based decision.
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Affiliation(s)
- Adam Brand
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Sweden
| | - Susanne May
- Department of Biostatistics, University of Washington, Seattle, Washington, USA
| | - James P. Hughes
- Department of Biostatistics, University of Washington, Seattle, Washington, USA
| | | | - Steven J. Reynolds
- Johns Hopkins University, School of Medicine, Baltimore, MD, USA
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Erin E. Gabriel
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Sweden
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5
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Rawlings SA, Scott B, Layman L, Naranatt P, Heltsley R, Ignacio C, Porrachia M, Gianella S, Smith D, Chaillon A. Can't Work From Home: Pooled Nucleic Acid Testing of Laboratory Workers During the COVID-19 Pandemic. Open Forum Infect Dis 2021; 8:ofab129. [PMID: 34327248 PMCID: PMC7989168 DOI: 10.1093/ofid/ofab129] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 03/11/2021] [Indexed: 11/29/2022] Open
Abstract
Together with protective measures, routine screening for severe acute respiratory syndrome coronavirus 2 infection helps provide a safe working environment. We evaluated a pooled nucleic acid testing strategy in a research laboratory. It allowed lab activity to be maintained and would save 25 920 person-hours and $1 684 800/year by increasing the margin of safety for returning to work.
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Affiliation(s)
- Stephen A Rawlings
- Division of Infectious Diseases and Global Public Health, University of California San Diego, San Diego, California, USA
- Veterans Affairs San Diego Healthsystem, San Diego, California, USA
| | - Brianna Scott
- Division of Infectious Diseases and Global Public Health, University of California San Diego, San Diego, California, USA
| | - Laura Layman
- Division of Infectious Diseases and Global Public Health, University of California San Diego, San Diego, California, USA
| | | | | | - Caroline Ignacio
- Division of Infectious Diseases and Global Public Health, University of California San Diego, San Diego, California, USA
| | - Magali Porrachia
- Division of Infectious Diseases and Global Public Health, University of California San Diego, San Diego, California, USA
| | - Sara Gianella
- Division of Infectious Diseases and Global Public Health, University of California San Diego, San Diego, California, USA
| | - Davey Smith
- Division of Infectious Diseases and Global Public Health, University of California San Diego, San Diego, California, USA
- Veterans Affairs San Diego Healthsystem, San Diego, California, USA
| | - Antoine Chaillon
- Division of Infectious Diseases and Global Public Health, University of California San Diego, San Diego, California, USA
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6
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Omooja J, Nannyonjo M, Sanyu G, Nabirye SE, Nassolo F, Lunkuse S, Kapaata A, Segujja F, Kateete DP, Ssebaggala E, Bbosa N, Aling E, Nsubuga RN, Kaleebu P, Ssemwanga D. Rates of HIV-1 virological suppression and patterns of acquired drug resistance among fisherfolk on first-line antiretroviral therapy in Uganda. J Antimicrob Chemother 2020; 74:3021-3029. [PMID: 31257432 PMCID: PMC6753497 DOI: 10.1093/jac/dkz261] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 05/17/2019] [Accepted: 05/22/2019] [Indexed: 01/13/2023] Open
Abstract
Objectives We examined virological outcomes, patterns of acquired HIV drug resistance (ADR), correlates of virological failure (VF) and acquired drug resistance among fisherfolk on first-line ART. Methods We enrolled 1169 adults on ART for a median duration of 6, 12, 24, 36 and ≥48 months and used a pooled VL testing approach to identify VF (VL ≥1000 copies/mL). We performed genotyping among VF cases and determined correlates of VF and ADR by logistic regression. Results The overall virological suppression rate was 91.7% and ADR was detected in 71/97 (73.2%) VF cases. The most prevalent mutations were M184V/I (53.6%) for NRTIs and K103N (39.2%) for NNRTIs. Thymidine analogue mutations were detected in 21.6% of VF cases while PI mutations were absent. A zidovudine-based ART regimen, duration on ART (≥24 months) and secondary/higher education level were significantly associated with VF. A nevirapine-based regimen [adjusted OR (aOR): 1.87; 95% CI: 0.03–0.54)] and VL ≥10000 copies/mL (aOR: 3.48; 95% CI: 1.37–8.85) were ADR correlates. The pooling strategies for VL testing with a negative predictive value (NPV) of ≥95.2% saved US $20320 (43.5%) in VL testing costs. Conclusions We observed high virological suppression rates among these highly mobile fisherfolk; however, there was widespread ADR among those with VF at the first VL testing prior to intensive adherence counselling. Timely treatment switching and adherence support is recommended for better treatment outcomes. Adoption of pooled VL testing could be cost effective, particularly in resource-limited settings.
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Affiliation(s)
- Jonah Omooja
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe, Uganda.,Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Maria Nannyonjo
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe, Uganda
| | - Grace Sanyu
- Uganda Virus Research Institute, Entebbe, Uganda
| | - Stella E Nabirye
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe, Uganda
| | - Faridah Nassolo
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe, Uganda
| | - Sandra Lunkuse
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe, Uganda
| | - Anne Kapaata
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe, Uganda
| | - Farouk Segujja
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe, Uganda.,Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - David Patrick Kateete
- Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda.,Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Eric Ssebaggala
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe, Uganda
| | - Nicholas Bbosa
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe, Uganda
| | - Emmanuel Aling
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe, Uganda
| | - Rebecca N Nsubuga
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe, Uganda
| | - Pontiano Kaleebu
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe, Uganda.,Uganda Virus Research Institute, Entebbe, Uganda
| | - Deogratius Ssemwanga
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe, Uganda.,Uganda Virus Research Institute, Entebbe, Uganda
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7
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Preiser W, van Zyl GU. Pooled testing: A tool to increase efficiency of infant HIV diagnosis and virological monitoring. Afr J Lab Med 2020; 9:1035. [PMID: 32934914 PMCID: PMC7479369 DOI: 10.4102/ajlm.v9i2.1035] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 04/15/2020] [Indexed: 01/04/2023] Open
Abstract
Background Pooled testing, or pooling, has been used for decades to efficiently diagnose relatively rare conditions, such as infection in blood donors. Programmes for the prevention of mother-to-child transmission of HIV and for antiretroviral therapy (ART) are being rolled out in much of Africa and are largely successful. This increases the need for early infant diagnosis (EID) of HIV using qualitative nucleic acid testing and for virological monitoring of patients on ART using viral load testing. While numbers of patients needing testing are increasing, infant HIV infections and ART failures are becoming rarer, opening an opportunity for pooled testing approaches. Aim This review highlights the need for universal EID and viral load coverage as well as the challenges faced. We introduce the concept of pooled testing and highlight some important considerations before giving an overview of studies exploring pooled testing for EID and virological monitoring. Results For ART monitoring, pooling has been shown to be accurate and efficient; for EID it has not been tried although modelling shows it to be promising. The final part attempts to place pooling into the context of current mother-to-child transmission of HIV and ART programmes and their expected trajectories over the next years. Conclusion Several points warrant consideration: pre-selection to exclude samples with an elevated pre-test probability of positivity from pooled testing, the use of dried blood or plasma spots, and choosing a pooling strategy that is both practically feasible and economical. Finally, novel ideas are suggested to make pooling even more attractive.
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Affiliation(s)
- Wolfgang Preiser
- Division of Medical Virology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.,National Health Laboratory Service (NHLS) Tygerberg, Cape Town, South Africa
| | - Gert U van Zyl
- Division of Medical Virology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.,National Health Laboratory Service (NHLS) Tygerberg, Cape Town, South Africa
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8
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[Optimizing resources to reduce costs to determine HIV viral load in limited resources settings]. BIOMEDICA 2017; 37:460-465. [PMID: 29373766 DOI: 10.7705/biomedica.v37i4.3318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Indexed: 11/21/2022]
Abstract
INTRODUCTION HIV viral load testing is a key factor to evaluate the accomplishment of the UNAIDS target of 90% of viral suppression among people receiving antiretroviral therapy. Pooled samples are a potentially accurate and economic approach in resource-constrained settings, but efficiency can be negatively affected by high prevalence rates of virological failure. OBJECTIVE Strategies were assessed to increase the relative efficiency of pooled HIV viral load testing in resource-constrained settings. MATERIALS AND METHODS We evaluated two strategies: a) plasma samples were not included in pools if patients had <12 months on antiretroviral therapy, patients had previous viral load >1,000 copies/ml, or were antiretroviral therapy naïve patients, and b) plasma pools were organized separately for first and second-line antiretroviral therapy regimens. Individual viral load tests were used to compare pooled results. RESULTS Negative predictive values were similar for patients on first (100.0%; 95% CI 99.5 to 100.0) and second-line antiretroviral therapy regimens (99.4%; 95% CI 96.9 to 99.9). However, the incidence of virological failure among individuals on first-line antiretroviral therapy was lower than second-line antiretroviral therapy patients (p <0.01), resulting in greater savings in laboratory tests in patients on first-line antiretroviral therapy (74.0%; 95% CI 71.0 to 76.7) compared with the group of patients on second-line antiretroviral therapy (50.9%; 95% CI 44.4 to 57.3) (p<0.01). CONCLUSION Selecting the samples to be included in the pools and selecting the pools according to ART regimens are criteria that could lead to decreased spending on laboratory tests for HIV viral load determination in resource-constrained settings.
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Improved HIV-1 Viral Load Monitoring Capacity Using Pooled Testing With Marker-Assisted Deconvolution. J Acquir Immune Defic Syndr 2017; 75:580-587. [PMID: 28489730 DOI: 10.1097/qai.0000000000001424] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVE Improve pooled viral load (VL) testing to increase HIV treatment monitoring capacity, particularly relevant for resource-limited settings. DESIGN We developed marker-assisted mini-pooling with algorithm (mMPA), a new VL pooling deconvolution strategy that uses information from low-cost, routinely collected clinical markers to determine an efficient order of sequential individual VL testing and dictates when the sequential testing can be stopped. METHODS We simulated the use of pooled testing to ascertain virological failure status on 918 participants from 3 studies conducted at the Academic Model Providing Access to Healthcare in Eldoret, Kenya, and estimated the number of assays needed when using mMPA and other pooling methods. We also evaluated the impact of practical factors, such as specific markers used, prevalence of virological failure, pool size, VL measurement error, and assay detection cutoffs on mMPA, other pooling methods, and single testing. RESULTS Using CD4 count as a marker to assist deconvolution, mMPA significantly reduces the number of VL assays by 52% [confidence interval (CI): 48% to 57%], 40% (CI: 38% to 42%), and 19% (CI: 15% to 22%) compared with individual testing, simple mini-pooling, and mini-pooling with algorithm, respectively. mMPA has higher sensitivity and negative/positive predictive values than mini-pooling with algorithm, and comparable high specificity. Further improvement is achieved with additional clinical markers, such as age and time on therapy, with or without CD4 values. mMPA performance depends on prevalence of virological failure and pool size but is insensitive to VL measurement error and VL assay detection cutoffs. CONCLUSIONS mMPA can substantially increase the capacity of VL monitoring.
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10
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Solomon SS. The holy grail of HIV programme effectiveness. Lancet HIV 2016; 4:e96-e98. [PMID: 27989575 DOI: 10.1016/s2352-3018(16)30210-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 11/10/2016] [Indexed: 11/18/2022]
Affiliation(s)
- Sunil Suhas Solomon
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA; Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
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11
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Rutstein SE, Hosseinipour MC, Weinberger M, Wheeler SB, Biddle AK, Wallis CL, Balakrishnan P, Mellors JW, Morgado M, Saravanan S, Tripathy S, Vardhanabhuti S, Eron JJ, Miller WC. Predicting resistance as indicator for need to switch from first-line antiretroviral therapy among patients with elevated viral loads: development of a risk score algorithm. BMC Infect Dis 2016; 16:280. [PMID: 27296625 PMCID: PMC4906700 DOI: 10.1186/s12879-016-1611-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 06/01/2016] [Indexed: 11/10/2022] Open
Abstract
Background In resource-limited settings, where resistance testing is unavailable, confirmatory testing for patients with high viral loads (VL) delays antiretroviral therapy (ART) switches for persons with resistance. We developed a risk score algorithm to predict need for ART change by identifying resistance among persons with persistently elevated VL. Methods We analyzed data from a Phase IV open-label trial. Using logistic regression, we identified demographic and clinical characteristics predictive of need for ART change among participants with VLs ≥1000 copies/ml, and assigned model-derived scores to predictors. We designed three models, including only variables accessible in resource-limited settings. Results Among 290 participants with at least one VL ≥1000 copies/ml, 51 % (148/290) resuppressed and did not have resistance testing; among those who did not resuppress and had resistance testing, 47 % (67/142) did not have resistance and 53 % (75/142) had resistance (ART change needed for 25.9 % (75/290)). Need for ART change was directly associated with higher baseline VL and higher VL at time of elevated measure, and inversely associated with treatment duration. Other predictors included body mass index and adherence. Area under receiver operating characteristic curves ranged from 0.794 to 0.817. At a risk score ≥9, sensitivity was 14.7–28.0 % and specificity was 96.7–98.6 %. Conclusions Our model performed reasonably well and may be a tool to quickly transition persons in need of ART change to more effective regimens when resistance testing is unavailable. Use of this algorithm may result in public health benefits and health system savings through reduced transmissions of resistant virus and costs on laboratory investigations. Electronic supplementary material The online version of this article (doi:10.1186/s12879-016-1611-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sarah E Rutstein
- Department of Health Policy and Management, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA. .,Division of Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Mina C Hosseinipour
- Division of Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,UNC Project, Lilongwe, Malawi
| | - Morris Weinberger
- Department of Health Policy and Management, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Stephanie B Wheeler
- Department of Health Policy and Management, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Andrea K Biddle
- Department of Health Policy and Management, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | - Pachamuthu Balakrishnan
- YRG Centre for AIDS Research and Education (YRG CARE), Voluntary Health Services, Taramani, Chennai, 600113, India
| | - John W Mellors
- Division of Infectious Diseases, University of Pittsburgh, Pittsburgh, PA, USA
| | - Mariza Morgado
- Department of STD, AIDS, and Viral Hepatitis, Brazilian National STD and AIDS Program, Rio de Janeiro, Brazil
| | | | - Srikanth Tripathy
- Institute for Leprosy and Other Mycobacterial Diseases, Tajganj, Agra, India
| | | | - Joseph J Eron
- Division of Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - William C Miller
- Division of Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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12
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Pooled Nucleic Acid Testing to Detect Antiretroviral Treatment Failure in HIV-Infected Patients in Mozambique. J Acquir Immune Defic Syndr 2016; 70:256-61. [PMID: 26135327 DOI: 10.1097/qai.0000000000000724] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
BACKGROUND In resource-limited settings, viral load monitoring of HIV-infected patients receiving antiretroviral therapy (ART) is not readily available because of high costs. Here, we compared the accuracy and costs of quantitative and qualitative pooled methods with standard viral load testing. METHODS Blood was collected prospectively from 461 patients receiving first-line ART in Mozambique who had not been evaluated previously with viral load testing. Screening for virologic failure of ART was performed quantitatively (ie, standard viral loads) and qualitatively [one and 2 rounds of polymerase chain reaction (PCR)]. Individual samples and minipools of 5 samples were then analyzed using both methods. The relative efficiency, accuracy, and costs of each method were calculated based on viral load thresholds for ART failure. RESULTS Standard viral load testing of individual samples revealed a high rate of ART failure (19%-23%) across all virologic failure thresholds, and the majority of the patients (93%) with viral loads >1500 copies per milliliter had genotypic resistance to drugs in their ART regimen. Pooled quantitative screening and deconvolution testing had positive and negative predictive values exceeding 95% with cost savings of $11,250 compared with quantitative testing of each sample individually. Pooled qualitative screening and deconvolution testing had a higher cost savings of $30,147 for 1 PCR round and $25,535 for 2 PCR rounds compared with quantitative testing each sample individually. Both pooled qualitative PCR methods had positive and negative predictive values ≥90%, but the pooled 1-round PCR method had a sensitivity of 64%. CONCLUSIONS Given the high rate of undiagnosed ART failure and drug resistance in this cohort, it is clear that virologic monitoring is urgently needed in this population. Here, we compared alternative methods of virologic monitoring with standard viral load testing of individual samples and found these methods to be cost saving and accurate. The test characteristics of each method will likely need to be considered for each local population before it is adopted.
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Abstract
In this article, we examine the concept of HIV viral load and how it has evolved over time (1995-2013) in the field of HIV/AIDS. Although the term viral load is used extensively in this field, few efforts have been directed toward the conceptualization of HIV viral load, which is often left unquestioned, undertheorized, and portrayed as a neutral and objective laboratory value that has remained relatively stable over time--with the exception of progressive advancements in technology, techniques, and sensitivity. The purpose of this article is to apply the evolutionary concept analysis method developed by Rodgers (1989, 2000a) to the concept of HIV viral load. To set the stage, we establish the need for a concept analysis of HIV viral load and provide an overview of the evolutionary view. Then, drawing on the steps proposed by Rodgers (2000a), we outline the process of data collection, management, and analysis. We then offer an in-depth discussion of the findings (attributes, antecedents, and consequences) informed by Wuest's (2000) critical approach to concept analysis. We conclude by highlighting the implications of this analysis for clinical practice, research, and theory.
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Cheng Z, Wang D, Tian X, Sun Y, Sun X, Xiao N, Zheng Z. Capture and Ligation Probe-PCR (CLIP-PCR) for Molecular Screening, with Application to Active Malaria Surveillance for Elimination. Clin Chem 2015; 61:821-8. [PMID: 25964304 DOI: 10.1373/clinchem.2014.237115] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Accepted: 03/19/2015] [Indexed: 11/06/2022]
Abstract
BACKGROUND Malaria control programs have achieved remarkable success during the past decade. Nonetheless, sensitive and affordable methods for active screening of malaria parasites in low-transmission settings remain urgently needed. METHODS We developed a molecular screening method, capture and ligation probe-PCR (CLIP-PCR), which achieved the sensitivity of reverse-transcription PCR but eliminated the reliance on RNA purification and reverse transcription. In this method, 18S rRNA of genus Plasmodium is released from blood, captured onto 96-well plates, and quantified by the amount of ligated probes that bind continuously to it. We first used laboratory-prepared samples to test the method across a range of parasite densities and pool sizes, then applied the method to an active screening of 3358 dried blood spot samples collected from 3 low-endemic areas in China. RESULTS Plasmodium falciparum diluted in whole blood lysate could be detected at a concentration as low as 0.01 parasites/μL, and a pool size of ≤36 did not significantly affect assay performance. When coupled with a matrix pooling strategy, the assay drastically increased throughput to thousands of samples per run while reducing the assay cost to cents per sample. In the active screening, CLIP-PCR identified 14 infections, including 4 asymptomatic ones, with <500 tests, costing <US$0.60 for each sample. All positive results were confirmed by standard quantitative PCR. CONCLUSIONS CLIP-PCR, by use of dried blood spots with a pooling strategy, efficiently offers a highly sensitive and high-throughput approach to detect asymptomatic submicroscopic infections with reduced cost and labor, making it an ideal tool for large-scale malaria surveillance in elimination settings.
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Affiliation(s)
- Zhibin Cheng
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Duoquan Wang
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, WHO Collaborating Center for Malaria, Schistosomiasis, and Filariasis, Key Laboratory of Parasite and Vector Biology, Ministry of Health, Shanghai, China
| | - Xiaoyi Tian
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Yu Sun
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Xiaodong Sun
- Yunnan Institute of Parasitic Diseases, Puer, Yunnan, China.
| | - Ning Xiao
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, WHO Collaborating Center for Malaria, Schistosomiasis, and Filariasis, Key Laboratory of Parasite and Vector Biology, Ministry of Health, Shanghai, China;
| | - Zhi Zheng
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, China.
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Black MS, Bilder CR, Tebbs JM. Optimal retesting configurations for hierarchical group testing. J R Stat Soc Ser C Appl Stat 2015; 64:693-710. [PMID: 26166904 DOI: 10.1111/rssc.12097] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Hierarchical group testing is widely used to test individuals for diseases. This testing procedure works by first amalgamating individual specimens into groups for testing. Groups testing negatively have their members declared negative. Groups testing positively are subsequently divided into smaller subgroups and are then retested to search for positive individuals. In our paper, we propose a new class of informative retesting procedures for hierarchical group testing that acknowledges heterogeneity among individuals. These procedures identify the optimal number of groups and their sizes at each testing stage in order to minimize the expected number of tests. We apply our proposals in two settings: 1) HIV testing programs that currently use three-stage hierarchical testing and 2) chlamydia and gonorrhea screening practices that currently use individual testing. For both applications, we show that substantial savings can be realized by our new procedures.
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Affiliation(s)
- Michael S Black
- Department of Mathematics, University of Wisconsin-Platteville, Platteville, WI 53818, USA,
| | - Christopher R Bilder
- Department of Statistics, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
| | - Joshua M Tebbs
- Department of Statistics, University of South Carolina, Columbia, SC 29208, USA,
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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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El Bouzidi K, Grant P, Edwards S, Benn P, Pillay D, Waters L, Nastouli E. Pooled Specimens for HIV RNA Monitoring: Cheaper, but Is It Reliable? Clin Infect Dis 2014; 59:1346-7. [DOI: 10.1093/cid/ciu562] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Kim SB, Kim HW, Kim HS, Ann HW, Kim JK, Choi H, Kim MH, Song JE, Ahn JY, Ku NS, Oh DH, Kim YC, Jeong SJ, Han SH, Kim JM, Smith DM, Choi JY. Pooled nucleic acid testing to identify antiretroviral treatment failure during HIV infection in Seoul, South Korea. ACTA ACUST UNITED AC 2013; 46:136-40. [PMID: 24228824 DOI: 10.3109/00365548.2013.851415] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
BACKGROUND There have been various efforts to identify less costly but still accurate methods for monitoring the response to HIV treatment. We evaluated a pooling method to determine if this could improve screening efficiency and reduce costs while maintaining accuracy in Seoul, South Korea. METHODS We conducted the first prospective study of pooled nucleic acid testing (NAT) using a 5 minipool + algorithm strategy versus individual viral load testing for patients receiving antiretroviral therapy (ART) between November 2011 and August 2012 at an urban hospital in Seoul, South Korea. The viral load assay used has a lower level of detection of 20 HIV RNA copies/ml, and the cost per assay is US$ 136. The 5 minipool +algorithm strategy was applied and 43 pooled samples were evaluated. The relative efficiency and accuracy of the pooled NAT were compared with those of individual testing. RESULTS Using the individual viral load assay, 15 of 215 (7%) plasma samples had more than 200 HIV RNA copies/ml. The pooled NAT using the 5 minipool + algorithm strategy was applied to 43 pooled samples; 111 tests were needed to test all samples when virologic failure was defined at HIV RNA ≥ 200 copies/ml. Therefore, 104 tests were saved over individual testing, with a relative efficiency of 0.48. When evaluating costs, a total of US$ 14,144 was saved for 215 individual samples during 10 months. The negative predictive value was 99.5% for all samples with HIV RNA ≥ 200 copies/ml. CONCLUSIONS The pooled NAT with 5 minipool + algorithm strategy seems to be a very promising approach to effectively monitor patients receiving ART and to save resources.
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Pooled HIV-1 viral load testing using dried blood spots to reduce the cost of monitoring antiretroviral treatment in a resource-limited setting. J Acquir Immune Defic Syndr 2013; 64:134-7. [PMID: 23892241 PMCID: PMC3815087 DOI: 10.1097/qai.0b013e3182a61e63] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Rollout of routine HIV-1 viral load monitoring is hampered by high costs and logistical difficulties associated with sample collection and transport. New strategies are needed to overcome these constraints. Dried blood spots from finger pricks have been shown to be more practical than the use of plasma specimens, and pooling strategies using plasma specimens have been demonstrated to be an efficient method to reduce costs. This study found that combination of finger-prick dried blood spots and a pooling strategy is a feasible and efficient option to reduce costs, while maintaining accuracy in the context of a district hospital in Malawi.
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20
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Rowley CF. Developments in CD4 and viral load monitoring in resource-limited settings. Clin Infect Dis 2013; 58:407-12. [PMID: 24218101 DOI: 10.1093/cid/cit733] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
CD4 counts and human immunodeficiency virus (HIV) load testing are essential components of HIV care, and making these tests available in resource-limited settings is critical to the roll-out of HIV treatment globally. Until recently, the evidence supporting the importance of laboratory monitoring in resource-limited settings was lacking, but there is now a consensus emerging that testing should become routine to ensure the longevity of treatment programs. Low-cost, point-of-care testing offers the potential to fill this role as it potentially improves all aspects of HIV care, ranging from the diagnosis and staging of HIV infection in both infants and adults to monitoring for treatment failure once antiretroviral therapy has been initiated. It is imperative for low-cost solutions to become a reality, but it is equally imperative that close scrutiny be given to each new device that hits the market to ensure they perform optimally in all settings.
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21
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Pooled HIV-1 RNA viral load testing for detection of antiretroviral treatment failure in Kenyan children. J Acquir Immune Defic Syndr 2013; 63:e87-93. [PMID: 23542638 DOI: 10.1097/qai.0b013e318292f9cd] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND Pooled viral load (VL) testing with 2 different testing strategies was evaluated as a potential cost saving method to monitor antiretroviral therapy (ART) in HIV-infected children receiving ART in a resource-limited setting. METHODS Archived samples collected from 250 HIV-1-infected children on first-line ART at various time points post-ART initiation were evaluated for pooled VL testing using a minipool + algorithm strategy. Additionally, samples collected in real time from 125 children on ART were assessed for virologic failure using a minipool strategy for pooled VL testing. Virologic failure was determined as HIV-1 RNA VLs >1500 copies/mL. RESULTS Minipool + algorithm strategy for pooled VL testing of archived samples had estimated viral failure of 13.6%, with a relative efficiency (RE) of 23.6% (95% CI: 18.5 to 29.4), and negative predictive value of 88%. This testing strategy would have resulted in 24% fewer assays needed for a cost savings of $1180 per 100 samples. The minipool strategy for pooled VL testing of samples obtained in real time yielded an estimated 23.2% of samples with viral failure and a RE of 8.0% (95% CI: 3.9 to 14.2); however, had a minipool + algorithm pooling strategy been used, the RE would have increased to 20%. CONCLUSIONS The minipool + algorithm strategy for pooled VL testing to detect virologic failure in HIV-1-infected children on ART was determined to be relatively efficient in detecting virologic failure, have high negative predictive value, with substantial cost savings. Pooling strategies may be important components of cost-effect strategies to reduce rates of viral failure and resistance, thus, improving clinical outcomes.
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Simulation of pooled nucleic acid testing to identify antiretroviral treatment failure during HIV infection in Seoul, South Korea. J Acquir Immune Defic Syndr 2013; 62:e104-5. [PMID: 23924640 DOI: 10.1097/qai.0b013e31827e8cc8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Finucane MM, Rowley CF, Paciorek CJ, Essex M, Pagano M. Estimating the prevalence of transmitted HIV drug resistance using pooled samples. Stat Methods Med Res 2013; 25:917-35. [PMID: 23376965 DOI: 10.1177/0962280212473514] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
In many resource-poor countries, hiv-infected patients receive a standardized antiretroviral cocktail. In these settings, population-level surveillance of drug resistance is needed to characterize the prevalence of resistance mutations and to enable antiretroviral therapy programs to select the optimal regimen for their local population. The surveillance strategy currently recommended by the World Health Organization is prohibitively expensive in some settings and may not provide a sufficiently precise rendering of the emergence of drug resistance. By using a novel assay on pooled sera samples, we decrease surveillance costs while simultaneously increasing the accuracy of drug resistance prevalence estimates for an important mutation that impacts first-line antiretroviral therapy. We present a Bayesian model for pooled-testing data that garners more information from each resistance assay conducted, compared with individual testing. We expand on previous pooling methods to account for uncertainty about the population distribution of within-subject resistance levels. In addition, our model accounts for measurement error of the resistance assay, and this added uncertainty naturally propagates through the Bayesian model to our inference on the prevalence parameter. We conduct a simulation study that informs our pool size recommendations and that shows that this model renders the prevalence parameter identifiable in instances when an existing non-model-based estimator fails.
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Affiliation(s)
- Mariel M Finucane
- The J. David Gladstone Institutes, University of California, San Francisco, USA
| | - Christopher F Rowley
- Division of Infectious Diseases, Beth Israel Deaconess Medical Center, Boston, USA Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, USA Harvard School of Public Health AIDS Initiative, Boston, USA
| | | | - Max Essex
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, USA Harvard School of Public Health AIDS Initiative, Boston, USA
| | - Marcello Pagano
- Department of Biostatistics, Harvard School of Public Health, Boston, USA
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Challenges and opportunities for the implementation of virological testing in resource-limited settings. J Int AIDS Soc 2012; 15:17324. [PMID: 23078767 PMCID: PMC3494160 DOI: 10.7448/ias.15.2.17324] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2012] [Revised: 08/31/2012] [Accepted: 09/19/2012] [Indexed: 11/18/2022] Open
Abstract
Though the advantages of routine virological monitoring for patients on anti-retroviral therapy have been established, cost and complexity limit its full implementation. Monitoring is important for diagnosing virological failure early on, before the development of drug resistance mutations, and to trigger early adherence interventions. Simple and cost-effective viral load tests that facilitate simplification and decentralization of testing and strategies, such as the use of dried blood spots and pooled sample testing, which further aid simplification, are becoming available. In addition, replacing immunological monitoring with virological monitoring in non-viremic patients in a phased manner will reduce the costs associated with dual immuno-virological monitoring. Going forward, the simplification of testing paired with price reducing strategies that will allow for healthy competition between multiple manufacturers will enable the implementation of viral load testing in resource-poor settings. It is important that future HIV and AIDS treatment guidelines provide clear recommendations for routine virological monitoring and that governments and donors fund the implementation of accurate and operationally proven testing platforms in a comprehensive manner.
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Tilghman MW, May S, Pérez-Santiago J, Ignacio CC, Little SJ, Richman DD, Smith DM. A combined screening platform for HIV treatment failure and resistance. PLoS One 2012; 7:e35401. [PMID: 22563383 PMCID: PMC3338506 DOI: 10.1371/journal.pone.0035401] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2012] [Accepted: 03/16/2012] [Indexed: 11/25/2022] Open
Abstract
Background To develop a low cost method to screen for virologic failure of antiretroviral therapy (ART) and HIV-1 drug resistance, we performed a retrospective evaluation of a screening assay using serial dilutions of HIV-1 RNA-spiked blood plasma and samples from patients receiving >6 months of first-line ART. Methods Serial dilution testing was used to assess sensitivity of a simple PCR-based assay (targeted at ≥1,000 HIV RNA copies/mL). We created blood plasma minipools of five samples, extracted HIV RNA from the pools, PCR amplified the reverse transcriptase (RT) coding region of the HIV-1 pol gene from extracted RNA, sequenced PCR product of positive pools, and used sequences to determine drug resistance. Sensitivity, specificity, and predictive values were determined for different levels of virologic failure based on maximum viral loads of individual samples within a pool. Results Of 295 samples analyzed, 43 (15%) had virologic failure at ≥50 copies/mL (range 50–10,500 copies/mL, four at ≥1,000 copies/mL). The assay demonstrated 100% sensitivity to detect virus from these four samples, requiring only one round of PCR, and 56% and 89% sensitivity to detect samples with ≥50 and ≥500 copies/mL using two rounds. Amplified PCR products of all positive pools were successfully sequenced and 30% harbored ≥1 major resistance mutation. This method would have cost 10% of the combined costs of individual viral load and resistance testing. Conclusions We present a novel method that can screen for both virologic failure of first-line ART and drug resistance. The method is much less expensive than current methods, which may offer sustainability in resource-limited settings.
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Affiliation(s)
- Myres W. Tilghman
- Department of Medicine, University of California San Diego, La Jolla, California, United States of America
- * E-mail: (MWT); (DMS)
| | - Susanne May
- Department of Biostatistics, University of Washington, Seattle, Washington, United States of America
| | - Josué Pérez-Santiago
- Department of Bioinformatics and Systems Biology, University of California San Diego, La Jolla, California, United States of America
| | - Caroline C. Ignacio
- Department of Medicine, University of California San Diego, La Jolla, California, United States of America
| | - Susan J. Little
- Department of Medicine, University of California San Diego, La Jolla, California, United States of America
| | - Douglas D. Richman
- Department of Medicine, University of California San Diego, La Jolla, California, United States of America
- Veterans Affairs San Diego Healthcare System, San Diego, California, United States of America
- Department of Pathology, University of California San Diego, La Jolla, California, United States of America
| | - Davey M. Smith
- Department of Medicine, University of California San Diego, La Jolla, California, United States of America
- Veterans Affairs San Diego Healthcare System, San Diego, California, United States of America
- * E-mail: (MWT); (DMS)
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26
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Walker AS, Gibb DM. Monitoring of highly active antiretroviral therapy in HIV infection. Curr Opin Infect Dis 2011; 24:27-33. [PMID: 21150591 DOI: 10.1097/qco.0b013e3283423e0e] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
PURPOSE OF REVIEW Patients on antiretroviral therapy (ART) in high-income countries have routine laboratory tests to monitor ART efficacy/toxicity. We review studies describing the outcomes and costs of different monitoring approaches, predominantly in low-income countries. RECENT FINDINGS CD4 cell counts, HIV RNA viral load and clinical events are frequently discordant; viral load suppression occurs with WHO-defined CD4 failure and, as expected, viral load failure often occurs before CD4 failure. Routine CD4 monitoring provides small but significant mortality/morbidity benefits over clinical monitoring, but, at current prices, is not yet cost-effective in many sub-Saharan African countries. Viral load monitoring is less cost-effective with modelling studies reporting variable results. More research into point-of-care tests, methods for targeting monitoring and thresholds for defining failure is needed. Most laboratory monitoring for toxicity is neither effective nor cost-effective. In terms of models for delivery of care, task-shifting with nurse-led and decentralized care appear as effective as doctor-led or centralized care. SUMMARY Recent studies have improved the evidence base for monitoring on ART. Future research to increase cost-effectiveness by better targeting of monitoring and/or evaluating implementation of less costly point-of-care tests will contribute to long-term success of ART while continuing to increase ART coverage.
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van Zyl GU, Preiser W, Potschka S, Lundershausen AT, Haubrich R, Smith D. Pooling strategies to reduce the cost of HIV-1 RNA load monitoring in a resource-limited setting. Clin Infect Dis 2011; 52:264-70. [PMID: 21288854 DOI: 10.1093/cid/ciq084] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Quantitative human immunodeficiency virus (HIV) RNA load testing surpasses CD4 cell count and clinical monitoring in detecting antiretroviral therapy (ART) failure; however, its cost can be prohibitive. Recently, the use of pooling strategies with a clinically appropriate viral load threshold was shown to be accurate and efficient for monitoring when the prevalence of virologic failure is low. METHODS We used laboratory request form information to identify specimens with a low pretest probability of virologic failure. Patients aged ≥15 years who were receiving first-line ART had individual viral load results available were eligible. Blood plasma, dried blood spots, and dried plasma spots were evaluated. Two pooling strategies were compared: minipools of 5 samples and a 10 ×10 matrix platform (liquid plasma specimens only). A deconvolution algorithm was used to identify specimens(s) with detectable viral loads. RESULTS The virologic failure rate in the study sample was <10%. Specimens included were liquid plasma specimens tested in minipools(n = 400), of which 300 were available for testing by matrix, and specimens tested with minipools only: dried blood spots (n = 100) and dried plasma spots (n = 185). Pooling methods resulted in 30.5%-60% fewer HIV RNA tests required to screen the study sample. For plasma pooling, the matrix strategy had the better efficiency, but minipools of 5 dried blood spots had the best efficiency overall and were accurate at a >95% negative predictive value with minimal technical requirements. CONCLUSIONS In resource-constrained settings, a combination of preselection of patients with low pretest probability of virologic failure and pooled testing can reduce the cost of virologic monitoring without compromising accuracy.
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Affiliation(s)
- G U van Zyl
- Division of Medical Virology, Stellenbosch University, and National Health Laboratory Service, Tygerberg, South Africa.
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Mehta SR, Nguyen VT, Osorio G, Little S, Smith DM. Evaluation of pooled rapid HIV antibody screening of patients admitted to a San Diego Hospital. J Virol Methods 2011; 174:94-8. [PMID: 21513744 DOI: 10.1016/j.jviromet.2011.04.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2010] [Revised: 03/28/2011] [Accepted: 04/05/2011] [Indexed: 11/19/2022]
Abstract
Current HIV screening guidelines in the United States recommend expanding the scope of HIV screening to include routine screening in health care settings; however, this will require increased resources. Since testing of pooled samples can decrease costs, the test characteristics of pooled rapid antibody testing were determined and optimal pool sizes were estimated for populations with HIV prevalence ranging from 0.25% to 10%. Based on these results, pooled testing methods were evaluated for screening patients admitted to hospital in San Diego, California. Evaluation of pooled antibody testing on samples collected from individuals with known HIV infection found only a modest reduction in sensitivity. These false negative results were only found among samples with very low optical density readings (<0.125 by the ADVIA Centaur® HIV assay). These readings are considered as HIV negative by the ADVIA Centaur® HIV assay, and therefore likely correspond to samples collected during acute infection. Further evaluation of pooled testing of samples collected from individuals during recent infection, found that mini-pool testing of five samples detected HIV antibody in 86% of samples taken within 60 days of the initial infection and 92% of samples taken within 90 days of the initial infection. Based on estimations of optimal pool sizes for low prevalence populations, it was decided to evaluate mini-pools consisting of 10 samples to screen the study's hospitalized patients. During this evaluation, the HIV prevalence among hospitalized patients was 0.8%, and the 10 sample mini-pool testing had 100% sensitivity and specificity. Additionally, pooled testing resulted in an 84.5% reduction in the number of rapid HIV antibody tests needed, as compared to testing each sample individually. Even when incorporating the increased costs of technician time, mini-pooled tested would have resulted in a net savings of 8760 USD for the 523 samples tested in the study. Taken together, these results indicate that pooled rapid antibody testing may reduce substantially the costs for HIV screening in low prevalence populations without a loss in accuracy.
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Affiliation(s)
- Sanjay R Mehta
- Division of Infectious Diseases, University of California, San Diego, La Jolla, CA 92093-0711, USA.
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Pooled nucleic acid testing to detect antiretroviral treatment failure in Mexico. J Acquir Immune Defic Syndr 2011; 56:e70-4. [PMID: 21124228 DOI: 10.1097/qai.0b013e3181ff63d7] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
BACKGROUND Similar to other resource-limited settings, cost restricts availability of viral load monitoring for most patients receiving antiretroviral therapy in Tijuana, Mexico. We evaluated if a pooling method could improve efficiency and reduce costs while maintaining accuracy. METHODS We evaluated 700 patient blood plasma specimens at a reference laboratory in Tijuana for detectable viremia, individually and in 10 × 10 matrix pools. Thresholds for virologic failure were set at ≥500, ≥1000 and ≥1500 HIV RNA copies per milliliter. Detectable pools were deconvoluted using pre-set algorithms. Accuracy and efficiency of the pooling method were compared with individual testing. Quality assurance (QA) measures were evaluated after 1 matrix demonstrated low efficiency relative to individual testing. RESULTS Twenty-two percent of the cohort had detectable HIV RNA (≥50 copies/mL). Pooling methods saved approximately one third of viral load assays over individual testing, while maintaining negative predictive values of >90% to detect samples with virologic failure (≥50 copies/mL). One matrix with low relative efficiency would have been detected earlier using the developed QA measures, but its exclusion would have only increased relative efficiency from 39% to 42%. These methods would have saved between $13,223 and $14,308 for monitoring this cohort. CONCLUSIONS Despite limited clinical data, high prevalence of detectable viral loads and a contaminated matrix, pooling greatly improved efficiency of virologic monitoring while maintaining accuracy. By improving cost-effectiveness, these methods could provide sustainability of virologic monitoring in resource-limited settings, and incorporation of developed QA measures will most likely maximize pooling efficiency in future uses.
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