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Saraiva GQ. Pool testing with dilution effects and heterogeneous priors. Health Care Manag Sci 2023; 26:651-672. [PMID: 37526758 DOI: 10.1007/s10729-023-09650-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 06/25/2023] [Indexed: 08/02/2023]
Abstract
The Dorfman pooled testing scheme is a process in which individual specimens (e.g., blood, urine, swabs, etc.) are pooled and tested together; if the merged sample tests positive for infection, then each specimen from the pool is tested individually. Through this procedure, laboratories can reduce the expected number of tests required to screen the population, as individual tests are only carried out when the pooled test detects an infection. Several different partitions of the population can be used to form the pools. In this study, we analyze the performance of ordered partitions, those in which subjects with similar probability of infection are pooled together. We derive sufficient conditions under which ordered partitions outperform other types of partitions in terms of minimizing the expected number of tests, the expected number of false negatives, and the expected number of false positive classifications. These sufficient conditions can be easily verified in practical applications once the dilution effect has been estimated. We also propose a measure of equity and present conditions under which this measure is maximized by ordered partitions.
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Affiliation(s)
- Gustavo Quinderé Saraiva
- Business School, Pontificia Universidad Católica de Chile, Vicuña Mackenna 4860, Macul, Santiago, Chile.
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Isibor PO, Onwaeze OO, Kayode-Edwards II, Agbontaen DO, Ifebem-Ezima IAM, Bilewu O, Onuselogu C, Akinniyi AP, Obafemi YD, Oniha MI. Investigating and combatting the key drivers of viral zoonoses in Africa: an analysis of eight epidemics. BRAZ J BIOL 2023; 84:e270857. [PMID: 37531478 DOI: 10.1590/1519-6984.270857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 03/02/2023] [Indexed: 08/04/2023] Open
Abstract
Investigating the interplay of factors that result in a viral zoonotic outbreak is difficult, though it is increasingly important. As anthropogenic influences shift the delicate balance of ecosystems, new zoonoses emerge in humans. Sub-Saharan Africa is a notable hotspot for zoonotic disease due to abundant competent mammalian reservoir hosts. Furthermore, poverty, corruption, and an overreliance on natural resources play considerable roles in depleting biological resources, exacerbating the population's susceptibility. Unsurprisingly, viral zoonoses have emerged in Africa, including HIV/AIDS, Ebola, Avian influenza, Lassa fever, Zika, and Monkeypox. These diseases are among the principal causes of death in endemic areas. Though typically distinct in their manifestations, viral zoonoses are connected by underlying, definitive factors. This review summarises vital findings on viral zoonoses in Africa using nine notable case studies as a benchmark for future studies. We discuss the importance of ecological recuperation and protection as a central strategy to control zoonotic diseases. Emphasis was made on moderating key drivers of zoonotic diseases to forestall future pandemics. This is in conjunction with attempts to redirect efforts from reactive to pre-emptive through a multidisciplinary "one health" approach.
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Affiliation(s)
- P O Isibor
- Covenant University, Department of Biological Sciences, Ota, Ogun State, Nigeria
| | - O O Onwaeze
- Covenant University, Department of Biological Sciences, Ota, Ogun State, Nigeria
| | - I I Kayode-Edwards
- Covenant University, Department of Biological Sciences, Ota, Ogun State, Nigeria
| | - D O Agbontaen
- University of South Wales, Department of Public Health, Pontypridd, United Kingdom
| | - I-A M Ifebem-Ezima
- Covenant University, Department of Biological Sciences, Ota, Ogun State, Nigeria
| | - O Bilewu
- Covenant University, Department of Biological Sciences, Ota, Ogun State, Nigeria
| | - C Onuselogu
- Covenant University, Department of Biological Sciences, Ota, Ogun State, Nigeria
| | - A P Akinniyi
- Covenant University, Department of Biological Sciences, Ota, Ogun State, Nigeria
| | - Y D Obafemi
- Covenant University, Department of Biological Sciences, Ota, Ogun State, Nigeria
| | - M I Oniha
- Covenant University, Department of Biological Sciences, Ota, Ogun State, Nigeria
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3
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Aguilera A, Fuentes A, Cea M, Carracedo R, Viñuela L, Ordóñez P, López-Fabal F, Sáez E, Cebrián R, Pérez-Revilla A, Pereira S, De Salazar A, García F. Real-life validation of a sample pooling strategy for screening of hepatitis C. Clin Microbiol Infect 2023; 29:112.e1-112.e4. [PMID: 36210627 DOI: 10.1016/j.cmi.2022.09.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 08/30/2022] [Accepted: 09/09/2022] [Indexed: 12/27/2022]
Abstract
OBJECTIVES To test a real-life sample pooling screening strategy which contributes to increasing the diagnostic capacity of clinical laboratories and expanding access to massive screening of hepatitis C. METHODS After evaluating the sensitivity of the pooling strategy for seven different commercial assays which are used to determine the concentration of hepatitis C virus (HCV)-RNA in the plasma or serum, consecutive samples submitted for HCV diagnosis during the first 3 weeks of November 2021 were tested for HCV antibodies and, in parallel and in a blinded way, were pooled into 100 samples and tested for HCV-RNA. When the result was positive, a strategy to un-mask the positive(s) pool(s), which needed up to 15 total HCV-RNA tests, was used. RESULTS All platforms were able to detect the presence of HCV-RNA in a single sample from a patient with viremic HCV present in pools of up to at least 10 000 HCV-RNA-free samples. A total of 1700 samples (17 pools) were analysed, with an overall prevalence of anti-HCV and HCV-RNA of 0.24%. After pooling, we could detect all samples previously detected using standard diagnosis tests (reflex testing) with a specificity and sensitivity of 100% (CI, 99.78-100%). Given the median current prices of anti-HCV and HCV-RNA on the market in Spain as well as personnel costs, testing using the pooling strategy would have resulted in a save of 3320€. CONCLUSIONS Here, we demonstrated that by improving cost effectiveness, with no loss of sensitivity and specificity, the strategy of pooling samples may serve as an appropriate tool for use in large-scale screening of HCV.
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Affiliation(s)
- Antonio Aguilera
- Servicio de Microbiología, Complexo Hospitalario Universitario de Santiago, Santiago de Compostela, Spain; Departamento de Microbiología, Universidade de Santiago de Compostela, Santiago de Compostela, Spain; Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Spain
| | - Ana Fuentes
- Servicio de Microbiología, Hospital Universitario Clínico San Cecilio, Granada, Spain; Instituto de Investigación Biosanitario Ibs.Granada, Spain
| | - María Cea
- Servicio de Microbiología, Complexo Hospitalario Universitario de Santiago, Santiago de Compostela, Spain
| | - Raquel Carracedo
- Servicio de Microbiología, Complexo Hospitalario Universitario de Santiago, Santiago de Compostela, Spain
| | - Laura Viñuela
- Servicio de Microbiología, Hospital Universitario Clínico San Cecilio, Granada, Spain; Instituto de Investigación Biosanitario Ibs.Granada, Spain
| | - Patricia Ordóñez
- Complejo Hospitalario Arquitecto Marcide-Profesor Novoa Santos, Ferrol, Spain
| | | | - Elena Sáez
- Laboratorio Central de la Comunidad de Madrid (URSALUD), Madrid, Spain
| | - Rubén Cebrián
- Servicio de Microbiología, Hospital Universitario Clínico San Cecilio, Granada, Spain; Instituto de Investigación Biosanitario Ibs.Granada, Spain
| | | | - Sara Pereira
- Servicio de Microbiología, Complexo Hospitalario Universitario de Santiago, Santiago de Compostela, Spain
| | - Adolfo De Salazar
- Servicio de Microbiología, Hospital Universitario Clínico San Cecilio, Granada, Spain; Instituto de Investigación Biosanitario Ibs.Granada, Spain; Ciber de Enfermedades Infecciosas, ISCIII, Spain
| | - Federico García
- Servicio de Microbiología, Hospital Universitario Clínico San Cecilio, Granada, Spain; Instituto de Investigación Biosanitario Ibs.Granada, Spain; Ciber de Enfermedades Infecciosas, ISCIII, Spain.
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Heckel S, Pacini A, Paredes F, Petreli MV, Perez M, Adriani N, Ibarra G, Menzella H, Colaneri A, Sesma J. Practical considerations to establish a validated platform for pooled detection of SARS-CoV-2 by droplet digital PCR. PLoS One 2022; 17:e0271860. [PMID: 36331920 PMCID: PMC9635689 DOI: 10.1371/journal.pone.0271860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 10/23/2022] [Indexed: 11/06/2022] Open
Abstract
Detection of SARS-CoV-2 has created an enormous workload for laboratories worldwide resulting in a restriction at the time of massive testing. Pool testing is a strategy that reduces time and costs. However, beyond the detection of infectious diseases in blood banks, this approach is rarely implemented in routine laboratories. Therefore, what was learned from the SARS-CoV-2 pool testing should represent an opportunity to increase diagnostic capabilities. The present work, carried out in the context of a diagnostic laboratory of a public hospital during the COVID-19 pandemic, represents a contribution to this end. The main limitation of pool testing is the risk of false negatives that could have been identified by individual tests. These limitations are the dilution of samples with a low virus load during pooling and that the integrity of the sample may be affected by the quality of the sample collection. Fortunately, both limitations coincide with the main strengths of droplet digital PCR (ddPCR). ddPCR is a third-generation PCR that splits the amplification into thousands of droplets that work in parallel, increasing sensitivity and resistance to inhibitors. Therefore, ddPCR is particularly useful for pool testing. Here we show how to factor between test sensitivity and savings in test time and resources. We have identified and optimized critical parameters for pool testing. The present study, which analyzed 1000 nasopharyngeal samples, showed that the pool testing could detect even a single positive sample with a CT value of up to 30 in pools of 34 samples. This test was performed using three different standard extraction methods, the simplest being heating only, which resulted in substantial savings of extraction reagents in addition to PCR reagents. Moreover, we show that pooling can be extended to use saliva, which is less invasive and allows self-collection, reducing the risk for health personnel.
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Affiliation(s)
- Sofía Heckel
- Molecular Biology Department, Hospital Provincial de Rosario (HPR), Rosario, Santa Fe, Argentina
- Instituto de Inmunología Clínica y Experimental de Rosario (IDICER-CONICET), Rosario, Santa Fe, Argentina
- Facultad de Ciencias Bioquímicas y Farmacéuticas de Rosario (FBioyF), Rosario, Santa Fe, Argentina
| | - Antonella Pacini
- Molecular Biology Department, Hospital Provincial de Rosario (HPR), Rosario, Santa Fe, Argentina
- Instituto de Inmunología Clínica y Experimental de Rosario (IDICER-CONICET), Rosario, Santa Fe, Argentina
| | - Franco Paredes
- Molecular Biology Department, Hospital Provincial de Rosario (HPR), Rosario, Santa Fe, Argentina
- Facultad de Ciencias Bioquímicas y Farmacéuticas de Rosario (FBioyF), Rosario, Santa Fe, Argentina
| | - Ma. Victoria Petreli
- Molecular Biology Department, Hospital Provincial de Rosario (HPR), Rosario, Santa Fe, Argentina
- Facultad de Ciencias Bioquímicas y Farmacéuticas de Rosario (FBioyF), Rosario, Santa Fe, Argentina
| | - Marilina Perez
- Molecular Biology Department, Hospital Provincial de Rosario (HPR), Rosario, Santa Fe, Argentina
| | - Natalia Adriani
- Molecular Biology Department, Hospital Provincial de Rosario (HPR), Rosario, Santa Fe, Argentina
| | - Guadalupe Ibarra
- Molecular Biology Department, Hospital Provincial de Rosario (HPR), Rosario, Santa Fe, Argentina
- Facultad de Ciencias Bioquímicas y Farmacéuticas de Rosario (FBioyF), Rosario, Santa Fe, Argentina
| | - Hugo Menzella
- Instituto de Procesos Biotecnológicos y Químicos Rosario (IPROByQ), Rosario, Santa Fe, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Alejandro Colaneri
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Juliana Sesma
- Molecular Biology Department, Hospital Provincial de Rosario (HPR), Rosario, Santa Fe, Argentina
- Instituto de Inmunología Clínica y Experimental de Rosario (IDICER-CONICET), Rosario, Santa Fe, Argentina
- Facultad de Ciencias Médicas (FCM-UNR), Rosario, Santa Fe, Argentina
- * E-mail:
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Sun HY, Chiang C, Huang SH, Guo WJ, Chuang YC, Huang YC, Yang CJ, Su LH, Chen YT, Chen YW, Hsu FC, Ho SY, Liu WC, Su YC, Chang SY, Hsiao CF, Hung CC, Yu ML. Three-Stage Pooled Plasma Hepatitis C Virus RNA Testing for the Identification of Acute HCV Infections in At-Risk Populations. Microbiol Spectr 2022; 10:e02437-21. [PMID: 35499354 PMCID: PMC9241589 DOI: 10.1128/spectrum.02437-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 04/11/2022] [Indexed: 01/26/2023] Open
Abstract
Timely diagnosis and treatment of hepatitis C virus (HCV) infection may prevent its transmission. We evaluated the performance and cost reductions of the pooled plasma HCV RNA testing strategy to identify acute HCV infections among people living with HIV (PLWH). PLWH with sexually transmitted infections, elevated aminotransferases within the past 6 months or past HCV infections (high-risk) and those without (low-risk) were enrolled prospectively. Participants underwent three-stage pooled plasma HCV RNA testing every 12 to 24 weeks until detection of HCV RNA or completion of a 48-week follow-up. The three-stage strategy combined 20 individual specimens into a stage 1 pool, 5 individual specimens from the stage 1 pool that tested positive for HCV RNA in the stage 2 mini-pool, followed by testing of individual specimens of the stage 2 mini-pool tested positive for HCV RNA. A simulation was constructed to investigate the cost reductions and pooled sensitivity and specificity under different combinations of HCV prevalence and pool/mini-pool sizes. Between June 25, 2019 and March 31, 2021, 32 cases of incident HCV viremia were identified in 760 high-risk PLWH that were enrolled 834 times, giving an incidence rate of 56.6 per 1000 person-years of follow-up (PYFU). No cases of HCV viremia were identified in 557 low-risk PLWH during a total of 269.2 PYFU. Simulation analysis suggested that this strategy could reduce HCV RNA testing cost by 50% to 86% with HCV viremia prevalence of 1% to 5% and various pooled sizes despite compromised pooled sensitivity. This pooled plasma HCV RNA testing strategy is cost-saving to identify acute HCV infections in high-risk populations with HCV viremia prevalence of 1% to 5%. IMPORTANCE Our three-stage pooled plasma HCV RNA testing successfully identified HCV viremia in high-risk PLWH with a testing cost reduction of 84.5%. Simulation analysis offered detailed information regarding the selection of pool and mini-pool sizes in settings of different HCV epidemiology and the performance of HCV RNA testing to optimize the cost reduction.
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Affiliation(s)
- Hsin-Yun Sun
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
- Department of Internal Medicine, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Chieh Chiang
- Department of Mathematics, Tamkang University, New Taipei City, Taiwan
| | - Sung-Hsi Huang
- Department of Internal Medicine, National Taiwan University Hospital Hsin-Chu Branch, Hsin-Chu, Taiwan
- Department of Tropical Medicine and Parasitology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Wen-Jin Guo
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Taiwan
| | - Yu-Chung Chuang
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
- Department of Internal Medicine, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Yi-Chia Huang
- Department of Internal Medicine, National Taiwan University Hospital Biomedical Park Branch, Hsin-Chu, Taiwan
| | - Chia-Jui Yang
- Department of Internal Medicine, Far Eastern Memorial Hospital, New Taipei City, Taiwan
- School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Li-Hsin Su
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
- Department of Internal Medicine, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Yi-Ting Chen
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
- Department of Internal Medicine, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Yea-Wen Chen
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
- Department of Internal Medicine, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Fu-Chiang Hsu
- Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan
- Department of Laboratory Medicine, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Shu-Yuan Ho
- Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan
- Department of Laboratory Medicine, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Wen-Chun Liu
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
- Department of Internal Medicine, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Yi-Ching Su
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
- Department of Internal Medicine, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Sui-Yuan Chang
- Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan
- Department of Laboratory Medicine, National Taiwan University College of Medicine, Taipei, Taiwan
- Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Chin-Fu Hsiao
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Taiwan
| | - Chien-Ching Hung
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
- Department of Internal Medicine, National Taiwan University College of Medicine, Taipei, Taiwan
- Department of Tropical Medicine and Parasitology, National Taiwan University College of Medicine, Taipei, Taiwan
- Department of Medical Research, China Medical University Hospital, Taichung, Taiwan
- China Medical University, Taichung, Taiwan
| | - Ming-Lung Yu
- Hepatobiliary Section, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
- Hepatitis Research Center, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
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El Hajj H, Bish DR, Bish EK, Aprahamian H. Screening multi-dimensional heterogeneous populations for infectious diseases under scarce testing resources, with application to COVID-19. NAVAL RESEARCH LOGISTICS 2022; 69:3-20. [PMID: 38607835 PMCID: PMC8251476 DOI: 10.1002/nav.21985] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 01/22/2021] [Accepted: 01/25/2021] [Indexed: 05/12/2023]
Abstract
Testing provides essential information for managing infectious disease outbreaks, such as the COVID-19 pandemic. When testing resources are scarce, an important managerial decision is who to test. This decision is compounded by the fact that potential testing subjects are heterogeneous in multiple dimensions that are important to consider, including their likelihood of being disease-positive, and how much potential harm would be averted through testing and the subsequent interventions. To increase testing coverage, pooled testing can be utilized, but this comes at a cost of increased false-negatives when the test is imperfect. Then, the decision problem is to partition the heterogeneous testing population into three mutually exclusive sets: those to be individually tested, those to be pool tested, and those not to be tested. Additionally, the subjects to be pool tested must be further partitioned into testing pools, potentially containing different numbers of subjects. The objectives include the minimization of harm (through detection and mitigation) or maximization of testing coverage. We develop data-driven optimization models and algorithms to design pooled testing strategies, and show, via a COVID-19 contact tracing case study, that the proposed testing strategies can substantially outperform the current practice used for COVID-19 contact tracing (individually testing those contacts with symptoms). Our results demonstrate the substantial benefits of optimizing the testing design, while considering the multiple dimensions of population heterogeneity and the limited testing capacity.
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Affiliation(s)
- Hussein El Hajj
- Department of Industrial and Systems EngineeringVirginia TechBlacksburgVirginiaUSA
| | - Douglas R. Bish
- Department of Information Systems, Statistics, and Management ScienceUniversity of AlabamaTuscaloosaAlabamaUSA
| | - Ebru K. Bish
- Department of Information Systems, Statistics, and Management ScienceUniversity of AlabamaTuscaloosaAlabamaUSA
| | - Hrayer Aprahamian
- Department of Industrial and Systems EngineeringTexas A&MCollege StationTexasUSA
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Chen R, Luo I, Rae M, Huang S. A cost-effective sample pooling strategy for line blot assay in detecting onconeural antibodies. J Immunol Methods 2022; 503:113235. [DOI: 10.1016/j.jim.2022.113235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 02/05/2022] [Accepted: 02/08/2022] [Indexed: 10/19/2022]
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Mintsa-Nguema R, Zoa-Assoumou S, Mewono L, M’Bondoukwé NP, Essono P, Mengue-Me-Ngou-Milama K, Boukandou-Mounanga M, Ndong-Ngomo JM, Mintsa-Ndong A, Ngoungou EB, Bouyou-Akotet MK, Mbongo-Kama E. Could pooled samples method affect SARS-CoV-2 diagnosis accuracy using BGI and Sansure-Biotech RT-PCR kits used in Gabon, Central Africa? PLoS One 2022; 17:e0262733. [PMID: 35061822 PMCID: PMC8782308 DOI: 10.1371/journal.pone.0262733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 01/04/2022] [Indexed: 11/29/2022] Open
Abstract
This study aims at establishing specimens pooling approach for the detection of SARS-CoV-2 using the RT-PCR BGI and Sansure-Biotech kits used in Gabon. To validate this approach, 14 positive samples, stored at -20°C for three to five weeks were analyzed individually (as gold standard) and in pools of five, eight and ten in the same plate. We created 14 pools of 5, 8 and 10 samples using 40 μL from each of the selected positive samples mixed with 4, 7 and 9 confirmed negative counterparts in a total volume of 200 μL, 320 μL and 400 μL for the pools of 5, 8 and 10 respectively. Both individual and pooled samples testing was conducted according to the BGI and Sansure-Biotech RT-PCR protocols used at the Professor Daniel Gahouma Laboratory (PDGL). Furthermore, the pooling method was also tested by comparing results of 470 unselected samples tested in 94 pools and individually. Results of our experiment showed that using a BGI single positive sample with cycle threshold (Ct) value of 28.42, confirmed by individual testing, detection occurred in all the pools. On the contrary samples with Ct >31 were not detected in pools of 10 and for these samples (Ct value as high as 37.17) their detection was possible in pool of 8. Regarding the Sansure-Biotech kit, positive samples were detected in all the pool sizes tested, irrespective of their Ct values. The specificity of the pooling method was 100% for the BGI and Sansure-Biotech RT-PCR assays. The present study found an increase in the Ct values with pool size for the BGI and Sansure-Biotech assays. This trend was statistically significant (Pearson’s r = 0.978; p = 0,022) using the BGI method where the mean Ct values were 24.04±1.1, 26.74±1.3, 27.91±1.1 and 28.32±1.1 for the individual, pool of 5, 8 and 10 respectively. The testing of the 470 samples showed that one of the 94 pools had a positive test similar to the individual test using the BGI and Sansure-Biotech kits. The saving of time and economizing test reagents by using the pooling method were demonstrated in this study. Ultimately, the pooling method could be used for the diagnosis of SARS-CoV-2 without modifying the accuracy of results in Gabon. We recommend a maximum pool size of 8 for the BGI kit. For the Sansure-Biotech kit, a maximum pool size of 10 can be used without affecting its accuracy compared to the individual testing.
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Affiliation(s)
- Rodrigue Mintsa-Nguema
- Research Institute in Tropical Ecology, National Center for Scientific and Technological Research, Libreville, Gabon
- Professor Daniel Gahouma Laboratory, Ministry of Health, Libreville, Gabon
- * E-mail:
| | - Samira Zoa-Assoumou
- Professor Daniel Gahouma Laboratory, Ministry of Health, Libreville, Gabon
- Department of Bacteriology-Virology, University of Health Science, Libreville, Gabon
| | - Ludovic Mewono
- Professor Daniel Gahouma Laboratory, Ministry of Health, Libreville, Gabon
- Department of Biology, Higher Normal School, Libreville, Gabon
| | - Noé P. M’Bondoukwé
- Professor Daniel Gahouma Laboratory, Ministry of Health, Libreville, Gabon
- Department of Parasitology-Mycology, University of Health Science, Libreville, Gabon
| | - Paulin Essono
- Professor Daniel Gahouma Laboratory, Ministry of Health, Libreville, Gabon
- National Laboratory of Public Health, Libreville, Gabon
| | - Krystina Mengue-Me-Ngou-Milama
- Professor Daniel Gahouma Laboratory, Ministry of Health, Libreville, Gabon
- National Laboratory of Public Health, Libreville, Gabon
| | - Marlaine Boukandou-Mounanga
- Professor Daniel Gahouma Laboratory, Ministry of Health, Libreville, Gabon
- Institute of Pharmacopeia and Traditional Medicine, National Center for Scientific and Technological Research, Libreville, Gabon
| | - Jacques M. Ndong-Ngomo
- Professor Daniel Gahouma Laboratory, Ministry of Health, Libreville, Gabon
- Department of Parasitology-Mycology, University of Health Science, Libreville, Gabon
| | | | - Edgard B. Ngoungou
- Department of Parasitology-Mycology, University of Health Science, Libreville, Gabon
| | | | - Elvyre Mbongo-Kama
- Professor Daniel Gahouma Laboratory, Ministry of Health, Libreville, Gabon
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Costa MS, Guimarães NS, de Andrade AB, Vaz-Tostes LP, Oliveira RB, Simões MDS, Gelape GDO, Alves CRL, Machado EL, da Fonseca FG, Teixeira SMR, Sato HI, Takahashi RHC, Tupinambás U. Detection of SARS-CoV-2 through pool testing for COVID-19: an integrative review. Rev Soc Bras Med Trop 2021; 54:e0276. [PMID: 34787261 PMCID: PMC8582953 DOI: 10.1590/0037-8682-0276-2021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Accepted: 08/19/2021] [Indexed: 12/18/2022] Open
Abstract
INTRODUCTION The pool testing technique optimizes the number of tests performed and reduces the delivery time of results, which is an interesting strategy for the health crisis caused by the COVID-19 pandemic. This integrative review investigated studies in which pool testing was carried out for epidemiological or screening purposes to analyze its clinical or cost effectiveness and assessed the applicability of this method in high-, middle-, and low-income countries. METHODS This integrative review used primary studies published in the MEDLINE, EMBASE, Literatura Latino-Americana e do Caribe em Ciências da Saúde (LILACS), and Cochrane Library databases. RESULTS A total of 435 studies were identified: 35.3% were carried out in Asia, 29.4% in Europe, 29.4% in North America, and 5.9% in Oceania. CONCLUSIONS This review suggests that pool testing in the general population may be a useful surveillance strategy to detect new variants of SARS-CoV-2 and to evaluate the period of immunogenicity and global immunity from vaccines.
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Affiliation(s)
- Murilo Soares Costa
- Universidade Federal de Minas Gerais, Programa de Pós-Graduação em Ciências da Saúde: Infectologia e Medicina Tropical, Belo Horizonte, MG, Brasil
| | - Nathalia Sernizon Guimarães
- Universidade Federal de Minas Gerais, Programa de Pós-Graduação em Ciências da Saúde: Infectologia e Medicina Tropical, Belo Horizonte, MG, Brasil
| | | | | | - Rhuan Braga Oliveira
- Universidade Federal de Minas Gerais, Faculdade de Medicina, Belo Horizonte, MG, Brasil
| | | | | | | | - Elaine Leandro Machado
- Universidade Federal de Minas Gerais, Departamento de Medicina Preventiva e Social, Belo Horizonte, MG, Brasil
| | | | | | - Hugo Itaru Sato
- Universidade Federal de Minas Gerais, Centro de Tecnologia de Vacinas, Belo Horizonte, MG, Brasil
| | | | - Unaí Tupinambás
- Universidade Federal de Minas Gerais, Programa de Pós-Graduação em Ciências da Saúde: Infectologia e Medicina Tropical, Belo Horizonte, MG, Brasil
- Universidade Federal de Minas Gerais, Departamento de Clínica Médica, Belo Horizonte , MG, Brasil
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10
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Evaluation of Sample Pooling for SARS-CoV-2 Detection in Nasopharyngeal Swab and Saliva Samples with the Idylla SARS-CoV-2 Test. Microbiol Spectr 2021; 9:e0099621. [PMID: 34756076 PMCID: PMC8579845 DOI: 10.1128/spectrum.00996-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Due to increased demand for testing, as well as restricted supply chain resources, testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection continues to face many hurdles. Pooling several samples has been proposed as an alternative approach to address these issues. We investigated the feasibility of pooling nasopharyngeal swab (NPS) or saliva samples for SARS-CoV-2 testing with a commercial assay (Idylla SARS-CoV-2 test; Biocartis). We evaluated the 10-pool and 20-pool approaches for 149 subjects, with 30 positive samples and 119 negative samples. The 10-pool approach had sensitivity of 78.95% (95% confidence interval [CI], 54.43% to 93.95%) and specificity of 100% (95% CI, 71.51% to 100%), whereas the 20-pool approach had sensitivity of 55.56% (95% CI, 21.20% to 86.30%) and specificity of 100% (95% CI, 25% to 100%). No significant difference was observed between the results obtained with pooled NPS and saliva samples. Given the rapidity, full automation, and practical advantages of the Idylla SARS-CoV-2 assay, pooling of 10 samples has the potential to significantly increase testing capacity for both NPS and saliva samples, with good sensitivity. IMPORTANCE To control outbreaks of coronavirus disease 2019 (COVID-19) and to avoid reagent shortages, testing strategies must be adapted and maintained for the foreseeable future. We analyzed the feasibility of pooling NPS and saliva samples for SARS-CoV-2 testing with the Idylla SARS-CoV-2 test, and we found that sensitivity was dependent on the pool size. The SARS-CoV-2 testing capacity with both NPS and saliva samples could be significantly expanded by pooling 10 samples; however, pooling 20 samples resulted in lower sensitivity.
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11
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Baccini M, Cereda G. Screening plans for SARS-CoV-2 based on sampling and rotation: An example in a European school setting. PLoS One 2021; 16:e0257099. [PMID: 34506536 PMCID: PMC8432749 DOI: 10.1371/journal.pone.0257099] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 08/23/2021] [Indexed: 11/20/2022] Open
Abstract
Screening plans for prevention and containment of SARS-CoV-2 infection should take into account the epidemic context, the fact that undetected infected individuals may transmit the disease and that the infection spreads through outbreaks, creating clusters in the population. In this paper, we compare through simulations the performance of six screening plans based on poorly sensitive individual tests, in detecting infection outbreaks at the level of single classes in a typical European school context. The performance evaluation is done by simulating different epidemic dynamics within the class during the four weeks following the day of the initial infection. The plans have different costs in terms of number of individual tests required for the screening and are based on recurrent evaluations on all students or subgroups of students in rotation. Especially in scenarios where the rate of contagion is high, at an equal cost, testing half of the class in rotation every week appears to be better in terms of sensitivity than testing all students every two weeks. Similarly, testing one-fourth of the students every week is comparable with testing all students every two weeks, despite the first one is a much cheaper strategy. In conclusion, we show that in the presence of natural clusters in the population, testing subgroups of individuals belonging to the same cluster in rotation may have a better performance than testing all the individuals less frequently. The proposed simulations approach can be extended to evaluate more complex screening plans than those presented in the paper.
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Affiliation(s)
- Michela Baccini
- Department of Statistics, Computer Science, Applications (DISIA), University of Florence, Florence, Italy
- * E-mail:
| | - Giulia Cereda
- Department of Statistics, Computer Science, Applications (DISIA), University of Florence, Florence, Italy
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12
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Verdun CM, Fuchs T, Harar P, Elbrächter D, Fischer DS, Berner J, Grohs P, Theis FJ, Krahmer F. Group Testing for SARS-CoV-2 Allows for Up to 10-Fold Efficiency Increase Across Realistic Scenarios and Testing Strategies. Front Public Health 2021; 9:583377. [PMID: 34490172 PMCID: PMC8416485 DOI: 10.3389/fpubh.2021.583377] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 07/26/2021] [Indexed: 11/24/2022] Open
Abstract
Background: Due to the ongoing COVID-19 pandemic, demand for diagnostic testing has increased drastically, resulting in shortages of necessary materials to conduct the tests and overwhelming the capacity of testing laboratories. The supply scarcity and capacity limits affect test administration: priority must be given to hospitalized patients and symptomatic individuals, which can prevent the identification of asymptomatic and presymptomatic individuals and hence effective tracking and tracing policies. We describe optimized group testing strategies applicable to SARS-CoV-2 tests in scenarios tailored to the current COVID-19 pandemic and assess significant gains compared to individual testing. Methods: We account for biochemically realistic scenarios in the context of dilution effects on SARS-CoV-2 samples and consider evidence on specificity and sensitivity of PCR-based tests for the novel coronavirus. Because of the current uncertainty and the temporal and spatial changes in the prevalence regime, we provide analysis for several realistic scenarios and propose fast and reliable strategies for massive testing procedures. Key Findings: We find significant efficiency gaps between different group testing strategies in realistic scenarios for SARS-CoV-2 testing, highlighting the need for an informed decision of the pooling protocol depending on estimated prevalence, target specificity, and high- vs. low-risk population. For example, using one of the presented methods, all 1.47 million inhabitants of Munich, Germany, could be tested using only around 141 thousand tests if the infection rate is below 0.4% is assumed. Using 1 million tests, the 6.69 million inhabitants from the city of Rio de Janeiro, Brazil, could be tested as long as the infection rate does not exceed 1%. Moreover, we provide an interactive web application, available at www.grouptexting.com, for visualizing the different strategies and designing pooling schemes according to specific prevalence scenarios and test configurations. Interpretation: Altogether, this work may help provide a basis for an efficient upscaling of current testing procedures, which takes the population heterogeneity into account and is fine-grained towards the desired study populations, e.g., mild/asymptomatic individuals vs. symptomatic ones but also mixtures thereof. Funding: German Science Foundation (DFG), German Federal Ministry of Education and Research (BMBF), Chan Zuckerberg Initiative DAF, and Austrian Science Fund (FWF).
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Affiliation(s)
- Claudio M. Verdun
- Department of Mathematics, Technical University of Munich, Garching, Germany
- Department of Electrical and Computer Engineering, Technical University of Munich, Munich, Germany
| | - Tim Fuchs
- Department of Mathematics, Technical University of Munich, Garching, Germany
| | - Pavol Harar
- Research Network Data Science, University of Vienna, Vienna, Austria
- Department of Telecommunications, Brno University of Technology, Brno, Czechia
| | | | - David S. Fischer
- Institute of Computational Biology, Helmholtz Zentrum München, Munich, Germany
| | - Julius Berner
- Faculty of Mathematics, University of Vienna, Vienna, Austria
| | - Philipp Grohs
- Research Network Data Science, University of Vienna, Vienna, Austria
- Faculty of Mathematics, University of Vienna, Vienna, Austria
- Johann Radon Institute for Computational and Applied Mathematics, Austrian Academy of Sciences, Linz, Austria
| | - Fabian J. Theis
- Department of Mathematics, Technical University of Munich, Garching, Germany
- Institute of Computational Biology, Helmholtz Zentrum München, Munich, Germany
| | - Felix Krahmer
- Department of Mathematics, Technical University of Munich, Garching, Germany
- Munich Data Science Institute, Technical University of Munich, Garching, Germany
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13
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Baccini M, Rocco E, Paganini I, Mattei A, Sani C, Vannucci G, Bisanzi S, Burroni E, Peluso M, Munnia A, Cellai F, Pompeo G, Micio L, Viti J, Mealli F, Carozzi FM. Pool testing on random and natural clusters of individuals: Optimisation of SARS-CoV-2 surveillance in the presence of low viral load samples. PLoS One 2021; 16:e0251589. [PMID: 34003878 PMCID: PMC8130965 DOI: 10.1371/journal.pone.0251589] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Accepted: 04/28/2021] [Indexed: 12/21/2022] Open
Abstract
Facing the SARS-CoV-2 epidemic requires intensive testing on the population to early identify and isolate infected subjects. During the first emergency phase of the epidemic, RT-qPCR on nasopharyngeal (NP) swabs, which is the most reliable technique to detect ongoing infections, exhibited limitations due to availability of reagents and budget constraints. This stressed the need to develop screening procedures that require fewer resources and are suitable to be extended to larger portions of the population. RT-qPCR on pooled samples from individual NP swabs seems to be a promising technique to improve surveillance. We performed preliminary experimental analyses aimed to investigate the performance of pool testing on samples with low viral load and we evaluated through Monte Carlo (MC) simulations alternative screening protocols based on sample pooling, tailored to contexts characterized by different infection prevalence. We focused on the role of pool size and the opportunity to develop strategies that take advantage of natural clustering structures in the population, e.g. families, school classes, hospital rooms. Despite the use of a limited number of specimens, our results suggest that, while high viral load samples seem to be detectable even in a pool with 29 negative samples, positive specimens with low viral load may be masked by the negative samples, unless smaller pools are used. The results of MC simulations confirm that pool testing is useful in contexts where the infection prevalence is low. The gain of pool testing in saving resources can be very high, and can be optimized by selecting appropriate group sizes. Exploiting natural groups makes the definition of larger pools convenient and potentially overcomes the issue of low viral load samples by increasing the probability of identifying more than one positive in the same pool.
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Affiliation(s)
- Michela Baccini
- Department of Statistics, Computer Science, Applications, University of Florence, Florence, Italy
- Florence Center for Data Science, University of Florence, Florence, Italy
- * E-mail: (MB); (FMC); (FM)
| | - Emilia Rocco
- Department of Statistics, Computer Science, Applications, University of Florence, Florence, Italy
- Florence Center for Data Science, University of Florence, Florence, Italy
| | - Irene Paganini
- Regional Laboratory of Cancer Prevention, Institute for Prevention, Research and Oncological Network (ISPRO), Florence, Italy
| | - Alessandra Mattei
- Department of Statistics, Computer Science, Applications, University of Florence, Florence, Italy
- Florence Center for Data Science, University of Florence, Florence, Italy
| | - Cristina Sani
- Regional Laboratory of Cancer Prevention, Institute for Prevention, Research and Oncological Network (ISPRO), Florence, Italy
| | - Giulia Vannucci
- Department of Statistics, Computer Science, Applications, University of Florence, Florence, Italy
- Florence Center for Data Science, University of Florence, Florence, Italy
| | - Simonetta Bisanzi
- Regional Laboratory of Cancer Prevention, Institute for Prevention, Research and Oncological Network (ISPRO), Florence, Italy
| | - Elena Burroni
- Regional Laboratory of Cancer Prevention, Institute for Prevention, Research and Oncological Network (ISPRO), Florence, Italy
| | - Marco Peluso
- Regional Laboratory of Cancer Prevention, Institute for Prevention, Research and Oncological Network (ISPRO), Florence, Italy
| | - Armelle Munnia
- Regional Laboratory of Cancer Prevention, Institute for Prevention, Research and Oncological Network (ISPRO), Florence, Italy
| | - Filippo Cellai
- Regional Laboratory of Cancer Prevention, Institute for Prevention, Research and Oncological Network (ISPRO), Florence, Italy
| | - Giampaolo Pompeo
- Regional Laboratory of Cancer Prevention, Institute for Prevention, Research and Oncological Network (ISPRO), Florence, Italy
| | - Laura Micio
- Regional Laboratory of Cancer Prevention, Institute for Prevention, Research and Oncological Network (ISPRO), Florence, Italy
| | - Jessica Viti
- Regional Laboratory of Cancer Prevention, Institute for Prevention, Research and Oncological Network (ISPRO), Florence, Italy
| | - Fabrizia Mealli
- Department of Statistics, Computer Science, Applications, University of Florence, Florence, Italy
- Florence Center for Data Science, University of Florence, Florence, Italy
- * E-mail: (MB); (FMC); (FM)
| | - Francesca Maria Carozzi
- Regional Laboratory of Cancer Prevention, Institute for Prevention, Research and Oncological Network (ISPRO), Florence, Italy
- * E-mail: (MB); (FMC); (FM)
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14
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Briggs J. Validation of Pooled SARS-CoV-2 Testing in the Outbreak Setting. Am J Trop Med Hyg 2021; 104:1165-1166. [PMID: 33684069 PMCID: PMC8045657 DOI: 10.4269/ajtmh.21-0202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 02/18/2021] [Indexed: 11/12/2022] Open
Affiliation(s)
- Jessica Briggs
- Address correspondence to Jessica Briggs, Department of Medicine, University of California San Francisco, SFGH, Building 3, Rm 525, 1001 Potrero Ave., San Francisco, CA 94110. E-mail:
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15
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Bish DR, Bish EK, El-Hajj H, Aprahamian H. A robust pooled testing approach to expand COVID-19 screening capacity. PLoS One 2021; 16:e0246285. [PMID: 33556129 PMCID: PMC7870054 DOI: 10.1371/journal.pone.0246285] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 01/18/2021] [Indexed: 12/28/2022] Open
Abstract
Limited testing capacity for COVID-19 has hampered the pandemic response. Pooling is a testing method wherein samples from specimens (e.g., swabs) from multiple subjects are combined into a pool and screened with a single test. If the pool tests positive, then new samples from the collected specimens are individually tested, while if the pool tests negative, the subjects are classified as negative for the disease. Pooling can substantially expand COVID-19 testing capacity and throughput, without requiring additional resources. We develop a mathematical model to determine the best pool size for different risk groups, based on each group's estimated COVID-19 prevalence. Our approach takes into consideration the sensitivity and specificity of the test, and a dynamic and uncertain prevalence, and provides a robust pool size for each group. For practical relevance, we also develop a companion COVID-19 pooling design tool (through a spread sheet). To demonstrate the potential value of pooling, we study COVID-19 screening using testing data from Iceland for the period, February-28-2020 to June-14-2020, for subjects stratified into high- and low-risk groups. We implement the robust pooling strategy within a sequential framework, which updates pool sizes each week, for each risk group, based on prior week's testing data. Robust pooling reduces the number of tests, over individual testing, by 88.5% to 90.2%, and 54.2% to 61.9%, respectively, for the low-risk and high-risk groups (based on test sensitivity values in the range [0.71, 0.98] as reported in the literature). This results in much shorter times, on average, to get the test results compared to individual testing (due to the higher testing throughput), and also allows for expanded screening to cover more individuals. Thus, robust pooling can potentially be a valuable strategy for COVID-19 screening.
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Affiliation(s)
- Douglas R. Bish
- University of Alabama, Information Systems, Statistics, and Management Science, Blacksburg, VA, United States of America
- * E-mail:
| | - Ebru K. Bish
- University of Alabama, Information Systems, Statistics, and Management Science, Blacksburg, VA, United States of America
| | - Hussein El-Hajj
- Virginia Tech, Industrial and Systems Engineering, Blacksburg, VA, United States of America
| | - Hrayer Aprahamian
- Industrial and Systems Engineering, Texas A&M University, College Station, TX, United States of America
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16
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Schulte PA, Weissman DN, Luckhaupt SE, de Perio MA, Beezhold D, Piacentino JD, Radonovich LJ, Hearl FJ, Howard J. Considerations for Pooled Testing of Employees for SARS-CoV-2. J Occup Environ Med 2021; 63:1-9. [PMID: 33378322 PMCID: PMC7773162 DOI: 10.1097/jom.0000000000002049] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVES To identify important background information on pooled tested of employees that employers workers, and health authorities should consider. METHODS This paper is a commentary based on the review by the authors of pertinent literature generally from preprints in medrixiv.org prior to August 2020. RESULTS/CONCLUSIONS Pooled testing may be particularly useful to employers in communities with low prevalence of COVID-19. It can be used to reduce the number of tests and associated financial costs. For effective and efficient pooled testing employers should consider it as part of a broader, more comprehensive workplace COVID-19 prevention and control program. Pooled testing of asymptomatic employees can prevent transmission of SARS-CoV-2 and help assure employers and customers that employees are not infectious.
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Affiliation(s)
- Paul A Schulte
- National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, 1090 Tusculum Avenue, Cincinnati, Ohio (Dr Schulte); National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, 1095 Willowdale Road, Morgantown, West Virginia (Dr Weissman, Dr Beezhold, Dr Radonovich); National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, 5555 Ridge Avenue, Cincinnati, Ohio (Dr Luckhaupt, Dr de Perio); National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, 395 E Street SW, Washington, DC 20024 (Dr Piacentino, Hearl, Dr Howard)
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17
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Yelin I, Aharony N, Tamar ES, Argoetti A, Messer E, Berenbaum D, Shafran E, Kuzli A, Gandali N, Shkedi O, Hashimshony T, Mandel-Gutfreund Y, Halberthal M, Geffen Y, Szwarcwort-Cohen M, Kishony R. Evaluation of COVID-19 RT-qPCR Test in Multi sample Pools. Clin Infect Dis 2020; 71:2073-2078. [PMID: 32358960 PMCID: PMC7197588 DOI: 10.1093/cid/ciaa531] [Citation(s) in RCA: 254] [Impact Index Per Article: 63.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 04/30/2020] [Indexed: 11/28/2022] Open
Abstract
Background The recent emergence of SARS-CoV-2 lead to a current pandemic of unprecedented scale. Though diagnostic tests are fundamental to the ability to detect and respond, overwhelmed healthcare systems are already experiencing shortages of reagents associated with this test, calling for a lean immediately-applicable protocol. Methods RNA extracts of positive samples were tested for the presence of SARS-CoV-2 using RT-qPCR, alone or in pools of different sizes (2-, 4-, 8- ,16-, 32- and 64-sample pools) with negative samples. Transport media of additional 3 positive samples were also tested when mixed with transport media of negative samples in pools of 8. Results A single positive sample can be detected in pools of up to 32 samples, using the standard kits and protocols, with an estimated false negative rate of 10%. Detection of positive samples diluted in even up to 64 samples may also be attainable, though may require additional amplification cycles. Single positive samples can be detected when pooling either after or prior to RNA extraction. Conclusions As it uses the standard protocols, reagents and equipment, this pooling method can be applied immediately in current clinical testing laboratories. We hope that such implementation of a pool test for COVID-19 would allow expanding current screening capacities thereby enabling the expansion of detection in the community, as well as in close organic groups, such as hospital departments, army units, or factory shifts.
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Affiliation(s)
- Idan Yelin
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel
| | - Noga Aharony
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel
| | - Einat Shaer Tamar
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel
| | - Amir Argoetti
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel
| | - Esther Messer
- Safety Unit, Technion - Israel Institute of Technology, Haifa, Israel
| | - Dina Berenbaum
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel
| | - Einat Shafran
- Virology laboratory, Rambam Health Care Campus, Haifa, Israel
| | - Areen Kuzli
- Virology laboratory, Rambam Health Care Campus, Haifa, Israel
| | - Nagham Gandali
- Virology laboratory, Rambam Health Care Campus, Haifa, Israel
| | - Omer Shkedi
- Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel
| | - Tamar Hashimshony
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel
| | - Yael Mandel-Gutfreund
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel.,Computer Science Department, Technion - Israel Institute of Technology, Haifa, Israel
| | - Michael Halberthal
- Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel.,Rambam Health Care Campus, Haifa, Israel
| | - Yuval Geffen
- Bacteriology laboratory, Rambam Health Care Campus, Haifa, Israel
| | | | - Roy Kishony
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel.,Computer Science Department, Technion - Israel Institute of Technology, Haifa, Israel
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18
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Smith DRM, Duval A, Pouwels KB, Guillemot D, Fernandes J, Huynh BT, Temime L, Opatowski L. Optimizing COVID-19 surveillance in long-term care facilities: a modelling study. BMC Med 2020; 18:386. [PMID: 33287821 PMCID: PMC7721547 DOI: 10.1186/s12916-020-01866-6] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 11/23/2020] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Long-term care facilities (LTCFs) are vulnerable to outbreaks of coronavirus disease 2019 (COVID-19). Timely epidemiological surveillance is essential for outbreak response, but is complicated by a high proportion of silent (non-symptomatic) infections and limited testing resources. METHODS We used a stochastic, individual-based model to simulate transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) along detailed inter-individual contact networks describing patient-staff interactions in a real LTCF setting. We simulated distribution of nasopharyngeal swabs and reverse transcriptase polymerase chain reaction (RT-PCR) tests using clinical and demographic indications and evaluated the efficacy and resource-efficiency of a range of surveillance strategies, including group testing (sample pooling) and testing cascades, which couple (i) testing for multiple indications (symptoms, admission) with (ii) random daily testing. RESULTS In the baseline scenario, randomly introducing a silent SARS-CoV-2 infection into a 170-bed LTCF led to large outbreaks, with a cumulative 86 (95% uncertainty interval 6-224) infections after 3 weeks of unmitigated transmission. Efficacy of symptom-based screening was limited by lags to symptom onset and silent asymptomatic and pre-symptomatic transmission. Across scenarios, testing upon admission detected just 34-66% of patients infected upon LTCF entry, and also missed potential introductions from staff. Random daily testing was more effective when targeting patients than staff, but was overall an inefficient use of limited resources. At high testing capacity (> 10 tests/100 beds/day), cascades were most effective, with a 19-36% probability of detecting outbreaks prior to any nosocomial transmission, and 26-46% prior to first onset of COVID-19 symptoms. Conversely, at low capacity (< 2 tests/100 beds/day), group testing strategies detected outbreaks earliest. Pooling randomly selected patients in a daily group test was most likely to detect outbreaks prior to first symptom onset (16-27%), while pooling patients and staff expressing any COVID-like symptoms was the most efficient means to improve surveillance given resource limitations, compared to the reference requiring only 6-9 additional tests and 11-28 additional swabs to detect outbreaks 1-6 days earlier, prior to an additional 11-22 infections. CONCLUSIONS COVID-19 surveillance is challenged by delayed or absent clinical symptoms and imperfect diagnostic sensitivity of standard RT-PCR tests. In our analysis, group testing was the most effective and efficient COVID-19 surveillance strategy for resource-limited LTCFs. Testing cascades were even more effective given ample testing resources. Increasing testing capacity and updating surveillance protocols accordingly could facilitate earlier detection of emerging outbreaks, informing a need for urgent intervention in settings with ongoing nosocomial transmission.
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Affiliation(s)
- David R M Smith
- Institut Pasteur, Epidemiology and Modelling of Antibiotic Evasion (EMAE), Paris, France.
- Université Paris-Saclay, UVSQ, Inserm, CESP, Anti-infective evasion and pharmacoepidemiology team, Montigny-Le-Bretonneux, France.
- Modélisation, épidémiologie et surveillance des risques sanitaires (MESuRS), Conservatoire national des arts et métiers, Paris, France.
| | - Audrey Duval
- Institut Pasteur, Epidemiology and Modelling of Antibiotic Evasion (EMAE), Paris, France
- Université Paris-Saclay, UVSQ, Inserm, CESP, Anti-infective evasion and pharmacoepidemiology team, Montigny-Le-Bretonneux, France
| | - Koen B Pouwels
- Health Economics Research Centre, Nuffield Department of Population Health, University of Oxford, Oxford, UK
- The National Institute for Health Research (NIHR) Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, UK
| | - Didier Guillemot
- Institut Pasteur, Epidemiology and Modelling of Antibiotic Evasion (EMAE), Paris, France
- Université Paris-Saclay, UVSQ, Inserm, CESP, Anti-infective evasion and pharmacoepidemiology team, Montigny-Le-Bretonneux, France
- AP-HP, Paris Saclay, Public Health, Medical Information, Clinical Research, Le Kremlin-Bicêtre, France
| | - Jérôme Fernandes
- Clinique de soins de suite et réadaptation, Choisy-Le-Roi, France
| | - Bich-Tram Huynh
- Institut Pasteur, Epidemiology and Modelling of Antibiotic Evasion (EMAE), Paris, France
- Université Paris-Saclay, UVSQ, Inserm, CESP, Anti-infective evasion and pharmacoepidemiology team, Montigny-Le-Bretonneux, France
| | - Laura Temime
- Modélisation, épidémiologie et surveillance des risques sanitaires (MESuRS), Conservatoire national des arts et métiers, Paris, France
- PACRI unit, Institut Pasteur, Conservatoire national des arts et métiers, Paris, France
| | - Lulla Opatowski
- Institut Pasteur, Epidemiology and Modelling of Antibiotic Evasion (EMAE), Paris, France
- Université Paris-Saclay, UVSQ, Inserm, CESP, Anti-infective evasion and pharmacoepidemiology team, Montigny-Le-Bretonneux, France
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19
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Deka S, Kalita D. Effectiveness of Sample Pooling Strategies for SARS-CoV-2 Mass Screening by RT-PCR: A Scoping Review. J Lab Physicians 2020; 12:212-218. [PMID: 33268939 PMCID: PMC7684986 DOI: 10.1055/s-0040-1721159] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The ongoing COVID-19 pandemic has hugely impacted the economy of many countries, and there is an acute shortage of diagnostic resources. With the exponential increase in the number of cases and necessity to screen large number of people, there is a steep increase in the demand for diagnostic kits. Pooled-sample testing is a promising strategy to screen a large population rapidly with limited resources. The aim of this work was to compile a cohesive literature review of the effectiveness and accuracy of pooled-sample testing in the detection of SARS-CoV-2 and critically analyze its limitations. Medline, Google Scholar, Embase, and preprint servers (e.g., bioRxiv) were searched for literature on pooled testing for diagnosis of COVID-19, and out of initial 60 articles/reports, nine original articles were retained. Optimal pool size (number of samples in a pool) seemed to be dependent on factors like prevalence or rate of positivity in community. In low-prevalence localities pool size of around 30 seemed to be effective as observed by some authors. All the researchers had found significant reduction in number of tests (depending on pool size, stages, and pooling design), leading to conservation of resources. Pooling can be done with extracted RNA eluate or directly with patient's sample before extraction. This leads to further reduction in consumables, time and manpower. Risk of false negativity in samples with high-threshold cycle (i.e., low-viral load) value was a concern. Some researchers suggest adding few additional cycles to lower the chances of missing positive cases with low-Ct value. Lower limit of detection (LoD) of RT-PCR kits, that is, sensitivity of kits was another factor to consider. Thus, in a country like India, given the economic benefit and scarcity of resources, pooling strategy can be very effective, especially in low-prevalence areas and in low-risk contacts.
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Affiliation(s)
- Sangeeta Deka
- Department of Microbiology, All India Institute of Medical Sciences, Rishikesh, Virbhadra Road, Rishikesh, Uttarakhand, India
| | - Deepjyoti Kalita
- Department of Microbiology, All India Institute of Medical Sciences, Rishikesh, Virbhadra Road, Rishikesh, Uttarakhand, India
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Yelin I, Aharony N, Tamar ES, Argoetti A, Messer E, Berenbaum D, Shafran E, Kuzli A, Gandali N, Shkedi O, Hashimshony T, Mandel-Gutfreund Y, Halberthal M, Geffen Y, Szwarcwort-Cohen M, Kishony R. Evaluation of COVID-19 RT-qPCR Test in Multi sample Pools. Clin Infect Dis 2020. [PMID: 32358960 DOI: 10.1101/2020.03.26.20039438] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2023] Open
Abstract
BACKGROUND The recent emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) led to a current pandemic of unprecedented scale. Although diagnostic tests are fundamental to the ability to detect and respond, overwhelmed healthcare systems are already experiencing shortages of reagents associated with this test, calling for a lean immediately applicable protocol. METHODS RNA extracts of positive samples were tested for the presence of SARS-CoV-2 using reverse transcription quantitative polymerase chain reaction, alone or in pools of different sizes (2-, 4-, 8-, 16-, 32-, and 64-sample pools) with negative samples. Transport media of additional 3 positive samples were also tested when mixed with transport media of negative samples in pools of 8. RESULTS A single positive sample can be detected in pools of up to 32 samples, using the standard kits and protocols, with an estimated false negative rate of 10%. Detection of positive samples diluted in even up to 64 samples may also be attainable, although this may require additional amplification cycles. Single positive samples can be detected when pooling either after or prior to RNA extraction. CONCLUSIONS As it uses the standard protocols, reagents, and equipment, this pooling method can be applied immediately in current clinical testing laboratories. We hope that such implementation of a pool test for coronavirus disease 2019 would allow expanding current screening capacities, thereby enabling the expansion of detection in the community, as well as in close organic groups, such as hospital departments, army units, or factory shifts.
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Affiliation(s)
- Idan Yelin
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel
| | - Noga Aharony
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel
| | - Einat Shaer Tamar
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel
| | - Amir Argoetti
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel
| | - Esther Messer
- Safety Unit, Technion - Israel Institute of Technology, Haifa, Israel
| | - Dina Berenbaum
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel
| | - Einat Shafran
- Virology laboratory, Rambam Health Care Campus, Haifa, Israel
| | - Areen Kuzli
- Virology laboratory, Rambam Health Care Campus, Haifa, Israel
| | - Nagham Gandali
- Virology laboratory, Rambam Health Care Campus, Haifa, Israel
| | - Omer Shkedi
- Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel
| | - Tamar Hashimshony
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel
| | - Yael Mandel-Gutfreund
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel
- Computer Science Department, Technion - Israel Institute of Technology, Haifa, Israel
| | - Michael Halberthal
- Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel
- Rambam Health Care Campus, Haifa, Israel
| | - Yuval Geffen
- Bacteriology laboratory, Rambam Health Care Campus, Haifa, Israel
| | | | - Roy Kishony
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel
- Computer Science Department, Technion - Israel Institute of Technology, Haifa, Israel
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21
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de Salazar A, Aguilera A, Trastoy R, Fuentes A, Alados JC, Causse M, Galán JC, Moreno A, Trigo M, Pérez-Ruiz M, Roldán C, Pena MJ, Bernal S, Serrano-Conde E, Barbeito G, Torres E, Riazzo C, Cortes-Cuevas JL, Chueca N, Coira A, Sanchez-Calvo JM, Marfil E, Becerra F, Gude MJ, Pallarés Á, Pérez Del Molino ML, García F. Sample pooling for SARS-CoV-2 RT-PCR screening. Clin Microbiol Infect 2020; 26:1687.e1-1687.e5. [PMID: 32919074 PMCID: PMC7481316 DOI: 10.1016/j.cmi.2020.09.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Revised: 09/01/2020] [Accepted: 09/03/2020] [Indexed: 11/21/2022]
Abstract
Objective To evaluate the efficacy of sample pooling compared to the individual analysis for the diagnosis of coronavirus disease 2019 (COVID-19) by using different commercial platforms for nucleic acid extraction and amplification. Methods A total of 3519 nasopharyngeal samples received at nine Spanish clinical microbiology laboratories were processed individually and in pools (342 pools of ten samples and 11 pools of nine samples) according to the existing methodology in place at each centre. Results We found that 253 pools (2519 samples) were negative and 99 pools (990 samples) were positive; with 241 positive samples (6.85%), our pooling strategy would have saved 2167 PCR tests. For 29 pools (made out of 290 samples), we found discordant results when compared to their correspondent individual samples, as follows: in 22 of 29 pools (28 samples), minor discordances were found; for seven pools (7 samples), we found major discordances. Sensitivity, specificity and positive and negative predictive values for pooling were 97.10% (95% confidence interval (CI), 94.11–98.82), 100%, 100% and 99.79% (95% CI, 99.56–99.90) respectively; accuracy was 99.80% (95% CI, 99.59–99.92), and the kappa concordant coefficient was 0.984. The dilution of samples in our pooling strategy resulted in a median loss of 2.87 (95% CI, 2.46–3.28) cycle threshold (Ct) for E gene, 3.36 (95% CI, 2.89–3.85) Ct for the RdRP gene and 2.99 (95% CI, 2.56–3.43) Ct for the N gene. Conclusions We found a high efficiency of pooling strategies for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA testing across different RNA extraction and amplification platforms, with excellent performance in terms of sensitivity, specificity and positive and negative predictive values.
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Affiliation(s)
- Adolfo de Salazar
- Clinical Microbiology Unit, Hospital Universitario Clínico San Cecilio, Granada, Spain; Instituto de Investigacion Biosanitaria Ibs.Granada, Granada, Spain
| | - Antonio Aguilera
- Clinical Microbiology Unit, Complexo Hospitalario Universitario de Santiago Santiago de Compostela, Spain; Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Spain
| | - Rocio Trastoy
- Clinical Microbiology Unit, Complexo Hospitalario Universitario de Santiago Santiago de Compostela, Spain; Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Spain
| | - Ana Fuentes
- Clinical Microbiology Unit, Hospital Universitario Clínico San Cecilio, Granada, Spain; Instituto de Investigacion Biosanitaria Ibs.Granada, Granada, Spain
| | - Juan Carlos Alados
- Clinical Microbiology Unit, Hospital Universitario de Jerez, Cádiz, Spain
| | - Manuel Causse
- Clinical Microbiology Unit, Hospital Universitario Reina Sofía, Córdoba, Spain; Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Córdoba, Spain
| | - Juan Carlos Galán
- Clinical Microbiology Unit, Hospital Universitario Ramón y Cajal, Madrid, Spain; Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), CIBER en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Antonio Moreno
- Clinical Microbiology Unit, Hospital Universitario Lucus Augusti de Lugo, Lugo, Spain
| | - Matilde Trigo
- Clinical Microbiology Unit, Complexo Hospitalario Universitario de Pontevedra, Pontevedra, Spain
| | - Mercedes Pérez-Ruiz
- Instituto de Investigacion Biosanitaria Ibs.Granada, Granada, Spain; Clinical Microbiology Unit, Hospital Universitario Virgen de las Nieves, Granada, Spain
| | - Carolina Roldán
- Clinical Microbiology Unit, Hospital Universitario de Jae, Jaen, Spain
| | - Maria José Pena
- Clinical Microbiology Unit, Hospital Universitario de Gran Canaria Dr. Negrín, Las Palmas de GC, Gran Canaria, Spain
| | - Samuel Bernal
- Unit of Infectious Disease and Clinical Microbiology, Hospital Universitario de Valme, Seville, Spain
| | - Esther Serrano-Conde
- Clinical Microbiology Unit, Hospital Universitario Clínico San Cecilio, Granada, Spain; Instituto de Investigacion Biosanitaria Ibs.Granada, Granada, Spain
| | - Gema Barbeito
- Clinical Microbiology Unit, Complexo Hospitalario Universitario de Santiago Santiago de Compostela, Spain; Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Spain
| | - Eva Torres
- Clinical Microbiology Unit, Hospital Universitario de Jerez, Cádiz, Spain
| | - Cristina Riazzo
- Clinical Microbiology Unit, Hospital Universitario Reina Sofía, Córdoba, Spain; Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Córdoba, Spain
| | | | - Natalia Chueca
- Clinical Microbiology Unit, Hospital Universitario Clínico San Cecilio, Granada, Spain; Instituto de Investigacion Biosanitaria Ibs.Granada, Granada, Spain
| | - Amparo Coira
- Clinical Microbiology Unit, Complexo Hospitalario Universitario de Santiago Santiago de Compostela, Spain; Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Spain
| | | | - Eduardo Marfil
- Clinical Microbiology Unit, Hospital Universitario Reina Sofía, Córdoba, Spain; Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Córdoba, Spain
| | - Federico Becerra
- Clinical Microbiology Unit, Hospital Universitario Ramón y Cajal, Madrid, Spain
| | - María José Gude
- Clinical Microbiology Unit, Hospital Universitario Lucus Augusti de Lugo, Lugo, Spain
| | - Ángeles Pallarés
- Clinical Microbiology Unit, Complexo Hospitalario Universitario de Pontevedra, Pontevedra, Spain
| | - María Luisa Pérez Del Molino
- Clinical Microbiology Unit, Complexo Hospitalario Universitario de Santiago Santiago de Compostela, Spain; Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Spain
| | - Federico García
- Clinical Microbiology Unit, Hospital Universitario Clínico San Cecilio, Granada, Spain; Instituto de Investigacion Biosanitaria Ibs.Granada, Granada, Spain.
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Abstract
Objective: Coronavirus disease (COVID-19) has emerged as a global pandemic for public health due to the large scale outbreak, therefore there is an urgent need to detect the infected cases quickly and isolate them in order to suppress the further spread of the disease. This study tries to identify a suitable pool testing method and algorithm for COVID-19. Methods: This study tries to derive a general equation for the number of tests required for a pooled sample to detect every infected individual in the specific pool. The gain in pool testing over the normal procedure is quantified by the percentage of tests required compared to individual testing. Results: The percentage of tests required by the pool testing strategy varies according to the different splitting procedures, the size of the pooled sample, and the probability of an individual being infected in the population. If the probability of infection is 0.05, then for a pool size of 32, only 14 tests are sufficient to detect every infected individual. Conclusion: The number of tests required to detect infected individuals by using the pooling method is much lower than individual testing. This may help us with increasing our testing capacity for COVID-19 by testing a large number of individuals in less time with limited resources.
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Implementation of Antibody Rapid Diagnostic Testing versus Real-Time Reverse Transcription-PCR Sample Pooling in the Screening of COVID-19: a Case of Different Testing Strategies in Africa. mSphere 2020; 5:5/4/e00524-20. [PMID: 32727861 PMCID: PMC7392544 DOI: 10.1128/msphere.00524-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) has wreaked havoc across the globe; although the number of cases in Africa remains lower than in other regions, it is on a gradual upward trajectory. To date, COVID-19 cases have been reported in 54 out of 55 African countries. However, due to limited severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) real-time reverse transcription-PCR (rRT-PCR) testing capacity and scarcity of testing reagents, it is probable that the total number of cases could far exceed published statistics. In this viewpoint, using Ghana, Malawi, South Africa, and Zimbabwe as examples of countries that have implemented different testing strategies, we argue that the implementation of sample pooling for rRT-PCR over antibody rapid diagnostic testing could have a greater impact in assessing disease burden. Sample pooling offers huge advantages compared to single test rRT-PCR, as it reduces diagnostic costs, personnel time, burnout, and analytical run times. Africa is already strained in terms of testing resources for COVID-19; hence, cheaper alternative ways need to be implemented to conserve resources, maximize mass testing, and reduce transmission in the wider population.
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24
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Petrovan V, Vrajmasu V, Bucur AC, Soare DS, Radu E, Dimon P, Zaulet M. Evaluation of Commercial qPCR Kits for Detection of SARS-CoV-2 in Pooled Samples. Diagnostics (Basel) 2020; 10:E472. [PMID: 32664511 PMCID: PMC7400658 DOI: 10.3390/diagnostics10070472] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 07/08/2020] [Accepted: 07/09/2020] [Indexed: 01/14/2023] Open
Abstract
Due to the current pandemic, a global shortage of reagents has drawn interest in developing alternatives to increase the number of coronavirus tests. One such alternative is sample pooling. We compared commercial kits that are used in COVID-19 diagnostics in terms of their sensitivity and feasibility for use in pooling. In this preliminary study, we showed that pooling of up to 80 samples did not affect the efficacy of the kits. Additionally, the RNA-dependent RNA polymerase (RdRp) gene is a more suitable target in pooled samples than the envelope (E) gene. This approach could provide an easy method of screening a large number of samples and help adjust different governmental regulations.
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Affiliation(s)
- Vlad Petrovan
- The Pirbright Institute, Woking, Surrey GU24 0NF, UK
| | | | - Ana Cristina Bucur
- Emergency Hospital Bucharest, Molecular Pathology Laboratory, 050098 Bucharest, Romania; (A.C.B.); (D.S.S.); (E.R.)
| | - Dan Sebastian Soare
- Emergency Hospital Bucharest, Molecular Pathology Laboratory, 050098 Bucharest, Romania; (A.C.B.); (D.S.S.); (E.R.)
| | - Eugen Radu
- Emergency Hospital Bucharest, Molecular Pathology Laboratory, 050098 Bucharest, Romania; (A.C.B.); (D.S.S.); (E.R.)
| | - Paula Dimon
- Personal Genetics, 010987 Bucharest, Romania;
| | - Mihaela Zaulet
- Department of Biochemistry and Molecular Biology, Faculty of Biology, University of Bucharest, 050095 Bucharest, Romania;
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25
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Pouwels KB, Roope LSJ, Barnett A, Hunter DJ, Nolan TM, Clarke PM. Group Testing for SARS-CoV-2: Forward to the Past? PHARMACOECONOMICS - OPEN 2020; 4:207-210. [PMID: 32347512 PMCID: PMC7187661 DOI: 10.1007/s41669-020-00217-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Affiliation(s)
- Koen B Pouwels
- Health Economics Research Centre, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Laurence S J Roope
- Health Economics Research Centre, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Adrian Barnett
- Institute of Health Biomedical Innovation (IHBI), Queensland University of Technology, Brisbane, QLD, Australia
| | - David J Hunter
- Translational Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Terry M Nolan
- The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Philip M Clarke
- Health Economics Research Centre, Nuffield Department of Population Health, University of Oxford, Oxford, UK.
- Centre for Health Policy, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, VIC, Australia.
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26
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Bukhari SUK, Khalid SS, Syed A, Shah SSH. Smart Pooled Sample Testing for COVID-19: A Possible Solution For Sparcity of Test Kits (Preprint). J Med Internet Res 2020. [DOI: 10.2196/20831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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