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Matsumura Y, Noguchi T, Shinohara K, Yamamoto M, Nagao M. Development and evaluation of three automated media pooling and molecular diagnostic systems for the detection of SARS-CoV-2. Microbiol Spectr 2024; 12:e0368423. [PMID: 38289934 PMCID: PMC10913432 DOI: 10.1128/spectrum.03684-23] [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: 10/19/2023] [Accepted: 12/22/2023] [Indexed: 02/01/2024] Open
Abstract
Pooled testing combined with molecular diagnostics for the detection of SARS-CoV-2 is a promising method that can increase testing capacities and save costs. However, pooled testing is also associated with the risks of decreased test sensitivity and specificity. To perform reliable pooled testing, we developed and validated three automated media pooling and molecular diagnostic systems. These pooling systems (geneLEAD-PS, Panther-PS, and Biomek-PS) comprised existing automated molecular detection platforms, corresponding automated media pooling devices, and laboratory information management systems. Analytical sensitivity analysis and mock sample evaluation were performed, and the obtained data were used to determine the sizes of the pool for the validation study. In the validation study, a total of 2,448, 3,228, and 6,420 upper respiratory samples were used for geneLEAD-PS, Panther-PS, and Biomek-PS, respectively, and the diagnostic performances were compared with the reference RT‒PCR assay. A pool size of 6 for geneLEAD-PS and a pool size of 4 for Panther-PS and Biomek-PS were selected for the validation studies. All three systems showed high positive percent agreement values of ≥90.5% and negative percent agreement values of ≥99.8% for any specimen type. Pooled testing resulted in a 65%-71% reduction in cost per sample. The testing capacities of geneLEAD-PS, Panther-PS, and Biomek-PS were 144 samples in 3 hours, 384 samples in 5.5 hours, and 376 samples in 4 hours, respectively. The developed pooling systems showed robust diagnostic performances and will increase the testing capacities of molecular diagnostic tests while saving costs and may contribute to infection control of COVID-19.IMPORTANCEDuring the COVID-19 pandemic, there have been surges in demand for accurate molecular diagnostic testing and laboratory supply shortages. Pooled testing combined with highly sensitive molecular testing, which entails mixing multiple samples as a single sample, is a promising approach to increase testing capacities while reducing the use of consumables. However, pooled testing is associated with risks that compromise diagnostic performance, such as false negatives due to dilution of positive samples or false positives due to cross-contamination. To perform reliable pooled testing, three different pooling systems (an automated pooling device, an automated molecular detection platform, and a laboratory information management system) were developed to accurately interpret pooled testing results. These three systems were validated using multiple clinical samples and showed high concordance with individual testing. The developed pooling systems will contribute to increasing reliable molecular testing capacities while using fewer consumables and saving costs.
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Affiliation(s)
- Yasufumi Matsumura
- Department of Clinical Laboratory Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Taro Noguchi
- Department of Clinical Laboratory Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Koh Shinohara
- Department of Clinical Laboratory Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Masaki Yamamoto
- Department of Clinical Laboratory Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Miki Nagao
- Department of Clinical Laboratory Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
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2
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Benede NSB, Tincho MB, Walters A, Subbiah V, Ngomti A, Baguma R, Butters C, Mennen M, Skelem S, Adriaanse M, van Graan S, Balla SR, Moyo-Gwete T, Moore PL, Botha M, Workman L, Zar HJ, Ntusi NAB, Zühlke L, Webb K, Riou C, Burgers WA, Keeton RS. Distinct T cell functional profiles in SARS-CoV-2 seropositive and seronegative children associated with endemic human coronavirus cross-reactivity. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.05.16.23290059. [PMID: 37292954 PMCID: PMC10246143 DOI: 10.1101/2023.05.16.23290059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
SARS-CoV-2 infection in children typically results in asymptomatic or mild disease. There is a paucity of studies on antiviral immunity in African children. We investigated SARS-CoV-2-specific T cell responses in 71 unvaccinated asymptomatic South African children who were seropositive or seronegative for SARS-CoV-2. SARS-CoV-2-specific CD4+ T cell responses were detectable in 83% of seropositive and 60% of seronegative children. Although the magnitude of the CD4+ T cell response did not differ significantly between the two groups, their functional profiles were distinct, with SARS-CoV-2 seropositive children exhibiting a higher proportion of polyfunctional T cells compared to their seronegative counterparts. The frequency of SARS-CoV-2-specific CD4+ T cells in seronegative children was associated with the endemic human coronavirus (HCoV) HKU1 IgG response. Overall, the presence of SARS-CoV-2-responding T cells in seronegative children may result from cross-reactivity to endemic coronaviruses and could contribute to the relative protection from disease observed in SARS-CoV-2-infected children.
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Affiliation(s)
- Ntombi S. B. Benede
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, South Africa
- Division of Medical Virology, Department of Pathology, University of Cape Town, Observatory, South Africa
| | - Marius B. Tincho
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, South Africa
- Division of Medical Virology, Department of Pathology, University of Cape Town, Observatory, South Africa
| | - Avril Walters
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, South Africa
- Division of Medical Virology, Department of Pathology, University of Cape Town, Observatory, South Africa
| | - Vennesa Subbiah
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, South Africa
- Division of Medical Virology, Department of Pathology, University of Cape Town, Observatory, South Africa
| | - Amkele Ngomti
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, South Africa
- Division of Medical Virology, Department of Pathology, University of Cape Town, Observatory, South Africa
| | - Richard Baguma
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, South Africa
- Division of Medical Virology, Department of Pathology, University of Cape Town, Observatory, South Africa
| | - Claire Butters
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, South Africa
| | - Mathilda Mennen
- Department of Medicine, University of Cape Town and Groote Schuur Hospital, Observatory, South Africa
| | - Sango Skelem
- Department of Medicine, University of Cape Town and Groote Schuur Hospital, Observatory, South Africa
| | - Marguerite Adriaanse
- Department of Medicine, University of Cape Town and Groote Schuur Hospital, Observatory, South Africa
| | - Strauss van Graan
- National Institute for Communicable Diseases of the National Health Laboratory Services, Johannesburg, South Africa
- MRC Antibody Immunity Research Unit, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Sashkia R. Balla
- National Institute for Communicable Diseases of the National Health Laboratory Services, Johannesburg, South Africa
- MRC Antibody Immunity Research Unit, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Thandeka Moyo-Gwete
- National Institute for Communicable Diseases of the National Health Laboratory Services, Johannesburg, South Africa
- MRC Antibody Immunity Research Unit, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Penny L. Moore
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, South Africa
- National Institute for Communicable Diseases of the National Health Laboratory Services, Johannesburg, South Africa
- MRC Antibody Immunity Research Unit, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
| | - Maresa Botha
- Department of Paediatrics and Child Health, University of Cape Town, Cape Town, South Africa
- Medical Research Council (MRC) Unit on Child and Adolescent Health, University of Cape Town, Cape Town, South Africa
| | - Lesley Workman
- Department of Paediatrics and Child Health, University of Cape Town, Cape Town, South Africa
- Medical Research Council (MRC) Unit on Child and Adolescent Health, University of Cape Town, Cape Town, South Africa
| | - Heather J. Zar
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, South Africa
- Department of Paediatrics and Child Health, University of Cape Town, Cape Town, South Africa
- Medical Research Council (MRC) Unit on Child and Adolescent Health, University of Cape Town, Cape Town, South Africa
- Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Observatory, South Africa
| | - Ntobeko A. B. Ntusi
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, South Africa
- Department of Medicine, University of Cape Town and Groote Schuur Hospital, Observatory, South Africa
- Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Observatory, South Africa
- Cape Heart Institute, Faculty of Health Sciences, University of Cape Town, Observatory, South Africa
| | - Liesl Zühlke
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, South Africa
- Department of Paediatrics and Child Health, University of Cape Town, Cape Town, South Africa
- Cape Heart Institute, Faculty of Health Sciences, University of Cape Town, Observatory, South Africa
- South African Medical Research Council, Francie Van Zijl Drive, Parow Cape Town, South Africa
| | - Kate Webb
- South African Medical Research Council, Francie Van Zijl Drive, Parow Cape Town, South Africa
- Crick African Network, The Francis Crick Institute, London, United Kingdom
| | - Catherine Riou
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, South Africa
- Division of Medical Virology, Department of Pathology, University of Cape Town, Observatory, South Africa
- Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Observatory, South Africa
| | - Wendy A. Burgers
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, South Africa
- Division of Medical Virology, Department of Pathology, University of Cape Town, Observatory, South Africa
- Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Observatory, South Africa
| | - Roanne S. Keeton
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, South Africa
- Division of Medical Virology, Department of Pathology, University of Cape Town, Observatory, South Africa
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Abstract
Scaling up SARS-CoV-2 testing during the COVID-19 pandemic was critical to maintaining clinical operations and an open society. Pooled testing and automation were two critical strategies used by laboratories to meet the unprecedented demand. Here, we review these and other cutting-edge strategies that sought to expand SARS-CoV-2 testing capacity while maintaining high individual test performance.
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Affiliation(s)
- Sanchita Das
- Department of Laboratory Medicine, National Institutes of Health Clinical Center, Bethesda, MD 20892, USA
| | - Karen M Frank
- Department of Laboratory Medicine, National Institutes of Health Clinical Center, Bethesda, MD 20892, USA.
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4
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Correa IA, de Souza Rodrigues T, Queiroz A, de França Nascimento L, Wolff T, Akamine RN, Kuriyama SN, da Costa LJ, Fidalgo-Neto AA. Boosting SARS-CoV-2 detection combining pooling and multiplex strategies. Sci Rep 2022; 12:8684. [PMID: 35606418 PMCID: PMC9126939 DOI: 10.1038/s41598-022-12747-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 04/28/2022] [Indexed: 11/09/2022] Open
Abstract
RT-qPCR is the gold standard technique available for SARS-CoV-2 detection. However, the long test run time and costs associated with this type of molecular testing are a challenge in a pandemic scenario. Due to high testing demand, especially for monitoring highly vaccinated populations facing the emergence of new SARS-CoV-2 variants, strategies that allow the increase in testing capacity and cost savings are needed. We evaluated a RT-qPCR pooling strategy either as a simplex and multiplex assay, as well as performed in-silico statistical modeling analysis validated with specimen samples obtained from a mass testing program of Industry Federation of the State of Rio de Janeiro (Brazil). Although the sensitivity reduction in samples pooled with 32 individuals in a simplex assay was observed, the high-test sensitivity was maintained even when 16 and 8 samples were pooled. This data was validated with the results obtained in our mass testing program with a cost saving of 51.5% already considering the expenditures with pool sampling that were analyzed individually. We also demonstrated that the pooling approach using 4 or 8 samples tested with a triplex combination in RT-qPCR is feasible to be applied without sensitivity loss, mainly combining Nucleocapsid (N) and Envelope (E) gene targets. Our data shows that the combination of pooling in a RT-qPCR multiplex assay could strongly contribute to mass testing programs with high-cost savings and low-reagent consumption while maintaining test sensitivity. In addition, the test capacity is predicted to be considerably increased which is fundamental for the control of the virus spread in the actual pandemic scenario.
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Affiliation(s)
- Isadora Alonso Correa
- Departamento de Virologia, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-617, Brazil.,Instituto Senai de Inovação em Química Verde, Rua Moraes e Silva, 53-9, Maracanã, Rio de Janeiro, RJ, 20271-030, Brazil
| | - Tamires de Souza Rodrigues
- Centro de Inovação SESI em Saúde Ocupacional, Rio de Janeiro, 20271-030, Brazil.,Centro de Pesquisa Leopoldo Américo Miguez de Mello (CENPES)-Petrobrás, Rio de Janeiro, 21941-915, Brazil
| | - Alex Queiroz
- Centro de Inovação SESI em Saúde Ocupacional, Rio de Janeiro, 20271-030, Brazil.,Centro de Pesquisa Leopoldo Américo Miguez de Mello (CENPES)-Petrobrás, Rio de Janeiro, 21941-915, Brazil
| | - Leon de França Nascimento
- Centro de Inovação SESI em Saúde Ocupacional, Rio de Janeiro, 20271-030, Brazil.,Centro de Pesquisa Leopoldo Américo Miguez de Mello (CENPES)-Petrobrás, Rio de Janeiro, 21941-915, Brazil
| | - Thiago Wolff
- Centro de Inovação SESI em Saúde Ocupacional, Rio de Janeiro, 20271-030, Brazil.,Centro de Pesquisa Leopoldo Américo Miguez de Mello (CENPES)-Petrobrás, Rio de Janeiro, 21941-915, Brazil
| | - Rubens Nobumoto Akamine
- Laboratório de Genética e Imunologia das Infecções Virais, Departamento de Virologia, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Avenida Carlos Chagas Filho, 373, CCS, Bloco I, Lab.I-SS 048, Cidade Universitária, Rio de Janeiro, RJ, 21941-902, Brazil
| | - Sergio Noboru Kuriyama
- Centro de Inovação SESI em Saúde Ocupacional, Rio de Janeiro, 20271-030, Brazil.,Centro de Pesquisa Leopoldo Américo Miguez de Mello (CENPES)-Petrobrás, Rio de Janeiro, 21941-915, Brazil
| | - Luciana Jesus da Costa
- Departamento de Virologia, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-617, Brazil. .,Instituto Senai de Inovação em Química Verde, Rua Moraes e Silva, 53-9, Maracanã, Rio de Janeiro, RJ, 20271-030, Brazil.
| | - Antonio Augusto Fidalgo-Neto
- Centro de Inovação SESI em Saúde Ocupacional, Rio de Janeiro, 20271-030, Brazil. .,Centro de Pesquisa Leopoldo Américo Miguez de Mello (CENPES)-Petrobrás, Rio de Janeiro, 21941-915, Brazil.
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5
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Bogere N, Bongomin F, Katende A, Ssebambulidde K, Ssengooba W, Ssenfuka H, Kigozi E, Biraro S, Kateete DP, Andia-Biraro I. Performance and cost-effectiveness of a pooled testing strategy for SARS-CoV-2 using real-time polymerase chain reaction in Uganda. Int J Infect Dis 2021; 113:355-358. [PMID: 34757007 PMCID: PMC8553367 DOI: 10.1016/j.ijid.2021.10.038] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Revised: 10/20/2021] [Accepted: 10/21/2021] [Indexed: 11/28/2022] Open
Abstract
Real-time polymerase chain reaction (RT-PCR) remains the gold standard for detection of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). This study tested the performance of a pooled testing strategy for RT-PCR and its cost-effectiveness. In total, 1280 leftover respiratory samples collected between 19 April and 6 May 2021 were tested in 128 pools of 10 samples each, out of which 16 pools were positive. The positivity rate of the unpooled samples was 1.9% (24/1280). After parallel testing using the individual and pooled testing strategies, positive agreement was 100% and negative agreement was 99.8%. The overall median cycle threshold (Ct) value of the unpooled samples was 29.8 (interquartile range 22.3-34.3). Pools that remained positive when compared with the results of individual samples had lower median Ct values compared with those that turned out to be negative (28.8 versus 34.8; P=0.0.035). Pooled testing reduced the cost >4-fold. Pooled testing may be a more cost-effective approach to diagnose SARS-CoV-2 in resource-limited settings without compromising diagnostic performance.
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Affiliation(s)
| | - Felix Bongomin
- Department of Medicine, School of Medicine, Makerere University, Kampala, Uganda; Department of Medical Microbiology and Immunology, Faculty of Medicine, Gulu University, Gulu, Uganda.
| | | | | | - Willy Ssengooba
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, Makerere University College of Health Sciences, Kampala, Uganda
| | - Henry Ssenfuka
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, Makerere University College of Health Sciences, Kampala, Uganda
| | - Edgar Kigozi
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, Makerere University College of Health Sciences, Kampala, Uganda
| | - Samuel Biraro
- Clockworks Research Company Limited, Kampala, Uganda
| | - David P Kateete
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, Makerere University College of Health Sciences, Kampala, Uganda
| | - Irene Andia-Biraro
- Department of Medicine, School of Medicine, Makerere University, Kampala, Uganda; Medical Research Council/Uganda Virus Research Institute and London School of Hygiene and Tropical Medicine Uganda Research Unit, Entebbe, Uganda
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6
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Daniel EA, Esakialraj L BH, S A, Muthuramalingam K, Karunaianantham R, Karunakaran LP, Nesakumar M, Selvachithiram M, Pattabiraman S, Natarajan S, Tripathy SP, Hanna LE. Pooled Testing Strategies for SARS-CoV-2 diagnosis: A comprehensive review. Diagn Microbiol Infect Dis 2021; 101:115432. [PMID: 34175613 PMCID: PMC8127528 DOI: 10.1016/j.diagmicrobio.2021.115432] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 05/09/2021] [Indexed: 12/23/2022]
Abstract
SARS-CoV-2 has surged across the globe causing the ongoing COVID-19 pandemic. Systematic testing to facilitate index case isolation and contact tracing is needed for efficient containment of viral spread. The major bottleneck in leveraging testing capacity has been the lack of diagnostic resources. Pooled testing is a potential approach that could reduce cost and usage of test kits. This method involves pooling individual samples and testing them 'en bloc'. Only if the pool tests positive, retesting of individual samples is performed. Upon reviewing recent articles on this strategy employed in various SARS-CoV-2 testing scenarios, we found substantial diversity emphasizing the requirement of a common protocol. In this article, we review various theoretically simulated and clinically validated pooled testing models and propose practical guidelines on applying this strategy for large scale screening. If implemented properly, the proposed approach could contribute to proper utilization of testing resources and flattening of infection curve.
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Affiliation(s)
- Evangeline Ann Daniel
- Department of HIV/AIDS, National Institute for Research in Tuberculosis, Chennai, India.
| | | | - Anbalagan S
- Department of HIV/AIDS, National Institute for Research in Tuberculosis, Chennai, India
| | | | | | | | - Manohar Nesakumar
- Department of HIV/AIDS, National Institute for Research in Tuberculosis, Chennai, India
| | | | | | - Sudhakar Natarajan
- Department of HIV/AIDS, National Institute for Research in Tuberculosis, Chennai, India
| | | | - Luke Elizabeth Hanna
- Department of HIV/AIDS, National Institute for Research in Tuberculosis, Chennai, India.
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7
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Chan CW, Kwon S, Matushek SM, Ciaglia C, Bethel C, Beavis KG. Implementation of a Sample Pooling Strategy for the Direct Detection of SARS-CoV-2 by Real-Time Polymerase Chain Reaction During the COVID-19 Pandemic. Am J Clin Pathol 2021; 156:15-23. [PMID: 33978164 PMCID: PMC8136033 DOI: 10.1093/ajcp/aqab035] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Objectives To report our institutional experience in devising and implementing a pooling protocol and process for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) reverse transcription polymerase chain reaction (RT-PCR) testing over a 3-month period in the fall of 2020. Methods The widespread testing implemented in the United States for detecting SARS-CoV-2 infection in response to the coronavirus disease 2019 pandemic has led to a significant shortage of testing supplies and therefore has become a major impediment to the public health response. To date, several institutions have implemented sample pooling, but publications documenting these experiences are sparse. Nasal and nasopharyngeal samples collected from low-positivity (<5%) areas were tested in pools of five on the Roche cobas 6800 analyzer system. Routine SARS-CoV-2 RT-PCR turnaround times between sample collection to result reporting were monitored and compared before and after sample pooling implementation. Results A total of 4,131 sample pools were tested over a 3-month period (during which 39,770 RT-PCR results were reported from the Roche system), allowing our laboratory to save 13,824 tests, equivalent to a conservation rate of 35%. A 48-hour or less turnaround time was generally maintained throughout the pooling period. Conclusions Sample pooling offers a viable means to mitigate shortfalls of PCR testing supplies in the ongoing pandemic without significantly compromising overall turnaround times.
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Affiliation(s)
| | | | - Scott M Matushek
- Clinical Microbiology and Immunology Laboratory, University of Chicago, Chicago, IL, USA
| | - Carol Ciaglia
- Clinical Microbiology and Immunology Laboratory, University of Chicago, Chicago, IL, USA
| | - Cindy Bethel
- Clinical Microbiology and Immunology Laboratory, University of Chicago, Chicago, IL, USA
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8
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Balasubramani B, Newsom KJ, Martinez KA, Starostik P, Clare-Salzler M, Chamala S. Pathology Informatics and Robotics Strategies for Improving Efficiency of COVID-19 Pooled Testing. Acad Pathol 2021; 8:23742895211020485. [PMID: 34189259 PMCID: PMC8209787 DOI: 10.1177/23742895211020485] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 04/19/2021] [Accepted: 05/05/2021] [Indexed: 11/25/2022] Open
Abstract
The global rise of the coronavirus disease 2019 pandemic resulted in an exponentially increasing demand for severe acute respiratory syndrome coronavirus 2 testing, which resulted in shortage of reagents worldwide. This shortage has been further worsened by screening of asymptomatic populations such as returning employees, students, and so on, as part of plans to reopen the economy. To optimize the utilization of testing reagents and human resources, pool testing of populations with low prevalence has emerged as a promising strategy. Although pooling is an effective solution to reduce the number of reagents used for testing, the process of pooling samples together and tracking them throughout the entire workflow is challenging. To be effective, samples must be tracked into each pool, pool-tested and reported individually. In this article, we address these challenges using robotics and informatics.
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Affiliation(s)
- Balaji Balasubramani
- Department of Computer and Information Science and Engineering, University of Florida, Gainesville, FL, USA.,Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL, USA
| | - Kimberly J Newsom
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL, USA
| | - Katherine A Martinez
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL, USA
| | - Petr Starostik
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL, USA
| | - Michael Clare-Salzler
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL, USA
| | - Srikar Chamala
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL, USA
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9
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Plantes PJ, Fragala MS, Clarke C, Goldberg ZN, Radcliff J, Goldberg SE. Model for Mitigation of Workplace Transmission of COVID-19 Through Population-Based Testing and Surveillance. Popul Health Manag 2021; 24:S16-S25. [PMID: 33493409 PMCID: PMC7875134 DOI: 10.1089/pop.2020.0322] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The coronavirus disease-2019 (COVID-19) pandemic is having a widespread impact on societies across the globe. As part of the effort to control transmission in the United States, many businesses either closed or instituted nonpharmaceutical control measures and allowed only essential workers on-site. During summer and fall of 2020, employers began formulating "return to work" strategies designed to mitigate the risk of transmission among employees. On a population level, several countries implemented national testing and surveillance strategies that proved effective in mitigating citizen-to-citizen transmission and contributed to suppressing COVID-19. A crucial component of many such strategies is population-based testing to identify and engage individuals with asymptomatic or presymptomatic infection, which also is relevant to return-to-work strategies. The authors describe an approach that multisite employers might use to help mitigate transmission of COVID-19 in the workplace. This approach leverages a bioinformatics platform informed by real-time PCR test data at the county and subcounty (eg, Public Use Microdata Area) level, allowing for population-based testing to be selectively targeted for employees in geographies with elevated SARS-CoV-2 positivity. A "Command Center" application integrates data from multiple sources (eg, local infection trends, employee symptom diaries, Bluetooth thermometers) in real time, which can be used to inform decisions regarding surveillance and employee self-isolation or quarantine; a mobile phone-based application provides for rapid, secure communication with employees. This overview is based on peer-reviewed literature and the early experience of a large employer with implementing bioinformatics tools to mitigate the impact of the pandemic on the workplace.
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10
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Kagan RM, Rogers AA, Borillo GA, Clarke NJ, Marlowe EM. Performance of Unobserved Self-Collected Nasal Swabs for Detection of SARS-CoV-2 by RT-PCR Utilizing a Remote Specimen Collection Strategy. Open Forum Infect Dis 2021; 8:ofab039. [PMID: 33954224 PMCID: PMC7928651 DOI: 10.1093/ofid/ofab039] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 01/25/2021] [Indexed: 12/23/2022] Open
Abstract
Background The use of a remote specimen collection strategy employing a kit designed for unobserved self-collection for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) reverse transcription polymerase chain reaction (RT-PCR) can decrease the use of personal protective equipment (PPE) and exposure risk. To assess the impact of unobserved specimen self-collection on test performance, we examined results from a SARS-CoV-2 qualitative RT-PCR test for self-collected specimens from participants in a return-to-work screening program and assessed the impact of a pooled testing strategy in this cohort. Methods Self-collected anterior nasal swabs from employee return-to-work programs were tested using the Quest Diagnostics Emergency Use Authorization SARS-CoV-2 RT-PCR. The cycle threshold (Ct) values for the N1 and N3 N-gene targets and a human RNase P (RP) gene control target were tabulated. For comparison, we utilized Ct values from a cohort of health care provider–collected specimens from patients with and without coronavirus disease 2019 symptoms. Results Among 47 923 participants, 1.8% were positive. RP failed to amplify for 13/115 435 (0.011%) specimens. The median (interquartile range) Cts were 32.7 (25.0–35.7) for N1 and 31.3 (23.8–34.2) for N3. Median Ct values in the self-collected cohort were significantly higher than those of symptomatic but not asymptomatic patients. Based on Ct values, pooled testing with 4 specimens would have yielded inconclusive results in 67/1268 (5.2%) specimens but only a single false-negative result. Conclusions Unobserved self-collection of nasal swabs provides adequate sampling for SARS-CoV-2 RT-PCR testing. These findings alleviate concerns of increased false negatives in this context. Specimen pooling could be used for this population, as the likelihood of false-negative results is very low when using a sensitive, dual-target methodology.
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Affiliation(s)
- Ron M Kagan
- Quest Diagnostics Infectious Disease, San Juan Capistrano, California, USA
| | - Amy A Rogers
- Quest Diagnostics Infectious Disease, San Juan Capistrano, California, USA
| | | | - Nigel J Clarke
- Quest Diagnostics Nichols Institute, San Juan Capistrano, California, USA
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