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Filiatreau LM, Zivich PN, Edwards JK, Mulholland GE, Max R, Westreich D. Optimizing SARS-CoV-2 Pooled Testing Strategies Through Differentiated Pooling for Distinct Groups. Am J Epidemiol 2023; 192:246-256. [PMID: 36222677 PMCID: PMC9620733 DOI: 10.1093/aje/kwac178] [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: 03/25/2021] [Revised: 08/02/2022] [Accepted: 10/06/2022] [Indexed: 02/07/2023] Open
Abstract
Pooled testing has been successfully used to expand SARS-CoV-2 testing, especially in settings requiring high volumes of screening of lower-risk individuals, but efficiency of pooling declines as prevalence rises. We propose a differentiated pooling strategy that independently optimizes pool sizes for distinct groups with different probabilities of infection to further improve the efficiency of pooled testing. We compared the efficiency (results obtained per test kit used) of the differentiated strategy with a traditional pooling strategy in which all samples are processed using uniform pool sizes under a range of scenarios. For most scenarios, differentiated pooling is more efficient than traditional pooling. In scenarios examined here, an improvement in efficiency of up to 3.94 results per test kit could be obtained through differentiated versus traditional pooling, with more likely scenarios resulting in 0.12 to 0.61 additional results per kit. Under circumstances similar to those observed in a university setting, implementation of our strategy could result in an improvement in efficiency between 0.03 to 3.21 results per test kit. Our results can help identify settings, such as universities and workplaces, where differentiated pooling can conserve critical testing resources.
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Affiliation(s)
- Lindsey M Filiatreau
- Correspondence Address: Department of Psychiatry, Washington University in St. Louis, 660 S. Euclid, St. Louis, MO 63110, E-mail:
| | - Paul N Zivich
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Carolina Population Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Jessie K Edwards
- Gillings Center for Coronavirus Testing, Screening, and Surveillance, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Grace E Mulholland
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Ryan Max
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Daniel Westreich
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Gillings Center for Coronavirus Testing, Screening, and Surveillance, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
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Mobini M, Matic N, Gugten JGVD, Ritchie G, Lowe CF, Holmes DT. End-to-End Data Automation for Pooled Sample SARS-CoV-2 Using R and Other Open-Source Tools. J Appl Lab Med 2023; 8:41-52. [PMID: 36610407 DOI: 10.1093/jalm/jfac109] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 10/17/2022] [Indexed: 01/09/2023]
Abstract
BACKGROUND Due to supply chain shortages of reagents for real-time (RT)-PCR for SARS-CoV-2 and increasing demand on technical staff, an end-to-end data automation strategy for SARS-CoV-2 sample pooling and singleton analysis became necessary in the summer of 2020. METHODS Using entirely open source software tools-Linux, bash, R, RShiny, ShinyProxy, and Docker-we developed a modular software application stack to manage the preanalytical, analytical, and postanalytical processes for singleton and pooled testing in a 5-week time frame. RESULTS Pooling was operationalized for 81 days, during which time 64 pooled runs were performed for a total of 5320 sample pools and approximately 21 280 patient samples in 4:1 format. A total of 17 580 negative pooled results were released in bulk. After pooling was discontinued, the application stack was used for singleton analysis and modified to release all viral RT-PCR results from our laboratory. To date, 236 109 samples have been processed avoiding over 610 000 transcriptions. CONCLUSIONS We present an end-to-end data automation strategy connecting 11 devices, one network attached storage, 2 Linux servers, and the laboratory information system.
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Affiliation(s)
- Mahdi Mobini
- St. Paul's Hospital Department of Pathology and Laboratory Medicine, Vancouver, BC, Canada.,Providence Health Emerging Technologies, Vancouver, BC, Canada
| | - Nancy Matic
- St. Paul's Hospital Department of Pathology and Laboratory Medicine, Vancouver, BC, Canada.,University of British Columbia Department of Pathology and Laboratory Medicine, Vancouver, BC, Canada
| | - J Grace Van Der Gugten
- St. Paul's Hospital Department of Pathology and Laboratory Medicine, Vancouver, BC, Canada
| | - Gordon Ritchie
- St. Paul's Hospital Department of Pathology and Laboratory Medicine, Vancouver, BC, Canada.,University of British Columbia Department of Pathology and Laboratory Medicine, Vancouver, BC, Canada
| | - Christopher F Lowe
- St. Paul's Hospital Department of Pathology and Laboratory Medicine, Vancouver, BC, Canada.,University of British Columbia Department of Pathology and Laboratory Medicine, Vancouver, BC, Canada
| | - Daniel T Holmes
- St. Paul's Hospital Department of Pathology and Laboratory Medicine, Vancouver, BC, Canada.,University of British Columbia Department of Pathology and Laboratory Medicine, Vancouver, BC, Canada
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Kästner A, Lücker P, Sombetzki M, Ehmke M, Koslowski N, Mittmann S, Hannich A, Schwarz A, Meinck K, Schmeyers L, Schmidt K, Reisinger EC, Hoffmann W. SARS-CoV-2 surveillance by RT-qPCR-based pool testing of saliva swabs (lollipop method) at primary and special schools—A pilot study on feasibility and acceptability. PLoS One 2022; 17:e0274545. [PMID: 36099277 PMCID: PMC9469960 DOI: 10.1371/journal.pone.0274545] [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: 05/22/2022] [Accepted: 08/30/2022] [Indexed: 12/03/2022] Open
Abstract
Background Since the onset of the COVID-19 pandemic, children have been mentally and physically burdened, particularly due to school closures, with an associated loss of learning. Therefore, efficient testing strategies with high sensitivity are necessary to keep schools open. Apart from individual rapid antigen testing, various methods have been investigated, such as PCR-based pool-testing of nasopharyngeal swabs, gargle, or saliva samples. To date, previous validation studies have found the PCR-based saliva swab pool testing method to be an effective screening method, however, the acceptability and feasibility of a widespread implementation in the school-setting among stakeholders has not been comprehensively evaluated. Methods In this pilot study, SARS-CoV-2 saliva swab pool testing of up to 15 swabs per pool was conducted in ten primary and special schools in Mecklenburg-Western Pomerania, Germany, over a period of one month. Thereafter, parents, teachers and school principals of the participating schools as well as the participating laboratories were surveyed about the feasibility and acceptability of this method, its large-scale implementation and challenges. Data were analyzed quantitatively and qualitatively. Results During the study period, 1,630 saliva swab pools were analyzed, of which 22 tested SARS-CoV-2 positive (1.3%). A total of N = 315 participants took part in the survey. Across all groups, the saliva swab pool testing method was perceived as more child-friendly (>87%), convenient (>82%), and easier (>81%) compared to rapid antigen testing by an anterior nasal swab. Over 80% of all participants favored widespread, regular use of the saliva swab method. Conclusion In school settings in particular, a high acceptability of the test method is crucial for a successful SARS-CoV-2 surveillance strategy. All respondents clearly preferred the saliva swab method, which can be used safely without complications in children six years of age and older. Hurdles and suggestions for improvement of an area-wide implementation were outlined.
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Affiliation(s)
- Anika Kästner
- Institute for Community Medicine, Section Epidemiology of Health Care and Community Health, University Medicine Greifswald, Greifswald, Germany
- * E-mail:
| | - Petra Lücker
- Institute for Community Medicine, Section Epidemiology of Health Care and Community Health, University Medicine Greifswald, Greifswald, Germany
| | - Martina Sombetzki
- Department of Tropical Medicine and Infectious Diseases, University Medical Center Rostock, Rostock, Germany
| | - Manja Ehmke
- Department of Tropical Medicine and Infectious Diseases, University Medical Center Rostock, Rostock, Germany
| | - Nicole Koslowski
- Department of Tropical Medicine and Infectious Diseases, University Medical Center Rostock, Rostock, Germany
| | - Swantje Mittmann
- Department of Tropical Medicine and Infectious Diseases, University Medical Center Rostock, Rostock, Germany
| | - Arne Hannich
- Institute for Community Medicine, Section Epidemiology of Health Care and Community Health, University Medicine Greifswald, Greifswald, Germany
| | | | | | - Lena Schmeyers
- Institute for Community Medicine, Section Epidemiology of Health Care and Community Health, University Medicine Greifswald, Greifswald, Germany
| | - Katrin Schmidt
- Department of Tropical Medicine and Infectious Diseases, University Medical Center Rostock, Rostock, Germany
| | - Emil C. Reisinger
- Department of Tropical Medicine and Infectious Diseases, University Medical Center Rostock, Rostock, Germany
| | - Wolfgang Hoffmann
- Institute for Community Medicine, Section Epidemiology of Health Care and Community Health, University Medicine Greifswald, Greifswald, Germany
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Phan T, Tran NYK, Gottlieb T, Siarakas S, McKew G. Evaluation of the influenza and respiratory syncytial virus (RSV) targets in the AusDiagnostics SARS-CoV-2, Influenza and RSV 8-well assay: sample pooling increases testing throughput. Pathology 2022; 54:466-471. [PMID: 35461715 PMCID: PMC9021007 DOI: 10.1016/j.pathol.2022.02.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 01/09/2022] [Accepted: 02/22/2022] [Indexed: 02/06/2023]
Abstract
During the COVID-19 pandemic, sample pooling has proven an effective strategy to overcome the limitations of reagent shortages and expand laboratory testing capacity. The inclusion of influenza and respiratory syncytial virus (RSV) in a multiplex tandem PCR platform with SARS-CoV-2 provides useful diagnostic and infection control information. This study aimed to evaluate the performance of the influenza and RSV targets in the AusDiagnostics SARS-CoV-2, Influenza and RSV 8-well assay, including the effect of pooling samples on target detection. RSV target detection in clinical samples was compared to the Cepheid Xpert Xpress Flu/RSV assay as a reference standard. Samples were then tested in pools of four and detection rates were compared. Owing to the unavailability of clinical samples for influenza, only the effect of sample pooling on simulated samples was evaluated for these targets. RSV was detected in neat clinical samples with a positive percent agreement (PPA) of 100% and negative percent agreement (NPA) of 99.5% compared to the reference standard, demonstrating 99.7% agreement. This study demonstrates that sample pooling by four increases the average Ct value by 2.24, 2.29, 2.20 and 1.91 cycles for the target's influenza A, influenza A typing, influenza B and RSV, respectively. The commercial AusDiagnostics SARS-CoV-2, Influenza and RSV 8-well assay was able to detect influenza and RSV at an intermediate concentration within the limit of detection of the assay. Further studies to explore the applicability of sample pooling at the lower limit of detection of the assay is needed. Nevertheless, sample pooling has shown to be a viable strategy to increase testing throughput and reduce reagent usage. In addition, the multiplexed platform targeting various respiratory viruses assists with public health and infection control responses, clinical care, and patient management.
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Affiliation(s)
- Thuy Phan
- Department of Microbiology and Infectious Disease, Concord Repatriation General Hospital, NSW Health Pathology, Concord, NSW, Australia
| | - Ngoc Yen Kim Tran
- Department of Microbiology and Infectious Disease, Concord Repatriation General Hospital, NSW Health Pathology, Concord, NSW, Australia,Address for correspondence: Dr Ngoc Yen Kim Tran, Department of Microbiology and Infectious Disease, Concord Repatriation General Hospital, Concord Road, Concord, NSW 2139, Australia
| | - Thomas Gottlieb
- Department of Microbiology and Infectious Disease, Concord Repatriation General Hospital, NSW Health Pathology, Concord, NSW, Australia,Faculty of Medicine and Health, The University of Sydney, Concord, NSW, Australia
| | - Steven Siarakas
- Department of Microbiology and Infectious Disease, Concord Repatriation General Hospital, NSW Health Pathology, Concord, NSW, Australia
| | - Genevieve McKew
- Department of Microbiology and Infectious Disease, Concord Repatriation General Hospital, NSW Health Pathology, Concord, NSW, Australia,Faculty of Medicine and Health, The University of Sydney, Concord, NSW, Australia
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Chang T, Draper JM, Van den Bout A, Kephart E, Maul-Newby H, Vasquez Y, Woodbury J, Randi S, Pedersen M, Nave M, La S, Gallagher N, McCabe MM, Dhillon N, Bjork I, Luttrell M, Dang F, MacMillan JB, Green R, Miller E, Kilpatrick AM, Vaske O, Stone MD, Sanford JR. A method for campus-wide SARS-CoV-2 surveillance at a large public university. PLoS One 2021; 16:e0261230. [PMID: 34919584 PMCID: PMC8682906 DOI: 10.1371/journal.pone.0261230] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 11/24/2021] [Indexed: 11/18/2022] Open
Abstract
The systematic screening of asymptomatic and pre-symptomatic individuals is a powerful tool for controlling community transmission of infectious disease on college campuses. Faced with a paucity of testing in the beginning of the COVID-19 pandemic, many universities developed molecular diagnostic laboratories focused on SARS-CoV-2 diagnostic testing on campus and in their broader communities. We established the UC Santa Cruz Molecular Diagnostic Lab in early April 2020 and began testing clinical samples just five weeks later. Using a clinically-validated laboratory developed test (LDT) that avoided supply chain constraints, an automated sample pooling and processing workflow, and a custom laboratory information management system (LIMS), we expanded testing from a handful of clinical samples per day to thousands per day with the testing capacity to screen our entire campus population twice per week. In this report we describe the technical, logistical, and regulatory processes that enabled our pop-up lab to scale testing and reporting capacity to thousands of tests per day.
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Affiliation(s)
- Terren Chang
- Colligan Clinical Diagnostic Laboratory, University of California Santa Cruz, Santa Cruz, California, United States of America
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California, United States of America
- UC Santa Cruz Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Jolene M. Draper
- Colligan Clinical Diagnostic Laboratory, University of California Santa Cruz, Santa Cruz, California, United States of America
- UC Santa Cruz Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, California, United States of America
- Department of Molecular, Cellular and Developmental Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Anouk Van den Bout
- Colligan Clinical Diagnostic Laboratory, University of California Santa Cruz, Santa Cruz, California, United States of America
- UC Santa Cruz Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, California, United States of America
- Department of Molecular, Cellular and Developmental Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Ellen Kephart
- Colligan Clinical Diagnostic Laboratory, University of California Santa Cruz, Santa Cruz, California, United States of America
- UC Santa Cruz Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, California, United States of America
- Department of Molecular, Cellular and Developmental Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Hannah Maul-Newby
- Colligan Clinical Diagnostic Laboratory, University of California Santa Cruz, Santa Cruz, California, United States of America
- UC Santa Cruz Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, California, United States of America
- Department of Molecular, Cellular and Developmental Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Yvonne Vasquez
- Colligan Clinical Diagnostic Laboratory, University of California Santa Cruz, Santa Cruz, California, United States of America
- UC Santa Cruz Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, California, United States of America
- Department of Molecular, Cellular and Developmental Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Jason Woodbury
- Thirdwave Analytics, San Francisco, California, United States of America
| | - Savanna Randi
- Colligan Clinical Diagnostic Laboratory, University of California Santa Cruz, Santa Cruz, California, United States of America
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Martina Pedersen
- Colligan Clinical Diagnostic Laboratory, University of California Santa Cruz, Santa Cruz, California, United States of America
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Maeve Nave
- Colligan Clinical Diagnostic Laboratory, University of California Santa Cruz, Santa Cruz, California, United States of America
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Scott La
- Colligan Clinical Diagnostic Laboratory, University of California Santa Cruz, Santa Cruz, California, United States of America
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Natalie Gallagher
- Colligan Clinical Diagnostic Laboratory, University of California Santa Cruz, Santa Cruz, California, United States of America
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Molly M. McCabe
- Colligan Clinical Diagnostic Laboratory, University of California Santa Cruz, Santa Cruz, California, United States of America
- Department of Molecular, Cellular and Developmental Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Namrita Dhillon
- Colligan Clinical Diagnostic Laboratory, University of California Santa Cruz, Santa Cruz, California, United States of America
- Department of Molecular, Cellular and Developmental Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Isabel Bjork
- Colligan Clinical Diagnostic Laboratory, University of California Santa Cruz, Santa Cruz, California, United States of America
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Michael Luttrell
- Business and Accounting Services, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Frank Dang
- University of California Davis, Davis, California, United States of America
| | - John B. MacMillan
- Colligan Clinical Diagnostic Laboratory, University of California Santa Cruz, Santa Cruz, California, United States of America
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Ralph Green
- University of California Davis, Davis, California, United States of America
| | - Elizabeth Miller
- Student Health Services, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Auston M. Kilpatrick
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Olena Vaske
- Colligan Clinical Diagnostic Laboratory, University of California Santa Cruz, Santa Cruz, California, United States of America
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California, United States of America
- UC Santa Cruz Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, California, United States of America
- Department of Molecular, Cellular and Developmental Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Michael D. Stone
- Colligan Clinical Diagnostic Laboratory, University of California Santa Cruz, Santa Cruz, California, United States of America
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California, United States of America
- UC Santa Cruz Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Jeremy R. Sanford
- Colligan Clinical Diagnostic Laboratory, University of California Santa Cruz, Santa Cruz, California, United States of America
- UC Santa Cruz Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, California, United States of America
- Department of Molecular, Cellular and Developmental Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, California, United States of America
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