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Rösch EL, Sack R, Chowdhury MS, Wolgast F, Zaborski M, Ludwig F, Schilling M, Viereck T, Rand U, Lak A. Amplification- and Enzyme-Free Magnetic Diagnostics Circuit for Whole-Genome Detection of SARS-CoV-2 RNA. Chembiochem 2024:e202400251. [PMID: 38709072 DOI: 10.1002/cbic.202400251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Revised: 04/30/2024] [Accepted: 05/06/2024] [Indexed: 05/07/2024]
Abstract
Polymerase chain reaction (PCR) requires thermal cycling and enzymatic reactions for sequence amplification, hampering their applications in point-of-care (POC) settings. Magnetic bioassays based on magnetic particle spectroscopy (MPS) and magnetic nanoparticles (MNPs) are isothermal, wash-free, and can be quantitative. Realizing them amplification- and enzyme-free on a benchtop device, they will become irreplaceable for POC applications. Here we demonstrate a first-in-class magnetic signal amplification circuit (MAC) that enables detection of whole genome of SARS-CoV-2 by combining the specificity of toehold-mediated DNA strand displacement with the magnetic response of MNPs to declustering processes. Using MAC, we detect the N gene of SARS-CoV-2 samples at a concentration of 104 RNA copies/μl as determined by droplet digital PCR. Further, we demonstrate that MAC can reliably distinguish between SARS-CoV-2 and other human coronaviruses. Being a wash-, amplification- and enzyme-free biosensing concept and working at isothermal conditions (25 °C) on a low-cost benchtop MPS device, our MAC biosensing concept offers several indispensable features for translating nucleic acid detection to POC applications.
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Affiliation(s)
- Enja Laureen Rösch
- Institute for Electrical Measurement Science and Fundamental Electrical Engineering and Laboratory for Emerging Nanometrology (LENA), Hans-Sommer-Str. 66, Braunschweig, 38106, Germany
| | - Rebecca Sack
- Institute for Electrical Measurement Science and Fundamental Electrical Engineering and Laboratory for Emerging Nanometrology (LENA), Hans-Sommer-Str. 66, Braunschweig, 38106, Germany
| | - Mohammad Suman Chowdhury
- Institute for Electrical Measurement Science and Fundamental Electrical Engineering and Laboratory for Emerging Nanometrology (LENA), Hans-Sommer-Str. 66, Braunschweig, 38106, Germany
| | - Florian Wolgast
- Institute for Electrical Measurement Science and Fundamental Electrical Engineering and Laboratory for Emerging Nanometrology (LENA), Hans-Sommer-Str. 66, Braunschweig, 38106, Germany
| | - Margarete Zaborski
- Leibniz Institute, German Collection of Microorganisms and Cell Cultures GmbH (DSMZ), Inhoffenstr. 7b, Braunschweig, 38124, Germany
| | - Frank Ludwig
- Institute for Electrical Measurement Science and Fundamental Electrical Engineering and Laboratory for Emerging Nanometrology (LENA), Hans-Sommer-Str. 66, Braunschweig, 38106, Germany
| | - Meinhard Schilling
- Institute for Electrical Measurement Science and Fundamental Electrical Engineering and Laboratory for Emerging Nanometrology (LENA), Hans-Sommer-Str. 66, Braunschweig, 38106, Germany
| | - Thilo Viereck
- Institute for Electrical Measurement Science and Fundamental Electrical Engineering and Laboratory for Emerging Nanometrology (LENA), Hans-Sommer-Str. 66, Braunschweig, 38106, Germany
| | - Ulfert Rand
- Leibniz Institute, German Collection of Microorganisms and Cell Cultures GmbH (DSMZ), Inhoffenstr. 7b, Braunschweig, 38124, Germany
| | - Aidin Lak
- Institute for Electrical Measurement Science and Fundamental Electrical Engineering and Laboratory for Emerging Nanometrology (LENA), Hans-Sommer-Str. 66, Braunschweig, 38106, Germany
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2
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Fagg J, Beale R, Futschik ME, Turek E, Chapman D, Halstead S, Jones M, Cole-Hamilton J, Gunson R, Sudhanva M, Klapper PE, Vansteenhouse H, Tunkel S, Dominiczak A, Peto TE, Fowler T. Swab pooling enables rapid expansion of high-throughput capacity for SARS-CoV-2 community testing. J Clin Virol 2023; 167:105574. [PMID: 37639778 DOI: 10.1016/j.jcv.2023.105574] [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: 03/25/2023] [Revised: 08/11/2023] [Accepted: 08/14/2023] [Indexed: 08/31/2023]
Abstract
BACKGROUND The challenges of rapid upscaling of testing capacity were a major lesson from the COVID-19 pandemic response. The need for process adjustments in high-throughput testing laboratories made sample pooling a challenging option to implement. OBJECTIVE This study aimed to evaluate whether pooling samples at source (swab pooling) was as effective as qRT-PCR testing of individuals in identifying cases of SARS-CoV-2 in real-world community testing conditions using the same high-throughput pipeline. METHODS Two cohorts of 10 (Pool10: 1,030 participants and 103 pools) and 6 (Pool6: 1,284 participants and 214 pools) samples per pool were tested for concordance, sensitivity, specificity, and Ct value differences with individual testing as reference. RESULTS Swab pooling allowed unmodified application of an existing high-throughput SARS-Cov-2 testing pipeline with only marginal loss of accuracy. For Pool10, concordance was 98.1% (95% Confidence interval: 93.3-99.8%), sensitivity was 95.7% (85.5-99.5%), and specificity was 100.0% (93.6-100.0%). For Pool6, concordance was 97.2% (94.0-99.0%), sensitivity was 97.5% (93.7-99.3%), and specificity was 96.4% (87.7-99.6%). Differences of outcomes measure between pool size were not significant. Most positive individual samples, which were not detected in pools, had very low viral concentration. If only individual samples with a viral concentration > 400 copies/ml (i.e. Ct value < 30) were considered positive, the overall sensitivity of pooling increased to 99.5%. CONCLUSION The study demonstrated high sensitivity and specificity by swab pooling and the immediate capability of high-throughput laboratories to implement this method making it an option in planning of rapid upscaling of laboratory capacity for future pandemics.
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Affiliation(s)
- Jamie Fagg
- Royal Free London NHS Foundation Trust, London, UK
| | - Rupert Beale
- Royal Free London NHS Foundation Trust, London, UK; University College London, Division of Medicine, Royal Free Hospital, London, UK
| | - Matthias E Futschik
- UK Health Security Agency, London, UK; Faculty of Health, School of Biomedical Sciences, University of Plymouth, Plymouth, UK
| | | | | | | | - Marc Jones
- Lighthouse Labs, University of Glasgow, UK
| | | | - Rory Gunson
- West of Scotland Specialist Virology Centre, Glasgow, UK
| | - Malur Sudhanva
- UK Health Security Agency, London, UK; King's College Hospital NHS Foundation Trust, London, UK
| | - Paul E Klapper
- UK Health Security Agency, London, UK; University of Manchester, Manchester, UK
| | | | | | | | | | - Tom Fowler
- UK Health Security Agency, London, UK; William Harvey Research Institute, Queen Mary University of London, London, UK.
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3
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Campbell WS, Donahue M, Williams RM, McCutchen E, Broadhurst J, Schnaubelt A, Staffend NJ, Hinrichs SH, Iwen PC. A Public Health Laboratory Information System in Support of Health Emergencies: The Nebraska Public Health Laboratory COVID-19 Experience. Public Health Rep 2023:333549231168459. [PMID: 37125740 PMCID: PMC10133861 DOI: 10.1177/00333549231168459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023] Open
Abstract
OBJECTIVES Public health laboratories (PHLs) are essential components of US Public Health Service operations. The health information technology that supports PHLs is central to effective and efficient laboratory operations and overall public health response to infectious disease management. This analysis presents key information on how the Nebraska Public Health Laboratory (NPHL) information technology system evolved to meet the demands of the COVID-19 pandemic. MATERIALS AND METHODS COVID-19 presented numerous, unforeseen information technology system challenges. The most notable challenges requiring changes to NPHL software systems and capability were improving efficiency of the laboratory operation due to high-volume testing, responding daily to demands for timely data for analysis by partner systems, interfacing with multiple testing (equipment) platforms, and supporting community-based specimen collection programs. RESULTS Improvements to the NPHL information technology system enabled NPHL to perform >121 000 SARS-CoV-2 polymerase chain reaction tests from March 2020 through January 2022 at a sustainable rate of 2000 SARS-CoV-2 tests per day, with no increase in laboratory staffing. Electronic reporting of 62 000 rapid antigen tests eliminated paper reporting and extended testing services throughout the state. Collection of COVID-19 symptom data before specimen collection enabled NPHL to make data-driven decisions to perform pool testing and conserve testing kits when supplies were low. PRACTICE IMPLICATIONS NPHL information technology applications proved essential for managing health care provider workload, prioritizing the use of scarce testing supplies, and managing Nebraska's overall pandemic response. The NPHL experience provides useful examples of a highly capable information technology system and suggests areas for additional attention in the PHL environment, including a focus on end users, collaboration with various partners, and investment in information technology.
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Affiliation(s)
- Walter S Campbell
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Matthew Donahue
- Epidemiology Unit, Nebraska Department of Health and Human Services, Lincoln, NE, USA
| | - Robin M Williams
- Epidemiology Unit, Nebraska Department of Health and Human Services, Lincoln, NE, USA
| | - Emily McCutchen
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Jana Broadhurst
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Andy Schnaubelt
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Nicholas J Staffend
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Steven H Hinrichs
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Peter C Iwen
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA
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Izadi R, Hatam N, Baberi F, Yousefzadeh S, Jafari A. Economic evaluation of strategies against coronavirus: a systematic review. HEALTH ECONOMICS REVIEW 2023; 13:18. [PMID: 36933043 PMCID: PMC10024293 DOI: 10.1186/s13561-023-00430-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 03/10/2023] [Indexed: 05/30/2023]
Abstract
BACKGROUND The COVID-19 outbreak was defined as a pandemic on 11 March 2020 by the World Health Organization. After that, COVID-19 has enormously influenced health systems around the world, and it has claimed more than 4.2 million deaths until July 2021. The pandemic has led to global health, social and economic costs. This situation has prompted a crucial search for beneficial interventions and treatments, but little is known about their monetary value. This study is aimed at systematically reviewing the articles conducted on the economic evaluation of preventive, control and treatment strategies against COVID-19. MATERIAL AND METHOD We searched PubMed, Web of Science, Scopus, and Google Scholar from December 2019 to October 2021 to find applicable literature to the economic evaluation of strategies against COVID-19. Two researchers screened potentially eligible titles and abstracts. The Consolidated Health Economic Evaluation Reporting Standards (CHEERS) checklist was used to quality assessment of studies. RESULTS Thirty-six studies were included in this review, and the average CHEERS score was 72. Cost-effectiveness analysis was the most common type of economic evaluation, used in 21 studies. And the quality-adjusted life year (QALY) was the main outcome applied to measure the effectiveness of interventions, which was used in 19 studies. In addition, articles were reported a wide range of incremental cost-effectiveness ratio (ICER), and the lowest cost per QALY ($321.14) was related to the use of vaccines. CONCLUSION Based on the results of this systematic review, it seems that all strategies are likely to be more cost-effective against COVID-19 than no intervention and vaccination was the most cost-effective strategy. This research provides insight for decision makers in choosing optimal interventions against the next waves of the current pandemic and possible future pandemics.
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Affiliation(s)
- Reyhane Izadi
- Department of Health Care Management, School of Management and Information Sciences, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Nahid Hatam
- Health Human Resources Research Center, School of Management and Medical Informatics, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Fatemeh Baberi
- Deputy of Research and Technology, School of Medicine, Shiraz University of Medical, Sciences, Shiraz, Iran
| | - Setareh Yousefzadeh
- Social Determinants of Health Research Center, Health Research Institute, Babol, University of Medical Sciences, Babol, Iran
| | - Abdosaleh Jafari
- Health Human Resources Research Centre, School of Health Management and Information Sciences, Shiraz University of Medical Sciences, Shiraz, Iran.
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Accelerating the Laboratory Testing Capacity through Saliva Pooling Prior to Direct RT-qPCR for SARS-CoV-2 Detection. Diagnostics (Basel) 2022; 12:diagnostics12123160. [PMID: 36553167 PMCID: PMC9777453 DOI: 10.3390/diagnostics12123160] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 12/04/2022] [Accepted: 12/09/2022] [Indexed: 12/23/2022] Open
Abstract
The testing capacity of the laboratory is paramount for better control of the pandemic caused by SARS-CoV-2. The pooling method is promising to increase testing capacity, and the use of direct NAAT-based detection of SARS-CoV-2 on a non-invasive specimen such as saliva will ultimately accelerate the testing capacity. This study aims to validate the pooling-of-four method to quadruple the testing capacity using RNA-extraction-free saliva specimens. In addition, we intend to investigate the preferable stage of pooling, including pre- or post-heating. The compatibility of this approach was also tested on five commercial kits. Saliva specimens stored at -80 °C for several months were proven viable and were used for various tests in this study. Our findings revealed that pooling-of-four specimens had an overall agreement rate of 98.18% with their individual testing. Moreover, we proved that the pooling procedure could be conducted either pre- or post-heating, with no discordance and no significant difference in Ct values generated. When compared to other commercial detection kits, it demonstrated an overall agreement greater than 85%, which exhibits broad compatibility and ensures easy adaptability in clinical settings. This method has been proven reliable and increases the testing capacity up to fourfold.
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6
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Performance of the TaqMan COVID-19 Pooling Kit for detection of SARS-CoV-2 in asymptomatic and symptomatic populations. PLoS One 2022; 17:e0269798. [PMID: 35687578 PMCID: PMC9187085 DOI: 10.1371/journal.pone.0269798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 05/30/2022] [Indexed: 11/24/2022] Open
Abstract
Clinical evidence for asymptomatic cases of coronavirus disease (COVID-19) has reinforced the significance of effective surveillance testing programs. Quantitative reverse transcriptase polymerase chain reaction (RT-qPCR) assays are considered the ‘gold standard’ for detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA. However, the labor and resource requirements can be prohibitive with respect to large testing volumes associated with the pandemic. Pooled testing algorithms may serve to increase testing capacity with more efficient resource utilization. Due to the lack of carefully curated cohorts, there is limited evidence for the applicability of RT-PCR pooling in asymptomatic COVID-19 cases. In this study, we compared the analytical sensitivity of the TaqMan™ SARS-CoV-2 Pooling Assay to detect one positive sample in a pool of five anterior nares swabs in symptomatic and asymptomatic cohorts at an institute of higher education. Positive pools were deconvoluted and each individual sample was retested using the TaqPath™ COVID-19 Combo Kit. Both assays target the open reading frame (ORF) 1ab, nucleocapsid (N), and spike (S) gene of the strain that originated in Wuhan, Hubei, China. Qualitative results demonstrated absolute agreement between pooled and deconvoluted samples in both cohorts. Independent t-test performed on Ct shifts supported an insignificant difference between cohorts with p-values of 0.306 (Orf1ab), 0.147 (N), and 0.052 (S). All negative pools were correctly reported as negative. Pooled PCR testing up to five samples is a valid method for surveillance testing of students and staff in a university setting, especially when the prevalence is expected to be low.
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Lee SS, Weitz M, Ardlie K, Bantham A, Schuckel MF, Goehringer K, Hogue C, Hosking R, Mortimer K, Saadat A, Seaman‐Chandler J, Linas BP, Ciaranello A. Resources Required for Implementation of SARS-CoV-2 Screening in Massachusetts K-12 Public Schools in Winter/Spring 2021. THE JOURNAL OF SCHOOL HEALTH 2022; 92:474-484. [PMID: 35253219 PMCID: PMC9115172 DOI: 10.1111/josh.13152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 01/25/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND The financial costs and human resource requirements at the school and district level to implement a SARS-CoV-2 screening program are not well known. METHODS A consortium of Massachusetts public K-12 schools was formed to implement and evaluate a range of SARS-CoV-2 screening approaches. Participating districts were surveyed weekly about their programs, including: type of assay used, individual vs. pooled screening, approaches to return of results and deconvolution of positive pools, number and type of personnel, and hours spent implementing the screening program, and hours spent on program implementation. RESULTS In 21 participating districts, over 21 weeks from January to June 2021, the positivity rate was 0.0% to 0.21% among students and 0.0% to 0.13% among educators/staff. The average weekly cost to implement a screening program, including assay and personnel costs, was $17.00 per person tested; this was $46.68 for individual screenings and $15.61 for pooled screenings. The total weekly costs by district ranged from $1,644 to $93,486, and districts screened between 58 and 3675 people per week. CONCLUSIONS Where screening is recommended for the 2021 to 2022 school year due to high COVID-19 incidence, understanding the human resources and finances required to implement screening will assist district policymakers in planning.
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Affiliation(s)
- Stephanie S. Lee
- Medical Practice Evaluation CenterMassachusetts General Hospital100 Cambridge St.BostonMA102114
| | - Michelle Weitz
- Section of Infectious DiseasesBoston Medical Center725 Albany St. 9th FloorBostonMA02118
| | - Kristin Ardlie
- GTEx LaboratoryBroad Institute of MIT & Harvard415 Main St.CambridgeMA02142
| | - Amy Bantham
- Move to Live MoreMove to Live More, LLCSomervilleMA02144
| | | | - Katey Goehringer
- Wellesley Education Foundation and Safer TeachersSafer Students CollaborativeP.O. Box 812321WellesleyMA02482
| | | | - Rosy Hosking
- Scientific Communications and Outreach, Stanley Center for Psychiatric ResearchBroad Institute of MIT and Harvard75 Ames St.CambridgeMA02142
| | - Kathleen Mortimer
- Medical Advisory Board MemberTown of Weston Public Health11 Town HouseWestonMA02493
| | - Alham Saadat
- Scientific EquityBroad Institute of MIT and Harvard415 Main St.CambridgeMA02142
| | | | - Benjamin P. Linas
- Boston University Schools of Medicine and Public Health and Section of Infectious DiseasesBoston Medical Center725 Albany St. 9th FloorBostonMA02118
| | - Andrea Ciaranello
- Division of Infectious Disease and Medical Practice Evaluation CenterMassachusetts General Hospital100 Cambridge St.BostonMA02114
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Campbell JR, Dion C, Uppal A, Yansouni CP, Menzies D. Systematic on-site testing for SARS-CoV-2 infection among asymptomatic essential workers in Montréal, Canada: a prospective observational and cost-assessment study. CMAJ Open 2022; 10:E409-E419. [PMID: 35537749 PMCID: PMC9259431 DOI: 10.9778/cmajo.20210290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Essential workers are at increased risk for SARS-CoV-2 infection. We aimed to estimate the yield, acceptability and cost of systematic workplace-based testing of asymptomatic essential workers for SARS-CoV-2 infection. METHODS From Jan. 27 to Mar. 12, 2021, we prospectively recruited non-health care essential businesses in Montréal, Canada, through email or telephone contact. Two trained mobile teams, each composed of 2 non-health care professionals, visited businesses. Consenting asymptomatic employees provided saline gargle samples under supervision. Samples were analyzed by means of reverse transcription polymerase chain reaction (RT-PCR). At businesses with outbreaks (≥ 2 participants with a positive result), we retested all participants with a negative result on initial testing. Our primary outcomes were yield (proportion of test results that were positive), acceptability (proportion of participants estimated to be present at the business who agreed to participate) and costs (including training, sample collection and analysis, and communicating results). Our secondary outcome was identification of factors associated with a positive test result on multivariable logistic regression. RESULTS Of the 366 businesses contacted, 69 (18.8%) agreed to participate. Nineteen businesses (28%) were manufacturers or suppliers, 12 (17%) were in auto sales or repair, and 11 (16%) were in childcare; the corresponding number of employees was 1225, 242 and 113. The median number of participants per business was 13 (interquartile range [IQR] 8-22). Of an estimated 2348 employees on site, 2128 (90.6%) participated (808 [38.0%] female, median age 48 [IQR 37-57] yr). Of the 2626 tests performed, 53 (2.0%) gave a positive result. Self-reported nonwhite ethnicity (adjusted odds ratio [OR] 3.7, 95% confidence interval [CI] 1.4-9.9) and a negative SARS-CoV-2 test result before the study (adjusted OR 0.4, 95% CI 0.2-0.8) were associated with a positive test result. Five businesses were experiencing an outbreak; at these businesses, 40/917 participants (4.4%) had a positive result on the initial test. We repeated testing for employees with initially negative results at 3 of these businesses over 2-3 weeks: 8/350 participants (2.3%) had a positive result on the second test, and none had a positive result on the third and fourth tests; no employer reported new positive results after our final visit (up to Mar. 26, 2021). At the remaining 64 businesses, 1211 participants were tested once, of whom 5 (0.4%) had a positive result. The per-person RT-PCR cost was $34, and all other costs, $8.67. INTERPRETATION On-site saline gargle sampling of essential workers for SARS-CoV-2 testing was acceptable and of modest cost, and appears most useful in the context of outbreaks. This sampling strategy should be evaluated further as a component of efforts to prevent SARS-CoV-2 transmission. PREPRINT: medRxiv - doi:10.1101/2021.05.12.21256956.
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Affiliation(s)
- Jonathon R Campbell
- Research Institute of the McGill University Health Centre (Campbell, Menzies, Dion, Yansouni, Uppal); Faculty of Medicine (Campbell, Menzies, Yansouni), McGill University; McGill International TB Centre (Campbell, Menzies); J.D. MacLean Centre for Tropical Diseases (Yansouni), Montréal, Que.
| | - Cynthia Dion
- Research Institute of the McGill University Health Centre (Campbell, Menzies, Dion, Yansouni, Uppal); Faculty of Medicine (Campbell, Menzies, Yansouni), McGill University; McGill International TB Centre (Campbell, Menzies); J.D. MacLean Centre for Tropical Diseases (Yansouni), Montréal, Que
| | - Aashna Uppal
- Research Institute of the McGill University Health Centre (Campbell, Menzies, Dion, Yansouni, Uppal); Faculty of Medicine (Campbell, Menzies, Yansouni), McGill University; McGill International TB Centre (Campbell, Menzies); J.D. MacLean Centre for Tropical Diseases (Yansouni), Montréal, Que
| | - Cedric P Yansouni
- Research Institute of the McGill University Health Centre (Campbell, Menzies, Dion, Yansouni, Uppal); Faculty of Medicine (Campbell, Menzies, Yansouni), McGill University; McGill International TB Centre (Campbell, Menzies); J.D. MacLean Centre for Tropical Diseases (Yansouni), Montréal, Que
| | - Dick Menzies
- Research Institute of the McGill University Health Centre (Campbell, Menzies, Dion, Yansouni, Uppal); Faculty of Medicine (Campbell, Menzies, Yansouni), McGill University; McGill International TB Centre (Campbell, Menzies); J.D. MacLean Centre for Tropical Diseases (Yansouni), Montréal, Que
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Abrego-Martinez JC, Jafari M, Chergui S, Pavel C, Che D, Siaj M. Aptamer-based electrochemical biosensor for rapid detection of SARS-CoV-2: Nanoscale electrode-aptamer-SARS-CoV-2 imaging by photo-induced force microscopy. Biosens Bioelectron 2022; 195:113595. [PMID: 34571481 PMCID: PMC8405239 DOI: 10.1016/j.bios.2021.113595] [Citation(s) in RCA: 73] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 08/15/2021] [Accepted: 08/25/2021] [Indexed: 02/07/2023]
Abstract
Rapid, mass diagnosis of the coronavirus disease 2019 (COVID-19) is critical to stop the ongoing infection spread. The two standard screening methods to confirm the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are polymerase chain reaction (PCR), through the RNA of the virus, and serology by detecting antibodies produced as a response to the viral infection. However, given the detection complexity, cost and relatively long analysis times of these techniques, novel technologies are urgently needed. Here, we report an aptamer-based biosensor developed on a screen-printed carbon electrode platform for rapid, sensitive, and user-friendly detection of SARS-CoV-2. The aptasensor relies on an aptamer targeting the receptor-binding domain (RBD) in the spike protein (S-protein) of the SARS-CoV-2. The aptamer immobilization on gold nanoparticles, and the presence of S-protein in the aptamer-target complex, investigated for the first time by photo-induced force microscopy mapping between 770 and 1910 cm−1 of the electromagnetic spectrum, revealed abundant S-protein homogeneously distributed on the sensing probe. The detection of SARS-CoV-2 S-protein was achieved by electrochemical impedance spectroscopy after 40 min incubation with several analyte concentrations, yielding a limit of detection of 1.30 pM (66 pg/mL). Moreover, the aptasensor was successfully applied for the detection of a SARS-CoV-2 pseudovirus, thus suggesting it is a promising tool for the diagnosis of COVID-19.
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Affiliation(s)
| | - Maziar Jafari
- Department of Chemistry and Biochemistry, Université Du Québec à Montréal, Montréal, QC, H3C 3P8, Canada
| | - Siham Chergui
- Department of Chemistry and Biochemistry, Université Du Québec à Montréal, Montréal, QC, H3C 3P8, Canada
| | - Catalin Pavel
- Azure Biosystems Canada, Montréal, QC, H4P 2N5, Canada
| | - Diping Che
- Azure Biosystems Canada, Montréal, QC, H4P 2N5, Canada
| | - Mohamed Siaj
- Department of Chemistry and Biochemistry, Université Du Québec à Montréal, Montréal, QC, H3C 3P8, Canada.
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10
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Yu J, Huang Y, Shen ZJ. Optimizing and evaluating PCR-based pooled screening during COVID-19 pandemics. Sci Rep 2021; 11:21460. [PMID: 34728759 PMCID: PMC8564549 DOI: 10.1038/s41598-021-01065-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 10/19/2021] [Indexed: 12/13/2022] Open
Abstract
Population screening played a substantial role in safely reopening the economy and avoiding new outbreaks of COVID-19. PCR-based pooled screening makes it possible to test the population with limited resources by pooling multiple individual samples. Our study compared different population-wide screening methods as transmission-mitigating interventions, including pooled PCR, individual PCR, and antigen screening. Incorporating testing-isolation process and individual-level viral load trajectories into an epidemic model, we further studied the impacts of testing-isolation on test sensitivities. Results show that the testing-isolation process could maintain a stable test sensitivity during the outbreak by removing most infected individuals, especially during the epidemic decline. Moreover, we compared the efficiency, accuracy, and cost of different screening methods during the pandemic. Our results show that PCR-based pooled screening is cost-effective in reversing the pandemic at low prevalence. When the prevalence is high, PCR-based pooled screening may not stop the outbreak. In contrast, antigen screening with sufficient frequency could reverse the epidemic, despite the high cost and the large numbers of false positives in the screening process.
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Affiliation(s)
- Jiali Yu
- Tsinghua-Berkeley Shenzhen Institute (TBSI), Tsinghua University, Shenzhen, China
| | - Yiduo Huang
- Department of Civil and Environmental Engineering, University of California Berkeley, Berkeley, CA, USA
| | - Zuo-Jun Shen
- College of Engineering, University of California Berkeley, Berkeley, CA, USA.
- Faculty of Engineering and Faculty of Business and Economics, University of Hong Kong, Hong Kong, China.
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11
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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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12
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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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13
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Ganz TJ, Donner R, Hines KM, Waithe-Alleyne ML, Slate DL, Abel G, Auclair JR. Two-Stage Hierarchical Group Testing Strategy to Increase SARS-CoV-2 Testing Capacity at an Institution of Higher Education: A Retrospective Analysis. J Mol Diagn 2021; 23:1691-1698. [PMID: 34562617 PMCID: PMC8457909 DOI: 10.1016/j.jmoldx.2021.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 08/11/2021] [Accepted: 09/09/2021] [Indexed: 11/02/2022] Open
Abstract
Population testing for severe acute respiratory syndrome coronavirus 2 is necessary because of the potential for viral transmission from asymptomatic cases, yet the scarcity of reagents and equipment has increased the cost-prohibitive implementation of screening campaigns at institutions of higher education. Significant analytical sensitivities of nucleic acid amplification methods permit sample pooling to increase testing capacity. Statistical models compared optimal testing configurations for pools of 3, 5, and 10 samples. Assessment of pooling using the TaqPath COVID-19 Combo Kit multiplex assay (ORF1ab, N, and S gene targets) involved a limit-of-detection study, matrix-effect study, and clinical comparison of neat with pooled samples. A limit of detection of 135.02 (ORF1ab; 95% CI, 117.21-155.52), 373.92 (N; 95% CI, 257.05-437.64), and 1001.32 (S; 95% CI, 896.62-1118.33) gene copy equivalents per milliliter was resolved. Seventy-two randomly selected samples showed slight suppression owing to a negative sample matrix. The resulting mean cycle threshold shifts were 2.09 (ORF1ab), 1.76 (N), and 2.31 (S) for the 3-sample pool, 2.83 (ORF1ab), 2.45 (N), and 3.24 (S) for the 5-sample pool, and 3.99 (ORF1ab), 3.46 (N), and 4.07 (S) for the 10-sample pool. Despite a quantitative sensitivity loss trend, the qualitative result was unaffected in each pool. According to the range of disease prevalence observed at the testing site (0.03% to 7.32%), a pool of five samples was deemed an optimal and cost-effective option for monitoring the Northeastern University community.
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Affiliation(s)
- Troy J Ganz
- Department of Chemistry and Chemical Biology, Life Sciences Testing Center, Northeastern University Innovation Campus in Burlington, Burlington, Massachusetts
| | - Rachel Donner
- Department of Chemistry and Chemical Biology, Life Sciences Testing Center, Northeastern University Innovation Campus in Burlington, Burlington, Massachusetts
| | - Kevin M Hines
- Department of Chemistry and Chemical Biology, Life Sciences Testing Center, Northeastern University Innovation Campus in Burlington, Burlington, Massachusetts
| | - Markus L Waithe-Alleyne
- Department of Chemistry and Chemical Biology, Life Sciences Testing Center, Northeastern University Innovation Campus in Burlington, Burlington, Massachusetts
| | - Deirdre L Slate
- Department of Chemistry and Chemical Biology, Life Sciences Testing Center, Northeastern University Innovation Campus in Burlington, Burlington, Massachusetts
| | - Gyorgy Abel
- Department of Chemistry and Chemical Biology, Life Sciences Testing Center, Northeastern University Innovation Campus in Burlington, Burlington, Massachusetts; Lahey Hospital and Medical Center, Burlington, Massachusetts.
| | - Jared R Auclair
- Department of Chemistry and Chemical Biology, Life Sciences Testing Center, Northeastern University Innovation Campus in Burlington, Burlington, Massachusetts.
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14
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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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15
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Mahmoud SA, Ibrahim E, Thakre B, Teddy JG, Raheja P, Ganesan S, Zaher WA. Evaluation of pooling of samples for testing SARS-CoV- 2 for mass screening of COVID-19. BMC Infect Dis 2021; 21:360. [PMID: 33865325 PMCID: PMC8052526 DOI: 10.1186/s12879-021-06061-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 04/07/2021] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND The current pandemic of the SARS-CoV-2 virus, widely known as COVID-19, has affected millions of people around the world. The World Health Organization (WHO) has recommended vigorous testing to differentiate SARS-CoV-2 from other respiratory infections to aid in guiding appropriate care and management. Situations like this have demanded robust testing strategies and pooled testing of samples for SARS-CoV-2 virus has provided the solution to mass screening of people for COVID-19. A pooled testing strategy can be very effective in testing when resources are limited, yet it comes with its own limitations. These benefits and limitations need critical consideration when it comes to testing highly infectious diseases like COVID-19. METHODS This study evaluated the pooled testing of nasopharyngeal swabs for SARS-COV-2 by comparing the sensitivity of individual sample testing with 4-and 8-pool sample testing. Median cycle threshold (Ct) values were compared, and the precision of pooled testing was assessed through an inter- and intra-assay of pooled samples. Coefficient of variance was calculated for inter- and intra-assay variability. RESULTS The sensitivity becomes considerably lower when the samples are pooled. There is a high percentage of false negative reports with larger sample pool size and when the patient viral load is low or weak positive samples. High variability was seen in the intra- and inter-assay, especially among weak positive samples and when more number of samples are pooled together. CONCLUSION As COVID - 19 infection numbers and need for testing remain high, we must meticulously evaluate the testing strategy for each country depending on its testing capacity, infrastructure, economic strength, and need to determine the optimal balance on the cost-effective strategy of resource saving and risk/ cost of missing positive patients.
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16
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Bilder CR, Tebbs JM, McMahan CS. Informative array testing with multiplex assays. Stat Med 2021; 40:3021-3034. [PMID: 33763901 DOI: 10.1002/sim.8954] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 02/12/2021] [Accepted: 03/01/2021] [Indexed: 11/07/2022]
Abstract
High-volume testing of clinical specimens for sexually transmitted diseases is performed frequently by a process known as group testing. This algorithmic process involves testing portions of specimens from separate individuals together as one unit (or "group") to detect diseases. Retesting is performed on groups that test positively in order to differentiate between positive and negative individual specimens. The overall goal is to use the least number of tests possible across all individuals without sacrificing diagnostic accuracy. One of the most efficient group testing algorithms is array testing. In its simplest form, specimens are arranged into a grid-like structure so that row and column groups can be formed. Positive-testing rows/columns indicate which specimens to retest. With the growing use of multiplex assays, the increasing number of diseases tested by these assays, and the availability of subject-specific risk information, opportunities exist to make this testing process even more efficient. We propose specific specimen arrangements within an array that can reduce the number of retests needed when compared with other array testing algorithms. We examine how to calculate operating characteristics, including the expected number of tests and the SD for the number of tests, and then subsequently find a best arrangement. Our methods are illustrated for chlamydia and gonorrhea detection with the Aptima Combo 2 Assay. We also provide R functions to make our research accessible to laboratories.
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Affiliation(s)
- Christopher R Bilder
- Department of Statistics, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Joshua M Tebbs
- Department of Statistics, University of South Carolina, Columbia, South Carolina, USA
| | - Christopher S McMahan
- School of Mathematical and Statistical Sciences, Clemson University, Clemson, South Carolina, USA
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