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Heath B, Villar SS, Robertson DS. How could a pooled testing policy have performed in managing the early stages of the COVID-19 pandemic? Results from a simulation study. Stat Med 2024; 43:2239-2262. [PMID: 38545961 DOI: 10.1002/sim.10062] [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: 05/26/2023] [Revised: 12/08/2023] [Accepted: 02/26/2024] [Indexed: 05/18/2024]
Abstract
A coordinated testing policy is an essential tool for responding to emerging epidemics, as was seen with COVID-19. However, it is very difficult to agree on the best policy when there are multiple conflicting objectives. A key objective is minimizing cost, which is why pooled testing (a method that involves pooling samples taken from multiple individuals and analyzing this with a single diagnostic test) has been suggested. In this article, we present results from an extensive and realistic simulation study comparing testing policies based on individually testing subjects with symptoms (a policy resembling the UK strategy at the start of the COVID-19 pandemic), individually testing subjects at random or pools of subjects randomly combined and tested. To compare these testing methods, a dynamic model compromised of a relationship network and an extended SEIR model is used. In contrast to most existing literature, testing capacity is considered as fixed and limited rather than unbounded. This article then explores the impact of the proportion of symptomatic infections on the expected performance of testing policies. Symptomatic testing performs better than pooled testing unless a low proportion of infections are symptomatic. Additionally, we include the novel feature for testing of non-compliance and perform a sensitivity analysis for different compliance assumptions. Our results suggest for the pooled testing scheme to be superior to testing symptomatic people individually, only a small proportion of the population (> 10 % $$ >10\% $$ ) needs to not comply with the testing procedure.
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Affiliation(s)
- Bethany Heath
- MRC Biostatistics Unit, University of Cambridge, Cambridge, UK
| | - Sofía S Villar
- MRC Biostatistics Unit, University of Cambridge, Cambridge, UK
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Schenk H, Caf Y, Knabl L, Mayerhofer C, Rauch W. High prevalence group testing in epidemiology with geometrically inspired algorithms. Sci Rep 2023; 13:18910. [PMID: 37919330 PMCID: PMC10622438 DOI: 10.1038/s41598-023-45639-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 10/22/2023] [Indexed: 11/04/2023] Open
Abstract
Demand for mass surveillance during peak times of the SARS-CoV-2 pandemic caused high workload for clinical laboratories. Efficient and cost conserving testing designs by means of group testing can substantially reduce resources during possible future emergency situations. The novel hypercube algorithm proposed by Mutesa et al. 2021 published in Nature provides methodological proof of concept and points out the applicability to epidemiological testing. In this work, the algorithm is explored and expanded for settings with high group prevalence. Numerical studies investigate the limits of the adapted hypercube methodology, allowing to optimize pooling designs for specific requirements (i.e. number of samples and group prevalence). Hyperparameter optimization is performed to maximize test-reduction. Standard deviation is examined to investigate resilience and precision. Moreover, empirical validation was performed by elaborately pooling SARS-CoV-2 virus samples according to numerically optimized pooling designs. Laboratory experiments with SARS-CoV-2 sample groups, ranging from 50 to 200 items, characterized by group prevalence up to 10%, are successfully processed and analysed. Test-reductions from 50 to 72.5% were achieved in the experimental setups when compared to individual testing. Higher theoretical test-reduction is possible, depending on the number of samples and the group prevalence, indicated by simulation results.
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Affiliation(s)
- Hannes Schenk
- Unit of Environmental Engineering, University of Innsbruck, Technikerstraße 13, 6020, Innsbruck, Austria
| | - Yasemin Caf
- Tyrolpath Obrist Brunhuber GmbH, Hauptplatz 4, 6511, Zams, Austria
| | - Ludwig Knabl
- Tyrolpath Obrist Brunhuber GmbH, Hauptplatz 4, 6511, Zams, Austria
| | | | - Wolfgang Rauch
- Unit of Environmental Engineering, University of Innsbruck, Technikerstraße 13, 6020, Innsbruck, Austria.
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Lancelot M, Fibben K, Sullivan J, O’Sick W, McLendon K, Wu H, Rao A, Bassit LC, Greenleaf M, Miller P, Krull W, Tyburski E, Roback JD, Lam WA, Damhorst GL. Effect of swab pooling on the Accula point-of-care RT-PCR for SARS-CoV-2 detection. Front Microbiol 2023; 14:1219214. [PMID: 37608952 PMCID: PMC10440424 DOI: 10.3389/fmicb.2023.1219214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 07/26/2023] [Indexed: 08/24/2023] Open
Abstract
Introduction Swab pooling may allow for more efficient use of point-of-care assays for SARS-CoV-2 detection in settings where widespread testing is warranted, but the effects of pooling on assay performance are not well described. Methods We tested the Thermo-Fisher Accula rapid point-of-care RT-PCR platform with contrived pooled nasal swab specimens. Results We observed a higher limit of detection of 3,750 copies/swab in pooled specimens compared to 2,250 copies/swab in individual specimens. Assay performance appeared worse in a specimen with visible nasal mucous and debris, although performance was improved when using a standard laboratory mechanical pipette compared to the transfer pipette included in the assay kit. Conclusion Clinicians and public health officials overseeing mass testing efforts must understand limitations and benefits of swab or sample pooling, including reduced assay performance from pooled specimens. We conclude that the Accula RT-PCR platform remains an attractive candidate assay for pooling strategies owing to the superior analytical sensitivity compared to most home use and point-of-care tests despite the inhibitory effects of pooled specimens we characterized.
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Affiliation(s)
- Moira Lancelot
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, United States
| | - Kirby Fibben
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, United States
| | - Julie Sullivan
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, GA, United States
- Department of Pediatrics, Emory University School of Medicine and Children’s Healthcare of Atlanta, Atlanta, GA, United States
| | - William O’Sick
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, United States
| | - Kaleb McLendon
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, United States
| | - Huixia Wu
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, United States
| | - Anuradha Rao
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, GA, United States
- Department of Pediatrics, Emory University School of Medicine and Children’s Healthcare of Atlanta, Atlanta, GA, United States
| | - Leda C. Bassit
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, GA, United States
- Department of Pediatrics, Emory University School of Medicine and Children’s Healthcare of Atlanta, Atlanta, GA, United States
- Laboratory of Biochemical Pharmacology, Emory University, Atlanta, GA, United States
| | - Morgan Greenleaf
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, GA, United States
| | - Pamela Miller
- Rapid Acceleration of Diagnostics (RADx), Maryland, MD, United States
| | - Wolfgang Krull
- Rapid Acceleration of Diagnostics (RADx), Maryland, MD, United States
| | - Erika Tyburski
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, GA, United States
| | - John D. Roback
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, United States
| | - Wilbur A. Lam
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, United States
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, GA, United States
- Department of Pediatrics, Emory University School of Medicine and Children’s Healthcare of Atlanta, Atlanta, GA, United States
- Aflac Cancer & Blood Disorders Center at Children's Healthcare of Atlanta, Atlanta, GA, United States
| | - Gregory L. Damhorst
- The Atlanta Center for Microsystems-Engineered Point-of-Care Technologies, Atlanta, GA, United States
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA, United States
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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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Evaluation of FAST COVID-19 SARS-CoV-2 Antigen Rapid Test Kit for Detection of SARS-CoV-2 in Respiratory Samples from Mildly Symptomatic or Asymptomatic Patients. Diagnostics (Basel) 2022; 12:diagnostics12030650. [PMID: 35328203 PMCID: PMC8947527 DOI: 10.3390/diagnostics12030650] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 02/25/2022] [Accepted: 03/05/2022] [Indexed: 02/07/2023] Open
Abstract
Molecular tests are the gold standard to diagnose severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection but are associated with a diagnostic delay, while antigen detection tests can generate results within 20 min even outside a laboratory. In order to evaluate the accuracy and reliability of the FAST COVID-19 SARS-CoV-2 Antigen Rapid Test Kit (Ag-RDT), two respiratory swabs were collected simultaneously from 501 patients, with mild or no coronavirus disease 2019 (COVID-19)-related symptoms, and analyzed with both the Reverse Transcriptase-quantitative Polymerase Chain Reaction (RT-qPCR) and the FAST COVID-19 SARS-CoV-2 Antigen Rapid Test. Results were then compared to determine clinical performance in a screening setting. We measured a precision of 97.41% (95% CI 92.42–99.15%) and a recall of 98.26% (95% CI 93.88–99.25%), with a specificity of 99.22% (95% CI 97.74–99.74%), a negative predictive value of 99.48% (95% CI 97.98–99.87%), and an overall accuracy of 99.00% (95% CI 97.69–99.68%). Concordance was described by a Kappa coefficient of 0.971 (95% CI 0.947–0.996). Considering short lead times, low cost, and opportunities for decentralized testing, the Ag-RDT test can enhance the efforts to control SARS-CoV-2 spread in several settings.
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Handous I, Hannachi N, Marzouk M, Hazgui O, Bouafif Ep Ben Alaya N, Boukadida J. Pooling Nasopharyngeal Swab Specimens to Improve Testing Capacity for SARS-CoV-2 by Real-Time RT-PCR. Biol Proced Online 2021; 23:19. [PMID: 34592917 PMCID: PMC8483732 DOI: 10.1186/s12575-021-00156-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 09/10/2021] [Indexed: 01/15/2023] Open
Abstract
Background The detection of SARS-CoV-2 using qRT-PCR with the pooling of samples can reduce workload and costs especially when the prevalence rate of COVID-19 in a population is low. To analyse the effect of pooling samples on the sensitivity of RT-qPCR for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detection, we compared the cycle threshold (Ct) values of pools of 5 and 10 that tested positive with Ct values of individual samples that tested positive in that pool. Twenty positive nasopharyngeal (NP) specimens with low to high viral load were selected and pooled individually with four and nine negative NP. Results In NP specimens, the sensitivity of pools of 5 and 10 were 90 and 85%, compared to individual sample testing, respectively. The RT-qPCR sensitivity of pools of 5 and 10 against individual testing were not significantly different (p > 0.05). Detection of positive samples with low Ct values (< 36) was consistently achieved in pools of 5 and 10. However, there were higher false negatives when samples with high ct values (> 36) were pooled and tested. The mean Ct values obtained with the 5-sample pooled testing exceeded individual sample testing by 1.85 ± 1.09 cycles, while Ct values obtained with the 10-sample pooling exceeded individual sample testing by 3.4 ± 1.65 cycles. Conclusions In a low prevalence setting, testing capacity can be increased by pooling 5 or 10 samples, but the risk of additional false negatives needs to be considered.
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Affiliation(s)
- Imene Handous
- Laboratoire de Microbiologie, UR12SP34, Hôpital Farhat Hached, Université de Sousse, Faculté de Médecine de Sousse, Sousse, 4000, Tunisie. .,Université de Sfax, Ecole Nationale d'Ingénieurs de Sfax, Sfax, 3038, Tunisie.
| | - Naila Hannachi
- Laboratoire de Microbiologie, UR12SP34, Hôpital Farhat Hached, Université de Sousse, Faculté de Médecine de Sousse, Sousse, 4000, Tunisie
| | - Manel Marzouk
- Laboratoire de Microbiologie, UR12SP34, Hôpital Farhat Hached, Université de Sousse, Faculté de Médecine de Sousse, Sousse, 4000, Tunisie
| | - Olfa Hazgui
- Laboratoire de Microbiologie, UR12SP34, Hôpital Farhat Hached, Université de Sousse, Faculté de Médecine de Sousse, Sousse, 4000, Tunisie
| | | | - Jalel Boukadida
- Laboratoire de Microbiologie, UR12SP34, Hôpital Farhat Hached, Université de Sousse, Faculté de Médecine de Sousse, Sousse, 4000, Tunisie
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Polvere I, Silvestri E, Sabatino L, Giacco A, Iervolino S, Peluso T, Guida R, Zerillo L, Varricchio R, D’Andrea S, Voccola S, Madera JR, Zullo A, Stilo R, Vito P, Zotti T. Sample-Pooling Strategy for SARS-CoV-2 Detection among Students and Staff of the University of Sannio. Diagnostics (Basel) 2021; 11:diagnostics11071166. [PMID: 34206932 PMCID: PMC8303429 DOI: 10.3390/diagnostics11071166] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 06/17/2021] [Accepted: 06/23/2021] [Indexed: 12/28/2022] Open
Abstract
Since the beginning of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) pandemic, it has been clear that testing large groups of the population was the key to stem infection and prevent the effects of the coronavirus disease of 2019, mostly among sensitive patients. On the other hand, time and cost-sustainability of virus detection by molecular analysis such as reverse transcriptase-quantitative polymerase chain reaction (RT-qPCR) may be a major issue if testing is extended to large communities, mainly asymptomatic large communities. In this context, sample-pooling and test grouping could offer an effective solution. Here we report the screening on 1195 oral-nasopharyngeal swabs collected from students and staff of the Università degli Studi del Sannio (University of Sannio, Benevento, Campania, Italy) and analyzed by an in-house developed multiplex RT-qPCR for SARS-CoV-2 detection through a simple monodimensional sample pooling strategy. Overall, 400 distinct pools were generated and, within 24 h after swab collection, five positive samples were identified. Out of them, four were confirmed by using a commercially available kit suitable for in vitro diagnostic use (IVD). High accuracy, sensitivity and specificity were also determined by comparing our results with a reference IVD assay for all deconvoluted samples. Overall, we conducted 463 analyses instead of 1195, reducing testing resources by more than 60% without lengthening diagnosis time and without significant losses in sensitivity, suggesting that our strategy was successful in recognizing positive cases in a community of asymptomatic individuals with minor requirements of reagents and time when compared to normal testing procedures.
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Affiliation(s)
- Immacolata Polvere
- Dipartimento di Scienze e Tecnologie, Università Degli Studi del Sannio, Via dei Mulini, 82100 Benevento, Italy; (I.P.); (E.S.); (L.S.); (A.G.); (S.I.); (T.P.); (R.G.); (L.Z.); (J.R.M.); (A.Z.); (R.S.)
- Genus Biotech, Università degli Studi del Sannio, SS Appia, 82030 Apollosa, Italy; (R.V.); (S.D.); (S.V.)
| | - Elena Silvestri
- Dipartimento di Scienze e Tecnologie, Università Degli Studi del Sannio, Via dei Mulini, 82100 Benevento, Italy; (I.P.); (E.S.); (L.S.); (A.G.); (S.I.); (T.P.); (R.G.); (L.Z.); (J.R.M.); (A.Z.); (R.S.)
| | - Lina Sabatino
- Dipartimento di Scienze e Tecnologie, Università Degli Studi del Sannio, Via dei Mulini, 82100 Benevento, Italy; (I.P.); (E.S.); (L.S.); (A.G.); (S.I.); (T.P.); (R.G.); (L.Z.); (J.R.M.); (A.Z.); (R.S.)
| | - Antonia Giacco
- Dipartimento di Scienze e Tecnologie, Università Degli Studi del Sannio, Via dei Mulini, 82100 Benevento, Italy; (I.P.); (E.S.); (L.S.); (A.G.); (S.I.); (T.P.); (R.G.); (L.Z.); (J.R.M.); (A.Z.); (R.S.)
| | - Stefania Iervolino
- Dipartimento di Scienze e Tecnologie, Università Degli Studi del Sannio, Via dei Mulini, 82100 Benevento, Italy; (I.P.); (E.S.); (L.S.); (A.G.); (S.I.); (T.P.); (R.G.); (L.Z.); (J.R.M.); (A.Z.); (R.S.)
| | - Teresa Peluso
- Dipartimento di Scienze e Tecnologie, Università Degli Studi del Sannio, Via dei Mulini, 82100 Benevento, Italy; (I.P.); (E.S.); (L.S.); (A.G.); (S.I.); (T.P.); (R.G.); (L.Z.); (J.R.M.); (A.Z.); (R.S.)
| | - Rosa Guida
- Dipartimento di Scienze e Tecnologie, Università Degli Studi del Sannio, Via dei Mulini, 82100 Benevento, Italy; (I.P.); (E.S.); (L.S.); (A.G.); (S.I.); (T.P.); (R.G.); (L.Z.); (J.R.M.); (A.Z.); (R.S.)
| | - Lucrezia Zerillo
- Dipartimento di Scienze e Tecnologie, Università Degli Studi del Sannio, Via dei Mulini, 82100 Benevento, Italy; (I.P.); (E.S.); (L.S.); (A.G.); (S.I.); (T.P.); (R.G.); (L.Z.); (J.R.M.); (A.Z.); (R.S.)
- Genus Biotech, Università degli Studi del Sannio, SS Appia, 82030 Apollosa, Italy; (R.V.); (S.D.); (S.V.)
| | - Romualdo Varricchio
- Genus Biotech, Università degli Studi del Sannio, SS Appia, 82030 Apollosa, Italy; (R.V.); (S.D.); (S.V.)
| | - Silvia D’Andrea
- Genus Biotech, Università degli Studi del Sannio, SS Appia, 82030 Apollosa, Italy; (R.V.); (S.D.); (S.V.)
| | - Serena Voccola
- Genus Biotech, Università degli Studi del Sannio, SS Appia, 82030 Apollosa, Italy; (R.V.); (S.D.); (S.V.)
- Consorzio Sannio Tech, SS Appia, 82030 Apollosa, Italy
| | - Jessica Raffaella Madera
- Dipartimento di Scienze e Tecnologie, Università Degli Studi del Sannio, Via dei Mulini, 82100 Benevento, Italy; (I.P.); (E.S.); (L.S.); (A.G.); (S.I.); (T.P.); (R.G.); (L.Z.); (J.R.M.); (A.Z.); (R.S.)
| | - Alberto Zullo
- Dipartimento di Scienze e Tecnologie, Università Degli Studi del Sannio, Via dei Mulini, 82100 Benevento, Italy; (I.P.); (E.S.); (L.S.); (A.G.); (S.I.); (T.P.); (R.G.); (L.Z.); (J.R.M.); (A.Z.); (R.S.)
| | - Romania Stilo
- Dipartimento di Scienze e Tecnologie, Università Degli Studi del Sannio, Via dei Mulini, 82100 Benevento, Italy; (I.P.); (E.S.); (L.S.); (A.G.); (S.I.); (T.P.); (R.G.); (L.Z.); (J.R.M.); (A.Z.); (R.S.)
| | - Pasquale Vito
- Dipartimento di Scienze e Tecnologie, Università Degli Studi del Sannio, Via dei Mulini, 82100 Benevento, Italy; (I.P.); (E.S.); (L.S.); (A.G.); (S.I.); (T.P.); (R.G.); (L.Z.); (J.R.M.); (A.Z.); (R.S.)
- Genus Biotech, Università degli Studi del Sannio, SS Appia, 82030 Apollosa, Italy; (R.V.); (S.D.); (S.V.)
- Correspondence: (P.V.); (T.Z.); Tel.: +39-0824305105 (P.V. & T.Z.)
| | - Tiziana Zotti
- Dipartimento di Scienze e Tecnologie, Università Degli Studi del Sannio, Via dei Mulini, 82100 Benevento, Italy; (I.P.); (E.S.); (L.S.); (A.G.); (S.I.); (T.P.); (R.G.); (L.Z.); (J.R.M.); (A.Z.); (R.S.)
- Genus Biotech, Università degli Studi del Sannio, SS Appia, 82030 Apollosa, Italy; (R.V.); (S.D.); (S.V.)
- Correspondence: (P.V.); (T.Z.); Tel.: +39-0824305105 (P.V. & T.Z.)
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