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Nambiar A, Pan C, Rana V, Cheraghchi M, Ribeiro J, Maslov S, Milenkovic O. Semi-quantitative group testing for efficient and accurate qPCR screening of pathogens with a wide range of loads. BMC Bioinformatics 2024; 25:195. [PMID: 38760692 PMCID: PMC11100062 DOI: 10.1186/s12859-024-05798-3] [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: 08/12/2023] [Accepted: 04/26/2024] [Indexed: 05/19/2024] Open
Abstract
BACKGROUND Pathogenic infections pose a significant threat to global health, affecting millions of people every year and presenting substantial challenges to healthcare systems worldwide. Efficient and timely testing plays a critical role in disease control and transmission prevention. Group testing is a well-established method for reducing the number of tests needed to screen large populations when the disease prevalence is low. However, it does not fully utilize the quantitative information provided by qPCR methods, nor is it able to accommodate a wide range of pathogen loads. RESULTS To address these issues, we introduce a novel adaptive semi-quantitative group testing (SQGT) scheme to efficiently screen populations via two-stage qPCR testing. The SQGT method quantizes cycle threshold (Ct) values into multiple bins, leveraging the information from the first stage of screening to improve the detection sensitivity. Dynamic Ct threshold adjustments mitigate dilution effects and enhance test accuracy. Comparisons with traditional binary outcome GT methods show that SQGT reduces the number of tests by 24% on the only complete real-world qPCR group testing dataset from Israel, while maintaining a negligible false negative rate. CONCLUSION In conclusion, our adaptive SQGT approach, utilizing qPCR data and dynamic threshold adjustments, offers a promising solution for efficient population screening. With a reduction in the number of tests and minimal false negatives, SQGT holds potential to enhance disease control and testing strategies on a global scale.
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Affiliation(s)
- Ananthan Nambiar
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, USA.
| | - Chao Pan
- Department of Electrical and Computer Engineering, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Center for Artificial Intelligence and Modeling, Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Vishal Rana
- Department of Electrical and Computer Engineering, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Mahdi Cheraghchi
- Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, MI, USA
| | - João Ribeiro
- NOVA LINCS and NOVA School of Science and Technology, Caparica, Portugal
| | - Sergei Maslov
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Center for Artificial Intelligence and Modeling, Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA.
| | - Olgica Milenkovic
- Department of Electrical and Computer Engineering, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Center for Artificial Intelligence and Modeling, Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA.
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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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Abdelrazik AM, Said MNE, Abdelaziz HM. Evaluation of pooling strategy of SARS-CoV-2 RT-PCR in limited resources setting in Egypt at low prevalence. COMPARATIVE CLINICAL PATHOLOGY 2023; 32:375-381. [PMID: 36778967 PMCID: PMC9906572 DOI: 10.1007/s00580-023-03445-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 01/23/2023] [Indexed: 02/10/2023]
Abstract
Sample pooling testing for SARS-COV-2 can be an effective tool in COVID-19 screening when resources are limited, yet it is important to assess the performance before implementation as pooling has its limitations. Our objective was to assess the efficacy of pooling samples for coronavirus 2019 (COVID-19) compared to an individual analysis by using commercial platforms for nucleic acid testing. A total of 2200 nasopharyngeal swabs for SARS-COV-2 were tested individually and in pools of 4, 8, and 10. The cycle threshold (Ct) values of the positive pooled samples were compared to their corresponding individual positive samples. In pool size 10 samples, an estimated increase of 3-Ct was obtained, which led to false negative results in low viral load positive samples. Pooling SARS COV-2 samples is an effective strategy of screening to increase laboratories' capacity and reduce costs without affecting diagnostic performance. A pool size of 8 is recommended.
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Affiliation(s)
| | - Manal Niazi El Said
- Clinical Pathology Department, Faculty of Medicine, Fayoum University, Fayoum, Egypt
| | - Hossam M. Abdelaziz
- Clinical Pathology Department, Faculty of Medicine, Fayoum University, Fayoum, Egypt
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de Sousa ARV, do Carmo Silva L, de Curcio JS, da Silva HD, Eduardo Anunciação C, Maria Salem Izacc S, Neto FOS, de Paula Silveira Lacerda E. "pySewage": a hybrid approach to predict the number of SARS-CoV-2-infected people from wastewater in Brazil. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:67260-67269. [PMID: 35524091 PMCID: PMC9075719 DOI: 10.1007/s11356-022-20609-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 04/30/2022] [Indexed: 05/21/2023]
Abstract
It is well known that the new coronavirus pandemic has global environmental, public health, and economic implications. In this sense, this study aims to monitor SARS-CoV-2 in the largest wastewater treatment plant of Goiânia, which processes wastewater from more than 700,000 inhabitants, and to correlate the molecular and clinical data collected. Influent and effluent samples were collected at Dr. Helio de Seixo Britto's wastewater treatment plant from January to August 2021. Viral concentration was performed with polyethylene glycol before viral RNA extraction. Real-time qPCR (N1 and N2 gene assays) was performed to detect and quantify the viral RNA present in the samples. The results showed that 43.63% of the samples were positive. There is no significant difference between the detection of primers N1 (mean 3.23 log10 genome copies/L, std 0.23) and N2 (mean 2.95 log10 genome copies/L, std 0.29); also, there is no significant difference between the detection of influent and effluent samples. Our molecular data revealed a positive correlation with clinical data, and infection prevalence was higher than clinical data. In addition, we developed a user-friendly web application to predict the number of infected people based on the detection of viral load present in wastewater samples and may be applied as a public policy strategy for monitoring ongoing outbreaks.
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Affiliation(s)
| | - Lívia do Carmo Silva
- Department of Genetics, Institute of Biological Sciences, Federal University of Goiás, Goiânia, Brazil
| | - Juliana Santana de Curcio
- Department of Genetics, Institute of Biological Sciences, Federal University of Goiás, Goiânia, Brazil
| | - Hugo Delleon da Silva
- Department of Genetics, Institute of Biological Sciences, Federal University of Goiás, Goiânia, Brazil
- Universitary Center of Goiás (UNIGOIÁS), Goiânia, Goiás, Brazil
| | - Carlos Eduardo Anunciação
- Department of Biochemistry and Molecular Biology, Institute of Biological Sciences, Federal University of Goiás, Goiânia, Brazil
| | - Silvia Maria Salem Izacc
- Department of Genetics, Institute of Biological Sciences, Federal University of Goiás, Goiânia, Brazil
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Progress and Challenges of Point-of-Need Photonic Biosensors for the Diagnosis of COVID-19 Infections and Immunity. BIOSENSORS 2022; 12:bios12090678. [PMID: 36140063 PMCID: PMC9496547 DOI: 10.3390/bios12090678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 08/13/2022] [Accepted: 08/16/2022] [Indexed: 11/25/2022]
Abstract
The new coronavirus disease, COVID-19, caused by SARS-CoV-2, continues to affect the world and after more than two years of the pandemic, approximately half a billion people are reported to have been infected. Due to its high contagiousness, our life has changed dramatically, with consequences that remain to be seen. To prevent the transmission of the virus, it is crucial to diagnose COVID-19 accurately, such that the infected cases can be rapidly identified and managed. Currently, the gold standard of testing is polymerase chain reaction (PCR), which provides the highest accuracy. However, the reliance on centralized rapid testing modalities throughout the COVID-19 pandemic has made access to timely diagnosis inconsistent and inefficient. Recent advancements in photonic biosensors with respect to cost-effectiveness, analytical performance, and portability have shown the potential for such platforms to enable the delivery of preventative and diagnostic care beyond clinics and into point-of-need (PON) settings. Herein, we review photonic technologies that have become commercially relevant throughout the COVID-19 pandemic, as well as emerging research in the field of photonic biosensors, shedding light on prospective technologies for responding to future health outbreaks. Therefore, in this article, we provide a review of recent progress and challenges of photonic biosensors that are developed for the testing of COVID-19, consisting of their working fundamentals and implementation for COVID-19 testing in practice with emphasis on the challenges that are faced in different development stages towards commercialization. In addition, we also present the characteristics of a biosensor both from technical and clinical perspectives. We present an estimate of the impact of testing on disease burden (in terms of Disability-Adjusted Life Years (DALYs), Quality Adjusted Life Years (QALYs), and Quality-Adjusted Life Days (QALDs)) and how improvements in cost can lower the economic impact and lead to reduced or averted DALYs. While COVID19 is the main focus of these technologies, similar concepts and approaches can be used and developed for future outbreaks of other infectious diseases.
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6
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Joly É, Mallein B. A tractable non-adaptative group testing method for non-binary measurements. ESAIM-PROBAB STAT 2022. [DOI: 10.1051/ps/2022007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
The original problem of group testing consists in the identification of defective items in a collection, by applying tests on groups of items that detect the presence of at least one defective element in the group. The aim is then to identify all defective items of the collection with as few tests as possible. This problem is relevant in several fields, among which biology and computer sciences. In the present article we consider that the tests applied to groups of items returns a load, measuring how defective the most defective item of the group is. In this setting, we propose a simple non-adaptative algorithm allowing the detection of all defective items of the collection. Items are put on an n × n grid and pools are organised as lines, columns and diagonals of this grid. This method improves on classical group testing algorithms using only the binary response of the test. Group testing recently gained attraction as a potential tool to solve a shortage of COVID-19 test kits, in particular for RT-qPCR. These tests return the viral load of the sample and the viral load varies greatly among individuals. Therefore our model presents some of the key features of this problem. We aim at using the extra piece of information that represents the viral load to construct a one-stage pool testing algorithm on this idealized version. We show that under the right conditions, the total number of tests needed to detect contaminated samples can be drastically diminished.
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Yang JR, Kuo CY, Huang HY, Yu IL, Hsieh CT, Chen BS, Liu MT. Evaluation of conventional and point-of-care real-time RT-PCR tests for the detection of SARS-CoV-2 through a pooled testing strategy. J Clin Lab Anal 2022; 36:e24491. [PMID: 35535393 PMCID: PMC9169176 DOI: 10.1002/jcla.24491] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 04/25/2022] [Accepted: 04/29/2022] [Indexed: 12/23/2022] Open
Abstract
Background The rapid identification and isolation of individuals infected with SARS‐CoV‐2 are fundamental countermeasures for the efficient control of the COVID‐19 pandemic, which has affected millions of people around the world. Real‐time RT‐PCR is one of the most commonly applied reference methods for virus detection, and the use of pooled testing has been proposed as an effective way to increase the throughput of routine diagnostic tests. However, the clinical applicability of different types of real‐time RT‐PCR tests in a given group size remains inconclusive due to inconsistent regional disease prevalence and test demands. Methods In this study, the performance of one dual‐target conventional and two point‐of‐care real‐time RT‐PCR tests in a 5‐specimen pooled testing strategy for the detection of SARS‐COV‐2 was evaluated. Results We demonstrated the proof of concept that all of these real‐time RT‐PCR tests could feasibly detect SARS‐CoV‐2 from nasopharyngeal and oropharyngeal specimens that contain viral RNA loads in the range of 3.48 × 105 to 3.42 × 102 copies/ml through pooled testing in a group size of 5 with overall positive percent agreement (pooling vs. individual testing) ranging from 100% to 93.75%. Furthermore, the two POC real‐time RT‐PCR tests exhibited comparable sensitivity to that of the dual‐target conventional one when clinical specimens were tested individually. Conclusion Our findings support the feasibility of using real‐time RT‐PCR tests developed as a variety of platforms in routine laboratory detection of suspected COVID‐19 cases through a pooled testing strategy that is beneficial to increasing the daily diagnostic capacity.
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Affiliation(s)
- Ji-Rong Yang
- Center for Diagnostics and Vaccine Development, Centers for Disease Control, Taipei, Taiwan
| | - Chuan-Yi Kuo
- Center for Diagnostics and Vaccine Development, Centers for Disease Control, Taipei, Taiwan
| | - Hsiang-Yi Huang
- Center for Diagnostics and Vaccine Development, Centers for Disease Control, Taipei, Taiwan
| | - I-Ling Yu
- Center for Diagnostics and Vaccine Development, Centers for Disease Control, Taipei, Taiwan
| | - Chih-Tsun Hsieh
- Center for Diagnostics and Vaccine Development, Centers for Disease Control, Taipei, Taiwan
| | - Bao-Shan Chen
- Center for Diagnostics and Vaccine Development, Centers for Disease Control, Taipei, Taiwan
| | - Ming-Tsan Liu
- Center for Diagnostics and Vaccine Development, Centers for Disease Control, Taipei, Taiwan
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8
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de Oliveira PSS, de Oliveira Silva B, e Silva RP, Galdino LV, de Carvalho VMF, de Almeida AR, da Rosa MM, de Melo Rêgo MJB, da Rocha Pitta MG, Pereira MC. Evaluation of long-term stability of SARS-CoV-2 nucleic acid extracted from human nasopharyngeal samples. J Virol Methods 2022; 305:114529. [PMID: 35398116 PMCID: PMC8985402 DOI: 10.1016/j.jviromet.2022.114529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 03/29/2022] [Accepted: 04/02/2022] [Indexed: 11/30/2022]
Abstract
The maintenance of SARS-Cov-2 RNA samples poses a new challenge for laboratories and researchers. In addition, it is a requirement in order to identify what strain of the new coronavirus is predominant in a region, for instance. Therefore, it is a must to keep the quality and viability of stored RNA to respond to this and other valid questions. In other to test the quality of our samples and storing protocols, we randomly checked RNA samples four different times over one year using a second RT-PCR assay after the first test. The virus genes, N1 and N2, showed no significant increase in the media of the CT value between the first assay and subsequent times with p > 0.05. However, the human RP gene showed differences in the first three times analyzed, but within the acceptable sample cut-off, according to the test manufacturer. After one year, the RNA extracted from human nasopharyngeal specimens are viable to detect the virus SARS-CoV-2 genes with minor changes.
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Gajpal Y, Appadoo SS, Shi V, Hu G. Optimal multi-stage group partition for efficient coronavirus screening. ANNALS OF OPERATIONS RESEARCH 2022:1-17. [PMID: 35221417 PMCID: PMC8860262 DOI: 10.1007/s10479-022-04543-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Accepted: 01/18/2022] [Indexed: 06/14/2023]
Abstract
The outbreak of COVID-19 has affected the economy worldwide due to entire countries being on lockdown. This has been highly challenging for governments facing constraints in terms of time and resources related to the availability of testing kits for the virus. This paper develops an optimal method for multiple-stage group partition for coronavirus screening using a dynamic programming approach. That is, in each stage, a group of people is divided into a certain number of subgroups, each will be tested as a whole. Only the subgroup(s) tested positive will be further divided into smaller subgroups in the next stage or individuals at the last stage. Our multiple-stage group partition scheme is able to minimize the total number of test kits and the number of stages. Our scheme can help solve the test kit shortage problem and save time. Finally, numerical examples with useful managerial insights for further investigation are presented. The results confirm the advantages of the multi-stage sampling method over the existing binary tree method.
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Affiliation(s)
- Yuvraj Gajpal
- Asper School of Business, University of Manitoba, Winnipeg, MB R3T 5V4 Canada
| | - S. S. Appadoo
- Asper School of Business, University of Manitoba, Winnipeg, MB R3T 5V4 Canada
| | - Victor Shi
- Lazaridis School of Business and Economics, Wilfrid Laurier University, Waterloo, ON N2L 3C5 Canada
| | - Guoping Hu
- School of Business Administration, Southwestern University of Finance and Economics, Chengdu, China
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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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Czuppon P, Schertzer E, Blanquart F, Débarre F. The stochastic dynamics of early epidemics: probability of establishment, initial growth rate, and infection cluster size at first detection. J R Soc Interface 2021; 18:20210575. [PMID: 34784776 PMCID: PMC8596012 DOI: 10.1098/rsif.2021.0575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 10/26/2021] [Indexed: 11/16/2022] Open
Abstract
Emerging epidemics and local infection clusters are initially prone to stochastic effects that can substantially impact the early epidemic trajectory. While numerous studies are devoted to the deterministic regime of an established epidemic, mathematical descriptions of the initial phase of epidemic growth are comparatively rarer. Here, we review existing mathematical results on the size of the epidemic over time, and derive new results to elucidate the early dynamics of an infection cluster started by a single infected individual. We show that the initial growth of epidemics that eventually take off is accelerated by stochasticity. As an application, we compute the distribution of the first detection time of an infected individual in an infection cluster depending on testing effort, and estimate that the SARS-CoV-2 variant of concern Alpha detected in September 2020 first appeared in the UK early August 2020. We also compute a minimal testing frequency to detect clusters before they exceed a given threshold size. These results improve our theoretical understanding of early epidemics and will be useful for the study and control of local infectious disease clusters.
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Affiliation(s)
- Peter Czuppon
- Institute of Ecology and Environmental Sciences of Paris (iEES-Paris, UMR 7618), Sorbonne Université, CNRS, UPEC, IRD, INRAE, Paris 75252, France
- Center for Interdisciplinary Research in Biology, CNRS, Collège de France, PSL Research University, Paris 75005, France
- Institute for Evolution and Biodiversity, University of Münster, Münster 48149, Germany
| | | | - François Blanquart
- Center for Interdisciplinary Research in Biology, CNRS, Collège de France, PSL Research University, Paris 75005, France
- Infection Antimicrobials Modelling Evolution, UMR 1137, INSERM, Université de Paris, Paris 75018, France
| | - Florence Débarre
- Institute of Ecology and Environmental Sciences of Paris (iEES-Paris, UMR 7618), Sorbonne Université, CNRS, UPEC, IRD, INRAE, Paris 75252, France
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12
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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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13
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Cui Y, Ni S, Shen S. A network-based model to explore the role of testing in the epidemiological control of the COVID-19 pandemic. BMC Infect Dis 2021; 21:58. [PMID: 33435892 PMCID: PMC7803001 DOI: 10.1186/s12879-020-05750-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 12/27/2020] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Testing is one of the most effective means to manage the COVID-19 pandemic. However, there is an upper bound on daily testing volume because of limited healthcare staff and working hours, as well as different testing methods, such as random testing and contact-tracking testing. In this study, a network-based epidemic transmission model combined with a testing mechanism was proposed to study the role of testing in epidemic control. The aim of this study was to determine how testing affects the spread of epidemics and the daily testing volume needed to control infectious diseases. METHODS We simulated the epidemic spread process on complex networks and introduced testing preferences to describe different testing strategies. Different networks were generated to represent social contact between individuals. An extended susceptible-exposed-infected-recovered (SEIR) epidemic model was adopted to simulate the spread of epidemics in these networks. The model establishes a testing preference of between 0 and 1; the larger the testing preference, the higher the testing priority for people in close contact with confirmed cases. RESULTS The numerical simulations revealed that the higher the priority for testing individuals in close contact with confirmed cases, the smaller the infection scale. In addition, the infection peak decreased with an increase in daily testing volume and increased as the testing start time was delayed. We also discovered that when testing and other measures were adopted, the daily testing volume required to keep the infection scale below 5% was reduced by more than 40% even if other measures only reduced individuals' infection probability by 10%. The proposed model was validated using COVID-19 testing data. CONCLUSIONS Although testing could effectively inhibit the spread of infectious diseases and epidemics, our results indicated that it requires a huge daily testing volume. Thus, it is highly recommended that testing be adopted in combination with measures such as wearing masks and social distancing to better manage infectious diseases. Our research contributes to understanding the role of testing in epidemic control and provides useful suggestions for the government and individuals in responding to epidemics.
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Affiliation(s)
- Yapeng Cui
- Institute of Public Safety Research, Tsinghua University, Beijing, China
- Department of Engineering Physics, Tsinghua University, Beijing, China
- Beijing Key Laboratory of City Integrated Emergency Response Science, Beijing, China
| | - Shunjiang Ni
- Institute of Public Safety Research, Tsinghua University, Beijing, China.
- Department of Engineering Physics, Tsinghua University, Beijing, China.
- Beijing Key Laboratory of City Integrated Emergency Response Science, Beijing, China.
| | - Shifei Shen
- Institute of Public Safety Research, Tsinghua University, Beijing, China
- Department of Engineering Physics, Tsinghua University, Beijing, China
- Beijing Key Laboratory of City Integrated Emergency Response Science, Beijing, China
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14
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Rosolanka R, Henao-Martinez AF, Pisney L, Franco-Paredes C, Krsak M. COVID-19: a review of current knowledge regarding exposure, quarantine, isolation and other preventive measures. Ther Adv Infect Dis 2021; 8:20499361211032039. [PMID: 34349986 PMCID: PMC8287266 DOI: 10.1177/20499361211032039] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 06/23/2021] [Indexed: 01/08/2023] Open
Abstract
Deeper understanding of the spread, morbidity, fatality, and development of immune response associated with coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2, is necessary in order to establish an appropriate epidemiological and clinical response. Exposure control represents a key part of the combat against COVID-19, as the effectiveness of current therapeutic options remains partial. Since the preventive measures have not been sufficiently able to slow down this pandemic, in this article we explore some of the pertinent knowledge gaps, while overall looking to effective vaccination strategies as a way out. Early on, such strategies may need to rely on counting the convalescents as protected in order to speed up the immunization of the whole population.
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Affiliation(s)
- Robert Rosolanka
- Department of Infectology and Travel Medicine, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Kollárova 2, Martin, 036 01, Slovakia
| | | | - Larissa Pisney
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO, USA
| | - Carlos Franco-Paredes
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO, USA
- Hospital Infantil de México, Federico Gomez, México City, México
| | - Martin Krsak
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO, USA
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15
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Abstract
It has long been known that pooling samples may be used to reduce the total number of tests required in order to identify each infected individual in a population. Pooling is most advantageous in populations with low infection (positivity) rates, but is expected to remain better than non-pooled testing in populations with infection rates up to 30%. For populations with infection rates lower than 10%, additional testing efficiency may be realized by performing a second round of pooling to test all the samples in the positive first-round pools. The present predictions are validated by recent COVID-19 (SARS-CoV-2) pooled testing and detection sensitivity measurements performed using non-optimal pool sizes, and quantify the additional improvement in testing efficiency that could have been obtained using optimal pooling. Although large pools are most advantageous for testing populations with very low infection rates, they are predicted to become highly non-optimal with increasing infection rate, while pool sizes smaller than 10 remain near-optimal over a broader range of infection rates.
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Affiliation(s)
- Dor Ben-Amotz
- Purdue University, Department of Chemistry, West Lafayette, IN 47907, United States of America.
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