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Liu Y, Yin Y, Ward MP, Li K, Chen Y, Duan M, Wong PPY, Hong J, Huang J, Shi J, Zhou X, Chen X, Xu J, Yuan R, Kong L, Zhang Z. Optimization of Screening Strategies for COVID-19: Scoping Review. JMIR Public Health Surveill 2024; 10:e44349. [PMID: 38412011 PMCID: PMC10933748 DOI: 10.2196/44349] [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: 11/17/2022] [Revised: 06/29/2023] [Accepted: 11/21/2023] [Indexed: 02/28/2024] Open
Abstract
BACKGROUND COVID-19 screening is an effective nonpharmaceutical intervention for identifying infected individuals and interrupting viral transmission. However, questions have been raised regarding its effectiveness in controlling the spread of novel variants and its high socioeconomic costs. Therefore, the optimization of COVID-19 screening strategies has attracted great attention. OBJECTIVE This review aims to summarize the evidence and provide a reference basis for the optimization of screening strategies for the prevention and control of COVID-19. METHODS We applied a methodological framework for scoping reviews and the PRISMA-ScR (Preferred Reporting Items for Systematic Reviews and Meta-Analyses Extension for Scoping Reviews) checklist. We conducted a scoping review of the present publications on the optimization of COVID-19 screening strategies. We searched the PubMed, Web of Science, and Elsevier ScienceDirect databases for publications up to December 31, 2022. English publications related to screening and testing strategies for COVID-19 were included. A data-charting form, jointly developed by 2 reviewers, was used for data extraction according to the optimization directions of the screening strategies. RESULTS A total of 2770 unique publications were retrieved from the database search, and 95 abstracts were retained for full-text review. There were 62 studies included in the final review. We summarized the results in 4 major aspects: the screening population (people at various risk conditions such as different regions and occupations; 12/62, 19%), the timing of screening (when the target population is tested before travel or during an outbreak; 12/62, 19%), the frequency of screening (appropriate frequencies for outbreak prevention, outbreak response, or community transmission control; 6/62, 10%), and the screening and detection procedure (the choice of individual or pooled detection and optimization of the pooling approach; 35/62, 56%). CONCLUSIONS This review reveals gaps in the optimization of COVID-19 screening strategies and suggests that a number of factors such as prevalence, screening accuracy, effective allocation of resources, and feasibility of strategies should be carefully considered in the development of future screening strategies.
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Affiliation(s)
- Yuanhua Liu
- Department of Epidemiology and Health Statistics, School of Public Health, Fudan University, Shanghai, China
- Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Yun Yin
- Department of Epidemiology and Health Statistics, School of Public Health, Fudan University, Shanghai, China
- Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Michael P Ward
- Sydney School of Veterinary Science, The University of Sydney, NSW, Australia
| | - Ke Li
- Department of Epidemiology and Health Statistics, School of Public Health, Fudan University, Shanghai, China
- Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Yue Chen
- School of Epidemiology and Public Health, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Mengwei Duan
- Department of Mathematics and Physics, North China Electric Power University, Baoding, China
| | | | - Jie Hong
- Department of Epidemiology and Health Statistics, School of Public Health, Fudan University, Shanghai, China
- Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Jiaqi Huang
- Department of Epidemiology and Health Statistics, School of Public Health, Fudan University, Shanghai, China
- Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Jin Shi
- Department of Epidemiology and Health Statistics, School of Public Health, Fudan University, Shanghai, China
- Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Xuan Zhou
- Department of Mathematics and Physics, North China Electric Power University, Baoding, China
| | - Xi Chen
- Department of Epidemiology and Health Statistics, School of Public Health, Fudan University, Shanghai, China
- Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Jiayao Xu
- Department of Epidemiology and Health Statistics, School of Public Health, Fudan University, Shanghai, China
- Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Rui Yuan
- Department of Epidemiology and Health Statistics, School of Public Health, Fudan University, Shanghai, China
- Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Lingcai Kong
- Department of Mathematics and Physics, North China Electric Power University, Baoding, China
| | - Zhijie Zhang
- Department of Epidemiology and Health Statistics, School of Public Health, Fudan University, Shanghai, China
- Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
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Heckel S, Pacini A, Paredes F, Petreli MV, Perez M, Adriani N, Ibarra G, Menzella H, Colaneri A, Sesma J. Practical considerations to establish a validated platform for pooled detection of SARS-CoV-2 by droplet digital PCR. PLoS One 2022; 17:e0271860. [PMID: 36331920 PMCID: PMC9635689 DOI: 10.1371/journal.pone.0271860] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 10/23/2022] [Indexed: 11/06/2022] Open
Abstract
Detection of SARS-CoV-2 has created an enormous workload for laboratories worldwide resulting in a restriction at the time of massive testing. Pool testing is a strategy that reduces time and costs. However, beyond the detection of infectious diseases in blood banks, this approach is rarely implemented in routine laboratories. Therefore, what was learned from the SARS-CoV-2 pool testing should represent an opportunity to increase diagnostic capabilities. The present work, carried out in the context of a diagnostic laboratory of a public hospital during the COVID-19 pandemic, represents a contribution to this end. The main limitation of pool testing is the risk of false negatives that could have been identified by individual tests. These limitations are the dilution of samples with a low virus load during pooling and that the integrity of the sample may be affected by the quality of the sample collection. Fortunately, both limitations coincide with the main strengths of droplet digital PCR (ddPCR). ddPCR is a third-generation PCR that splits the amplification into thousands of droplets that work in parallel, increasing sensitivity and resistance to inhibitors. Therefore, ddPCR is particularly useful for pool testing. Here we show how to factor between test sensitivity and savings in test time and resources. We have identified and optimized critical parameters for pool testing. The present study, which analyzed 1000 nasopharyngeal samples, showed that the pool testing could detect even a single positive sample with a CT value of up to 30 in pools of 34 samples. This test was performed using three different standard extraction methods, the simplest being heating only, which resulted in substantial savings of extraction reagents in addition to PCR reagents. Moreover, we show that pooling can be extended to use saliva, which is less invasive and allows self-collection, reducing the risk for health personnel.
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Affiliation(s)
- Sofía Heckel
- Molecular Biology Department, Hospital Provincial de Rosario (HPR), Rosario, Santa Fe, Argentina
- Instituto de Inmunología Clínica y Experimental de Rosario (IDICER-CONICET), Rosario, Santa Fe, Argentina
- Facultad de Ciencias Bioquímicas y Farmacéuticas de Rosario (FBioyF), Rosario, Santa Fe, Argentina
| | - Antonella Pacini
- Molecular Biology Department, Hospital Provincial de Rosario (HPR), Rosario, Santa Fe, Argentina
- Instituto de Inmunología Clínica y Experimental de Rosario (IDICER-CONICET), Rosario, Santa Fe, Argentina
| | - Franco Paredes
- Molecular Biology Department, Hospital Provincial de Rosario (HPR), Rosario, Santa Fe, Argentina
- Facultad de Ciencias Bioquímicas y Farmacéuticas de Rosario (FBioyF), Rosario, Santa Fe, Argentina
| | - Ma. Victoria Petreli
- Molecular Biology Department, Hospital Provincial de Rosario (HPR), Rosario, Santa Fe, Argentina
- Facultad de Ciencias Bioquímicas y Farmacéuticas de Rosario (FBioyF), Rosario, Santa Fe, Argentina
| | - Marilina Perez
- Molecular Biology Department, Hospital Provincial de Rosario (HPR), Rosario, Santa Fe, Argentina
| | - Natalia Adriani
- Molecular Biology Department, Hospital Provincial de Rosario (HPR), Rosario, Santa Fe, Argentina
| | - Guadalupe Ibarra
- Molecular Biology Department, Hospital Provincial de Rosario (HPR), Rosario, Santa Fe, Argentina
- Facultad de Ciencias Bioquímicas y Farmacéuticas de Rosario (FBioyF), Rosario, Santa Fe, Argentina
| | - Hugo Menzella
- Instituto de Procesos Biotecnológicos y Químicos Rosario (IPROByQ), Rosario, Santa Fe, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Alejandro Colaneri
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Juliana Sesma
- Molecular Biology Department, Hospital Provincial de Rosario (HPR), Rosario, Santa Fe, Argentina
- Instituto de Inmunología Clínica y Experimental de Rosario (IDICER-CONICET), Rosario, Santa Fe, Argentina
- Facultad de Ciencias Médicas (FCM-UNR), Rosario, Santa Fe, Argentina
- * E-mail:
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Nyaruaba R, Mwaliko C, Dobnik D, Neužil P, Amoth P, Mwau M, Yu J, Yang H, Wei H. Digital PCR Applications in the SARS-CoV-2/COVID-19 Era: a Roadmap for Future Outbreaks. Clin Microbiol Rev 2022; 35:e0016821. [PMID: 35258315 PMCID: PMC9491181 DOI: 10.1128/cmr.00168-21] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The ongoing coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has led to a global public health disaster. The current gold standard for the diagnosis of infected patients is real-time reverse transcription-quantitative PCR (RT-qPCR). As effective as this method may be, it is subject to false-negative and -positive results, affecting its precision, especially for the detection of low viral loads in samples. In contrast, digital PCR (dPCR), the third generation of PCR, has been shown to be more effective than the gold standard, RT-qPCR, in detecting low viral loads in samples. In this review article, we selected publications to show the broad-spectrum applications of dPCR, including the development of assays and reference standards, environmental monitoring, mutation detection, and clinical diagnosis of SARS-CoV-2, while comparing it analytically to the gold standard, RT-qPCR. In summary, it is evident that the specificity, sensitivity, reproducibility, and detection limits of RT-dPCR are generally unaffected by common factors that may affect RT-qPCR. As this is the first time that dPCR is being tested in an outbreak of such a magnitude, knowledge of its applications will help chart a course for future diagnosis and monitoring of infectious disease outbreaks.
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Affiliation(s)
- Raphael Nyaruaba
- Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China
- International College, University of Chinese Academy of Sciences, Beijing, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
| | - Caroline Mwaliko
- International College, University of Chinese Academy of Sciences, Beijing, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
- CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - David Dobnik
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Pavel Neužil
- Northwestern Polytechnical University, Xi’an, Shaanxi, China
| | - Patrick Amoth
- Ministry of Health, Government of Kenya, Nairobi, Kenya
| | - Matilu Mwau
- Center for Infectious and Parasitic Diseases Control Research, Kenya Medical Research Institute, Busia, Kenya
| | - Junping Yu
- Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Hang Yang
- Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Hongping Wei
- Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China
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