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Cabrera Alvargonzalez JJ, Larrañaga A, Martinez J, Pérez Castro S, Rey Cao S, Daviña Nuñez C, Del Campo Pérez V, Duran Parrondo C, Suarez Luque S, González Alonso E, Silva Tojo AJ, Porteiro J, Regueiro B. Assessment of the Effective Sensitivity of SARS-CoV-2 Sample Pooling Based on a Large-Scale Screening Experience: Retrospective Analysis. JMIR Public Health Surveill 2024; 10:e54503. [PMID: 39316785 DOI: 10.2196/54503] [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: 12/19/2023] [Revised: 05/18/2024] [Accepted: 07/18/2024] [Indexed: 09/26/2024] Open
Abstract
BACKGROUND The development of new large-scale saliva pooling detection strategies can significantly enhance testing capacity and frequency for asymptomatic individuals, which is crucial for containing SARS-CoV-2. OBJECTIVE This study aims to implement and scale-up a SARS-CoV-2 screening method using pooled saliva samples to control the virus in critical areas and assess its effectiveness in detecting asymptomatic infections. METHODS Between August 2020 and February 2022, our laboratory received a total of 928,357 samples. Participants collected at least 1 mL of saliva using a self-sampling kit and registered their samples via a smartphone app. All samples were directly processed using AutoMate 2550 for preanalytical steps and then transferred to Microlab STAR, managed with the HAMILTON Pooling software for pooling. The standard pool preset size was 20 samples but was adjusted to 5 when the prevalence exceeded 2% in any group. Real-time polymerase chain reaction (RT-PCR) was conducted using the Allplex SARS-CoV-2 Assay until July 2021, followed by the Allplex SARS-CoV-2 FluA/FluB/RSV assay for the remainder of the study period. RESULTS Of the 928,357 samples received, 887,926 (95.64%) were fully processed into 56,126 pools. Of these pools, 4863 tested positive, detecting 5720 asymptomatic infections. This allowed for a comprehensive analysis of pooling's impact on RT-PCR sensitivity and false-negative rate (FNR), including data on positive samples per pool (PPP). We defined Ctref as the minimum cycle threshold (Ct) of each data set from a sample or pool and compared these Ctref results from pooled samples with those of the individual tests (ΔCtP). We then examined their deviation from the expected offset due to dilution [ΔΔCtP = ΔCtP - log2]. In this work, the ΔCtP and ΔΔCtP were 2.23 versus 3.33 and -0.89 versus 0.23, respectively, comparing global results with results for pools with 1 positive sample per pool. Therefore, depending on the number of genes used in the test and the size of the pool, we can evaluate the FNR and effective sensitivity (1 - FNR) of the test configuration. In our scenario, with a maximum of 20 samples per pool and 3 target genes, statistical observations indicated an effective sensitivity exceeding 99%. From an economic perspective, the focus is on pooling efficiency, measured by the effective number of persons that can be tested with 1 test, referred to as persons per test (PPT). In this study, the global PPT was 8.66, reflecting savings of over 20 million euros (US $22 million) based on our reagent prices. CONCLUSIONS Our results demonstrate that, as expected, pooling reduces the sensitivity of RT-PCR. However, with the appropriate pool size and the use of multiple target genes, effective sensitivity can remain above 99%. Saliva pooling may be a valuable tool for screening and surveillance in asymptomatic individuals and can aid in controlling SARS-CoV-2 transmission. Further studies are needed to assess the effectiveness of these strategies for SARS-CoV-2 and their application to other microorganisms or biomarkers detected by PCR.
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Affiliation(s)
- Jorge J Cabrera Alvargonzalez
- Microbiology Department, Complexo Hospitalario Universitario de Vigo, Servicio Galego de Saude, Vigo, Spain
- Galicia Sur Health Research Institute (IIS Galicia Sur), Microbiology and Infectology Research Group, Vigo, Spain
| | - Ana Larrañaga
- Centro de Investigación en Tecnologías, Energía y Procesos Industriales, University of Vigo, Lagoas-Marcosende, Vigo, Spain
| | - Javier Martinez
- Applied Mathematics I, Telecommunications Engineering School, University of Vigo, Vigo, Spain
| | - Sonia Pérez Castro
- Microbiology Department, Complexo Hospitalario Universitario de Vigo, Servicio Galego de Saude, Vigo, Spain
- Galicia Sur Health Research Institute (IIS Galicia Sur), Microbiology and Infectology Research Group, Vigo, Spain
| | - Sonia Rey Cao
- Microbiology Department, Complexo Hospitalario Universitario de Vigo, Servicio Galego de Saude, Vigo, Spain
- Galicia Sur Health Research Institute (IIS Galicia Sur), Microbiology and Infectology Research Group, Vigo, Spain
| | - Carlos Daviña Nuñez
- Galicia Sur Health Research Institute (IIS Galicia Sur), Microbiology and Infectology Research Group, Vigo, Spain
| | - Víctor Del Campo Pérez
- Department of Preventive Medicine and Public Health, Complexo Hospitalario, Universitario de Vigo, Vigo, Spain
| | - Carmen Duran Parrondo
- Dirección Xeral de Saúde Pública, Consellería de Sanidade, Xunta de Galicia, Santiago de Compostela, Spain
| | - Silvia Suarez Luque
- Dirección Xeral de Saúde Pública, Consellería de Sanidade, Xunta de Galicia, Santiago de Compostela, Spain
| | - Elena González Alonso
- Galicia Sur Health Research Institute (IIS Galicia Sur), Microbiology and Infectology Research Group, Vigo, Spain
| | - Alfredo José Silva Tojo
- Dirección Xeral de Maiores y atención Sociosanitaria, Conselleria de Politica Social e Xuventude, Xunta de Galicia, Santiago de Compostela, Spain
| | - Jacobo Porteiro
- Centro de Investigación en Tecnologías, Energía y Procesos Industriales, University of Vigo, Lagoas-Marcosende, Vigo, Spain
| | - Benito Regueiro
- Microbiology Department, Complexo Hospitalario Universitario de Vigo, Servicio Galego de Saude, Vigo, Spain
- Galicia Sur Health Research Institute (IIS Galicia Sur), Microbiology and Infectology Research Group, Vigo, Spain
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Lin B, Li B, Zeng W, Zhao Y, Li H, Gu Y, Liu P. Needle-Plug/Piston-Based Modular Mesoscopic Design Paradigm Coupled With Microfluidic Device for Point-of-Care Pooled Testing. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2406076. [PMID: 39269286 DOI: 10.1002/advs.202406076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Revised: 07/26/2024] [Indexed: 09/15/2024]
Abstract
Emerging diagnostic scenarios, such as population surveillance by pooled testing and on-site rapid diagnosis, highlight the importance of advanced microfluidic systems for in vitro diagnostics. However, the widespread adoption of microfluidic technology faces challenges due to the lack of standardized design paradigms, posing difficulties in managing macro-micro fluidic interfaces, reagent storage, and complex macrofluidic operations. This paper introduces a novel modular-based mesoscopic design paradigm, featuring a core "needle-plug/piston" structure with versatile variants for complex fluidic operations. These structures can be easily coupled with various microfluidic platforms to achieve truly self-contained microsystems. Incorporated into a "3D extensible" design architecture, the mesoscopic design meets the demands of function integration, macrofluid manipulations, and flexible throughputs for point-of-care nucleic acid testing. Using this approach, an ultra-sensitive nucleic acid detection system is developed with a limit of detection of ten copies of SARS-CoV-2 per mL. This system efficiently conducts large-scale pooled testing from 50 pharyngeal swabs in a tube with an uncompromised sensitivity, enabling a truly "sample-in-answer-out" microsystem with exceptional performance.
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Affiliation(s)
- Baobao Lin
- Department of Biomedical Engineering, Tsinghua University, Beijing, 100084, China
| | - Bao Li
- Department of Biomedical Engineering, Tsinghua University, Beijing, 100084, China
| | - Wu Zeng
- Department of Biomedical Engineering, Tsinghua University, Beijing, 100084, China
- Changping Laboratory, Beijing, 102206, China
| | - Yulan Zhao
- Changping Laboratory, Beijing, 102206, China
| | - Huiping Li
- Department of Biomedical Engineering, Tsinghua University, Beijing, 100084, China
| | - Yin Gu
- State Key Laboratory of Space Medicine, China Astronaut Research and Training Center, Beijing, 100094, China
| | - Peng Liu
- Department of Biomedical Engineering, Tsinghua University, Beijing, 100084, China
- Changping Laboratory, Beijing, 102206, China
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Lin J, Aprahamian H, Golovko G. A proactive/reactive mass screening approach with uncertain symptomatic cases. PLoS Comput Biol 2024; 20:e1012308. [PMID: 39141678 PMCID: PMC11346970 DOI: 10.1371/journal.pcbi.1012308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 08/26/2024] [Accepted: 07/09/2024] [Indexed: 08/16/2024] Open
Abstract
We study the problem of mass screening of heterogeneous populations under limited testing budget. Mass screening is an essential tool that arises in various settings, e.g., the COVID-19 pandemic. The objective of mass screening is to classify the entire population as positive or negative for a disease as efficiently and accurately as possible. Under limited budget, testing facilities need to allocate a portion of the budget to target sub-populations (i.e., proactive screening) while reserving the remaining budget to screen for symptomatic cases (i.e., reactive screening). This paper addresses this decision problem by taking advantage of accessible population-level risk information to identify the optimal set of sub-populations for proactive/reactive screening. The framework also incorporates two widely used testing schemes: Individual and Dorfman group testing. By leveraging the special structure of the resulting bilinear optimization problem, we identify key structural properties, which in turn enable us to develop efficient solution schemes. Furthermore, we extend the model to accommodate customized testing schemes across different sub-populations and introduce a highly efficient heuristic solution algorithm for the generalized model. We conduct a comprehensive case study on COVID-19 in the US, utilizing geographically-based data. Numerical results demonstrate a significant improvement of up to 52% in total misclassifications compared to conventional screening strategies. In addition, our case study offers valuable managerial insights regarding the allocation of proactive/reactive measures and budget across diverse geographic regions.
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Affiliation(s)
- Jiayi Lin
- Department of Industrial and Systems Engineering, Texas A&M University College Station, Texas, United States of America
| | - Hrayer Aprahamian
- Department of Industrial and Systems Engineering, Texas A&M University College Station, Texas, United States of America
| | - George Golovko
- Department of Pharmacology and Toxicology, The University of Texas Medical Branch Galveston, Texas, United States of America
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Liang Z, Hu S, Dong Y, Miao L, Zhu W, Feng B, Fu J, Luo M, Wang L, Dong Z. Molecular characterization and function of hif1a and fih1 in response to acute thermal stress in American shad (Alosa sapidissima). FISH PHYSIOLOGY AND BIOCHEMISTRY 2024; 50:1563-1581. [PMID: 38789648 DOI: 10.1007/s10695-024-01356-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 05/03/2024] [Indexed: 05/26/2024]
Abstract
In order to evaluate the function of hypoxia-inducible factor-1 alpha (hif1α) and factor inhibiting hif1α (fih1) in response to thermal stress, we first conducted a functional analysis of A. sapidissima hif1α and fih1, and determined hif1α and fih1 expressions in different tissues in response to thermal stress based on identified housekeeping genes (HKGs). The results showed that hif1α and fih1 were mainly located in the nucleus and cytoplasm. The full length cDNA sequence of hif1α and fih1 was 4073 bp and 2759 bp, respectively. The cDNA sequence of hif1α includes 15 exons encoding 750 amino acid residues, and the full length cDNA sequence of fih1 contains 9 exons encoding 354 amino acid residues. During the acute thermal stress transferring from 16 ± 0.5 °C (control) to 20 ± 0.5 °C, 25 ± 0.5 °C, and 30 ± 0.5 °C for 15 min, it was found that the expression trends of hif1α and fih1 showed an inhibitory regulation in the heart, while they consistently expressed in brain, intestine, muscle, gill, kidney and liver. In conclusion, this is the first study to identify the tissue-specific HKGs in A. sapidissima and found that ef1α and β-actin are the most suitable HKGs. Hif1α and Fih1 are mainly the nuclear and cytoplasmic proteins, respectively, having high levels in the heart and brain. Alosa sapidissima countered a temperature increase from 16 to 25 ℃ by regulating the expressions of hif1α and fih1, but their physiological regulatory functions were unable to cope with acute thermal stress when the temperature difference was 14 ℃ (from 16 to 30 ℃).
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Affiliation(s)
- Zhengyuan Liang
- Wuxi Fisheries College, Nanjing Agricultural University, No.9 East Shanshui Road, Wuxi Jiangsu, 214081, China
- Wuxi Raysun Fishery Science and Technology Company, Xingyuan North Road No. 401, P.O. Box D20-501, Wuxi Jiangsu, 214000, China
| | - Songqin Hu
- Wuxi Fisheries College, Nanjing Agricultural University, No.9 East Shanshui Road, Wuxi Jiangsu, 214081, China
| | - Yalun Dong
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs; Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi Jiangsu, 214081, China
| | - Linghong Miao
- Wuxi Fisheries College, Nanjing Agricultural University, No.9 East Shanshui Road, Wuxi Jiangsu, 214081, China
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs; Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi Jiangsu, 214081, China
| | - Wenbin Zhu
- Wuxi Fisheries College, Nanjing Agricultural University, No.9 East Shanshui Road, Wuxi Jiangsu, 214081, China
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs; Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi Jiangsu, 214081, China
| | - Bingbing Feng
- Fisheries Technology Extension Center of Jiangsu Province, Hanzhongmen Street No. 300, Nanjing Jiangsu, 210036, China
| | - Jianjun Fu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs; Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi Jiangsu, 214081, China
| | - Mingkun Luo
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs; Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi Jiangsu, 214081, China
| | - Lanmei Wang
- Wuxi Fisheries College, Nanjing Agricultural University, No.9 East Shanshui Road, Wuxi Jiangsu, 214081, China
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs; Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi Jiangsu, 214081, China
| | - Zaije Dong
- Wuxi Fisheries College, Nanjing Agricultural University, No.9 East Shanshui Road, Wuxi Jiangsu, 214081, China.
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs; Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi Jiangsu, 214081, China.
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Sharma S, Caputi M, Asghar W. Development of a Diagnostic Microfluidic Chip for SARS-CoV-2 Detection in Saliva and Nasopharyngeal Samples. Viruses 2024; 16:1190. [PMID: 39205164 PMCID: PMC11360425 DOI: 10.3390/v16081190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 07/15/2024] [Accepted: 07/16/2024] [Indexed: 09/04/2024] Open
Abstract
The novel coronavirus SARS-CoV-2 was first isolated in late 2019; it has spread to all continents, infected over 700 million people, and caused over 7 million deaths worldwide to date. The high transmissibility of the virus and the emergence of novel strains with altered pathogenicity and potential resistance to therapeutics and vaccines are major challenges in the study and treatment of the virus. Ongoing screening efforts aim to identify new cases to monitor the spread of the virus and help determine the danger connected to the emergence of new variants. Given its sensitivity and specificity, nucleic acid amplification tests (NAATs) such as RT-qPCR are the gold standard for SARS-CoV-2 detection. However, due to high costs, complexity, and unavailability in low-resource and point-of-care (POC) settings, the available RT-qPCR assays cannot match global testing demands. An alternative NAAT, RT-LAMP-based SARS-CoV-2 detection offers scalable, low-cost, and rapid testing capabilities. We have developed an automated RT-LAMP-based microfluidic chip that combines the RNA isolation, purification, and amplification steps on the same device and enables the visual detection of SARS-CoV-2 within 40 min from saliva and nasopharyngeal samples. The entire assay is executed inside a uniquely designed, inexpensive disposable microfluidic chip, where assay components and reagents have been optimized to provide precise and qualitative results and can be effectively deployed in POC settings. Furthermore, this technology could be easily adapted for other novel emerging viruses.
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Affiliation(s)
- Sandhya Sharma
- Department of Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FL 33431, USA
- Asghar-Lab, Micro and Nanotechnology in Medicine, College of Engineering and Computer Science, Boca Raton, FL 33431, USA
| | - Massimo Caputi
- Charles E. Schmidt College of Medicine, Florida Atlantic University, Boca Raton, FL 33431, USA;
| | - Waseem Asghar
- Department of Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FL 33431, USA
- Asghar-Lab, Micro and Nanotechnology in Medicine, College of Engineering and Computer Science, Boca Raton, FL 33431, USA
- Department of Biological Sciences (Courtesy Appointment), Florida Atlantic University, Boca Raton, FL 33431, USA
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Miguel F, Baleizão AR, Gomes AG, Caria H, Serralha FN, Justino MC. Strategies for Increasing the Throughput of Genetic Screening: Lessons Learned from the COVID-19 Pandemic within a University Community. BIOTECH 2024; 13:26. [PMID: 39051341 PMCID: PMC11270334 DOI: 10.3390/biotech13030026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Revised: 06/29/2024] [Accepted: 07/08/2024] [Indexed: 07/27/2024] Open
Abstract
Amidst the COVID-19 pandemic, the Polytechnic University of Setúbal (IPS) used its expertise in molecular genetics to establish a COVID-19 laboratory, addressing the demand for community-wide testing. Following standard protocols, the IPS COVID Lab received national accreditation in October 2020 and was registered in February 2021. With the emergence of new SARS-CoV-2 variants and safety concerns for students and staff, the lab was further challenged to develop rapid and sensitive diagnostic technologies. Methodologies such as sample-pooling extraction and multiplex protocols were developed to enhance testing efficiency without compromising accuracy. Through Real-Time Reverse Transcription Polymerase Chain Reaction (RT-qPCR) analysis, the effectiveness of sample pooling was validated, proving to be a clear success in COVID-19 screening. Regarding multiplex analysis, the IPS COVID Lab developed an in-house protocol, achieving a sensitivity comparable to that of standard methods while reducing operational time and reagent consumption. This approach, requiring only two wells of a PCR plate (instead of three for samples), presents a more efficient alternative for future testing scenarios, increasing its throughput and testing capacity while upholding accuracy standards. The lessons learned during the SARS-CoV-2 pandemic provide added value for future pandemic situations.
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Affiliation(s)
- Fernanda Miguel
- IPS COVID Lab, Instituto Politécnico de Setúbal, Rua Américo da Silva Marinho, 2839-001 Lavradio, Portugal (A.G.G.); (H.C.)
| | - A. Raquel Baleizão
- IPS COVID Lab, Instituto Politécnico de Setúbal, Rua Américo da Silva Marinho, 2839-001 Lavradio, Portugal (A.G.G.); (H.C.)
| | - A. Gabriela Gomes
- IPS COVID Lab, Instituto Politécnico de Setúbal, Rua Américo da Silva Marinho, 2839-001 Lavradio, Portugal (A.G.G.); (H.C.)
- RESILIENCE—Center for Regional Resilience and Sustainability, Escola Superior de Tecnologia do Barreiro, Instituto Politécnico de Setúbal, Rua Américo da Silva Marinho, 2839-001 Lavradio, Portugal;
- MARE—Marine and Environmental Sciences Centre, Escola Superior de Tecnologia do Barreiro, Instituto Politécnico de Setúbal, Campus do IPS, Estefanilha, 2910-761 Setúbal, Portugal
- Departamento de Engenharia Química e Biológica, Escola Superior de Tecnologia do Barreiro, Instituto Politécnico de Setúbal, Rua Américo da Silva Marinho, 2839-001 Lavradio, Portugal
| | - Helena Caria
- IPS COVID Lab, Instituto Politécnico de Setúbal, Rua Américo da Silva Marinho, 2839-001 Lavradio, Portugal (A.G.G.); (H.C.)
- Departamento de Engenharia Química e Biológica, Escola Superior de Tecnologia do Barreiro, Instituto Politécnico de Setúbal, Rua Américo da Silva Marinho, 2839-001 Lavradio, Portugal
- BioISI—Instituto de Biosistemas e Ciências Integrativas, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
- Departamento de Ciências Biomédicas, Escola Superior de Saúde, Instituto Politécnico de Setúbal, Campus do IPS, Estefanilha, 2914-503 Setúbal, Portugal
| | - Fátima N. Serralha
- RESILIENCE—Center for Regional Resilience and Sustainability, Escola Superior de Tecnologia do Barreiro, Instituto Politécnico de Setúbal, Rua Américo da Silva Marinho, 2839-001 Lavradio, Portugal;
- Departamento de Engenharia Química e Biológica, Escola Superior de Tecnologia do Barreiro, Instituto Politécnico de Setúbal, Rua Américo da Silva Marinho, 2839-001 Lavradio, Portugal
| | - Marta C. Justino
- IPS COVID Lab, Instituto Politécnico de Setúbal, Rua Américo da Silva Marinho, 2839-001 Lavradio, Portugal (A.G.G.); (H.C.)
- RESILIENCE—Center for Regional Resilience and Sustainability, Escola Superior de Tecnologia do Barreiro, Instituto Politécnico de Setúbal, Rua Américo da Silva Marinho, 2839-001 Lavradio, Portugal;
- MARE—Marine and Environmental Sciences Centre, Escola Superior de Tecnologia do Barreiro, Instituto Politécnico de Setúbal, Campus do IPS, Estefanilha, 2910-761 Setúbal, Portugal
- Departamento de Engenharia Química e Biológica, Escola Superior de Tecnologia do Barreiro, Instituto Politécnico de Setúbal, Rua Américo da Silva Marinho, 2839-001 Lavradio, Portugal
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Bouska O, Koudelakova V, Gurska S, Kubanova K, Slavkovsky R, Jaworek H, Vrbkova J, Dzubak P, Hajduch M. Pooling of samples to optimise SARS-CoV-2 detection in nasopharyngeal swabs and gargle lavage self-samples for covid-19 diagnostics and surveillance. Infect Dis (Lond) 2024; 56:531-542. [PMID: 38549542 DOI: 10.1080/23744235.2024.2333438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 03/16/2024] [Indexed: 06/04/2024] Open
Abstract
BACKGROUND Testing of pooled samples is an effective strategy for increasing testing capacity while saving resources and time. This study aimed to validate pooled testing and gather real-life data on its use for Covid-19 surveillance with a gargle lavage (GL) self-sampling strategy. METHODS Two-stage pooled testing with pools of 6 and 12 samples was used for preventive testing of an asymptomatic population and Covid-19 surveillance in Czech schools. Both GL and nasopharyngeal swabs were used for sampling. RESULTS In total, 61,111 samples were tested. The use of pooled testing for large-scale Covid-19 surveillance reduced consumable costs by almost 75% and increased testing capacity up to 3.8-fold compared to standard methods. RT-PCR experiments revealed a minimal loss of sensitivity (0-2.2%) when using pooled samples, enabling the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genes with Ct values >35. The minor loss of sensitivity was counterbalanced by a significantly increased throughput and the ability to substantially increase testing frequencies. CONCLUSIONS Pooled testing is considerably more cost-effective and less time-consuming than standard testing for large-scale Covid-19 surveillance even when the prevalence of SARS-CoV-2 is fluctuating. Gargle lavage self-sampling is a non-invasive technique suitable for sample collection without a healthcare worker's assistance.
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Affiliation(s)
- Ondrej Bouska
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic
| | - Vladimira Koudelakova
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic
- Laboratory of Experimental Medicine, University Hospital Olomouc, Olomouc, Czech Republic
| | - Sona Gurska
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic
| | - Katerina Kubanova
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic
| | - Rastislav Slavkovsky
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic
| | - Hana Jaworek
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic
- Laboratory of Experimental Medicine, University Hospital Olomouc, Olomouc, Czech Republic
| | - Jana Vrbkova
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic
| | - Petr Dzubak
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic
| | - Marian Hajduch
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic
- Laboratory of Experimental Medicine, University Hospital Olomouc, Olomouc, Czech Republic
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Liu H, Cai J, Zhou J, Xu X, Ajelli M, Yu H. Assessing the impact of interventions on the major Omicron BA.2 outbreak in spring 2022 in Shanghai. Infect Dis Model 2024; 9:519-526. [PMID: 38463154 PMCID: PMC10924171 DOI: 10.1016/j.idm.2024.02.013] [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: 01/25/2024] [Revised: 02/26/2024] [Accepted: 02/26/2024] [Indexed: 03/12/2024] Open
Abstract
Background Shanghai experienced a significant surge in Omicron BA.2 infections from March to June 2022. In addition to the standard interventions in place at that time, additional interventions were implemented in response to the outbreak. However, the impact of these interventions on BA.2 transmission remains unclear. Methods We systematically collected data on the daily number of newly reported infections during this wave and utilized a Bayesian approach to estimate the daily effective reproduction number. Data on public health responses were retrieved from the Oxford COVID-19 Government Response Tracker and served as a proxy for the interventions implemented during this outbreak. Using a log-linear regression model, we assessed the impact of these interventions on the reproduction number. Furthermore, we developed a mathematical model of BA.2 transmission. By combining the estimated effect of the interventions from the regression model and the transmission model, we estimated the number of infections and deaths averted by the implemented interventions. Results We found a negative association (-0.0069, 95% CI: 0.0096 to -0.0045) between the level of interventions and the number of infections. If interventions did not ramp up during the outbreak, we estimated that the number of infections and deaths would have increased by 22.6% (95% CI: 22.4-22.8%), leading to a total of 768,576 (95% CI: 768,021-769,107) infections and 722 (95% CI: 722-723) deaths. If no interventions were deployed during the outbreak, we estimated that the number of infections and deaths would have increased by 46.0% (95% CI: 45.8-46.2%), leading to a total of 915,099 (95% CI: 914,639-915,518) infections and 860 (95% CI: 860-861) deaths. Conclusion Our findings suggest that the interventions adopted during the Omicron BA.2 outbreak in spring 2022 in Shanghai were effective in reducing SARS-CoV-2 transmission and disease burden. Our findings emphasize the importance of non-pharmacological interventions in controlling quick surges of cases during epidemic outbreaks.
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Affiliation(s)
- Hengcong Liu
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Jun Cai
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Jiaxin Zhou
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Xiangyanyu Xu
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Marco Ajelli
- Laboratory for Computational Epidemiology and Public Health, Department of Epidemiology and Biostatistics, Indiana University School of Public Health, Bloomington, IN, USA
| | - Hongjie Yu
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
- Shanghai Institute of Infectious Disease and Biosecurity, School of Public Health, Fudan University, Shanghai, China
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9
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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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10
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Kamari F, Eller E, Bøgebjerg ME, Capella IM, Galende BA, Korim T, Øland P, Borup ML, Frederiksen AR, Ranjouriheravi A, Al-Jwadi AF, Mansour M, Hansen S, Diethelm I, Burek M, Alvarez F, Buch AG, Mojtahedi N, Röttger R, Segtnan EA. Clinical performance of AI-integrated risk assessment pooling reveals cost savings even at high prevalence of COVID-19. Sci Rep 2024; 14:8853. [PMID: 38632289 PMCID: PMC11024139 DOI: 10.1038/s41598-024-59068-6] [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: 09/06/2023] [Accepted: 04/06/2024] [Indexed: 04/19/2024] Open
Abstract
Individual testing of samples is time- and cost-intensive, particularly during an ongoing pandemic. Better practical alternatives to individual testing can significantly decrease the burden of disease on the healthcare system. Herein, we presented the clinical validation of Segtnan™ on 3929 patients. Segtnan™ is available as a mobile application entailing an AI-integrated personalized risk assessment approach with a novel data-driven equation for pooling of biological samples. The AI was selected from a comparison between 15 machine learning classifiers (highest accuracy = 80.14%) and a feed-forward neural network with an accuracy of 81.38% in predicting the rRT-PCR test results based on a designed survey with minimal clinical questions. Furthermore, we derived a novel pool-size equation from the pooling data of 54 published original studies. The results demonstrated testing capacity increase of 750%, 60%, and 5% at prevalence rates of 0.05%, 22%, and 50%, respectively. Compared to Dorfman's method, our novel equation saved more tests significantly at high prevalence, i.e., 28% (p = 0.006), 40% (p = 0.00001), and 66% (p = 0.02). Lastly, we illustrated the feasibility of the Segtnan™ usage in clinically complex settings like emergency and psychiatric departments.
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Affiliation(s)
- Farzin Kamari
- Department of Neurophysiology, Institute of Physiology, Eberhard Karls University of Tübingen, Tübingen, Germany
| | | | - Mathias Emil Bøgebjerg
- Department of Mathematics and Computer Science, University of Southern Denmark, Odense, Denmark
| | | | - Borja Arroyo Galende
- Grupo de Aplicación de Telecomunicaciones Visuales, Universidad Politécnica de Madrid, Madrid, Spain
| | | | | | | | | | - Amir Ranjouriheravi
- Research Center for Translational Medicine (KUTTAM), Graduate School of Sciences and Engineering, Koç University, Istanbul, Turkey
| | | | - Mostafa Mansour
- SDU Health Informatics and Technology, Maersk Mc-Kinney Moller Institute, Faculty of Engineering, University of Southern Denmark, Odense, Denmark
| | - Sara Hansen
- SDU Health Informatics and Technology, Maersk Mc-Kinney Moller Institute, Faculty of Engineering, University of Southern Denmark, Odense, Denmark
| | - Isabella Diethelm
- SDU Health Informatics and Technology, Maersk Mc-Kinney Moller Institute, Faculty of Engineering, University of Southern Denmark, Odense, Denmark
| | - Marta Burek
- SDU Health Informatics and Technology, Maersk Mc-Kinney Moller Institute, Faculty of Engineering, University of Southern Denmark, Odense, Denmark
| | - Federico Alvarez
- Grupo de Aplicación de Telecomunicaciones Visuales, Universidad Politécnica de Madrid, Madrid, Spain
| | - Anders Glent Buch
- Department of Engineering, Maersk Mc-Kinney Moller Institute, Faculty of Engineering, University of Southern Denmark, Odense, Denmark
| | - Nima Mojtahedi
- Department of Neurophysiology, Institute of Physiology, Eberhard Karls University of Tübingen, Tübingen, Germany
| | - Richard Röttger
- Department of Mathematics and Computer Science, University of Southern Denmark, Odense, Denmark
| | - Eivind Antonsen Segtnan
- Department of Neurosurgery, Odense University Hospital, Odense, Denmark.
- Synaptic ApS, Copenhagen, Denmark.
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11
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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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12
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Cerda A, Rivera M, Armijo G, Ibarra-Henriquez C, Reyes J, Blázquez-Sánchez P, Avilés J, Arce A, Seguel A, Brown AJ, Vásquez Y, Cortez-San Martín M, Cubillos FA, García P, Ferres M, Ramírez-Sarmiento CA, Federici F, Gutiérrez RA. An Open One-Step RT-qPCR for SARS-CoV-2 detection. PLoS One 2024; 19:e0297081. [PMID: 38271448 PMCID: PMC10810446 DOI: 10.1371/journal.pone.0297081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 12/26/2023] [Indexed: 01/27/2024] Open
Abstract
The COVID-19 pandemic has resulted in millions of deaths globally, and while several diagnostic systems were proposed, real-time reverse transcription polymerase chain reaction (RT-PCR) remains the gold standard. However, diagnostic reagents, including enzymes used in RT-PCR, are subject to centralized production models and intellectual property restrictions, which present a challenge for less developed countries. With the aim of generating a standardized One-Step open RT-qPCR protocol to detect SARS-CoV-2 RNA in clinical samples, we purified and tested recombinant enzymes and a non-proprietary buffer. The protocol utilized M-MLV RT and Taq DNA pol enzymes to perform a Taqman probe-based assay. Synthetic RNA samples were used to validate the One-Step RT-qPCR components, demonstrating sensitivity comparable to a commercial kit routinely employed in clinical settings for patient diagnosis. Further evaluation on 40 clinical samples (20 positive and 20 negative) confirmed its comparable diagnostic accuracy. This study represents a proof of concept for an open approach to developing diagnostic kits for viral infections and diseases, which could provide a cost-effective and accessible solution for less developed countries.
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Affiliation(s)
- Ariel Cerda
- ANID—Millennium Science Initiative Program—Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- FONDAP Center for Genome Regulation, Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Maira Rivera
- ANID—Millennium Science Initiative Program—Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Grace Armijo
- ANID—Millennium Science Initiative Program—Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- FONDAP Center for Genome Regulation, Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Catalina Ibarra-Henriquez
- ANID—Millennium Science Initiative Program—Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- FONDAP Center for Genome Regulation, Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Javiera Reyes
- ANID—Millennium Science Initiative Program—Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Paula Blázquez-Sánchez
- ANID—Millennium Science Initiative Program—Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Javiera Avilés
- ANID—Millennium Science Initiative Program—Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Aníbal Arce
- ANID—Millennium Science Initiative Program—Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Aldo Seguel
- ANID—Millennium Science Initiative Program—Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Alexander J. Brown
- Department of Biomedical Research, National Jewish Health, Denver, CO, United States of America
- Department of Immunology & Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States of America
| | - Yesseny Vásquez
- Escuela de Ciencias Médicas, Facultad de Medicina, Universidad de Santiago de Chile, USACH, Santiago, Chile
| | - Marcelo Cortez-San Martín
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, USACH, Santiago, Chile
| | - Francisco A. Cubillos
- ANID—Millennium Science Initiative Program—Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, USACH, Santiago, Chile
| | - Patricia García
- Departamento de Laboratorios Clínicos, Escuela de Medicina, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Marcela Ferres
- Departamento de Laboratorios Clínicos, Escuela de Medicina, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - César A. Ramírez-Sarmiento
- ANID—Millennium Science Initiative Program—Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Fernán Federici
- ANID—Millennium Science Initiative Program—Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- FONDAP Center for Genome Regulation, Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, Chile
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Rodrigo A. Gutiérrez
- ANID—Millennium Science Initiative Program—Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- FONDAP Center for Genome Regulation, Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, Chile
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13
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Rahmasari R, Raekiansyah M, Aliyah SH, Yodi P, Baihaqy F, Irhamsyah M, Sari KCDP, Suryadi H, Moi ML, Sauriasari R. Development and validation of cost-effective SYBR Green-based RT-qPCR and its evaluation in a sample pooling strategy for detecting SARS-CoV-2 infection in the Indonesian setting. Sci Rep 2024; 14:1817. [PMID: 38245603 PMCID: PMC10799953 DOI: 10.1038/s41598-024-52250-w] [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: 04/27/2023] [Accepted: 01/16/2024] [Indexed: 01/22/2024] Open
Abstract
A low-cost SYBR Green-based RT-qPCR method to detect SARS-CoV-2 were developed and validated. Primers targeting a conserved and vital region of the N genes of SARS-CoV-2 were designed. In-silico study was performed to analyse the compatibility of the selected primer pair with Indonesian SARS-CoV-2 genome sequences available from the GISAID database. We determined the linearity of our new assay using serial dilution of SARS-CoV-2 RNA from clinical samples with known virus concentration. The assay was then evaluated using clinically relevant samples in comparison to a commercial TaqMan-based test kit. Finally, we applied the assay in sample pooling strategies for SARS-CoV-2 detection. The SYBR Green-based RT-qPCR method was successfully developed with sufficient sensitivity. There is a very low prevalence of genome variation in the selected N primer binding regions, indicating their high conservation. The validation of the assay using clinical samples demonstrated similar performance to the TaqMan method suggesting the SYBR methods is reliable. The pooling strategy by combining 5 RNA samples for SARS-CoV-2 detection using the SYBR RT-qPCR methods is feasible and provides a high diagnostic yield. However, when dealing with samples having a very low viral load, it may increase the risk of missing positive cases.
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Affiliation(s)
- Ratika Rahmasari
- Microbiology and Biotechnology Laboratory, Faculty of Pharmacy, Universitas Indonesia, Depok, West Java, Indonesia.
| | | | - Siti Hana Aliyah
- Microbiology and Biotechnology Laboratory, Faculty of Pharmacy, Universitas Indonesia, Depok, West Java, Indonesia
| | - Priska Yodi
- Microbiology and Biotechnology Laboratory, Faculty of Pharmacy, Universitas Indonesia, Depok, West Java, Indonesia
| | - Fathan Baihaqy
- Helix Laboratory & Clinic, Depok, West Java, Indonesia
- Department of Microbiology, School of Life Sciences & Technology, Institut Teknologi Bandung, Bandung, West Java, Indonesia
| | | | | | - Herman Suryadi
- Microbiology and Biotechnology Laboratory, Faculty of Pharmacy, Universitas Indonesia, Depok, West Java, Indonesia
| | - Meng Ling Moi
- School of International Health, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Rani Sauriasari
- Clinical Pharmacy and Social Pharmacy Laboratory, Faculty of Pharmacy, Universitas Indonesia, Depok, West Java, Indonesia
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14
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Liu AB, Lee D, Jalihal AP, Hanage WP, Springer M. Quantitatively assessing early detection strategies for mitigating COVID-19 and future pandemics. Nat Commun 2023; 14:8479. [PMID: 38123536 PMCID: PMC10733317 DOI: 10.1038/s41467-023-44199-7] [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: 09/19/2023] [Accepted: 12/04/2023] [Indexed: 12/23/2023] Open
Abstract
Researchers and policymakers have proposed systems to detect novel pathogens earlier than existing surveillance systems by monitoring samples from hospital patients, wastewater, and air travel, in order to mitigate future pandemics. How much benefit would such systems offer? We developed, empirically validated, and mathematically characterized a quantitative model that simulates disease spread and detection time for any given disease and detection system. We find that hospital monitoring could have detected COVID-19 in Wuhan 0.4 weeks earlier than it was actually discovered, at 2,300 cases (standard error: 76 cases) compared to 3,400 (standard error: 161 cases). Wastewater monitoring would not have accelerated COVID-19 detection in Wuhan, but provides benefit in smaller catchments and for asymptomatic or long-incubation diseases like polio or HIV/AIDS. Air travel monitoring does not accelerate outbreak detection in most scenarios we evaluated. In sum, early detection systems can substantially mitigate some future pandemics, but would not have changed the course of COVID-19.
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Affiliation(s)
- Andrew Bo Liu
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA.
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
| | - Daniel Lee
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - William P Hanage
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Michael Springer
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA.
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15
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Saraiva GQ. Pool testing with dilution effects and heterogeneous priors. Health Care Manag Sci 2023; 26:651-672. [PMID: 37526758 DOI: 10.1007/s10729-023-09650-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 06/25/2023] [Indexed: 08/02/2023]
Abstract
The Dorfman pooled testing scheme is a process in which individual specimens (e.g., blood, urine, swabs, etc.) are pooled and tested together; if the merged sample tests positive for infection, then each specimen from the pool is tested individually. Through this procedure, laboratories can reduce the expected number of tests required to screen the population, as individual tests are only carried out when the pooled test detects an infection. Several different partitions of the population can be used to form the pools. In this study, we analyze the performance of ordered partitions, those in which subjects with similar probability of infection are pooled together. We derive sufficient conditions under which ordered partitions outperform other types of partitions in terms of minimizing the expected number of tests, the expected number of false negatives, and the expected number of false positive classifications. These sufficient conditions can be easily verified in practical applications once the dilution effect has been estimated. We also propose a measure of equity and present conditions under which this measure is maximized by ordered partitions.
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Affiliation(s)
- Gustavo Quinderé Saraiva
- Business School, Pontificia Universidad Católica de Chile, Vicuña Mackenna 4860, Macul, Santiago, Chile.
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16
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Shan X, Gong F, Yang Y, Qian J, Tan Z, Tian S, He Z, Ji X. Nucleic Acid Amplification-Free Digital Detection Method for SARS-CoV-2 RNA Based on Droplet Microfluidics and CRISPR-Cas13a. Anal Chem 2023; 95:16489-16495. [PMID: 37910547 DOI: 10.1021/acs.analchem.3c02007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2023]
Abstract
Most of the methods currently developed for RNA detection based on CRISPR were combined with nucleic acid amplification. As a result, such methods inevitably led to certain disadvantages such as multiple operations, expensive reagents, and amplification bias. To solve the above problems, we developed a highly sensitive and specific nucleic acid amplification-free digital detection method for SARS-CoV-2 RNA based on droplet microfluidics and CRISPR-Cas13a. In this assay, thousands of monodisperse droplets with a size of 30 μm were generated within 2 min by a negative pressure-driven microfluidic chip. By confining a single target RNA recognition event to an independent droplet, the collateral cleavage products of activated Cas13a could be accumulated in one droplet. By combining the droplet microfluidics and CRISPR-Cas13a, SARS-CoV-2 RNA could be easily detected within 30 min with a detection limit of 470 aM. The performance of this assay was verified by specificity experiments and spiking and recovery experiments with human saliva. Compared with many developed methods for SARS-CoV-2 RNA detection, our method is time- and reagent-saving and easy to operate. Taken together, this digital detection method based on droplet microfluidics and CRISPR-Cas13a provides a promising approach for RNA detection in clinical diagnostics.
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Affiliation(s)
- Xiaoyun Shan
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Feng Gong
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Yixia Yang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Jingjing Qian
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Zhiyou Tan
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Songbai Tian
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Zhike He
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
- Wuhan Research Center for Infectious Diseases and Cancer, Chinese Academy of Medical Sciences, Wuhan 430071, China
| | - Xinghu Ji
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
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17
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Liu AB, Lee D, Jalihal AP, Hanage WP, Springer M. Quantitatively assessing early detection strategies for mitigating COVID-19 and future pandemics. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.06.08.23291050. [PMID: 37398047 PMCID: PMC10312821 DOI: 10.1101/2023.06.08.23291050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Researchers and policymakers have proposed systems to detect novel pathogens earlier than existing surveillance systems by monitoring samples from hospital patients, wastewater, and air travel, in order to mitigate future pandemics. How much benefit would such systems offer? We developed, empirically validated, and mathematically characterized a quantitative model that simulates disease spread and detection time for any given disease and detection system. We find that hospital monitoring could have detected COVID-19 in Wuhan 0.4 weeks earlier than it was actually discovered, at 2,300 cases (standard error: 76 cases) compared to 3,400 (standard error: 161 cases). Wastewater monitoring would not have accelerated COVID-19 detection in Wuhan, but provides benefit in smaller catchments and for asymptomatic or long-incubation diseases like polio or HIV/AIDS. Monitoring of air travel provides little benefit in most scenarios we evaluated. In sum, early detection systems can substantially mitigate some future pandemics, but would not have changed the course of COVID-19.
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Affiliation(s)
- Andrew Bo Liu
- Department of Systems Biology, Harvard Medical School; Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School; Boston, MA, USA
| | - Daniel Lee
- Department of Biomedical Informatics, Harvard Medical School; Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard; Cambridge, MA, USA
| | | | - William P. Hanage
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health; Boston, MA, USA
| | - Michael Springer
- Department of Systems Biology, Harvard Medical School; Boston, MA, USA
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18
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Vuchas C, Teyim P, Dang BF, Neh A, Keugni L, Che M, Che PN, Beloko H, Fondoh V, Ndi NN, Wandji IAG, Fundoh M, Manga H, Mbuli C, Creswell J, Bisso A, Donkeng V, Sander M. Implementation of large-scale pooled testing to increase rapid molecular diagnostic test coverage for tuberculosis: a retrospective evaluation. Sci Rep 2023; 13:15358. [PMID: 37717043 PMCID: PMC10505184 DOI: 10.1038/s41598-023-41904-w] [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: 03/06/2023] [Accepted: 09/01/2023] [Indexed: 09/18/2023] Open
Abstract
In 2021, only 6.4 million of the 10.6 million people with tuberculosis (TB) were diagnosed and treated for the disease. Although the World Health Organization recommends initial diagnostic testing using a rapid sensitive molecular assay, only 38% of people diagnosed with TB benefited from these, due to barriers including the high cost of available assays. Pooled testing has been used as an approach to increase testing efficiency in many resource-constrained situations, such as the COVID-19 pandemic, but it has not yet been widely adopted for TB diagnostic testing. Here we report a retrospective analysis of routine pooled testing of 10,117 sputum specimens using the Xpert MTB/RIF and Xpert MTB/RIF Ultra assays that was performed from July 2020 to February 2022. Pooled testing saved 48% of assays and enabled rapid molecular testing for 4156 additional people as compared to individual testing, with 6.6% of specimens positive for TB. From an in silico analysis, the positive percent agreement of pooled testing in pools of 3 as compared with individual testing for the Xpert MTB/RIF Ultra assay was estimated as 99.4% (95% CI, 96.6% to 100%). These results support the scale-up of pooled testing for efficient TB diagnosis.
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Affiliation(s)
- Comfort Vuchas
- Center for Health Promotion and Research, Bamenda, Northwest, Cameroon.
| | - Pride Teyim
- Tuberculosis Reference Laboratory Douala, Douala, Littoral, Cameroon
| | | | - Angela Neh
- Center for Health Promotion and Research, Bamenda, Northwest, Cameroon
| | - Liliane Keugni
- Tuberculosis Reference Laboratory Douala, Douala, Littoral, Cameroon
| | - Mercy Che
- Center for Health Promotion and Research, Bamenda, Northwest, Cameroon
| | - Pantalius Nji Che
- Center for Health Promotion and Research, Bamenda, Northwest, Cameroon
| | - Hamada Beloko
- Tuberculosis Reference Laboratory Douala, Douala, Littoral, Cameroon
| | - Victor Fondoh
- Bamenda Regional Hospital, Bamenda, Northwest, Cameroon
| | - Norah Nyah Ndi
- Baptist Convention Health Services and Baptist Institute of Health Sciences, Bamenda, Northwest, Cameroon
| | | | - Mercy Fundoh
- National TB Program- Northwest Region, Bamenda, Northwest, Cameroon
| | - Henri Manga
- National TB Program, Yaoundé, Center, Cameroon
| | - Cyrille Mbuli
- Center for Health Promotion and Research, Bamenda, Northwest, Cameroon
| | | | - Annie Bisso
- National TB Program, Yaoundé, Center, Cameroon
| | | | - Melissa Sander
- Center for Health Promotion and Research, Bamenda, Northwest, Cameroon.
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19
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Balakrishnan S, Palathingal S. An adaptive testing strategy for efficient utilization of healthcare resources during an epidemic. J Theor Biol 2023; 571:111555. [PMID: 37290500 PMCID: PMC10245284 DOI: 10.1016/j.jtbi.2023.111555] [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: 11/28/2022] [Revised: 05/29/2023] [Accepted: 06/01/2023] [Indexed: 06/10/2023]
Abstract
Lockdowns are found to be effective against rapidly spreading epidemics like COVID-19. Two downsides to strategies rooted in social distancing and lockdowns are that they adversely affect the economy and prolong the duration of the epidemic. The extended duration observed in these strategies is often due to the under-utilization of medical facilities. Even though an under-utilized health care system is preferred over an overwhelmed one, an alternate strategy could be to maintain medical facilities close to their capacity, with a factor of safety. We explore the practicality of this alternate mitigation strategy and show that it can be achieved by varying the testing rate. We present an algorithm to calculate the number of tests per day to maintain medical facilities close to their capacity. We illustrate the efficacy of our strategy by showing that it reduced the epidemic duration by 40% in comparison to lockdown-based strategies.
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Affiliation(s)
- Sreenath Balakrishnan
- School of Mechanical Sciences, Indian Institute of Technology Goa, Ponda, 403401, Goa, India; School of Interdisciplinary Life Sciences, Indian Institute of Technology Goa, Ponda, 403401, Goa, India.
| | - Safvan Palathingal
- Department of Mechanical and Aerospace Engineering, Indian Institute of Technology Hyderabad, Hyderabad, 502284, Telangana, India
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20
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Yuwen L, Zhang S, Chao J. Recent Advances in DNA Nanotechnology-Enabled Biosensors for Virus Detection. BIOSENSORS 2023; 13:822. [PMID: 37622908 PMCID: PMC10452139 DOI: 10.3390/bios13080822] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 08/05/2023] [Accepted: 08/12/2023] [Indexed: 08/26/2023]
Abstract
Virus-related infectious diseases are serious threats to humans, which makes virus detection of great importance. Traditional virus-detection methods usually suffer from low sensitivity and specificity, are time-consuming, have a high cost, etc. Recently, DNA biosensors based on DNA nanotechnology have shown great potential in virus detection. DNA nanotechnology, specifically DNA tiles and DNA aptamers, has achieved atomic precision in nanostructure construction. Exploiting the programmable nature of DNA nanostructures, researchers have developed DNA nanobiosensors that outperform traditional virus-detection methods. This paper reviews the history of DNA tiles and DNA aptamers, and it briefly describes the Baltimore classification of virology. Moreover, the advance of virus detection by using DNA nanobiosensors is discussed in detail and compared with traditional virus-detection methods. Finally, challenges faced by DNA nanobiosensors in virus detection are summarized, and a perspective on the future development of DNA nanobiosensors in virus detection is also provided.
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Affiliation(s)
- Lihui Yuwen
- State Key Laboratory of Organic Electronics and Information Displays, Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing 210023, China; (L.Y.); (S.Z.)
| | - Shifeng Zhang
- State Key Laboratory of Organic Electronics and Information Displays, Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing 210023, China; (L.Y.); (S.Z.)
| | - Jie Chao
- School of Geography and Biological Information, Nanjing University of Posts and Telecommunications, Nanjing 210023, China
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21
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Millward GG, Popelka SM, Gutierrez AG, Kowallis WJ, von Tersch RL, Yerramilli SV. A novel strategy to avoid sensitivity loss in pooled testing for SARS-CoV-2 surveillance: validation using nasopharyngeal swab and saliva samples. Front Public Health 2023; 11:1190308. [PMID: 37637813 PMCID: PMC10450028 DOI: 10.3389/fpubh.2023.1190308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 07/18/2023] [Indexed: 08/29/2023] Open
Abstract
At the peak of the COVID-19 pandemic, pooled surveillance strategies were employed to alleviate the overwhelming demand for clinical testing facilities. A major drawback of most pooled-testing methods is the dilution of positive samples, which leads to a loss of detection sensitivity and the potential for false negatives. We developed a novel pooling strategy that compensates for the initial dilution with an appropriate concentration during nucleic acid extraction and real-time PCR. We demonstrated the proof of principle using laboratory-created 10-sample pools with one positive and corresponding individual positive samples by spiking a known amount of heat-inactivated SARS-CoV-2 into viral transport medium (VTM) or pooled negative saliva. No Ct difference was observed between a 10-sample pool with one positive vs. the corresponding individually analyzed positive sample by this method, suggesting that there is no detectable loss of sensitivity. We further validated this approach by using nasopharyngeal swab (NPS) specimens and showed that there is no loss of sensitivity. Serial dilutions of the virus were spiked into VTM and pooled with negative saliva in simulated 10-sample pools containing one positive to determine the LOD and process efficiency of this pooling methodology. The LOD of this approach was 10 copies/PCR, and the process efficiencies are ~95%-103% for N1 and ~87%-98% for N2 with samples in different matrices and with two different master mixes tested. Relative to TaqPath 1-step master mix, the TaqMan Fast Virus 1-Step master mix showed better sensitivity for the N2 assay, while the N1 assay showed no Ct difference. Our pooled testing strategy can facilitate large-scale, cost-effective SARS-CoV-2 surveillance screening and maintain the same level of sensitivity when analyzed individually or in a pool. This approach is highly relevant for public health surveillance efforts aimed at mitigating SARS-CoV-2 spread.
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Affiliation(s)
| | | | | | | | | | - Subrahmanyam V. Yerramilli
- Emerging Biological Threats Branch, Molecular Biology Division, Laboratory Sciences, Defense Centers for Public Health - Aberdeen “Formerly the Army Public Health Center”, Aberdeen Proving Ground, Edgewood, MD, United States
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22
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Cabrera ODLC, Alsehibani R. Statistical modeling and evaluation of the impact of multiplicity classification thresholds on the COVID-19 pool testing accuracy. PLoS One 2023; 18:e0283874. [PMID: 37494364 PMCID: PMC10370739 DOI: 10.1371/journal.pone.0283874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 03/17/2023] [Indexed: 07/28/2023] Open
Abstract
Prior research on pool testing focus on developing testing methods with the main objective of reducing the total number of tests. However, pool testing can also be used to improve the accuracy of the testing process. The objective of this paper is to improve the accuracy of pool testing using the same number of tests as that of individual testing taking into consideration the probability of testing errors and pool multiplicity classification thresholds. Statistical models are developed to evaluate the impact of pool multiplicity classiffcation thresholds on pool testing accuracy using the receiver operating characteristic (ROC) curve and the area under the curve (AUC). The findings indicate that under certain conditions, pool testing multiplicity yields superior testing accuracy compared to individual testing without additional cost. The results reveal that selecting the multiplicity classification threshold is a critical factor in improving the pool testing accuracy and show that the lower the prevalence level the higher the gains in accuracy using multiplicity pool testing. The findings also indicate that performance can be improved using a batch size that is inversely proportional to the prevalence level. Furthermore, the results indicate that multiplicity pool testing not only improves the testing accuracy but also reduces the total cost of the testing process. Based on the findings, the manufacturer's test sensitivity has more significant impact on the accuracy of multiplicity pool testing compared to that of manufacturer's test specificity.
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Affiliation(s)
- Omar De La Cruz Cabrera
- Department of Mathematical Sciences, Kent State University, Kent, OH, United States of America
| | - Razan Alsehibani
- Department of Mathematical Sciences, Kent State University, Kent, OH, United States of America
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23
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Cabrera A, Al Mutawah F, Kadour M, Schofield S, Conkey B, Fuller J, Payne M, Elsayed S, Delport J. Increasing SARS-CoV-2 testing capacity through specimen pooling: An acute care center experience. PLoS One 2023; 18:e0267137. [PMID: 37379564 DOI: 10.1371/journal.pone.0267137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 04/01/2022] [Indexed: 06/30/2023] Open
Abstract
Innovation in laboratory testing algorithms to address seemingly uncontrollable global supply chain shortages in plastics and other consumables during emergencies such as the current COVID-19 pandemic have been urgently needed. We report our experience with specimen pooling on SARS-CoV-2 testing in an acute care hospital microbiology laboratory during a high testing demand period that exceeded available processing capacity. A fully automated four-in-one pooling algorithm was designed and validated. Correlation and agreement were calculated. A custom Microsoft Excel tool was designed for use by the technologists to aid interpretation, verification and result entry. Cost-per-test impact for pooling was measured in reference to the consumable cost and was denoted as the percentage reduction of cost versus the baseline cost-per-test of testing specimens individually. Validation showed a strong correlation between the signals observed when testing specimens individually versus those that were pooled. Average crossing point difference was 1.352 cycles (95% confidence interval of -0.235 and 2.940). Overall agreement observed between individually and pooled tested specimens was 96.8%. Stratified agreement showed an expected decreased performance of pooling for weakly positive specimens dropping below 60% after a crossing point of 35. Post-implementation data showed the consumable cost-savings achieved through this algorithm was 85.5% after 8 months, creating both testing and resource capacity. Pooling is an effective method to be used for SARS-CoV-2 testing during the current pandemic to address resource shortages and provide quick turnaround times for high test volumes without compromising performance.
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Affiliation(s)
- Ana Cabrera
- Pathology and Laboratory Medicine Department, London Health Sciences Centre, London, Ontario, Canada
- Pathology and Laboratory Medicine Department, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
- Microbiology and Immunology Department, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Fatimah Al Mutawah
- Pathology and Laboratory Medicine Department, London Health Sciences Centre, London, Ontario, Canada
- Pathology and Laboratory Medicine Department, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Mike Kadour
- Pathology and Laboratory Medicine Department, London Health Sciences Centre, London, Ontario, Canada
- Pathology and Laboratory Medicine Department, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Shannon Schofield
- Pathology and Laboratory Medicine Department, London Health Sciences Centre, London, Ontario, Canada
| | - Beverley Conkey
- Pathology and Laboratory Medicine Department, London Health Sciences Centre, London, Ontario, Canada
| | - Jeffrey Fuller
- Pathology and Laboratory Medicine Department, London Health Sciences Centre, London, Ontario, Canada
- Pathology and Laboratory Medicine Department, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Michael Payne
- Pathology and Laboratory Medicine Department, London Health Sciences Centre, London, Ontario, Canada
- Pathology and Laboratory Medicine Department, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Sameer Elsayed
- Pathology and Laboratory Medicine Department, London Health Sciences Centre, London, Ontario, Canada
- Pathology and Laboratory Medicine Department, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
- Department of Medicine, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
- Department of Epidemiology and Biostatistics, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Johan Delport
- Pathology and Laboratory Medicine Department, London Health Sciences Centre, London, Ontario, Canada
- Pathology and Laboratory Medicine Department, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
- Microbiology and Immunology Department, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
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24
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Choi JW, Seo WH, Kang T, Kang T, Chung BG. Droplet digital recombinase polymerase amplification for multiplexed detection of human coronavirus. LAB ON A CHIP 2023; 23:2389-2398. [PMID: 37083004 DOI: 10.1039/d3lc00025g] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Since the outbreak of coronavirus 2019 (COVID-19), detection technologies have been attracting a great deal of attention in molecular diagnosis applications. In particular, the droplet digital PCR (ddPCR) has become a promising tool as it offers absolute quantification of target nucleic acids with high specificity and sensitivity. In recent years, the combination of the isothermal amplification strategies has made ddPCR a popular method for on-site testing by enabling amplification at a constant temperature. However, the current isothermal ddPCR assays are still challenging due to inherent non-specific amplification. In this paper, we present a multiplexed droplet digital recombinase polymerase amplification (MddRPA) with precise initiation of the reaction. First, the reaction temperature and dynamic range of reverse transcription (RT) and RPA were characterized by real-time monitoring of fluorescence intensities. Using a droplet-based microfluidic chip, the master mix and the initiator were fractionated and rapidly mixed within well-confined droplets. Due to the high heat transfer and mass transfer of the droplets, the precise initiation of the amplification was enabled and the entire assay could be conducted within 30 min. The concentrations of target RNA in the range from 5 copies per μL to 2500 copies per μL could be detected with high linearity (R2 > 0.999). Furthermore, the multiplexed detection of three types of human coronaviruses was successfully demonstrated with high specificity (>96%). Finally, we compared the performance of the assay with a commercial RT-qPCR system using COVID-19 clinical samples. The MddRPA assay showed a 100% concordance with the RT-qPCR results, indicating its reliability and accuracy in detecting SARS-CoV-2 nucleic acids in clinical samples. Therefore, our MddRPA assay with rapid detection, precise quantification, and multiplexing capability would be an interesting method for molecular diagnosis of viral infections.
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Affiliation(s)
- Ji Wook Choi
- Department of Mechanical Engineering, Sogang University, Seoul, Korea.
| | - Won Ho Seo
- Department of Biomedical Engineering, Sogang University, Seoul, Korea
| | - Taejoon Kang
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Korea
- School of Pharmacy, Sungkyunkwan University (SKKU), Suwon, Korea
| | - Taewook Kang
- Department of Chemical and Biomolecular Engineering, Sogang University, Seoul, Korea
- Institute of Integrated Biotechnology, Sogang University, Seoul, Korea
| | - Bong Geun Chung
- Department of Mechanical Engineering, Sogang University, Seoul, Korea.
- Institute of Integrated Biotechnology, Sogang University, Seoul, Korea
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25
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Effectiveness of sample pooling strategies for diagnosis of SARS-CoV-2: Specimen pooling vs. RNA elutes pooling. Indian J Med Microbiol 2023; 42:34-38. [PMID: 36967213 PMCID: PMC9870240 DOI: 10.1016/j.ijmmb.2022.12.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 11/13/2022] [Accepted: 12/31/2022] [Indexed: 01/24/2023]
Abstract
PURPOSE The pandemic of SARS-CoV-2 or COVID-19 has hugely created an economic imbalance worldwide. With the exponential increase in the number of cases and to keep in check on the community transmission, there is high demand and acute shortage of diagnostic kits. The pooled-sample strategy turns out to be the promising strategy intended to determine the optimal testing for specimens with limited resources and without losing the test sensitivity and specificity. The study was performed with standard molecular biology graded lab equipment, FDA-approved COVID-19 RNA extraction, and SARS-CoV-2 tests kits. MATERIALS AND METHODS The study aims to comparatively analyze the pooling strategy of the naso-oropharyngeal specimen sample and RNA extracted from the same patient samples in the pool of 3,5, and 8 with no significant loss in test usability. Another primary focus of the study was detection of low or borderline SARS-CoV-2 positives in the pooling strategy. A total of 300 samples (240 positives and 60 negatives) were tested for 3, 5, and 8 pools of specimen samples and RNA elutes. RESULTS The comparative analysis determined the sensitivity for three and five pool strategy to be above 98% and eight pool strategy to be 100%. CONCLUSION The RNA elutes pooling strategy concordance rate is better than that of specimen pooling with 100% specificity. Thus, in the substantial crisis of resources with the global pandemic, pooling approaches for SARS-CoV-2 can be practical in a low prevalence rate of 5%.
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26
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Eales O, Page AJ, Tang SN, Walters CE, Wang H, Haw D, Trotter AJ, Le Viet T, Foster-Nyarko E, Prosolek S, Atchison C, Ashby D, Cooke G, Barclay W, Donnelly CA, O’Grady J, Volz E, Darzi A, Ward H, Elliott P, Riley S. The use of representative community samples to assess SARS-CoV-2 lineage competition: Alpha outcompetes Beta and wild-type in England from January to March 2021. Microb Genom 2023; 9:mgen000887. [PMID: 36745545 PMCID: PMC9997751 DOI: 10.1099/mgen.0.000887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Genomic surveillance for SARS-CoV-2 lineages informs our understanding of possible future changes in transmissibility and vaccine efficacy and will be a high priority for public health for the foreseeable future. However, small changes in the frequency of one lineage over another are often difficult to interpret because surveillance samples are obtained using a variety of methods all of which are known to contain biases. As a case study, using an approach which is largely free of biases, we here describe lineage dynamics and phylogenetic relationships of the Alpha and Beta variant in England during the first 3 months of 2021 using sequences obtained from a random community sample who provided a throat and nose swab for rt-PCR as part of the REal-time Assessment of Community Transmission-1 (REACT-1) study. Overall, diversity decreased during the first quarter of 2021, with the Alpha variant (first identified in Kent) becoming predominant, driven by a reproduction number 0.3 higher than for the prior wild-type. During January, positive samples were more likely to be Alpha in those aged 18 to 54 years old. Although individuals infected with the Alpha variant were no more likely to report one or more classic COVID-19 symptoms compared to those infected with wild-type, they were more likely to be antibody-positive 6 weeks after infection. Further, viral load was higher in those infected with the Alpha variant as measured by cycle threshold (Ct) values. The presence of infections with non-imported Beta variant (first identified in South Africa) during January, but not during February or March, suggests initial establishment in the community followed by fade-out. However, this occurred during a period of stringent social distancing. These results highlight how sequence data from representative community surveys such as REACT-1 can augment routine genomic surveillance during periods of lineage diversity.
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Affiliation(s)
- Oliver Eales
- School of Public Health, Imperial College London, London, UK
- MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
- *Correspondence: Oliver Eales,
| | | | - Sonja N. Tang
- School of Public Health, Imperial College London, London, UK
| | - Caroline E. Walters
- School of Public Health, Imperial College London, London, UK
- MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - Haowei Wang
- School of Public Health, Imperial College London, London, UK
- MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | - David Haw
- School of Public Health, Imperial College London, London, UK
- MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | | | | | | | | | | | - Deborah Ashby
- School of Public Health, Imperial College London, London, UK
| | - Graham Cooke
- Department of Infectious Disease, Imperial College London, London, UK
- Imperial College Healthcare NHS Trust, London, UK
- National Institute for Health Research Imperial Biomedical Research Centre, London, UK
| | - Wendy Barclay
- Department of Infectious Disease, Imperial College London, London, UK
| | - Christl A. Donnelly
- School of Public Health, Imperial College London, London, UK
- MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
- Department of Statistics, University of Oxford, Oxford, UK
| | | | - Erik Volz
- School of Public Health, Imperial College London, London, UK
- MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
| | | | - Ara Darzi
- Imperial College Healthcare NHS Trust, London, UK
- National Institute for Health Research Imperial Biomedical Research Centre, London, UK
- Institute of Global Health Innovation at Imperial College London, London, UK
| | - Helen Ward
- School of Public Health, Imperial College London, London, UK
- Imperial College Healthcare NHS Trust, London, UK
- National Institute for Health Research Imperial Biomedical Research Centre, London, UK
| | - Paul Elliott
- School of Public Health, Imperial College London, London, UK
- Imperial College Healthcare NHS Trust, London, UK
- National Institute for Health Research Imperial Biomedical Research Centre, London, UK
- MRC Centre for Environment and Health, School of Public Health, Imperial College London, London, UK
- Health Data Research (HDR) UK London at Imperial College, London, UK
- UK Dementia Research Institute at Imperial College, London, UK
- *Correspondence: Paul Elliott,
| | - Steven Riley
- School of Public Health, Imperial College London, London, UK
- MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergency Analytics, Imperial College London, London, UK
- *Correspondence: Steven Riley,
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27
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Filiatreau LM, Zivich PN, Edwards JK, Mulholland GE, Max R, Westreich D. Optimizing SARS-CoV-2 Pooled Testing Strategies Through Differentiated Pooling for Distinct Groups. Am J Epidemiol 2023; 192:246-256. [PMID: 36222677 PMCID: PMC9620733 DOI: 10.1093/aje/kwac178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 08/02/2022] [Accepted: 10/06/2022] [Indexed: 02/07/2023] Open
Abstract
Pooled testing has been successfully used to expand SARS-CoV-2 testing, especially in settings requiring high volumes of screening of lower-risk individuals, but efficiency of pooling declines as prevalence rises. We propose a differentiated pooling strategy that independently optimizes pool sizes for distinct groups with different probabilities of infection to further improve the efficiency of pooled testing. We compared the efficiency (results obtained per test kit used) of the differentiated strategy with a traditional pooling strategy in which all samples are processed using uniform pool sizes under a range of scenarios. For most scenarios, differentiated pooling is more efficient than traditional pooling. In scenarios examined here, an improvement in efficiency of up to 3.94 results per test kit could be obtained through differentiated versus traditional pooling, with more likely scenarios resulting in 0.12 to 0.61 additional results per kit. Under circumstances similar to those observed in a university setting, implementation of our strategy could result in an improvement in efficiency between 0.03 to 3.21 results per test kit. Our results can help identify settings, such as universities and workplaces, where differentiated pooling can conserve critical testing resources.
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Affiliation(s)
- Lindsey M Filiatreau
- Correspondence Address: Department of Psychiatry, Washington University in St. Louis, 660 S. Euclid, St. Louis, MO 63110, E-mail:
| | - Paul N Zivich
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Carolina Population Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Jessie K Edwards
- Gillings Center for Coronavirus Testing, Screening, and Surveillance, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Grace E Mulholland
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Ryan Max
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Daniel Westreich
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Gillings Center for Coronavirus Testing, Screening, and Surveillance, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
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28
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DUYURAN R, GÜRBÜZ H, BAYRAKÇI S, ÇİÇEK H. Serum oxidant, antioxidant, and paraoxonase levels in COVID-19 patients. CUKUROVA MEDICAL JOURNAL 2022. [DOI: 10.17826/cumj.1167711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Purpose: The aim of his study was to determine serum oxidant status (TOS), antioxidant status (TAS), and paraoxonase (PON1) levels and to determine their diagnostic values in patients diagnosed with COVID-19.
Materials and Methods: The research was carried out on patients diagnosed with COVID-19. Within the scope of the study, a total of 87 patients with a diagnosis of COVID-19, 48 (55.1%) male and 39 (44.9%) were evaluated. Total antioxidant determination was performed using a microplate reader according to the Erel method. To calculate the Oxidative stress index (OSI), TOS and TAS levels were determined.
Results: Male gender was associated with high PON1, smoking with high TOS, the presence of hypertension and Diabetes mellitus (DM) diseases with low OSI, and the presence of asthma with low PON1. High PON1 was found to be associated with shorter hospitalization duration and high TOS was associated with longer hospitalization duration. TAS and TOS levels increased significantly due to the increase in CRP, TOS levels due to the increase in neutrophil level, OSI levels due to the increase in leukocyte level, PON1 levels increased due to the increase in LDH level TAS, TOS, OSI, and PON1 cut-off values were 1.41 (AUC: 0.647), 4.56 (AUC: 0.493), 0.421 (AUC: 0.505) and 340 (AUC: 0.536), sensitivity values were 65.5, 55.2, 48.3 and 51.7; specificity values were calculated respectively as 62.1, 46.6, 34.5 and 53.4.
Conclusion: Although it is seen that oxidative stress types have diagnostic value, there is a need for more comprehensive studies with larger samples on the subject.
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Affiliation(s)
| | - Hüseyin GÜRBÜZ
- 2. Dr. Ersin Arslan Training and Research Hospital, Department of Emergency Medicine
| | - Sinem BAYRAKÇI
- 3. Dr. Ersin Arslan Training and Research Hospital, Department of Intensive Care
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Chen Y, Ma Y, Han Y, Diao Z, Chang L, Li J, Zhang R. Evaluation of Four Strategies for SARS-CoV-2 Detection: Characteristics and Prospects. Microbiol Spectr 2022; 10:e0214322. [PMID: 36287010 PMCID: PMC9769534 DOI: 10.1128/spectrum.02143-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 09/27/2022] [Indexed: 01/06/2023] Open
Abstract
The pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has posed an enormous burden on the global public health system and has had disastrous socioeconomic consequences. Currently, single sampling tests, 20-in-1 pooling tests, nucleic acid point-of-care tests (POCTs), and rapid antigen tests are implemented in different scenarios to detect SARS-CoV-2, but a comprehensive evaluation of them is scarce and remains to be explored. In this study, 3 SARS-CoV-2 inactivated cell culture supernatants were used to evaluate the analytical performance of these strategies. Additionally, 5 recombinant SARS-CoV-2 nucleocapsid (N) proteins were also used for rapid antigen tests. For the wild-type (WT), Delta, and Omicron strains, the lowest inactivated virus concentrations to achieve 100% detection rates of single sampling tests ranged between 1.28 × 102 to 1.02 × 103, 1.28 × 102 to 4.10 × 103, and 1.28 × 102 to 2.05 × 103 copies/mL. The 20-in-1 pooling tests ranged between 1.30 × 102 to 1.04 × 103, 5.19 × 102 to 2.07 × 103, and 2.59 × 102 to 1.04 × 103 copies/mL. The nucleic acid POCTs were all 1.42 × 103 copies/mL. The rapid antigen tests ranged between 2.84 × 105 to 7.14 × 106, 8.68 × 104 to 7.14 × 106, and 1.12 × 105 to 3.57 × 106 copies/mL. For the WT, Delta AY.2, Delta AY.1/AY.3, Omicron BA.1, and Omicron BA.2 recombinant N proteins, the lowest concentrations to achieve 100% detection rates of rapid antigen tests ranged between 3.47 to 142.86, 1.74 to 142.86, 3.47 to 142.86, 3.47 to 142.86, and 5.68-142.86 ng/mL, respectively. This study provided helpful insights into the scientific deployment of tests and recommended the full-scale consideration of the testing purpose, resource availability, cost performance, result rapidity, and accuracy to facilitate a profound pathway toward the long-term surveillance of coronavirus disease 2019 (COVID-19). IMPORTANCE In the study, we reported an evaluation of 4 detection strategies implemented in different scenarios for SARS-CoV-2 detection: single sampling tests, 20-in-1 pooling tests, nucleic acid point-of-care tests, and rapid antigen tests. 3 SARS-CoV-2-inactivated SARS-CoV-2 cell culture supernatants and 5 recombinant SARS-CoV-2 nucleocapsid proteins were used for evaluation. In this analysis, we found that for the WT, Delta, and Omicron supernatants, the lowest concentrations to achieve 100% detection rates of single sampling tests ranged between 1.28 × 102 to 1.02 × 103, 1.28 × 102 to 4.10 × 103, and 1.28 × 102 to 2.05 × 103 copies/mL. The 20-in-1 pooling tests ranged between 1.30 × 102 to 1.04 × 103, 5.19 × 102 to 2.07 × 103, and 2.59 × 102 to 1.04 × 103 copies/mL. The nucleic acid POCTs were all 1.42 × 103 copies/mL. The rapid antigen tests ranged between 2.84 × 105 to 7.14 × 106, 8.68 × 104 to 7.14 × 106, and 1.12 × 105 to 3.57 × 106 copies/mL. For the WT, Delta AY.2, Delta AY.1/AY.3, Omicron BA.1, and Omicron BA.2 recombinant N proteins, the lowest concentrations to achieve 100% detection rates of rapid antigen tests ranged between 3.47 to 142.86, 1.74 to 142.86, 3.47 to 142.86, 3.47 to 142.86, and 5.68 to 142.86 ng/mL, respectively.
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Affiliation(s)
- Yuqing Chen
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, People’s Republic of China
- Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, People’s Republic of China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People’s Republic of China
| | - Yu Ma
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, People’s Republic of China
- Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, People’s Republic of China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People’s Republic of China
| | - Yanxi Han
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, People’s Republic of China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People’s Republic of China
| | - Zhenli Diao
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, People’s Republic of China
- Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, People’s Republic of China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People’s Republic of China
| | - Lu Chang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, People’s Republic of China
- Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, People’s Republic of China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People’s Republic of China
| | - Jinming Li
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, People’s Republic of China
- Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, People’s Republic of China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People’s Republic of China
| | - Rui Zhang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, People’s Republic of China
- Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, People’s Republic of China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People’s Republic of China
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30
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Chung HY, Jian MJ, Chang CK, Lin JC, Yeh KM, Chen CW, Yang YS, Hsieh SS, Chen ES, Yang MH, Tang SH, Perng CL, Yang JR, Liu MT, Chang FY, Shang HS. Multicenter study evaluating novel multi-specimen pooling assay for the detection of SARS-CoV-2: High sensitivity and high throughput testing. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2022; 55:1069-1075. [PMID: 34538568 PMCID: PMC8411585 DOI: 10.1016/j.jmii.2021.08.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/30/2021] [Accepted: 08/16/2021] [Indexed: 12/27/2022]
Abstract
BACKGROUND/PURPOSE Mass screening for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is important to prevent the spread of coronavirus disease 2019 (COVID-19). Pooling samples can increase the number of tests processed. LabTurbo AIO 48 is an automated platform that allows ribonucleic acid extraction and sample analysis on the same instrument. We created a novel pooling assay on this platform for SARS-CoV-2 detection and demonstrated that the pooling strategy increases testing capacity without affecting accuracy and sensitivity. METHODS Comparative limit of detection (LoD) assessment was performed on the LabTurbo AIO 48 platform and the current standard detection system based on real-time reverse transcription polymerase chain reaction (rRT-PCR) using 55 clinically positive samples. An additional 330 primary clinical samples were assessed. RESULTS Six samples pooled into one reaction tube were detected in approximately 2.5 h using the World Health Organization rRT-PCR protocol. LabTurbo AIO 48 also demonstrated a higher throughput than our reference rRT-PCR assay, with an LoD of 1000 copies/mL. The overall percentage agreement between the methods for the 330 samples was 100%. CONCLUSION We created a novel multi-specimen pooling assay using LabTurbo AIO 48 for the robust detection of SARS-CoV-2, allowing high-throughput results; this assay will aid in better control and prevention of COVID-19. The diagnostic assay was cost-effective and time-efficient; thus, the pooling strategy is a practical and effective method for diagnosing large quantities of specimens without compromising precision.
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Affiliation(s)
- Hsing-Yi Chung
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROC
| | - Ming-Jr Jian
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROC
| | - Chih-Kai Chang
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROC
| | - Jung-Chung Lin
- Division of Infectious Diseases and Tropical Medicine, Department of Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROC
| | - Kuo-Ming Yeh
- Division of Infectious Diseases and Tropical Medicine, Department of Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROC
| | - Chien-Wen Chen
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROC
| | - Ya-Sung Yang
- Division of Infectious Diseases and Tropical Medicine, Department of Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROC
| | - Shan-Shan Hsieh
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROC
| | - En-Sung Chen
- Department of Clinical Pathology, Cathay General Hospital, Taipei, Taiwan
| | - Mei-Hsiu Yang
- Department of Clinical Pathology, Cathay General Hospital, Taipei, Taiwan
| | - Sheng-Hui Tang
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROC
| | - Cherng-Lih Perng
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROC
| | | | | | - Feng-Yee Chang
- Division of Infectious Diseases and Tropical Medicine, Department of Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROC
| | - Hung-Sheng Shang
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROC,Corresponding author. Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, No.325, Sec.2, Chenggong Rd., Neihu District, Taipei City 11490, Taiwan, ROC. Fax: +886 2 87927226
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31
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Dong T, Han C, Jiang M, Zhang T, Kang Q, Wang P, Zhou F. A Four-Channel Surface Plasmon Resonance Sensor Functionalized Online for Simultaneous Detections of Anti-SARS-CoV-2 Antibody, Free Viral Particles, and Neutralized Viral Particles. ACS Sens 2022; 7:3560-3570. [PMID: 36382569 DOI: 10.1021/acssensors.2c02067] [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: 11/18/2022]
Abstract
Current tests for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detect either the constituent nucleic acids/proteins of the viral particles or antibodies specific to the virus, but cannot provide information about viral neutralization by an antibody and the efficacy of an antibody. Such information is important about individuals' vulnerability to severe symptoms or their likelihood of showing no symptoms. We immobilized online SARS-CoV-2 spike (S1) protein and angiotensin-converting enzyme 2 (ACE2) into separate surface plasmon resonance (SPR) channels of a tris-nitrilotriacetic acid (tris-NTA) chip to simultaneously detect the anti-S1 antibody and viral particles in serum samples. In addition, with a high-molecular-weight-cutoff filter, we separated the neutralized viral particles from the free antibody molecules and used a sensing channel immobilized with Protein G to determine antibody-neutralized viral particles. The optimal density of probe molecules in each fluidic channel can be precisely controlled through the closure and opening of the specific ports. By utilizing the high surface density of ACE2, multiple assays can be carried out without regenerations. These three species can be determined with a short analysis time (<12 min per assay) and excellent sensor-to-sensor/cycle-to-cycle reproducibility (RSD < 5%). When coupled with an autosampler, continuous assays can be performed in an unattended manner at a single chip for up to 6 days. Such a sensor capable of assaying serum samples containing the three species at different levels provides additional insights into the disease status and immunity of persons being tested, which should be helpful for containing the SARS-CoV-2 spread during the era of incessant viral mutations.
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Affiliation(s)
- Tianbao Dong
- Institute of Surface Analysis and Chemical Biology, University of Jinan, Jinan, Shandong, P. R. China, 250022
| | - Chaowei Han
- Institute of Surface Analysis and Chemical Biology, University of Jinan, Jinan, Shandong, P. R. China, 250022
| | - Meng Jiang
- Institute of Surface Analysis and Chemical Biology, University of Jinan, Jinan, Shandong, P. R. China, 250022
| | - Tiantian Zhang
- University Hospital, University of Jinan, Jinan, Shandong, P. R. China, 250022
| | - Qing Kang
- Institute of Surface Analysis and Chemical Biology, University of Jinan, Jinan, Shandong, P. R. China, 250022
| | - Pengcheng Wang
- Institute of Surface Analysis and Chemical Biology, University of Jinan, Jinan, Shandong, P. R. China, 250022
| | - Feimeng Zhou
- Institute of Surface Analysis and Chemical Biology, University of Jinan, Jinan, Shandong, P. R. China, 250022
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32
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Xie L, Li J, Ai Y, He H, Chen X, Yin M, Li W, Huang W, Luo MY, He J. Current strategies for SARS-CoV-2 molecular detection. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2022; 14:4625-4642. [PMID: 36349688 DOI: 10.1039/d2ay01313d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The molecular detection of SARS-CoV-2 is extremely important for the discovery and prevention of pandemic dissemination. Because SARS-CoV-2 is not always present in the samples that can be collected, the sample chosen for testing has inevitably become the key to the SARS-CoV-2 positive cases screening. The nucleotide amplification strategy mainly includes Q-PCR assays and isothermal amplification assays. The Q-PCR assay is the most used SARS-CoV-2 detection assay. Due to heavy expenditures and other drawbacks, isothermal amplification cannot replace the dominant position of the Q-PCR assay. The antibody-based detection combined with Q-PCR can help to find more positive cases than only using nucleotide amplification-based assays. Pooled testing based on Q-PCR significantly increases efficiency and reduces the cost of massive-scale screening. The endless stream of variants emerging across the world poses a great challenge to SARS-CoV-2 molecular detection. The multi-target assays and several other strategies have proved to be efficient in the detection of mutated SARS-CoV-2 variants. Further research work should concentrate on: (1) identifying more ideal sample plucking strategies, (2) ameliorating the Q-PCR primer and probes targeted toward mutated SARS-CoV-2 variants, (3) exploring more economical and precise isothermal amplification assays, and (4) developing more advanced strategies for antibody/antigen or engineered antibodies to ameliorate the antibody/antigen-based strategy.
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Affiliation(s)
- Lei Xie
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, No. 12 Jichang Road, Guangzhou 510080, China.
| | - Junlin Li
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, No. 12 Jichang Road, Guangzhou 510080, China.
| | - Ying Ai
- Artemisinin Research Center, Guangzhou University of Chinese Medicine, Guangzhou 510080, China
| | - Haolan He
- Guangzhou Eighth People's Hospital, Guangzhou 510080, China
| | - Xiuyun Chen
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, No. 12 Jichang Road, Guangzhou 510080, China.
| | - Mingyu Yin
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, No. 12 Jichang Road, Guangzhou 510080, China.
| | - Wanxi Li
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, No. 12 Jichang Road, Guangzhou 510080, China.
| | - Wenguan Huang
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, No. 12 Jichang Road, Guangzhou 510080, China.
| | - Min-Yi Luo
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, No. 12 Jichang Road, Guangzhou 510080, China.
| | - Jinyang He
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, No. 12 Jichang Road, Guangzhou 510080, China.
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Validation of SARS-CoV-2 pooled testing for surveillance using the Panther Fusion® system: Impact of pool size, automation, and assay chemistry. PLoS One 2022; 17:e0276729. [PMID: 36342921 PMCID: PMC9639840 DOI: 10.1371/journal.pone.0276729] [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: 07/29/2022] [Accepted: 10/12/2022] [Indexed: 11/09/2022] Open
Abstract
Combining diagnostic specimens into pools has been considered as a strategy to augment throughput, decrease turnaround time, and leverage resources. This study utilized a multi-parametric approach to assess optimum pool size, impact of automation, and effect of nucleic acid amplification chemistries on the detection of SARS-CoV-2 RNA in pooled samples for surveillance testing on the Hologic Panther Fusion® System. Dorfman pooled testing was conducted with previously tested SARS-CoV-2 nasopharyngeal samples using Hologic’s Aptima® and Panther Fusion® SARS-CoV-2 Emergency Use Authorization assays. A manual workflow was used to generate pool sizes of 5:1 (five samples: one positive, four negative) and 10:1. An automated workflow was used to generate pool sizes of 3:1, 4:1, 5:1, 8:1 and 10:1. The impact of pool size, pooling method, and assay chemistry on sensitivity, specificity, and lower limit of detection (LLOD) was evaluated. Both the Hologic Aptima® and Panther Fusion® SARS-CoV-2 assays demonstrated >85% positive percent agreement between neat testing and pool sizes ≤5:1, satisfying FDA recommendation. Discordant results between neat and pooled testing were more frequent for positive samples with CT>35. Fusion® CT (cycle threshold) values for pooled samples increased as expected for pool sizes of 5:1 (CT increase of 1.92–2.41) and 10:1 (CT increase of 3.03–3.29). The Fusion® assay demonstrated lower LLOD than the Aptima® assay for pooled testing (956 vs 1503 cp/mL, pool size of 5:1). Lowering the cut-off threshold of the Aptima® assay from 560 kRLU (manufacturer’s setting) to 350 kRLU improved the assay sensitivity to that of the Fusion® assay for pooled testing. Both Hologic’s SARS-CoV-2 assays met the FDA recommended guidelines for percent positive agreement (>85%) for pool sizes ≤5:1. Automated pooling increased test throughput and enabled automated sample tracking while requiring less labor. The Fusion® SARS-CoV-2 assay, which demonstrated a lower LLOD, may be more appropriate for surveillance testing.
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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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35
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Moura AV, de Oliveira DC, Silva AAR, da Rosa JR, Garcia PHD, Sanches PHG, Garza KY, Mendes FMM, Lambert M, Gutierrez JM, Granado NM, dos Santos AC, de Lima IL, Negrini LDDO, Antonio MA, Eberlin MN, Eberlin LS, Porcari AM. Urine Metabolites Enable Fast Detection of COVID-19 Using Mass Spectrometry. Metabolites 2022; 12:1056. [PMID: 36355139 PMCID: PMC9697918 DOI: 10.3390/metabo12111056] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 10/19/2022] [Accepted: 10/27/2022] [Indexed: 08/27/2023] Open
Abstract
The COVID-19 pandemic boosted the development of diagnostic tests to meet patient needs and provide accurate, sensitive, and fast disease detection. Despite rapid advancements, limitations related to turnaround time, varying performance metrics due to different sampling sites, illness duration, co-infections, and the need for particular reagents still exist. As an alternative diagnostic test, we present urine analysis through flow-injection-tandem mass spectrometry (FIA-MS/MS) as a powerful approach for COVID-19 diagnosis, targeting the detection of amino acids and acylcarnitines. We adapted a method that is widely used for newborn screening tests on dried blood for urine samples in order to detect metabolites related to COVID-19 infection. We analyzed samples from 246 volunteers with diagnostic confirmation via PCR. Urine samples were self-collected, diluted, and analyzed with a run time of 4 min. A Lasso statistical classifier was built using 75/25% data for training/validation sets and achieved high diagnostic performances: 97/90% sensitivity, 95/100% specificity, and 95/97.2% accuracy. Additionally, we predicted on two withheld sets composed of suspected hospitalized/symptomatic COVID-19-PCR negative patients and patients out of the optimal time-frame collection for PCR diagnosis, with promising results. Altogether, we show that the benchmarked FIA-MS/MS method is promising for COVID-19 screening and diagnosis, and is also potentially useful after the peak viral load has passed.
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Affiliation(s)
- Alexandre Varao Moura
- MSLife Laboratory of Mass Spectrometry, Health Sciences Postgraduate Program, São Francisco University, Bragança Paulista 12916-900, SP, Brazil
| | - Danilo Cardoso de Oliveira
- MSLife Laboratory of Mass Spectrometry, Health Sciences Postgraduate Program, São Francisco University, Bragança Paulista 12916-900, SP, Brazil
| | - Alex Ap. R. Silva
- MSLife Laboratory of Mass Spectrometry, Health Sciences Postgraduate Program, São Francisco University, Bragança Paulista 12916-900, SP, Brazil
| | - Jonas Ribeiro da Rosa
- MSLife Laboratory of Mass Spectrometry, Health Sciences Postgraduate Program, São Francisco University, Bragança Paulista 12916-900, SP, Brazil
| | - Pedro Henrique Dias Garcia
- MSLife Laboratory of Mass Spectrometry, Health Sciences Postgraduate Program, São Francisco University, Bragança Paulista 12916-900, SP, Brazil
| | - Pedro Henrique Godoy Sanches
- MSLife Laboratory of Mass Spectrometry, Health Sciences Postgraduate Program, São Francisco University, Bragança Paulista 12916-900, SP, Brazil
| | - Kyana Y. Garza
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712, USA
| | - Flavio Marcio Macedo Mendes
- MSLife Laboratory of Mass Spectrometry, Health Sciences Postgraduate Program, São Francisco University, Bragança Paulista 12916-900, SP, Brazil
| | - Mayara Lambert
- MSLife Laboratory of Mass Spectrometry, Health Sciences Postgraduate Program, São Francisco University, Bragança Paulista 12916-900, SP, Brazil
| | - Junier Marrero Gutierrez
- MSLife Laboratory of Mass Spectrometry, Health Sciences Postgraduate Program, São Francisco University, Bragança Paulista 12916-900, SP, Brazil
| | - Nicole Marino Granado
- MSLife Laboratory of Mass Spectrometry, Health Sciences Postgraduate Program, São Francisco University, Bragança Paulista 12916-900, SP, Brazil
| | - Alicia Camacho dos Santos
- Department of Material Engineering and Nanotechnology, Mackenzie Presbyterian University, São Paulo 01302-907, SP, Brazil
| | - Iasmim Lopes de Lima
- Department of Material Engineering and Nanotechnology, Mackenzie Presbyterian University, São Paulo 01302-907, SP, Brazil
| | | | - Marcia Aparecida Antonio
- Integrated Unit of Pharmacology and Gastroenterology, UNIFAG, Bragança Paulista 12916-900, SP, Brazil
| | - Marcos N. Eberlin
- Department of Material Engineering and Nanotechnology, Mackenzie Presbyterian University, São Paulo 01302-907, SP, Brazil
| | - Livia S. Eberlin
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712, USA
- Department of Surgery, Baylor College of Medicine, Houston, TX 77030, USA
| | - Andreia M. Porcari
- MSLife Laboratory of Mass Spectrometry, Health Sciences Postgraduate Program, São Francisco University, Bragança Paulista 12916-900, SP, Brazil
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Butler KS, Carson BD, Podlevsky JD, Mayes CM, Rowland JM, Campbell D, Ricken JB, Wudiri G, Timlin JA. Singleplex, multiplex and pooled sample real-time RT-PCR assays for detection of SARS-CoV-2 in an occupational medicine setting. Sci Rep 2022; 12:17733. [PMID: 36273023 PMCID: PMC9587995 DOI: 10.1038/s41598-022-22106-2] [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: 02/14/2022] [Accepted: 10/10/2022] [Indexed: 01/18/2023] Open
Abstract
For workplaces which cannot operate as telework or remotely, there is a critical need for routine occupational SARS-CoV-2 diagnostic testing. Although diagnostic tests including the CDC 2019-Novel Coronavirus (2019-nCoV) Real-Time RT-PCR Diagnostic Panel (CDC Diagnostic Panel) (EUA200001) were made available early in the pandemic, resource scarcity and high demand for reagents and equipment necessitated priority of symptomatic patients. There is a clearly defined need for flexible testing methodologies and strategies with rapid turnaround of results for (1) symptomatic, (2) asymptomatic with high-risk exposures and (3) asymptomatic populations without preexisting conditions for routine screening to address the needs of an on-site work force. We developed a distinct SARS-CoV-2 diagnostic assay based on the original CDC Diagnostic Panel (EUA200001), yet, with minimum overlap for currently employed reagents to eliminate direct competition for limited resources. As the pandemic progressed with testing loads increasing, we modified the assay to include 5-sample pooling and amplicon target multiplexing. Analytical sensitivity of the pooled and multiplexed assays was rigorously tested with contrived positive samples in realistic patient backgrounds. Assay performance was determined with clinical samples previously assessed with an FDA authorized assay. Throughout the pandemic we successfully tested symptomatic, known contact and travelers within our occupational population with a ~ 24-48-h turnaround time to limit the spread of COVID-19 in the workplace. Our singleplex assay had a detection limit of 31.25 copies per reaction. The three-color multiplexed assay maintained similar sensitivity to the singleplex assay, while tripling the throughput. The pooling assay further increased the throughput to five-fold the singleplex assay, albeit with a subtle loss of sensitivity. We subsequently developed a hybrid 'multiplex-pooled' strategy to testing to address the need for both rapid analysis of samples from personnel at high risk of COVID infection and routine screening. Herein, our SARS-CoV-2 assays specifically address the needs of occupational healthcare for both rapid analysis of personnel at high-risk of infection and routine screening that is essential for controlling COVID-19 disease transmission. In addition to SARS-CoV-2 and COVID-19, this work demonstrates successful flexible assays developments and deployments with implications for emerging highly transmissible diseases and future pandemics.
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Affiliation(s)
- Kimberly S Butler
- Molecular and Microbiology Department, Sandia National Laboratories, Albuquerque, NM, 87123, USA
| | - Bryan D Carson
- Molecular and Microbiology Department, Sandia National Laboratories, Albuquerque, NM, 87123, USA
| | - Joshua D Podlevsky
- Molecular and Microbiology Department, Sandia National Laboratories, Albuquerque, NM, 87123, USA
| | - Cathryn M Mayes
- WMD Threats and Aerosol Science, Sandia National Laboratories, Albuquerque, NM, 87123, USA
| | - Jessica M Rowland
- Global Chemical and Biological Security, Sandia National Laboratories, Albuquerque, NM, 87123, USA
| | - DeAnna Campbell
- Biological and Chemical Sensors Department, Sandia National Laboratories, Albuquerque, NM, 87123, USA
| | - J Bryce Ricken
- Molecular and Microbiology Department, Sandia National Laboratories, Albuquerque, NM, 87123, USA
| | - George Wudiri
- Cooperative Nuclear Counterproliferation, Sandia National Laboratories, Albuquerque, NM, 87123, USA
| | - Jerilyn A Timlin
- Molecular and Microbiology Department, Sandia National Laboratories, Albuquerque, NM, 87123, USA.
- Computational Biology and Biophysics Department, Sandia National Laboratories, Albuquerque, NM, 87123, USA.
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Mladonicky J, Bedada A, Yoder C, VanderWaal K, Torrison J, Wells SJ. Pooled surveillance testing for asymptomatic SARS-CoV-2 infections at a Veterinary Teaching Hospital College, University of Minnesota, December 2020-April 2021. Front Public Health 2022; 10:879107. [PMID: 35991058 PMCID: PMC9388852 DOI: 10.3389/fpubh.2022.879107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 07/01/2022] [Indexed: 11/13/2022] Open
Abstract
To evaluate the use of asymptomatic surveillance, we implemented a surveillance program for asymptomatic SARS-CoV-2 infection in a voluntary sample of individuals at the College of Veterinary Medicine at the University of Minnesota. Self-collected anterior nasal samples were tested using real time reverse transcription-polymerase chain reaction (RT-PCR), in a 5:1 pooled testing strategy, twice weekly for 18 weeks. Positive pools were deconvoluted into individual tests, revealing an observed prevalence of 0.07% (3/4,525). Pooled testing allowed for large scale testing with an estimated cost savings of 79.3% and modeling demonstrated this testing strategy prevented up to 2 workplace transmission events, averting up to 4 clinical cases. At the study endpoint, antibody testing revealed 80.7% of participants had detectable vaccine antibody levels while 9.6% of participants had detectable antibodies to natural infection.
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Affiliation(s)
- Janice Mladonicky
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, United States
| | - Addisalem Bedada
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, United States
| | - Colin Yoder
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, United States
| | - Kimberly VanderWaal
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, United States
| | - Jerry Torrison
- Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, United States
| | - Scott J. Wells
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, United States
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38
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Shapiro M, Landau R, Shay S, Kaminski M, Verhovsky G. Early Detection of COVID-19 outbreaks using Textual Analysis of Electronic Medical Records. J Clin Virol 2022; 155:105251. [PMID: 35973330 PMCID: PMC9347140 DOI: 10.1016/j.jcv.2022.105251] [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: 03/21/2022] [Revised: 07/10/2022] [Accepted: 08/02/2022] [Indexed: 11/26/2022]
Abstract
Purpose Our objective was to develop a tool promoting early detection of COVID-19 cases by focusing epidemiological investigations and PCR examinations during a period of limited testing capabilities. Methods We developed an algorithm for analyzing medical records recorded by healthcare providers in the Israeli Defense Forces. The algorithm utilized textual analysis to detect patients presenting with suspicious symptoms and was tested among 92 randomly selected units. Detection of a potential cluster of patients in a unit prompted a focused epidemiological investigation aided by data provided by the algorithm. Results During a month of follow up, the algorithm has flagged 17 of the units for investigation. The subsequent epidemiological investigations led to the testing of 78 persons and the detection of eight cases in four clusters that were previously gone unnoticed. The resulting positive test rate of 10.25% was five time higher than the IDF average at the time of the study. No cases of COVID-19 in the examined units were missed by the algorithm. Conclusions This study depicts the successful development and large scale deployment of a textual analysis based algorithm for early detection of COVID-19 cases, demonstrating the potential of natural language processing of medical text as a tool for promoting public health.
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Liu L. Modeling the optimization of COVID-19 pooled testing: How many samples can be included in a single test? INFORMATICS IN MEDICINE UNLOCKED 2022; 32:101037. [PMID: 35966127 PMCID: PMC9357440 DOI: 10.1016/j.imu.2022.101037] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 07/26/2022] [Accepted: 08/01/2022] [Indexed: 11/29/2022] Open
Abstract
Objectives This study tries to answer the crucial question of how many biological samples can be optimally included in a single test for COVID-19 pooled testing. Methods It builds a novel theoretical model which links the local population to be tested in a region, the number of biological samples included in a single test, the “attitude” toward resource cost saving and time taken in a single test, as well as the corresponding resource cost function and time function, together. The numerical simulation results are then used to formulate the resource cost function as well as the time function. Finally, a loss function to be minimized is constructed and the optimal number of samples included is calculated. Results In a numerical example, we consider a region of 1 million population which needs to be tested for the infection of COVID-19. The solution calculates the optimal number of biological samples included in a single test as 4.254 when the time taken is given the weight of 50% under the infection probability of 10%. Other combinations of numerical results are also presented. Conclusions As we can see in our simulation results, given the infection probability at 10%, setting the number of biological samples included in a single test (in the integer level) at [4,6] is reasonable for a wide range of the subjective attitude between time and resource costs. Therefore, in the current practice, 5-mixed samples would sound better than the commonly used 10-mixed samples.
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Affiliation(s)
- Lu Liu
- School of Economics, Southwestern University of Finance and Economics, China
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40
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Tekeli T, Dénes A, Röst G. Adaptive group testing in a compartmental model of COVID-19 . MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2022; 19:11018-11033. [PMID: 36124578 DOI: 10.3934/mbe.2022513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Various measures have been implemented around the world to prevent the spread of SARS-CoV-2. A potential tool to reduce disease transmission is regular mass testing of a high percentage of the population, possibly with pooling (testing a compound of several samples with one single test). We develop a compartmental model to study the applicability of this method and compare different pooling strategies: regular and Dorfman pooling. The model includes isolated compartments as well, from where individuals rejoin the active population after some time delay. We develop a method to optimize Dorfman pooling depending on disease prevalence and establish an adaptive strategy to select variable pool sizes during the course of the epidemic. It is shown that optimizing the pool size can avert a significant number of infections. The adaptive strategy is much more efficient, and may prevent an epidemic outbreak even in situations when a fixed pool size strategy can not.
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Affiliation(s)
- Tamás Tekeli
- Bolyai Institute, University of Szeged, Aradi vértanúk tere 1., H-6720 Szeged, Hungary
| | - Attila Dénes
- Bolyai Institute, University of Szeged, Aradi vértanúk tere 1., H-6720 Szeged, Hungary
| | - Gergely Röst
- Bolyai Institute, University of Szeged, Aradi vértanúk tere 1., H-6720 Szeged, Hungary
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41
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Eales O, Page AJ, de Oliveira Martins L, Wang H, Bodinier B, Haw D, Jonnerby J, Atchison C, Ashby D, Barclay W, Taylor G, Cooke G, Ward H, Darzi A, Riley S, Chadeau-Hyam M, Donnelly CA, Elliott P. SARS-CoV-2 lineage dynamics in England from September to November 2021: high diversity of Delta sub-lineages and increased transmissibility of AY.4.2. BMC Infect Dis 2022; 22:647. [PMID: 35896970 PMCID: PMC9326417 DOI: 10.1186/s12879-022-07628-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 07/04/2022] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Since the emergence of SARS-CoV-2, evolutionary pressure has driven large increases in the transmissibility of the virus. However, with increasing levels of immunity through vaccination and natural infection the evolutionary pressure will switch towards immune escape. Genomic surveillance in regions of high immunity is crucial in detecting emerging variants that can more successfully navigate the immune landscape. METHODS We present phylogenetic relationships and lineage dynamics within England (a country with high levels of immunity), as inferred from a random community sample of individuals who provided a self-administered throat and nose swab for rt-PCR testing as part of the REal-time Assessment of Community Transmission-1 (REACT-1) study. During round 14 (9 September-27 September 2021) and 15 (19 October-5 November 2021) lineages were determined for 1322 positive individuals, with 27.1% of those which reported their symptom status reporting no symptoms in the previous month. RESULTS We identified 44 unique lineages, all of which were Delta or Delta sub-lineages, and found a reduction in their mutation rate over the study period. The proportion of the Delta sub-lineage AY.4.2 was increasing, with a reproduction number 15% (95% CI 8-23%) greater than the most prevalent lineage, AY.4. Further, AY.4.2 was less associated with the most predictive COVID-19 symptoms (p = 0.029) and had a reduced mutation rate (p = 0.050). Both AY.4.2 and AY.4 were found to be geographically clustered in September but this was no longer the case by late October/early November, with only the lineage AY.6 exhibiting clustering towards the South of England. CONCLUSIONS As SARS-CoV-2 moves towards endemicity and new variants emerge, genomic data obtained from random community samples can augment routine surveillance data without the potential biases introduced due to higher sampling rates of symptomatic individuals.
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Affiliation(s)
- Oliver Eales
- School of Public Health, Imperial College London, Norfolk Place, London, W2 1PG, UK
- MRC Centre for Global Infectious Disease Analysis and Jameel Institute, Imperial College London, London, UK
| | | | | | - Haowei Wang
- School of Public Health, Imperial College London, Norfolk Place, London, W2 1PG, UK
- MRC Centre for Global Infectious Disease Analysis and Jameel Institute, Imperial College London, London, UK
| | - Barbara Bodinier
- School of Public Health, Imperial College London, Norfolk Place, London, W2 1PG, UK
- MRC Centre for Environment and Health, School of Public Health, Imperial College London, London, UK
| | - David Haw
- School of Public Health, Imperial College London, Norfolk Place, London, W2 1PG, UK
- MRC Centre for Global Infectious Disease Analysis and Jameel Institute, Imperial College London, London, UK
| | - Jakob Jonnerby
- School of Public Health, Imperial College London, Norfolk Place, London, W2 1PG, UK
- MRC Centre for Global Infectious Disease Analysis and Jameel Institute, Imperial College London, London, UK
| | - Christina Atchison
- School of Public Health, Imperial College London, Norfolk Place, London, W2 1PG, UK
| | - Deborah Ashby
- School of Public Health, Imperial College London, Norfolk Place, London, W2 1PG, UK
| | - Wendy Barclay
- Department of Infectious Disease, Imperial College London, London, UK
| | - Graham Taylor
- Department of Infectious Disease, Imperial College London, London, UK
| | - Graham Cooke
- Department of Infectious Disease, Imperial College London, London, UK
- Imperial College Healthcare NHS Trust, London, UK
- National Institute for Health Research Imperial Biomedical Research Centre, London, UK
| | - Helen Ward
- School of Public Health, Imperial College London, Norfolk Place, London, W2 1PG, UK
- Imperial College Healthcare NHS Trust, London, UK
- National Institute for Health Research Imperial Biomedical Research Centre, London, UK
| | - Ara Darzi
- Imperial College Healthcare NHS Trust, London, UK
- National Institute for Health Research Imperial Biomedical Research Centre, London, UK
- Institute of Global Health Innovation, Imperial College London, London, UK
| | - Steven Riley
- School of Public Health, Imperial College London, Norfolk Place, London, W2 1PG, UK
- MRC Centre for Global Infectious Disease Analysis and Jameel Institute, Imperial College London, London, UK
| | - Marc Chadeau-Hyam
- School of Public Health, Imperial College London, Norfolk Place, London, W2 1PG, UK
- MRC Centre for Environment and Health, School of Public Health, Imperial College London, London, UK
| | - Christl A Donnelly
- School of Public Health, Imperial College London, Norfolk Place, London, W2 1PG, UK.
- MRC Centre for Global Infectious Disease Analysis and Jameel Institute, Imperial College London, London, UK.
- Department of Statistics, University of Oxford, Oxford, UK.
| | - Paul Elliott
- School of Public Health, Imperial College London, Norfolk Place, London, W2 1PG, UK.
- MRC Centre for Global Infectious Disease Analysis and Jameel Institute, Imperial College London, London, UK.
- Imperial College Healthcare NHS Trust, London, UK.
- National Institute for Health Research Imperial Biomedical Research Centre, London, UK.
- Health Data Research (HDR) UK, Imperial College London, London, UK.
- UK Dementia Research Institute Centre at Imperial, Imperial College London, London, UK.
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Charles CM, Osman NB, Arijama D, Matingane B, Sitoé T, Kenga D, Lorenzoni C, Luís E, Pacagnella RDC, Sacarlal J. Clinical and epidemiological aspects of SARS-CoV-2 infection among pregnant and postpartum women in Mozambique: a prospective cohort study. Reprod Health 2022; 19:164. [PMID: 35854384 PMCID: PMC9297548 DOI: 10.1186/s12978-022-01469-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 06/21/2022] [Indexed: 12/03/2022] Open
Abstract
Background Although there is a significant increase of evidence regarding the prevalence and impact of COVID-19 on maternal and perinatal outcomes, data on the effects of the pandemic on the obstetric population in sub-Saharan African countries are still scarce. Therefore, the study aims were to assess the prevalence and impact of COVID-19 on maternal and neonatal outcomes in the obstetric population at Central Hospital of Maputo (HCM), Mozambique. Methods Prospective cohort study conducted at teaching and referral maternity, HCM, from 20 October 2020 to 22 July 2021. We collected maternal and perinatal outcomes up to 6 weeks postpartum of eligible women (pregnant and postpartum women—up to the 14th day postpartum) screened for COVID-19 (individual test for symptomatic participants and pool testing for asymptomatic). The primary outcome was maternal death, Severe Acute Respiratory Syndrome (SARS) and Intensive Care Unit (ICU) admission. We estimated the COVID-19 prevalence and the unadjusted RR (95% CI) for maternal and perinatal outcomes. We used the chi-square or Fisher's exact test to compare categorical variables (two-sided p-value < 0.05 for statistical significance). Results We included 239 participants. The overall prevalence of COVID-19 was 9.2% (22/239) and in the symptomatic group was 32.4% (11/34). About 50% of the participants with COVID-19 were symptomatic. Moreover, the most frequent symptoms were dyspnoea (33.3%), cough (28.6%), anosmia (23.8%), and fever (19%). Not having a partner, being pregnant, and alcohol consumption were vulnerability factors for SARS-CoV-2 infection. The risk of adverse maternal and neonatal outcomes (abortion, foetal death, preterm birth, Apgar, and NICU admission) was not significantly increased with COVID-19. Moreover, we did not observe a significant difference in the primary outcomes (SARS, ICU admission and maternal death) between COVID-19 positive and COVID-19 negative groups. Conclusion The prevalence of COVID-19 in the obstetric population is higher than in the general population, and fifty percent of pregnant and postpartum women with COVID-19 infection are asymptomatic. Not having a partner and alcohol consumption were factors of greatest vulnerability to SARS-COV-2 infection. Moreover, being pregnant versus postpartum was associated with increased vulnerability to COVID-19. Data suggest that pregnant women with COVID-19 may have a higher frequency of COVID-19 infection, reinforcing the need for universal testing, adequate follow-up for this population, and increasing COVID-19 therapy facilities in Mozambique. Moreover, provide counselling during Antenatal care for COVID-19 preventive measures. However, more prospective and robust studies are needed to assess these findings. The epidemiological pattern of the COVID-19 pandemic in Africa is heterogeneous, and many African countries are still struggling to establish efficient testing policy, guarantee sufficient laboratory supply and achieve or maintain adequate testing capacity. In addition, evidence suggests that sexual and reproductive health services were the most affected by the pandemic; this scenario might have devastating effects on maternal and perinatal health. Moreover, data from non-sub-Saharan countries the SARS-CoV-2 infection among pregnant and postpartum women is associated with an increased risk of adverse maternal and neonatal health (preterm birth, preeclampsia and maternal death). Although there is a significant increase of evidence regarding the prevalence and impact of COVID-19 on maternal and perinatal health, data on the effects of this condition on the obstetric population in low-income countries are scarce. Therefore, the study objective were to assess the prevalence and impact of COVID-19 on maternal and neonatal health at referral maternity in Maputo, Mozambique. Our findings suggest that the prevalence of COVID-19 in the obstetric population is higher than the general population, and most pregnant and postpartum women are asymptomatic. Being pregnant, not having a partner and alcohol consumption were factors of greatest vulnerability to SARS-COV-2 infection. Moreover, the risk of COVID-19 among pregnant was seven-fold higher than in postpartum women. Pregnant women with COVID-19 may have a higher frequency of adverse gestational outcomes (foetal death and abortion). Although the risk of adverse maternal outcomes (death, Severe Acute Respiratory Syndrome and Intensive Care Unit admission) did not differ significantly between the COVID-19 and COVID-19 negative groups, universal screening for COVID-19 should be implemented to ensure adequate management of pregnant women and newborns.
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Affiliation(s)
- Charles M'poca Charles
- Provincial Health Administration, DPS Manica, Chimoio, Manica Province, Mozambique. .,Department of Obstetrics and Gynecology, School of Medicine, University of Campinas, Campinas, São Paulo, Brazil.
| | - Nafissa Bique Osman
- Department of Obstetrics and Gynecology, Maputo Central Hospital, Maputo, Mozambique.,Department of Obstetrics and Gynecology, Faculty of Medicine, Eduardo Mondlane University, Maputo, Mozambique
| | - Domingos Arijama
- Department of Obstetrics and Gynecology, Maputo Central Hospital, Maputo, Mozambique
| | - Benjamim Matingane
- Department of Obstetrics and Gynecology, Maputo Central Hospital, Maputo, Mozambique.,Department of Obstetrics and Gynecology, Faculty of Medicine, Eduardo Mondlane University, Maputo, Mozambique
| | - Tomás Sitoé
- Department of Obstetrics and Gynecology, Maputo Central Hospital, Maputo, Mozambique
| | - Darlene Kenga
- Department of Microbiology, Faculty of Medicine, Eduardo Mondlane University, Maputo, Mozambique
| | - Cesaltina Lorenzoni
- Pathology Department, Faculty of Medicine, Eduardo Mondlane University, Maputo, Mozambique.,Pathological Anatomy Service, Maputo Central Hospital, Maputo, Mozambique
| | - Elvira Luís
- Department of Obstetrics and Gynecology, Maputo Central Hospital, Maputo, Mozambique.,Department of Obstetrics and Gynecology, Faculty of Medicine, Eduardo Mondlane University, Maputo, Mozambique
| | | | - Jahit Sacarlal
- Department of Microbiology, Faculty of Medicine, Eduardo Mondlane University, Maputo, Mozambique
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Hong KH, Kim GJ, Roh KH, Sung H, Lee J, Kim SY, Kim TS, Park JS, Huh HJ, Park Y, Kim JS, Kim HS, Seong MW, Ryoo NH, Song SH, Lee H, Kwon GC, Yoo CK. Update of Guidelines for Laboratory Diagnosis of COVID-19 in Korea. Ann Lab Med 2022; 42:391-397. [PMID: 35177559 PMCID: PMC8859556 DOI: 10.3343/alm.2022.42.4.391] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 01/25/2022] [Accepted: 02/07/2022] [Indexed: 11/19/2022] Open
Abstract
Korean Society for Laboratory Medicine and the Korea Disease Prevention and Control Agency have announced guidelines for diagnosing coronavirus disease (COVID-19) in clinical laboratories in Korea. With the ongoing pandemic, we propose an update of the previous guidelines based on new scientific data. This update includes recommendations for tests that were not included in the previous guidelines, including the rapid molecular test, antigen test, antibody test, and self-collected specimens, and a revision of the previous recommendations. This update will aid clinical laboratories in performing laboratory tests for diagnosing COVID-19.
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Affiliation(s)
- Ki Ho Hong
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - Gab Jung Kim
- Bureau of Infectious Disease Diagnosis Control, the Korea Disease Control and Prevention Agency, Osong, Korea
| | - Kyoung Ho Roh
- Department of Laboratory Medicine, National Health Insurance Service Ilsan Hospital, Goyang, Korea
| | - Heungsup Sung
- Department of Laboratory Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Jaehyeon Lee
- Department of Laboratory Medicine, Jeonbuk National University Medical School and Hospital, Jeonju, Korea
| | - So Yeon Kim
- Department of Laboratory Medicine, National Medical Center, Seoul, Korea
| | - Taek Soo Kim
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Korea
| | - Jae-Sun Park
- Bureau of Infectious Disease Diagnosis Control, the Korea Disease Control and Prevention Agency, Osong, Korea
| | - Hee Jae Huh
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Younhee Park
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - Jae-Seok Kim
- Department of Laboratory Medicine, Hallym University College of Medicine, Chuncheon, Korea
| | - Hyun Soo Kim
- Department of Laboratory Medicine, Hallym University College of Medicine, Chuncheon, Korea
| | - Moon-Woo Seong
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Korea
| | - Nam Hee Ryoo
- Department of Laboratory Medicine, Keimyung University School of Medicine, Daegu, Korea
| | - Sang Hoon Song
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Korea
| | - Hyukmin Lee
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - Gye Cheol Kwon
- Department of Laboratory Medicine, College of Medicine, Chungnam National University, Daejeon, Korea
| | - Cheon Kwon Yoo
- Bureau of Infectious Disease Diagnosis Control, the Korea Disease Control and Prevention Agency, Osong, Korea
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44
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Song Y, Wang X, Xiao Y, Wang H. A review of pooled‐sample strategy: Does complexity lead to better performance? VIEW 2022. [DOI: 10.1002/viw.20210005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Affiliation(s)
- Yu Song
- Department of Molecular Biology Shanghai Centre for Clinical Laboratory Shanghai China
| | - XueLiang Wang
- Department of Molecular Biology Shanghai Centre for Clinical Laboratory Shanghai China
| | - YanQun Xiao
- Department of Molecular Biology Shanghai Centre for Clinical Laboratory Shanghai China
| | - Hualiang Wang
- Department of Molecular Biology Shanghai Centre for Clinical Laboratory Shanghai China
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45
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Mandhan P, Sharma M, Pandey S, Chandel N, Chourasia N, Moun A, Sharma D, Sukar R, Singh N, Mathur S, Kotnala A, Negi N, Gupta A, Kumar A, Suresh Kumar R, Kumar P, Singh S. A Regional Pooling Intervention in a High-Throughput COVID-19 Diagnostic Laboratory to Enhance Throughput, Save Resources and Time Over a Period of 6 Months. Front Microbiol 2022; 13:858555. [PMID: 35756046 PMCID: PMC9218601 DOI: 10.3389/fmicb.2022.858555] [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: 01/20/2022] [Accepted: 03/31/2022] [Indexed: 11/13/2022] Open
Abstract
An effective and rapid diagnosis has great importance in tackling the ongoing COVID-19 pandemic through isolation of the infected individuals to curb the transmission and initiation of specialized treatment for the disease. It has been proven that enhanced testing capacities contribute to efficiently curbing SARS-CoV-2 transmission during the initial phases of the outbreaks. RT-qPCR is considered a gold standard for the diagnosis of COVID-19. However, in resource-limited countries expenses for molecular diagnosis limits the diagnostic capacities. Here, we present interventions of two pooling strategies as 5 sample pooling (P-5) and 10 sample pooling (P-10) in a high-throughput COVID-19 diagnostic laboratory to enhance throughput and save resources and time over a period of 6 months. The diagnostic capacity was scaled-up 2.15-folds in P-5 and 1.8-fold in P-10, reagents (toward RNA extraction and RT-qPCR) were preserved at 75.24% in P-5 and 86.21% in P-10, and time saved was 6,290.93 h in P-5 and 3147.3 h in P-10.
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Affiliation(s)
- Prerna Mandhan
- ICMR-National Institute of Cancer Prevention and Research, Noida, India
| | - Mansi Sharma
- ICMR-National Institute of Cancer Prevention and Research, Noida, India
| | - Sushmita Pandey
- ICMR-National Institute of Cancer Prevention and Research, Noida, India
| | - Neha Chandel
- ICMR-National Institute of Cancer Prevention and Research, Noida, India
| | - Nidhi Chourasia
- ICMR-National Institute of Cancer Prevention and Research, Noida, India
| | - Amit Moun
- ICMR-National Institute of Cancer Prevention and Research, Noida, India
| | - Divyani Sharma
- ICMR-National Institute of Cancer Prevention and Research, Noida, India
| | - Rubee Sukar
- ICMR-National Institute of Cancer Prevention and Research, Noida, India
| | - Niyati Singh
- ICMR-National Institute of Cancer Prevention and Research, Noida, India
| | - Shubhangi Mathur
- ICMR-National Institute of Cancer Prevention and Research, Noida, India
| | - Aarti Kotnala
- ICMR-National Institute of Cancer Prevention and Research, Noida, India
| | - Neetu Negi
- ICMR-National Institute of Cancer Prevention and Research, Noida, India
| | - Ashish Gupta
- ICMR-National Institute of Cancer Prevention and Research, Noida, India
| | - Anuj Kumar
- ICMR-National Institute of Cancer Prevention and Research, Noida, India
| | - R Suresh Kumar
- ICMR-National Institute of Cancer Prevention and Research, Noida, India
| | - Pramod Kumar
- ICMR-National Institute of Cancer Prevention and Research, Noida, India
| | - Shalini Singh
- ICMR-National Institute of Cancer Prevention and Research, Noida, India
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Raypah ME, Faris AN, Mohd Azlan M, Yusof NY, Suhailin FH, Shueb RH, Ismail I, Mustafa FH. Near-Infrared Spectroscopy as a Potential COVID-19 Early Detection Method: A Review and Future Perspective. SENSORS 2022; 22:s22124391. [PMID: 35746172 PMCID: PMC9229781 DOI: 10.3390/s22124391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 05/16/2022] [Accepted: 05/23/2022] [Indexed: 02/05/2023]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic is a worldwide health anxiety. The rapid dispersion of the infection globally results in unparalleled economic, social, and health impacts. The pathogen that causes COVID-19 is known as a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). A fast and low-cost diagnosis method for COVID-19 disease can play an important role in controlling its proliferation. Near-infrared spectroscopy (NIRS) is a quick, non-destructive, non-invasive, and inexpensive technique for profiling the chemical and physical structures of a wide range of samples. Furthermore, the NIRS has the advantage of incorporating the internet of things (IoT) application for the effective control and treatment of the disease. In recent years, a significant advancement in instrumentation and spectral analysis methods has resulted in a remarkable impact on the NIRS applications, especially in the medical discipline. To date, NIRS has been applied as a technique for detecting various viruses including zika (ZIKV), chikungunya (CHIKV), influenza, hepatitis C, dengue (DENV), and human immunodeficiency (HIV). This review aims to outline some historical and contemporary applications of NIRS in virology and its merit as a novel diagnostic technique for SARS-CoV-2.
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Affiliation(s)
- Muna E. Raypah
- School of Physics, Universiti Sains Malaysia, George Town 11800, Pulau Pinang, Malaysia;
| | - Asma Nadia Faris
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia Health Campus, Kubang Kerian 16150, Kelantan, Malaysia; (A.N.F.); (M.M.A.); (N.Y.Y.); (R.H.S.)
| | - Mawaddah Mohd Azlan
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia Health Campus, Kubang Kerian 16150, Kelantan, Malaysia; (A.N.F.); (M.M.A.); (N.Y.Y.); (R.H.S.)
| | - Nik Yusnoraini Yusof
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia Health Campus, Kubang Kerian 16150, Kelantan, Malaysia; (A.N.F.); (M.M.A.); (N.Y.Y.); (R.H.S.)
| | - Fariza Hanim Suhailin
- Department of Physics, Faculty of Science, Universiti Teknologi Malaysia, Skudai 81310, Johor, Malaysia;
| | - Rafidah Hanim Shueb
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia Health Campus, Kubang Kerian 16150, Kelantan, Malaysia; (A.N.F.); (M.M.A.); (N.Y.Y.); (R.H.S.)
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, Kubang Kerian 16150, Kelantan, Malaysia
| | - Irneza Ismail
- Advanced Devices & System (ADS) Research Group, Department of Electrical & Electronic Engineering, Faculty of Engineering and Built Environment, Universiti Sains Islam Malaysia, Bandar Baru Nilai, Nilai 71800, Negeri Sembilan, Malaysia
- Correspondence: (I.I.); (F.H.M.); Tel.: +60-7986569 (I.I.); +60-9-7672432 (F.H.M.)
| | - Fatin Hamimi Mustafa
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia Health Campus, Kubang Kerian 16150, Kelantan, Malaysia; (A.N.F.); (M.M.A.); (N.Y.Y.); (R.H.S.)
- Correspondence: (I.I.); (F.H.M.); Tel.: +60-7986569 (I.I.); +60-9-7672432 (F.H.M.)
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Yu M, Zhang X, Zhang X, Zahra QUA, Huang Z, Chen Y, Song C, Song M, Jiang H, Luo Z, Lu Y. An electrochemical aptasensor with N protein binding aptamer-complementary oligonucleotide as probe for ultra-sensitive detection of COVID-19. Biosens Bioelectron 2022; 213:114436. [PMID: 35716641 PMCID: PMC9176179 DOI: 10.1016/j.bios.2022.114436] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 05/24/2022] [Accepted: 05/27/2022] [Indexed: 01/08/2023]
Abstract
The emergence of the COVID-19 epidemic has affected the lives of hundreds of millions of people globally. There is no doubt that the development of fast and sensitive detection methods is crucial while the worldwide effective vaccination programs are miles away from actualization. In this study, we have reported an electrochemical N protein aptamer sensor with complementary oligonucleotide as probe for the specific detection of COVID-19. The electrochemical aptasensor was prepared by fixing the double-stranded DNA hybrid obtained by the hybridization of N protein aptamer and its Fc-labeled complementary strand on the surface of a gold electrode. After incubation with the target, the aptamer dissociated from the labeled complementary DNA oligonucleotide hybrid to preferentially bind with N protein in the solution. The concentration of N protein was measured by detecting the changes in electrochemical current signals induced by the conformational transformation of the complementary DNA oligonucleotide left on the electrode surface. The sensor had a linear relationship between the logarithm of the N protein concentration from 10 fM to 100 nM (ΔIp = 0.098 log CN protein/fM - 0.08433, R2 = 0.99), and the detection limitation was 1 fM (S/N = 3). The electrochemical aptamer sensor was applied to test the spiked concentrations of throat swabs and blood samples from three volunteers, and the obtained results proved that the sensor has great potentials for the early detection of COVID-19 in patients.
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Affiliation(s)
- Mengdi Yu
- Department of Applied Chemistry, Key Laboratory of Agricultural Sensors, Ministry of Agriculture and Rural Affairs, Anhui Agricultural University, Hefei, 230036, PR China
| | - Xiaohui Zhang
- Department of Applied Chemistry, Key Laboratory of Agricultural Sensors, Ministry of Agriculture and Rural Affairs, Anhui Agricultural University, Hefei, 230036, PR China
| | - Xin Zhang
- Department of Applied Chemistry, Key Laboratory of Agricultural Sensors, Ministry of Agriculture and Rural Affairs, Anhui Agricultural University, Hefei, 230036, PR China
| | - Qurat Ul Ain Zahra
- Hefei National Lab for Physical Sciences at the Microscale and the Centers for Biomedical Engineering, University of Science and Technology of China, Hefei, 230026, PR China; Core Facility Center for Life Sciences, Department of Molecular Biology and Cell Biology, University of Sciences and Technology of China, Hefei, 230026, PR China
| | - Zenghui Huang
- Department of Applied Chemistry, Key Laboratory of Agricultural Sensors, Ministry of Agriculture and Rural Affairs, Anhui Agricultural University, Hefei, 230036, PR China
| | - Ying Chen
- Department of Applied Chemistry, Key Laboratory of Agricultural Sensors, Ministry of Agriculture and Rural Affairs, Anhui Agricultural University, Hefei, 230036, PR China
| | - Chunxia Song
- Department of Applied Chemistry, Key Laboratory of Agricultural Sensors, Ministry of Agriculture and Rural Affairs, Anhui Agricultural University, Hefei, 230036, PR China
| | - Min Song
- Affiliated Hospital of Anhui Agricultural University, Hefei, 230036, PR China
| | - Hongjuan Jiang
- Affiliated Hospital of Anhui Agricultural University, Hefei, 230036, PR China
| | - Zhaofeng Luo
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, PR China; The Cancer Hospital of the University of Chinese Academy of Sciences, Aptamer Selection Center, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, 310022, PR China
| | - Ying Lu
- Department of Applied Chemistry, Key Laboratory of Agricultural Sensors, Ministry of Agriculture and Rural Affairs, Anhui Agricultural University, Hefei, 230036, PR China.
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Bandawe G, Chitenje M, Bitiliyu-Bangoh J, Kampira E. Approaches to Deployment of Molecular Testing for SARS-CoV-2 in Resource-Limited Settings. Clin Lab Med 2022; 42:283-298. [PMID: 35636827 PMCID: PMC8885302 DOI: 10.1016/j.cll.2022.02.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Deployment of molecular testing for SARS-CoV-2 in resource-limited settings is challenging. Scale-up of molecular had to be conducted with a laboratory system strengthening approach that emphasize laboratory integration. National reference laboratories play a central role. In Malawi the molecular testing was underpinned by existing pathogen control programs for human immunodeficiency virus and tuberculosis that use Abbott and GeneXpert machines and reagents. Despite this, the impact on these programs was well managed. Antigen testing increased access to testing. Pooled testing and direct-to-polymerase chain reaction methods have the potential to save costs and further increase access to molecular tests.
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Affiliation(s)
- Gama Bandawe
- Biological Sciences Department, Academy of Medical Sciences, Malawi University of Science and Technology, P. O. Box 5196, Limbe, Malawi.
| | - Moses Chitenje
- International Teaching and Education Centre for Health (ITECH), PO Box 30369, Capital City Lilongwe 3, Plot 13/14, 1st Floor ARWA House, City Center, Lilongwe, Malawi; Public Health Institute of Malawi, Ministry of Health, Lilongwe, Malawi
| | | | - Elizabeth Kampira
- Centres for Disease Control and Prevention, P. O. Box 30016, NICO House, City Centre, Lilongwe 3, Lilongwe, Malawi
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Cohen Y, Bamberger N, Mor O, Walfisch R, Fleishon S, Varkovitzky I, Younger A, Levi DO, Kohn Y, Steinberg DM, Zeevi D, Erster O, Mendelson E, Livneh Z. Effective bubble-based testing for SARS-CoV-2 using swab-pooling. Clin Microbiol Infect 2022; 28:859-864. [PMID: 35182758 PMCID: PMC8849906 DOI: 10.1016/j.cmi.2022.02.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 02/03/2022] [Accepted: 02/08/2022] [Indexed: 12/15/2022]
Abstract
OBJECTIVES Despite the success in developing COVID-19 vaccines, containment of the disease is obstructed worldwide by vaccine production bottlenecks, logistics hurdles, vaccine refusal, transmission through unvaccinated children, and the appearance of new viral variants. This underscores the need for effective strategies for identifying carriers/patients, which was the main aim of this study. METHODS We present a bubble-based PCR testing approach using swab-pooling into lysis buffer. A bubble is a cluster of people who can be periodically tested for SARS-CoV-2 by swab-pooling. A positive test of a pool mandates quarantining each of its members, who are then individually tested while in isolation to identify the carrier(s) for further epidemiological contact tracing. RESULTS We tested an overall sample of 25 831 individuals, divided into 1273 bubbles, with an average size of 20.3 ± 7.7 swabs/test tube, obtaining for all pools (≤37 swabs/pool) a specificity of 97.5% (lower bound 96.6%) and a sensitivity of 86.3% (lower bound 78.2%) and a post hoc analyzed sensitivity of 94.6% (lower bound 86.7%) and a specificity of 97.2% (lower bound 96.2%) in pools with ≤25 swabs, relative to individual testing. DISCUSSION This approach offers a significant scale-up in sampling and testing throughput and savings in testing cost, without reducing sensitivity or affecting the standard PCR testing laboratory routine. It can be used in school classes, airplanes, hospitals, military units, and workplaces, and may be applicable to future pandemics.
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Affiliation(s)
- Yuval Cohen
- Directorate of Defense Research & Development, Israeli Ministry of Defense, Tel Aviv, Israel
| | - Nadav Bamberger
- Directorate of Defense Research & Development, Israeli Ministry of Defense, Tel Aviv, Israel
| | - Orna Mor
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Tel-Hashomer, Israel; Department of Epidemiology and Preventive Medicine, School of Public Health, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.
| | - Ronen Walfisch
- Directorate of Defense Research & Development, Israeli Ministry of Defense, Tel Aviv, Israel
| | | | - Itay Varkovitzky
- Directorate of Defense Research & Development, Israeli Ministry of Defense, Tel Aviv, Israel
| | | | | | - Yishai Kohn
- Directorate of Defense Research & Development, Israeli Ministry of Defense, Tel Aviv, Israel
| | - David M Steinberg
- Department of Statistics and Operations Research, Tel Aviv University, Tel Aviv, Israel
| | - Danny Zeevi
- Department of Biotechnology, Hadassah Academic College, Jerusalem, Israel
| | - Oran Erster
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Tel-Hashomer, Israel
| | - Ella Mendelson
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Tel-Hashomer, Israel; Department of Epidemiology and Preventive Medicine, School of Public Health, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Zvi Livneh
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel.
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50
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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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