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de Souza LR, da Silva IEP, Celis-Silva G, Raddatz BW, Imamura LM, Kim EYS, Valderrama GV, Riedi HDP, Rogal SR, de Almeida BMM, Figueredo MVM, Bengtson MH, Massirer KB. Improved protocol for Bst polymerase and reverse transcriptase production and application to a point-of-care diagnostics system. Exp Biol Med (Maywood) 2023; 248:1671-1683. [PMID: 38088106 PMCID: PMC10723028 DOI: 10.1177/15353702231215815] [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] [Indexed: 12/17/2023] Open
Abstract
The pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has raised awareness in the scientific community about the importance of being prepared for sanitary emergencies. Many measures implemented during the COVID pandemic are now being expanded to other applications. In the field of molecular and immunological diagnostics, the need to massively test the population worldwide resulted in the application of a variety of methods to detect viral infection. Besides gold standard reverse transcription quantitative polymerase chain reaction (RT-qPCR), the use of reverse transcription loop-mediated isothermal amplification (RT-LAMP) arose as an alternative and sensitive method to amplify and detect viral genetic material. We have used openly available protocols and have improved the protein production of RT-LAMP enzymes Bst polymerase and HIV-reverse transcriptase. To optimize enzyme production, we tested different protein tags, and we shortened the protein purification protocol, resulting in reduced processing time and handling of the enzymes and, thus, preserved the protein activity with high purity. The enzymes showed significant stability at 4 °C and 25 °C, over 60 days, and were highly reliable when used as a one-step RT-LAMP reaction in a portable point-of-care device with clinical samples. The enzymes and the reaction setup can be further expanded to detect other infectious diseases agents.
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Affiliation(s)
- Lucas Rodrigo de Souza
- Center for Molecular Biology and Genetic Engineering (CBMEG), Universidade Estadual de Campinas (UNICAMP), Campinas/SP 13083-875, Brazil
- Center for Medicinal Chemistry (CQMED), Universidade Estadual de Campinas (UNICAMP), Campinas/SP 13083-886, Brazil
| | - Italo Esposti Poly da Silva
- Center for Molecular Biology and Genetic Engineering (CBMEG), Universidade Estadual de Campinas (UNICAMP), Campinas/SP 13083-875, Brazil
- Center for Medicinal Chemistry (CQMED), Universidade Estadual de Campinas (UNICAMP), Campinas/SP 13083-886, Brazil
- Department of Biochemistry and Tissue Biology, Institute of Biology, Universidade Estadual de Campinas (UNICAMP), Campinas/SP 13083-862, Brazil
| | - Gabriele Celis-Silva
- Center for Molecular Biology and Genetic Engineering (CBMEG), Universidade Estadual de Campinas (UNICAMP), Campinas/SP 13083-875, Brazil
- Center for Medicinal Chemistry (CQMED), Universidade Estadual de Campinas (UNICAMP), Campinas/SP 13083-886, Brazil
| | | | | | | | - Gabriel Vieira Valderrama
- Center for Molecular Biology and Genetic Engineering (CBMEG), Universidade Estadual de Campinas (UNICAMP), Campinas/SP 13083-875, Brazil
- Center for Medicinal Chemistry (CQMED), Universidade Estadual de Campinas (UNICAMP), Campinas/SP 13083-886, Brazil
| | | | | | | | | | - Mario Henrique Bengtson
- Center for Medicinal Chemistry (CQMED), Universidade Estadual de Campinas (UNICAMP), Campinas/SP 13083-886, Brazil
- Department of Biochemistry and Tissue Biology, Institute of Biology, Universidade Estadual de Campinas (UNICAMP), Campinas/SP 13083-862, Brazil
| | - Katlin Brauer Massirer
- Center for Molecular Biology and Genetic Engineering (CBMEG), Universidade Estadual de Campinas (UNICAMP), Campinas/SP 13083-875, Brazil
- Center for Medicinal Chemistry (CQMED), Universidade Estadual de Campinas (UNICAMP), Campinas/SP 13083-886, Brazil
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2
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Pena JM, Manning BJ, Li X, Fiore ES, Carlson L, Shytle K, Nguyen PP, Azmi I, Larsen A, Wilson MK, Singh S, DeMeo MC, Ramesh P, Boisvert H, Blake WJ. Real-Time, Multiplexed SHERLOCK for in Vitro Diagnostics. J Mol Diagn 2023; 25:428-437. [PMID: 37088139 PMCID: PMC10122965 DOI: 10.1016/j.jmoldx.2023.03.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 03/08/2023] [Accepted: 03/16/2023] [Indexed: 04/25/2023] Open
Abstract
The pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has highlighted the need for simple, low-cost, and scalable diagnostics that can be widely deployed for rapid testing. Clustered regularly interspaced short palindromic repeats (CRISPR)-based diagnostics have emerged as a promising technology, but its implementation in clinical laboratories has been limited by the requirement of a separate amplification step prior to CRISPR-associated (Cas) enzyme-based detection. This article reports the discovery of two novel Cas12 enzymes (SLK9 and SLK5-2) that exhibit enzymatic activity at 60°C, which, when combined with loop-mediated isothermal amplification (LAMP), enable a real-time, single-step nucleic acid detection method [real-time SHERLOCK (real-time SLK)]. Real-time SLK was demonstrated to provide accurate results comparable to those from real-time quantitative RT-PCR in clinical samples, with 100% positive and 100% negative percent agreement. The method is further demonstrated to be compatible with direct testing (real-time SLK Direct) of samples from anterior nasal swabs, without the need for standard nucleic acid extraction. Lastly, SLK9 was combined with either Alicyclobacillus acidoterrestris AacCas12b or with SLK5-2 to generate a real-time, multiplexed CRISPR-based diagnostic assay for the simultaneous detection of SARS-CoV-2 and a human-based control in a single reaction, with sensitivity down to 5 copies/μL and a time to result of under 30 minutes.
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Affiliation(s)
| | | | - Xiang Li
- Sherlock Biosciences, Watertown, Massachusetts
| | | | | | | | | | - Ishara Azmi
- Sherlock Biosciences, Watertown, Massachusetts
| | - Alex Larsen
- Sherlock Biosciences, Watertown, Massachusetts
| | | | - Subha Singh
- Sherlock Biosciences, Watertown, Massachusetts
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3
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McPhillips L, MacSharry J. Saliva as an alternative specimen to nasopharyngeal swabs for COVID-19 diagnosis: Review. Access Microbiol 2022; 4:acmi000366. [PMID: 36003360 PMCID: PMC9394527 DOI: 10.1099/acmi.0.000366] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 04/25/2022] [Indexed: 12/12/2022] Open
Abstract
Almost 2 years ago, the novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was discovered to be the causative agent of the disease COVID-19. Subsequently, SARS-CoV-2 has spread across the world infecting millions of people, resulting in the ongoing COVID-19 pandemic. The current 'gold standard' for COVID-19 diagnosis involves obtaining a nasopharyngeal swab (NPS) from the patient and testing for the presence of SARS-CoV-2 RNA in the specimen using real-time reverse transcription PCR (RT-qPCR). However, obtaining a NPS specimen is an uncomfortable and invasive procedure for the patient and is limited in its applicability to mass testing. Interest in saliva as an alternative diagnostic specimen is of increasing global research interest due to its malleability to mass testing, greater patient acceptability and overall ease of specimen collection. However, the current literature surrounding the sensitivity of saliva compared to NPS is conflicting. The aim of this review was to analyse the recent literature to assess the viability of saliva in COVID-19 diagnosis. We hypothesize that the discrepancies in the current literature are likely due to the variations in the saliva collection and processing protocols used between studies. The universal adaptation of an optimised protocol could alleviate these discrepancies and see saliva specimens be as sensitive, if not more, than NPS for COVID-19 diagnosis. Whilst saliva specimens are more complimentary to mass-testing, with the possibility of samples being collected from home, the RT-qPCR diagnostic process remains to be the rate-limiting step and therefore interest in salivary rapid antigen tests, which negate the wait-times of RT-qPCR with results available within 15-30 min, may be an answer to this.
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Affiliation(s)
- Leah McPhillips
- School of Microbiology, University College Cork, Cork, Ireland
- Present address: Department of Molecular Microbiology, The John Innes Centre, Norwich, UK
| | - John MacSharry
- School of Microbiology, University College Cork, Cork, Ireland
- School of Medicine, University College Cork, Cork, Ireland
- The APC Microbiome Ireland, University College Cork, Cork, Ireland
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4
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Rapid Same-Day Detection of Listeria monocytogenes, Salmonella spp., and Escherichia coli O157 by Colorimetric LAMP in Dairy Products. FOOD ANAL METHOD 2022. [DOI: 10.1007/s12161-022-02345-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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5
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Effect of thermal and chemical treatments used for SARS-COV-2 inactivation in the measurement of saliva analytes. Sci Rep 2022; 12:9434. [PMID: 35676391 PMCID: PMC9174913 DOI: 10.1038/s41598-022-13491-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 05/17/2022] [Indexed: 11/20/2022] Open
Abstract
The present study aims to assess the effects of thermal and chemical inactivating procedures, that can be used for SARS-CoV-2 inactivation, on different salivary analytes. SDS–Polyacrylamide Gel Electrophoresis (SDS-PAGE) protein profile and a panel of 25 specific biomarkers of oxidative status, stress, metabolism and tissue damage were evaluated in samples subjected to different treatments: thermal (65 °C or 92 °C) and chemical with detergents [sodium dodecyl sulphate (SDS), Triton X-100 or NP-40]. Salivary SDS-PAGE profile was most affected by heating at 92 °C, with three and two protein bands decreasing and increasing their expression levels, respectively. This treatment also affected the results of several enzymes, with some of them being also affected by heating at 65 °C and incubation with SDS. The use of Triton X-100 or NP-40 resulted in increased values of cortisol, triglycerides and glucose, not affecting the other tested biomarkers. The present results will help researchers and clinicians to select the best protocols to work in safe conditions with saliva, taking into account the target analyte planned to be measured.
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6
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Papadakis G, Pantazis AK, Fikas N, Chatziioannidou S, Tsiakalou V, Michaelidou K, Pogka V, Megariti M, Vardaki M, Giarentis K, Heaney J, Nastouli E, Karamitros T, Mentis A, Zafiropoulos A, Sourvinos G, Agelaki S, Gizeli E. Portable real-time colorimetric LAMP-device for rapid quantitative detection of nucleic acids in crude samples. Sci Rep 2022; 12:3775. [PMID: 35260588 PMCID: PMC8904468 DOI: 10.1038/s41598-022-06632-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 01/27/2022] [Indexed: 02/08/2023] Open
Abstract
Loop-mediated isothermal amplification is known for its high sensitivity, specificity and tolerance to inhibiting-substances. In this work, we developed a device for performing real-time colorimetric LAMP combining the accuracy of lab-based quantitative analysis with the simplicity of point-of-care testing. The device innovation lies on the use of a plastic tube anchored vertically on a hot surface while the side walls are exposed to a mini camera able to take snapshots of the colour change in real time during LAMP amplification. Competitive features are the rapid analysis (< 30 min), quantification over 9 log-units, crude sample-compatibility (saliva, tissue, swabs), low detection limit (< 5 copies/reaction), smartphone-operation, fast prototyping (3D-printing) and ability to select the dye of interest (Phenol red, HNB). The device’s clinical utility is demonstrated in cancer mutations-analysis during the detection of 0.01% of BRAF-V600E-to-wild-type molecules from tissue samples and COVID-19 testing with 97% (Ct < 36.8) and 98% (Ct < 30) sensitivity when using extracted RNA and nasopharyngeal-swabs, respectively. The device high technology-readiness-level makes it a suitable platform for performing any colorimetric LAMP assay; moreover, its simple and inexpensive fabrication holds promise for fast deployment and application in global diagnostics.
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Affiliation(s)
- G Papadakis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, 100 N. Plastira Str., 70013, Heraklion, Greece. .,BIOPIX DNA TECHNOLOGY PC, Science and Technology Park of Crete, 100 N. Plastira Str., 70013, Heraklion, Greece.
| | - A K Pantazis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, 100 N. Plastira Str., 70013, Heraklion, Greece.,BIOPIX DNA TECHNOLOGY PC, Science and Technology Park of Crete, 100 N. Plastira Str., 70013, Heraklion, Greece
| | - N Fikas
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, 100 N. Plastira Str., 70013, Heraklion, Greece.,BIOPIX DNA TECHNOLOGY PC, Science and Technology Park of Crete, 100 N. Plastira Str., 70013, Heraklion, Greece
| | - S Chatziioannidou
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, 100 N. Plastira Str., 70013, Heraklion, Greece.,BIOPIX DNA TECHNOLOGY PC, Science and Technology Park of Crete, 100 N. Plastira Str., 70013, Heraklion, Greece.,Department of Biology, University of Crete, 70013, Voutes, Heraklion, Greece
| | - V Tsiakalou
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, 100 N. Plastira Str., 70013, Heraklion, Greece
| | - K Michaelidou
- Laboratory of Translational Oncology, School of Medicine, University of Crete, 71500, Heraklion, Greece
| | - V Pogka
- National SARS-CoV-2 Reference Laboratory, Hellenic Pasteur Institute, 127 Vas. Sofias Ave., 11521, Athens, Greece
| | - M Megariti
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, 100 N. Plastira Str., 70013, Heraklion, Greece
| | - M Vardaki
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, 100 N. Plastira Str., 70013, Heraklion, Greece.,Department of Biology, University of Crete, 70013, Voutes, Heraklion, Greece
| | - K Giarentis
- Department of Biology, University of Crete, 70013, Voutes, Heraklion, Greece
| | - J Heaney
- Advanced Pathogens Diagnostics Unit, University College London Hospitals NHS Trust, London, WC1H 9AX, UK.,UCL Great Ormond Street Institute of Child Health, London, UK
| | - E Nastouli
- Advanced Pathogens Diagnostics Unit, University College London Hospitals NHS Trust, London, WC1H 9AX, UK.,UCL Great Ormond Street Institute of Child Health, London, UK
| | - T Karamitros
- National SARS-CoV-2 Reference Laboratory, Hellenic Pasteur Institute, 127 Vas. Sofias Ave., 11521, Athens, Greece
| | - A Mentis
- National SARS-CoV-2 Reference Laboratory, Hellenic Pasteur Institute, 127 Vas. Sofias Ave., 11521, Athens, Greece
| | - A Zafiropoulos
- Laboratory of Clinical Virology, School of Medicine, University of Crete, 71500, Heraklion, Greece
| | - G Sourvinos
- Laboratory of Clinical Virology, School of Medicine, University of Crete, 71500, Heraklion, Greece
| | - S Agelaki
- Department of Biology, University of Crete, 70013, Voutes, Heraklion, Greece.,Department of Medical Oncology, University General Hospital, 71110, Heraklion, Greece
| | - E Gizeli
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, 100 N. Plastira Str., 70013, Heraklion, Greece. .,Department of Biology, University of Crete, 70013, Voutes, Heraklion, Greece.
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7
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Viana LG, Lebkuchen A, Schuch RA, Okai GG, Salgueiro JS, Cardozo KHM, Carvalho VM. Mass Spectrometry Multiplexed Detection of SARS-CoV-2. Methods Mol Biol 2022; 2511:161-174. [PMID: 35838959 DOI: 10.1007/978-1-0716-2395-4_12] [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] [Indexed: 06/15/2023]
Abstract
Testing of large populations for virus infection is now a reality worldwide due to the coronavirus (SARS-CoV-2) pandemic. The demand for SARS-CoV-2 testing using alternatives other than PCR led to the development of mass spectrometry (MS)-based assays. However, MS for SARS-CoV-2 large-scale testing have some downsides, including complex sample preparation and slow data analysis. Here, we describe a high-throughput targeted proteomics method to detect SARS-CoV-2 directly from nasopharyngeal and oropharyngeal swabs. This strategy employs fully automated sample preparation mediated by magnetic particles, followed by detection of SARS-CoV-2 nucleoprotein peptides by turbulent flow chromatography coupled with tandem mass spectrometry.
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Affiliation(s)
| | - Adriana Lebkuchen
- Division of Research and Development, Fleury Group, São Paulo, SP, Brazil
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8
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Lai MY, Bukhari FDM, Zulkefli NZ, Ismail I, Mustapa NI, Soh TST, Hassan AH, Peariasamy KM, Lee YL, Suppiah J, Thayan R, Lau YL. Two extraction-free reverse transcription loop-mediated isothermal amplification assays for detection of SARS-CoV-2. BMC Infect Dis 2021; 21:1162. [PMID: 34789179 PMCID: PMC8595270 DOI: 10.1186/s12879-021-06876-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 11/10/2021] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Current assays for detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) rely on time consuming, costly and laboratory based methods for virus isolation, purification and removing inhibitors. To address this limitation, we propose a simple method for testing RNA from nasopharyngeal swab samples that bypasses the RNA purification step. METHODS In the current project, we have described two extraction-free reverse transcription loop-mediated isothermal amplification (RT-LAMP) assays for the detection of SARS-CoV-2 by using E gene and RdRp gene as the targets. RESULTS Here, results showed that reverse transcription loop-mediated isothermal amplification assays with 88.4% sensitive (95% CI: 74.9-96.1%) and 67.4% sensitive (95% CI: 51.5-80.9%) for E gene and RdRp gene, respectively. CONCLUSION Without the need of RNA purification, our developed RT-LAMP assays for direct detection of SARS-CoV-2 from nasopharyngeal swab samples could be turned into alternatives to qRT-PCR for rapid screening.
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Affiliation(s)
- Meng Yee Lai
- Department of Parasitology, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Fatma Diyana Mohd Bukhari
- Department of Parasitology, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Nur Zulaikha Zulkefli
- Department of Parasitology, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Ilyiana Ismail
- Department of Pathology, Hospital Sungai Buloh, Ministry of Health, Kuala Lumpur, Malaysia
| | - Nur Izati Mustapa
- Department of Pathology, Hospital Sungai Buloh, Ministry of Health, Kuala Lumpur, Malaysia
| | - Tuan Suhaila Tuan Soh
- Department of Pathology, Hospital Sungai Buloh, Ministry of Health, Kuala Lumpur, Malaysia
| | - Afifah Haji Hassan
- Department of Pathology, Hospital Sungai Buloh, Ministry of Health, Kuala Lumpur, Malaysia
| | - Kalaiarasu M Peariasamy
- Institute for Clinical Research, National Institutes of Health, Ministry of Health, Kuala Lumpur, Malaysia
| | - Yee Leng Lee
- Clinical Research Centre, Hospital Sungai Buloh, Ministry of Health, Kuala Lumpur, Malaysia
| | - Jeyanthi Suppiah
- Virology Unit, Infectious Disease Research Centre, Institute for Medical Research, National Institutes of Health, Ministry of Health, Kuala Lumpur, Malaysia
| | - Ravindran Thayan
- Virology Unit, Infectious Disease Research Centre, Institute for Medical Research, National Institutes of Health, Ministry of Health, Kuala Lumpur, Malaysia
| | - Yee Ling Lau
- Department of Parasitology, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia.
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9
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SARS-CoV-2 detection using reverse transcription strand invasion based amplification and a portable compact size instrument. Sci Rep 2021; 11:22214. [PMID: 34782681 PMCID: PMC8593107 DOI: 10.1038/s41598-021-01744-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 11/03/2021] [Indexed: 12/26/2022] Open
Abstract
Rapid nucleic-acid based tests that can be performed by non-professionals outside laboratory settings could help the containment of the pandemic SARS-CoV-2 virus and may potentially prevent further widespread lockdowns. Here, we present a novel compact portable detection instrument (the Egoo Health System) for extraction-free detection of SARS-CoV-2 using isothermal reverse transcription strand invasion based amplification (RT-SIBA). The SARS-CoV-2 RT-SIBA assay can be performed directly on crude oropharyngeal swabs without nucleic acid extraction with a reaction time of 30 min. The Egoo Health system uses a capsule system, which is automatically sealed tight in the Egoo instrument after applying the sample, resulting in a closed system optimal for molecular isothermal amplification. The performance of the Egoo Health System is comparable to the PCR instrument with an analytical sensitivity of 25 viral RNA copies per SARS-CoV-2 RT-SIBA reaction and a clinical sensitivity and specificity between 87.0–98.4% and 96.6–98.2% respectively.
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10
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Yusuf L, Appeaning M, Amole TG, Musa BM, Galadanci HS, Quashie PK, Aliyu IA. Rapid, Cheap, and Effective COVID-19 Diagnostics for Africa. Diagnostics (Basel) 2021; 11:diagnostics11112105. [PMID: 34829451 PMCID: PMC8625903 DOI: 10.3390/diagnostics11112105] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 09/27/2021] [Accepted: 10/13/2021] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Although comprehensive public health measures such as mass quarantine have been taken internationally, this has generally been ineffective, leading to a high infection and mortality rate. Despite the fact that the COVID-19 pandemic has been downgraded to epidemic status in many countries, the real number of infections is unknown, particularly in low-income countries. However, precision shielding is used in COVID-19 management, and requires estimates of mass infection in key groups. As a result, rapid tests for the virus could be a useful screening tool for asymptomatic virus shedders who are about to come into contact with sensitive groups. In Africa and other low- and middle-income countries there is high rate of COVID-19 under-diagnosis, due to the high cost of molecular assays. Exploring alternate assays to the reverse transcriptase polymerase chain reaction (RT-PCR) for COVID-19 diagnosis is highly warranted. AIM This review explored the feasibility of using alternate molecular, rapid antigen, and serological diagnostic assays to accurately and precisely diagnose COVID-19 in African populations, and to mitigate severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RT-PCR diagnostic challenges in Africa. METHOD We reviewed publications from internet sources and searched for appropriate documents available in English. This included Medline, Google Scholar, and Ajol. We included primary literature and some review articles that presented knowledge on the current trends on SARS-CoV-2 diagnostics in Africa and globally. RESULTS Based on our analysis, we highlight the utility of four different alternatives to RT-PCR. These include two isothermal nucleic acid amplification assays (loop-mediated isothermal amplification (LAMP) and recombinase polymerase amplification (RPA)), rapid antigen testing, and antibody testing for tackling difficulties posed by SARS-CoV-2 RT-PCR testing in Africa. CONCLUSION The economic burden associated COVID-19 mass testing by RT-PCR will be difficult for low-income nations to meet. We provide evidence for the utility and deployment of these alternate testing methods in Africa and other LMICs.
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Affiliation(s)
- Lukman Yusuf
- Department of Medical Laboratory Science, College of Health Sciences, Bayero University Kano, Kano 700233, Nigeria;
| | - Mark Appeaning
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), College of Basic and Applied Sciences, University of Ghana, P.O. Box LG54, Legon, Accra 23321, Ghana;
- Department of Medical Laboratory Science, Faculty of Health and Allied Sciences, Koforidua Technical University, P.O. Box KF981, Koforidua 03420, Ghana
| | - Taiwo Gboluwaga Amole
- Africa Center of Excellence for Population Health and Policy, Bayero University Kano (ACEPHAP), Kano 700233, Nigeria; (T.G.A.); (B.M.M.); (H.S.G.)
- Department of Community Medicine, Bayero University Kano, Aminu Kano Teaching Hospital, Kano 700233, Nigeria
| | - Baba Maiyaki Musa
- Africa Center of Excellence for Population Health and Policy, Bayero University Kano (ACEPHAP), Kano 700233, Nigeria; (T.G.A.); (B.M.M.); (H.S.G.)
- Department of Medicine, College of Health Sciences, Bayero University Kano, Aminu Kano Teaching Hospital, Kano 700233, Nigeria
| | - Hadiza Shehu Galadanci
- Africa Center of Excellence for Population Health and Policy, Bayero University Kano (ACEPHAP), Kano 700233, Nigeria; (T.G.A.); (B.M.M.); (H.S.G.)
- Department of Gynecology and Obstetrics, College of Health Sciences, Bayero University Kano, Kano 700233, Nigeria
| | - Peter Kojo Quashie
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), College of Basic and Applied Sciences, University of Ghana, P.O. Box LG54, Legon, Accra 23321, Ghana;
- Correspondence: (P.K.Q.); (I.A.A.)
| | - Isah Abubakar Aliyu
- Department of Medical Laboratory Science, College of Health Sciences, Bayero University Kano, Kano 700233, Nigeria;
- Africa Center of Excellence for Population Health and Policy, Bayero University Kano (ACEPHAP), Kano 700233, Nigeria; (T.G.A.); (B.M.M.); (H.S.G.)
- Correspondence: (P.K.Q.); (I.A.A.)
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11
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A semi-automated, isolation-free, high-throughput SARS-CoV-2 reverse transcriptase (RT) loop-mediated isothermal amplification (LAMP) test. Sci Rep 2021; 11:21385. [PMID: 34725400 PMCID: PMC8560768 DOI: 10.1038/s41598-021-00827-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 10/12/2021] [Indexed: 12/15/2022] Open
Abstract
Shortages of reverse transcriptase (RT)-polymerase chain reaction (PCR) reagents and related equipment during the COVID-19 pandemic have demonstrated the need for alternative, high-throughput methods for severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2)-mass screening in clinical diagnostic laboratories. A robust, SARS-CoV-2 RT-loop-mediated isothermal amplification (RT-LAMP) assay with high-throughput and short turnaround times in a clinical laboratory setting was established and compared to two conventional RT-PCR protocols using 323 samples of individuals with suspected SARS-CoV-2 infection. Limit of detection (LoD) and reproducibility of the isolation-free SARS-CoV-2 RT-LAMP test were determined. An almost perfect agreement (Cohen's kappa > 0.8) between the novel test and two classical RT-PCR protocols with no systematic difference (McNemar's test, P > 0.05) was observed. Sensitivity and specificity were in the range of 89.5 to 100% and 96.2 to 100% dependent on the reaction condition and the RT-PCR method used as reference. The isolation-free RT-LAMP assay showed high reproducibility (Tt intra-run coefficient of variation [CV] = 0.4%, Tt inter-run CV = 2.1%) with a LoD of 95 SARS-CoV-2 genome copies per reaction. The established SARS-CoV-2 RT-LAMP assay is a flexible and efficient alternative to conventional RT-PCR protocols, suitable for SARS-CoV-2 mass screening using existing laboratory infrastructure in clinical diagnostic laboratories.
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12
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Brown TA, Schaefer KS, Tsang A, Yi HA, Grimm JB, Lemire AL, Jradi FM, Kim C, McGowan K, Ritola K, Armstrong DT, Mostafa HH, Korff W, Vale RD, Lavis LD. Direct detection of SARS-CoV-2 RNA using high-contrast pH-sensitive dyes. J Biomol Tech 2021; 32:121-133. [PMID: 35027870 PMCID: PMC8730524 DOI: 10.7171/jbt.21-3203-007] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
The worldwide coronavirus disease 2019 pandemic has had devastating effects on health, healthcare infrastructure, social structure, and economics. One of the limiting factors in containing the spread of this virus has been the lack of widespread availability of fast, inexpensive, and reliable methods for testing of individuals. Frequent screening for infected and often asymptomatic people is a cornerstone of pandemic management plans. Here, we introduce 2 pH-sensitive "LAMPshade" dyes as novel readouts in an isothermal Reverse Transcriptase Loop-mediated isothermal AMPlification amplification assay for severe acute respiratory syndrome coronavirus 2 RNA. The resulting JaneliaLAMP assay is robust, simple, inexpensive, and has low technical requirements, and we describe its use and performance in direct testing of contrived and clinical samples without RNA extraction.
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Affiliation(s)
- Timothy A. Brown
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147
| | | | - Arthur Tsang
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147
| | - Hyun Ah Yi
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147
| | - Jonathan B. Grimm
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147
| | - Andrew L. Lemire
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147
| | - Fadi M. Jradi
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147
| | - Charles Kim
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147
| | - Kevin McGowan
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147
| | - Kimberly Ritola
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147
| | - Derek T. Armstrong
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287-7093
| | - Heba H. Mostafa
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287-7093
| | - Wyatt Korff
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147
| | - Ronald D. Vale
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147
| | - Luke D. Lavis
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147
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13
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Lin Q, Fang X, Chen H, Weng W, Liu B, Kong J. Dual-modality loop-mediated isothermal amplification for pretreatment-free detection of Septin9 methylated DNA in colorectal cancer. Mikrochim Acta 2021; 188:307. [PMID: 34453211 PMCID: PMC8396143 DOI: 10.1007/s00604-021-04979-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 08/07/2021] [Indexed: 12/25/2022]
Abstract
Currently, the determination of DNA methylation is still a challenge due to the limited efficiency of enrichment, bisulfite modification, and detection. In this study, a dual-modality loop-mediated isothermal amplification integrated with magnetic bead isolation is proposed for the determination of methylated Septin9 gene in colorectal cancer. Magnetic beads modified with anti-methyl cytosine antibody were prepared for fast enrichment of methylated DNA through specific immunoaffinity (30 min). One-pot real-time fluorescence and colorimetric loop-mediated isothermal amplification were simultaneously developed for detecting methylated Septin9 gene (60 min). The real-time fluorescence generating by SYTO-9 dye (excitation: 470 nm and emission: 525 nm) and pH indicator (neutral red) was used for quantitative and visualized detection of methylated DNA. This method was demonstrated to detect methylated DNA from HCT 116 cells ranging from 2 to 0.02 ng/μL with a limit of detection of 0.02 ± 0.002 ng/μL (RSD: 9.75%). This method also could discriminate methylated Septin9 in 0.1% HCT 116 cells (RSD: 6.60%), suggesting its high specificity and sensitivity. The feasibility of this assay was further evaluated by clinical plasma samples from 20 colorectal cancer patients and 20 healthy controls, which shows the potential application in simple, low cost, quantitative, and visualized detection of methylated nucleic acids.
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Affiliation(s)
- Qiuyuan Lin
- Department of Chemistry, Fudan University, Shanghai, 200438, People's Republic of China
| | - Xueen Fang
- Department of Chemistry, Fudan University, Shanghai, 200438, People's Republic of China
| | - Hui Chen
- Department of Chemistry, Fudan University, Shanghai, 200438, People's Republic of China.
| | - Wenhao Weng
- Department of Clinical Laboratory, Yangpu Hospital, Tongji University School of Medicine, Shanghai, 200090, China.
| | - Baohong Liu
- Department of Chemistry, Fudan University, Shanghai, 200438, People's Republic of China
- Shanghai Stomatological Hospital, Shanghai, 200438, People's Republic of China
| | - Jilie Kong
- Department of Chemistry, Fudan University, Shanghai, 200438, People's Republic of China.
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14
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Amaral C, Antunes W, Moe E, Duarte AG, Lima LMP, Santos C, Gomes IL, Afonso GS, Vieira R, Teles HSS, Reis MS, da Silva MAR, Henriques AM, Fevereiro M, Ventura MR, Serrano M, Pimentel C. A molecular test based on RT-LAMP for rapid, sensitive and inexpensive colorimetric detection of SARS-CoV-2 in clinical samples. Sci Rep 2021; 11:16430. [PMID: 34385527 PMCID: PMC8361189 DOI: 10.1038/s41598-021-95799-6] [Citation(s) in RCA: 79] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 07/23/2021] [Indexed: 12/26/2022] Open
Abstract
Until there is an effective implementation of COVID-19 vaccination program, a robust testing strategy, along with prevention measures, will continue to be the most viable way to control disease spread. Such a strategy should rely on disparate diagnostic tests to prevent a slowdown in testing due to lack of materials and reagents imposed by supply chain problems, which happened at the beginning of the pandemic. In this study, we have established a single-tube test based on RT-LAMP that enables the visual detection of less than 100 viral genome copies of SARS-CoV-2 within 30 min. We benchmarked the assay against the gold standard test for COVID-19 diagnosis, RT-PCR, using 177 nasopharyngeal RNA samples. For viral loads above 100 copies, the RT-LAMP assay had a sensitivity of 100% and a specificity of 96.1%. Additionally, we set up a RNA extraction-free RT-LAMP test capable of detecting SARS-CoV-2 directly from saliva samples, albeit with lower sensitivity. The saliva was self-collected and the collection tube remained closed until inactivation, thereby ensuring the protection of the testing personnel. As expected, RNA extraction from saliva samples increased the sensitivity of the test. To lower the costs associated with RNA extraction, we performed this step using an alternative protocol that uses plasmid DNA extraction columns. We also produced the enzymes needed for the assay and established an in-house-made RT-LAMP test independent of specific distribution channels. Finally, we developed a new colorimetric method that allowed the detection of LAMP products by the visualization of an evident color shift, regardless of the reaction pH.
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Affiliation(s)
- Catarina Amaral
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. República, 2780-157, Oeiras, Portugal
| | - Wilson Antunes
- Centro de Investigação da Academia Militar (CINAMIL), Unidade Militar Laboratorial de Defesa Biológica e Química (UMLDBQ), Av. Dr. Alfredo Bensaúde, 1849-012, Lisbon, Portugal
| | - Elin Moe
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. República, 2780-157, Oeiras, Portugal
| | - Américo G Duarte
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. República, 2780-157, Oeiras, Portugal
| | - Luís M P Lima
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. República, 2780-157, Oeiras, Portugal
| | - Cristiana Santos
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. República, 2780-157, Oeiras, Portugal
| | - Inês L Gomes
- Centro de Investigação da Academia Militar (CINAMIL), Unidade Militar Laboratorial de Defesa Biológica e Química (UMLDBQ), Av. Dr. Alfredo Bensaúde, 1849-012, Lisbon, Portugal
| | - Gonçalo S Afonso
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. República, 2780-157, Oeiras, Portugal
| | - Ricardo Vieira
- Centro de Investigação da Academia Militar (CINAMIL), Unidade Militar Laboratorial de Defesa Biológica e Química (UMLDBQ), Av. Dr. Alfredo Bensaúde, 1849-012, Lisbon, Portugal
| | - Helena Sofia S Teles
- Centro de Medicina Naval-Marinha Portuguesa, Alfeite, 2810-001, Almada, Portugal
| | - Marisa S Reis
- Centro de Medicina Naval-Marinha Portuguesa, Alfeite, 2810-001, Almada, Portugal
| | | | - Ana Margarida Henriques
- Instituto Nacional de Investigação Agrária e Veterinária, I.P., Laboratório de Virologia, Av. República, Quinta do Marquês, 2780-157, Oeiras, Portugal
| | - Miguel Fevereiro
- Instituto Nacional de Investigação Agrária e Veterinária, I.P., Laboratório de Virologia, Av. República, Quinta do Marquês, 2780-157, Oeiras, Portugal
| | - M Rita Ventura
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. República, 2780-157, Oeiras, Portugal
| | - Mónica Serrano
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. República, 2780-157, Oeiras, Portugal.
| | - Catarina Pimentel
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. República, 2780-157, Oeiras, Portugal.
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15
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Colorimetric RT-LAMP SARS-CoV-2 diagnostic sensitivity relies on color interpretation and viral load. Sci Rep 2021; 11:9026. [PMID: 33907239 PMCID: PMC8079700 DOI: 10.1038/s41598-021-88506-y] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Accepted: 04/06/2021] [Indexed: 12/23/2022] Open
Abstract
The use of RT-LAMP (reverse transcriptase—loop mediated isothermal amplification) has been considered as a promising point-of-care method to diagnose COVID-19. In this manuscript we show that the RT-LAMP reaction has a sensitivity of only 200 RNA virus copies, with a color change from pink to yellow occurring in 100% of the 62 clinical samples tested positive by RT-qPCR. We also demonstrated that this reaction is 100% specific for SARS-CoV-2 after testing 57 clinical samples infected with dozens of different respiratory viruses and 74 individuals without any viral infection. Although the majority of manuscripts recently published using this technique describe only the presence of two-color states (pink = negative and yellow = positive), we verified by naked-eye and absorbance measurements that there is an evident third color cluster (orange), in general related to positive samples with low viral loads, but which cannot be defined as positive or negative by the naked eye. Orange colors should be repeated or tested by RT-qPCR to avoid a false diagnostic. RT-LAMP is therefore very reliable for samples with a RT-qPCR Ct < 30 being as sensitive and specific as a RT-qPCR test. All reactions were performed in 30 min at 65 °C. The use of reaction time longer than 30 min is also not recommended since nonspecific amplifications may cause false positives.
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16
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Yang Q, Meyerson NR, Clark SK, Paige CL, Fattor WT, Gilchrist AR, Barbachano-Guerrero A, Healy BG, Worden-Sapper ER, Wu SS, Muhlrad D, Decker CJ, Saldi TK, Lasda E, Gonzales P, Fink MR, Tat KL, Hager CR, Davis JC, Ozeroff CD, Brisson GR, McQueen MB, Leinwand LA, Parker R, Sawyer SL. Saliva TwoStep for rapid detection of asymptomatic SARS-CoV-2 carriers. eLife 2021; 10:e65113. [PMID: 33779548 PMCID: PMC8057811 DOI: 10.7554/elife.65113] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 03/26/2021] [Indexed: 01/01/2023] Open
Abstract
Here, we develop a simple molecular test for SARS-CoV-2 in saliva based on reverse transcription loop-mediated isothermal amplification. The test has two steps: (1) heat saliva with a stabilization solution and (2) detect virus by incubating with a primer/enzyme mix. After incubation, saliva samples containing the SARS-CoV-2 genome turn bright yellow. Because this test is pH dependent, it can react falsely to some naturally acidic saliva samples. We report unique saliva stabilization protocols that rendered 295 healthy saliva samples compatible with the test, producing zero false positives. We also evaluated the test on 278 saliva samples from individuals who were infected with SARS-CoV-2 but had no symptoms at the time of saliva collection, and from 54 matched pairs of saliva and anterior nasal samples from infected individuals. The Saliva TwoStep test described herein identified infections with 94% sensitivity and >99% specificity in individuals with sub-clinical (asymptomatic or pre-symptomatic) infections.
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Affiliation(s)
- Qing Yang
- BioFrontiers Institute, University of Colorado BoulderBoulderUnited States
- Department of Molecular, Cellular and Developmental Biology, University of Colorado BoulderBoulderUnited States
| | - Nicholas R Meyerson
- BioFrontiers Institute, University of Colorado BoulderBoulderUnited States
- Darwin Biosciences IncBoulderUnited States
| | - Stephen K Clark
- BioFrontiers Institute, University of Colorado BoulderBoulderUnited States
- Darwin Biosciences IncBoulderUnited States
| | - Camille L Paige
- BioFrontiers Institute, University of Colorado BoulderBoulderUnited States
| | - Will T Fattor
- BioFrontiers Institute, University of Colorado BoulderBoulderUnited States
| | - Alison R Gilchrist
- BioFrontiers Institute, University of Colorado BoulderBoulderUnited States
- Department of Molecular, Cellular and Developmental Biology, University of Colorado BoulderBoulderUnited States
| | | | - Benjamin G Healy
- Department of Mechanical Engineering, University of Colorado BoulderBoulderUnited States
| | - Emma R Worden-Sapper
- BioFrontiers Institute, University of Colorado BoulderBoulderUnited States
- Department of Molecular, Cellular and Developmental Biology, University of Colorado BoulderBoulderUnited States
| | - Sharon S Wu
- BioFrontiers Institute, University of Colorado BoulderBoulderUnited States
- Department of Molecular, Cellular and Developmental Biology, University of Colorado BoulderBoulderUnited States
- Interdisciplinary Quantitative Biology Graduate Program, University of Colorado BoulderBoulderUnited States
| | - Denise Muhlrad
- Department of Biochemistry, University of Colorado BoulderBoulderUnited States
- Howard Hughes Medical Institute, University of Colorado BoulderBoulderUnited States
| | - Carolyn J Decker
- Department of Biochemistry, University of Colorado BoulderBoulderUnited States
- Howard Hughes Medical Institute, University of Colorado BoulderBoulderUnited States
| | - Tassa K Saldi
- BioFrontiers Institute, University of Colorado BoulderBoulderUnited States
| | - Erika Lasda
- BioFrontiers Institute, University of Colorado BoulderBoulderUnited States
| | - Patrick Gonzales
- BioFrontiers Institute, University of Colorado BoulderBoulderUnited States
- Department of Integrative Physiology, University of Colorado BoulderBoulderUnited States
| | - Morgan R Fink
- BioFrontiers Institute, University of Colorado BoulderBoulderUnited States
| | - Kimngan L Tat
- BioFrontiers Institute, University of Colorado BoulderBoulderUnited States
| | - Cole R Hager
- BioFrontiers Institute, University of Colorado BoulderBoulderUnited States
| | - Jack C Davis
- Department of Molecular, Cellular and Developmental Biology, University of Colorado BoulderBoulderUnited States
| | | | - Gloria R Brisson
- Wardenburg Health Center, University of Colorado BoulderBoulderUnited States
| | - Matthew B McQueen
- Department of Integrative Physiology, University of Colorado BoulderBoulderUnited States
| | - Leslie A Leinwand
- BioFrontiers Institute, University of Colorado BoulderBoulderUnited States
- Department of Molecular, Cellular and Developmental Biology, University of Colorado BoulderBoulderUnited States
| | - Roy Parker
- BioFrontiers Institute, University of Colorado BoulderBoulderUnited States
- Department of Molecular, Cellular and Developmental Biology, University of Colorado BoulderBoulderUnited States
- Department of Biochemistry, University of Colorado BoulderBoulderUnited States
- Howard Hughes Medical Institute, University of Colorado BoulderBoulderUnited States
| | - Sara L Sawyer
- BioFrontiers Institute, University of Colorado BoulderBoulderUnited States
- Department of Molecular, Cellular and Developmental Biology, University of Colorado BoulderBoulderUnited States
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17
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Dinnes J, Deeks JJ, Berhane S, Taylor M, Adriano A, Davenport C, Dittrich S, Emperador D, Takwoingi Y, Cunningham J, Beese S, Domen J, Dretzke J, Ferrante di Ruffano L, Harris IM, Price MJ, Taylor-Phillips S, Hooft L, Leeflang MM, McInnes MD, Spijker R, Van den Bruel A. Rapid, point-of-care antigen and molecular-based tests for diagnosis of SARS-CoV-2 infection. Cochrane Database Syst Rev 2021; 3:CD013705. [PMID: 33760236 PMCID: PMC8078597 DOI: 10.1002/14651858.cd013705.pub2] [Citation(s) in RCA: 298] [Impact Index Per Article: 99.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
BACKGROUND Accurate rapid diagnostic tests for SARS-CoV-2 infection could contribute to clinical and public health strategies to manage the COVID-19 pandemic. Point-of-care antigen and molecular tests to detect current infection could increase access to testing and early confirmation of cases, and expediate clinical and public health management decisions that may reduce transmission. OBJECTIVES To assess the diagnostic accuracy of point-of-care antigen and molecular-based tests for diagnosis of SARS-CoV-2 infection. We consider accuracy separately in symptomatic and asymptomatic population groups. SEARCH METHODS Electronic searches of the Cochrane COVID-19 Study Register and the COVID-19 Living Evidence Database from the University of Bern (which includes daily updates from PubMed and Embase and preprints from medRxiv and bioRxiv) were undertaken on 30 Sept 2020. We checked repositories of COVID-19 publications and included independent evaluations from national reference laboratories, the Foundation for Innovative New Diagnostics and the Diagnostics Global Health website to 16 Nov 2020. We did not apply language restrictions. SELECTION CRITERIA We included studies of people with either suspected SARS-CoV-2 infection, known SARS-CoV-2 infection or known absence of infection, or those who were being screened for infection. We included test accuracy studies of any design that evaluated commercially produced, rapid antigen or molecular tests suitable for a point-of-care setting (minimal equipment, sample preparation, and biosafety requirements, with results within two hours of sample collection). We included all reference standards that define the presence or absence of SARS-CoV-2 (including reverse transcription polymerase chain reaction (RT-PCR) tests and established diagnostic criteria). DATA COLLECTION AND ANALYSIS Studies were screened independently in duplicate with disagreements resolved by discussion with a third author. Study characteristics were extracted by one author and checked by a second; extraction of study results and assessments of risk of bias and applicability (made using the QUADAS-2 tool) were undertaken independently in duplicate. We present sensitivity and specificity with 95% confidence intervals (CIs) for each test and pooled data using the bivariate model separately for antigen and molecular-based tests. We tabulated results by test manufacturer and compliance with manufacturer instructions for use and according to symptom status. MAIN RESULTS Seventy-eight study cohorts were included (described in 64 study reports, including 20 pre-prints), reporting results for 24,087 samples (7,415 with confirmed SARS-CoV-2). Studies were mainly from Europe (n = 39) or North America (n = 20), and evaluated 16 antigen and five molecular assays. We considered risk of bias to be high in 29 (50%) studies because of participant selection; in 66 (85%) because of weaknesses in the reference standard for absence of infection; and in 29 (45%) for participant flow and timing. Studies of antigen tests were of a higher methodological quality compared to studies of molecular tests, particularly regarding the risk of bias for participant selection and the index test. Characteristics of participants in 35 (45%) studies differed from those in whom the test was intended to be used and the delivery of the index test in 39 (50%) studies differed from the way in which the test was intended to be used. Nearly all studies (97%) defined the presence or absence of SARS-CoV-2 based on a single RT-PCR result, and none included participants meeting case definitions for probable COVID-19. Antigen tests Forty-eight studies reported 58 evaluations of antigen tests. Estimates of sensitivity varied considerably between studies. There were differences between symptomatic (72.0%, 95% CI 63.7% to 79.0%; 37 evaluations; 15530 samples, 4410 cases) and asymptomatic participants (58.1%, 95% CI 40.2% to 74.1%; 12 evaluations; 1581 samples, 295 cases). Average sensitivity was higher in the first week after symptom onset (78.3%, 95% CI 71.1% to 84.1%; 26 evaluations; 5769 samples, 2320 cases) than in the second week of symptoms (51.0%, 95% CI 40.8% to 61.0%; 22 evaluations; 935 samples, 692 cases). Sensitivity was high in those with cycle threshold (Ct) values on PCR ≤25 (94.5%, 95% CI 91.0% to 96.7%; 36 evaluations; 2613 cases) compared to those with Ct values >25 (40.7%, 95% CI 31.8% to 50.3%; 36 evaluations; 2632 cases). Sensitivity varied between brands. Using data from instructions for use (IFU) compliant evaluations in symptomatic participants, summary sensitivities ranged from 34.1% (95% CI 29.7% to 38.8%; Coris Bioconcept) to 88.1% (95% CI 84.2% to 91.1%; SD Biosensor STANDARD Q). Average specificities were high in symptomatic and asymptomatic participants, and for most brands (overall summary specificity 99.6%, 95% CI 99.0% to 99.8%). At 5% prevalence using data for the most sensitive assays in symptomatic people (SD Biosensor STANDARD Q and Abbott Panbio), positive predictive values (PPVs) of 84% to 90% mean that between 1 in 10 and 1 in 6 positive results will be a false positive, and between 1 in 4 and 1 in 8 cases will be missed. At 0.5% prevalence applying the same tests in asymptomatic people would result in PPVs of 11% to 28% meaning that between 7 in 10 and 9 in 10 positive results will be false positives, and between 1 in 2 and 1 in 3 cases will be missed. No studies assessed the accuracy of repeated lateral flow testing or self-testing. Rapid molecular assays Thirty studies reported 33 evaluations of five different rapid molecular tests. Sensitivities varied according to test brand. Most of the data relate to the ID NOW and Xpert Xpress assays. Using data from evaluations following the manufacturer's instructions for use, the average sensitivity of ID NOW was 73.0% (95% CI 66.8% to 78.4%) and average specificity 99.7% (95% CI 98.7% to 99.9%; 4 evaluations; 812 samples, 222 cases). For Xpert Xpress, the average sensitivity was 100% (95% CI 88.1% to 100%) and average specificity 97.2% (95% CI 89.4% to 99.3%; 2 evaluations; 100 samples, 29 cases). Insufficient data were available to investigate the effect of symptom status or time after symptom onset. AUTHORS' CONCLUSIONS Antigen tests vary in sensitivity. In people with signs and symptoms of COVID-19, sensitivities are highest in the first week of illness when viral loads are higher. The assays shown to meet appropriate criteria, such as WHO's priority target product profiles for COVID-19 diagnostics ('acceptable' sensitivity ≥ 80% and specificity ≥ 97%), can be considered as a replacement for laboratory-based RT-PCR when immediate decisions about patient care must be made, or where RT-PCR cannot be delivered in a timely manner. Positive predictive values suggest that confirmatory testing of those with positive results may be considered in low prevalence settings. Due to the variable sensitivity of antigen tests, people who test negative may still be infected. Evidence for testing in asymptomatic cohorts was limited. Test accuracy studies cannot adequately assess the ability of antigen tests to differentiate those who are infectious and require isolation from those who pose no risk, as there is no reference standard for infectiousness. A small number of molecular tests showed high accuracy and may be suitable alternatives to RT-PCR. However, further evaluations of the tests in settings as they are intended to be used are required to fully establish performance in practice. Several important studies in asymptomatic individuals have been reported since the close of our search and will be incorporated at the next update of this review. Comparative studies of antigen tests in their intended use settings and according to test operator (including self-testing) are required.
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Affiliation(s)
- Jacqueline Dinnes
- Test Evaluation Research Group, Institute of Applied Health Research, University of Birmingham, Birmingham , UK
- NIHR Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust and University of Birmingham, Birmingham, UK
| | - Jonathan J Deeks
- NIHR Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust and University of Birmingham, Birmingham, UK
- Test Evaluation Research Group, Institute of Applied Health Research, University of Birmingham, Birmingham, UK
| | - Sarah Berhane
- NIHR Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust and University of Birmingham, Birmingham, UK
| | - Melissa Taylor
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Ada Adriano
- Test Evaluation Research Group, Institute of Applied Health Research, University of Birmingham, Birmingham, UK
| | - Clare Davenport
- NIHR Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust and University of Birmingham, Birmingham, UK
- Test Evaluation Research Group, Institute of Applied Health Research, University of Birmingham, Birmingham, UK
| | | | | | - Yemisi Takwoingi
- NIHR Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust and University of Birmingham, Birmingham, UK
- Test Evaluation Research Group, Institute of Applied Health Research, University of Birmingham, Birmingham, UK
| | - Jane Cunningham
- Global Malaria Programme, World Health Organization, Geneva , Switzerland
| | - Sophie Beese
- Test Evaluation Research Group, Institute of Applied Health Research, University of Birmingham, Birmingham, UK
| | - Julie Domen
- Department of Public Health and Primary Care, KU Leuven, Leuven, Belgium
| | - Janine Dretzke
- Test Evaluation Research Group, Institute of Applied Health Research, University of Birmingham, Birmingham, UK
| | - Lavinia Ferrante di Ruffano
- Test Evaluation Research Group, Institute of Applied Health Research, University of Birmingham, Birmingham, UK
| | - Isobel M Harris
- Test Evaluation Research Group, Institute of Applied Health Research, University of Birmingham, Birmingham, UK
| | - Malcolm J Price
- Test Evaluation Research Group, Institute of Applied Health Research, University of Birmingham, Birmingham, UK
| | - Sian Taylor-Phillips
- Division of Health Sciences, Warwick Medical School, University of Warwick , Coventry, UK
| | - Lotty Hooft
- Cochrane Netherlands, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht , Netherlands
| | - Mariska Mg Leeflang
- Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
| | | | - René Spijker
- Medical Library, Amsterdam UMC, University of Amsterdam, Amsterdam Public Health, Amsterdam, Netherlands
- Cochrane Netherlands, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Ann Van den Bruel
- Department of Public Health and Primary Care, KU Leuven, Leuven, Belgium
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18
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Byrnes SA, Gallagher R, Steadman A, Bennett C, Rivera R, Ortega C, Motley ST, Jain P, Weigl BH, Connelly JT. Multiplexed and Extraction-Free Amplification for Simplified SARS-CoV-2 RT-PCR Tests. Anal Chem 2021; 93:4160-4165. [PMID: 33631932 PMCID: PMC7927279 DOI: 10.1021/acs.analchem.0c03918] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 01/11/2021] [Indexed: 02/07/2023]
Abstract
The rapid onset of the global COVID-19 pandemic has led to challenges for accurately diagnosing the disease, including supply shortages for sample collection, preservation, and purification. Currently, most diagnostic tests require RNA extraction and detection by RT-PCR; however, extraction is expensive and time-consuming and requires technical expertise. With these challenges in mind, we report extraction-free, multiplexed amplification of SARS-CoV-2 RNA from 246 clinical samples, resulting in 86% sensitivity and 100% specificity. The multiplex RT-PCR uses the CDC singleplex targets and has an LoD of 2 c/μL. We also report on amplification using a range of master mixes in different transport media. This work can help guide which combinations of reagents will enable accurate results when availability of supplies changes throughout the pandemic. Implementing these methods can reduce complexity and cost, minimize reagent usage, expedite time to results, and increase testing capacity.
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Affiliation(s)
| | - Ryan Gallagher
- Global
Health Labs, Bellevue, Washington 98007, United States
| | - Amy Steadman
- Global
Health Labs, Bellevue, Washington 98007, United States
| | - Crissa Bennett
- Global
Good, Intellectual Ventures, Bellevue, Washington 98007, United States
| | - Rafael Rivera
- Global
Health Labs, Bellevue, Washington 98007, United States
| | - Corrie Ortega
- Global
Health Labs, Bellevue, Washington 98007, United States
| | - S. Timothy Motley
- Global
Good, Intellectual Ventures, Bellevue, Washington 98007, United States
| | - Paras Jain
- Global
Good, Intellectual Ventures, Bellevue, Washington 98007, United States
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19
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García-Bernalt Diego J, Fernández-Soto P, Domínguez-Gil M, Belhassen-García M, Bellido JLM, Muro A. A Simple, Affordable, Rapid, Stabilized, Colorimetric, Versatile RT-LAMP Assay to Detect SARS-CoV-2. Diagnostics (Basel) 2021; 11:438. [PMID: 33806456 PMCID: PMC8000859 DOI: 10.3390/diagnostics11030438] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 02/25/2021] [Accepted: 02/28/2021] [Indexed: 02/06/2023] Open
Abstract
The SARS-CoV-2 pandemic has forced all countries worldwide to rapidly develop and implement widespread testing to control and manage the Coronavirus Disease 2019 (COVID-19). reverse-transcription (RT)-qPCR is the gold standard molecular diagnostic method for COVID-19, mostly in automated testing platforms. These systems are accurate and effective, but also costly, time-consuming, high-technological, infrastructure-dependent, and currently suffer from commercial reagent supply shortages. The reverse-transcription loop-mediated isothermal amplification (RT-LAMP) can be used as an alternative testing method. Here, we present a novel versatile (real-time and colorimetric) RT-LAMP for the simple (one-step), affordable (~1.7 €/sample), and rapid detection of SARS-CoV-2 targeting both ORF1ab and N genes of the novel virus genome. We demonstrate the assay on RT-qPCR-positive clinical samples, obtaining most positive results under 25 min. In addition, a novel 30-min one-step drying protocol has been developed to stabilize the RT-LAMP reaction mixtures, allowing them to be stored at room temperature functionally for up to two months, as predicted by the Q10. This Dry-RT-LAMP methodology is suitable for potentially ready-to-use COVID-19 diagnosis. After further testing and validation, it could be easily applied both in developed and in low-income countries yielding rapid and reliable results.
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Affiliation(s)
- Juan García-Bernalt Diego
- Infectious and Tropical Diseases Research Group (e-INTRO), Biomedical Research Institute of Salamanca-Research Centre for Tropical Diseases at the University of Salamanca (IBSAL-CIETUS), Faculty of Pharmacy, University of Salamanca, 37007 Salamanca, Spain; (J.G.-B.D.); (M.B.-G.); (A.M.)
| | - Pedro Fernández-Soto
- Infectious and Tropical Diseases Research Group (e-INTRO), Biomedical Research Institute of Salamanca-Research Centre for Tropical Diseases at the University of Salamanca (IBSAL-CIETUS), Faculty of Pharmacy, University of Salamanca, 37007 Salamanca, Spain; (J.G.-B.D.); (M.B.-G.); (A.M.)
| | - Marta Domínguez-Gil
- Microbiology Service, Hospital Universitario Río Hortega, 47012 Valladolid, Spain;
| | - Moncef Belhassen-García
- Infectious and Tropical Diseases Research Group (e-INTRO), Biomedical Research Institute of Salamanca-Research Centre for Tropical Diseases at the University of Salamanca (IBSAL-CIETUS), Faculty of Pharmacy, University of Salamanca, 37007 Salamanca, Spain; (J.G.-B.D.); (M.B.-G.); (A.M.)
- Internal Medicine Service, Sección de Enfermedades Infecciosas, Complejo Asistencial Universitario de Salamanca, University of Salamanca, 37007 Salamanca, Spain
| | - Juan Luis Muñoz Bellido
- Microbiology and Parasitology Service, Complejo Asistencial Universitario de Salamanca, University of Salamanca, 37007 Salamanca, Spain;
| | - Antonio Muro
- Infectious and Tropical Diseases Research Group (e-INTRO), Biomedical Research Institute of Salamanca-Research Centre for Tropical Diseases at the University of Salamanca (IBSAL-CIETUS), Faculty of Pharmacy, University of Salamanca, 37007 Salamanca, Spain; (J.G.-B.D.); (M.B.-G.); (A.M.)
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20
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Vandenberg O, Martiny D, Rochas O, van Belkum A, Kozlakidis Z. Considerations for diagnostic COVID-19 tests. Nat Rev Microbiol 2021; 19:171-183. [PMID: 33057203 PMCID: PMC7556561 DOI: 10.1038/s41579-020-00461-z] [Citation(s) in RCA: 459] [Impact Index Per Article: 153.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/17/2020] [Indexed: 02/07/2023]
Abstract
During the early phase of the coronavirus disease 2019 (COVID-19) pandemic, design, development, validation, verification and implementation of diagnostic tests were actively addressed by a large number of diagnostic test manufacturers. Hundreds of molecular tests and immunoassays were rapidly developed, albeit many still await clinical validation and formal approval. In this Review, we summarize the crucial role of diagnostic tests during the first global wave of COVID-19. We explore the technical and implementation problems encountered during this early phase in the pandemic, and try to define future directions for the progressive and better use of (syndromic) diagnostics during a possible resurgence of COVID-19 in future global waves or regional outbreaks. Continuous global improvement in diagnostic test preparedness is essential for more rapid detection of patients, possibly at the point of care, and for optimized prevention and treatment, in both industrialized countries and low-resource settings.
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Affiliation(s)
- Olivier Vandenberg
- Innovation and Business Development Unit, Laboratoire Hospitalier Universtaire de Bruxelles - Universitair Laboratorium Brussel, Université Libre de Bruxelles, Brussels, Belgium.
- Center for Environmental Health and Occupational Health, School of Public Health, Université Libre de Bruxelles, Brussels, Belgium.
- Division of Infection and Immunity, Faculty of Medical Sciences, University College London, London, UK.
| | - Delphine Martiny
- Department of Microbiology, Laboratoire Hospitalier Universtaire de Bruxelles - Universitair Laboratorium Brussel, Université Libre de Bruxelles, Brussels, Belgium
| | - Olivier Rochas
- Strategic Intelligence, Corporate Business Development, bioMérieux, Chemin de L'Orme, France
| | - Alex van Belkum
- Open Innovation and Partnerships, bioMérieux, La Balme Les Grottes, France.
| | - Zisis Kozlakidis
- Laboratory Services and Biobank Group, International Agency for Research on Cancer, World Health Organization, Lyon, France
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21
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Newman CM, Ramuta MD, McLaughlin MT, Wiseman RW, Karl JA, Dudley DM, Stauss MR, Maddox RJ, Weiler AM, Bliss MI, Fauser KN, Haddock LA, Shortreed CG, Haj AK, Accola MA, Heffron AS, Bussan HE, Reynolds MR, Harwood OE, Moriarty RV, Stewart LM, Crooks CM, Prall TM, Neumann EK, Somsen ED, Burmeister CB, Hall KL, Rehrauer WM, Friedrich TC, O’Connor SL, O’Connor DH. Initial evaluation of a mobile SARS-CoV-2 RT-LAMP testing strategy. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2020.07.28.20164038. [PMID: 33655260 PMCID: PMC7924282 DOI: 10.1101/2020.07.28.20164038] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) control in the United States remains hampered, in part, by testing limitations. We evaluated a simple, outdoor, mobile, colorimetric reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay workflow where self-collected saliva is tested for SARS-CoV-2 RNA. From July 16 to November 19, 2020, 4,704 surveillance samples were collected from volunteers and tested for SARS-CoV-2 at 5 sites. A total of 21 samples tested positive for SARS-CoV-2 by RT-LAMP; 12 were confirmed positive by subsequent quantitative reverse-transcription polymerase chain reaction (qRT-PCR) testing, while 8 were negative for SARS-CoV-2 RNA, and 1 could not be confirmed because the donor did not consent to further molecular testing. We estimated the RT-LAMP assay's false-negative rate from July 16 to September 17, 2020 by pooling residual heat-inactivated saliva that was unambiguously negative by RT-LAMP into groups of 6 or less and testing for SARS-CoV-2 RNA by qRT-PCR. We observed a 98.8% concordance between the RT-LAMP and qRT-PCR assays, with only 5 of 421 RT-LAMP negative pools (2,493 samples) testing positive in the more sensitive qRT-PCR assay. Overall, we demonstrate a rapid testing method that can be implemented outside the traditional laboratory setting by individuals with basic molecular biology skills and can effectively identify asymptomatic individuals who would not typically meet the criteria for symptom-based testing modalities.
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Affiliation(s)
- Christina M. Newman
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Mitchell D. Ramuta
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Matthew T. McLaughlin
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Roger W. Wiseman
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Julie A. Karl
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Dawn M. Dudley
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | | | | | | | - Mason I. Bliss
- Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Luis A. Haddock
- Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Cecilia G. Shortreed
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Amelia K. Haj
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Molly A. Accola
- University of Wisconsin Hospitals and Clinics, Madison, WI, USA
| | - Anna S. Heffron
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Hailey E. Bussan
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Matthew R. Reynolds
- Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA
- Wisconsin National Primate Research Center, Madison, WI, USA
| | - Olivia E. Harwood
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Ryan V. Moriarty
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Laurel M. Stewart
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Chelsea M. Crooks
- Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Trent M. Prall
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Emma K. Neumann
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Elizabeth D. Somsen
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Corrie B. Burmeister
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Kristi L. Hall
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - William M. Rehrauer
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
- University of Wisconsin Hospitals and Clinics, Madison, WI, USA
| | - Thomas C. Friedrich
- Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA
- Wisconsin National Primate Research Center, Madison, WI, USA
| | - Shelby L. O’Connor
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
- Wisconsin National Primate Research Center, Madison, WI, USA
| | - David H. O’Connor
- Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
- Wisconsin National Primate Research Center, Madison, WI, USA
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22
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Yang Q, Meyerson NR, Clark SK, Paige CL, Fattor WT, Gilchrist AR, Barbachano-Guerrero A, Healy BG, Worden-Sapper ER, Wu SS, Muhlrad D, Decker CJ, Saldi TK, Lasda E, Gonzales PK, Fink MR, Tat KL, Hager CR, Davis JC, Ozeroff CD, Brisson GR, McQueen MB, Leinwand L, Parker R, Sawyer SL. Saliva TwoStep for rapid detection of asymptomatic SARS-CoV-2 carriers. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2020.07.16.20150250. [PMID: 33619503 PMCID: PMC7899473 DOI: 10.1101/2020.07.16.20150250] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Here, we develop a simple molecular test for SARS-CoV-2 in saliva based on reverse transcription loop-mediated isothermal amplification (RT-LAMP). The test has two steps: 1) heat saliva with a stabilization solution, and 2) detect virus by incubating with a primer/enzyme mix. After incubation, saliva samples containing the SARS-CoV-2 genome turn bright yellow. Because this test is pH dependent, it can react falsely to some naturally acidic saliva samples. We report unique saliva stabilization protocols that rendered 295 healthy saliva samples compatible with the test, producing zero false positives. We also evaluated the test on 278 saliva samples from individuals who were infected with SARS-CoV-2 but had no symptoms at the time of saliva collection, and from 54 matched pairs of saliva and anterior nasal samples from infected individuals. The Saliva TwoStep test described herein identified infections with 94% sensitivity and >99% specificity in individuals with sub-clinical (asymptomatic or pre-symptomatic) infections.
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Affiliation(s)
- Qing Yang
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, 80303
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, Colorado, 80303
| | - Nicholas R Meyerson
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, 80303
- Darwin Biosciences Inc., Boulder, Colorado, 80303, USA
| | - Stephen K Clark
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, 80303
- Darwin Biosciences Inc., Boulder, Colorado, 80303, USA
| | - Camille L Paige
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, 80303
| | - Will T Fattor
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, 80303
| | - Alison R Gilchrist
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, 80303
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, Colorado, 80303
| | | | - Benjamin G Healy
- Department of Mechanical Engineering, University of Colorado Boulder, Boulder, Colorado, 80303
| | - Emma R Worden-Sapper
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, 80303
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, Colorado, 80303
| | - Sharon S Wu
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, 80303
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, Colorado, 80303
- Interdisciplinary Quantitative Biology Graduate Program, University of Colorado Boulder, Boulder, Colorado, 80303
| | - Denise Muhlrad
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado, 80303
- Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, Colorado, 80303
| | - Carolyn J Decker
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado, 80303
- Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, Colorado, 80303
| | - Tassa K Saldi
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, 80303
| | - Erika Lasda
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, 80303
| | - Patrick K Gonzales
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, 80303
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, Colorado, 80303
| | - Morgan R Fink
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, 80303
| | - Kimngan L Tat
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, 80303
| | - Cole R Hager
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, 80303
| | - Jack C Davis
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, Colorado, 80303
| | | | - Gloria R Brisson
- Wardenburg Health Center, University of Colorado Boulder, Boulder, Colorado, 80303
| | - Matthew B McQueen
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, Colorado, 80303
| | - Leslie Leinwand
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, 80303
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, Colorado, 80303
| | - Roy Parker
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, 80303
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, Colorado, 80303
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado, 80303
- Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, Colorado, 80303
| | - Sara L Sawyer
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, 80303
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, Colorado, 80303
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23
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Márquez-Ipiña AR, González-González E, Rodríguez-Sánchez IP, Lara-Mayorga IM, Mejía-Manzano LA, Sánchez-Salazar MG, González-Valdez JG, Ortiz-López R, Rojas-Martínez A, Trujillo-de Santiago G, Alvarez MM. Serological Test to Determine Exposure to SARS-CoV-2: ELISA Based on the Receptor-Binding Domain of the Spike Protein (S-RBD N318-V510) Expressed in Escherichia coli. Diagnostics (Basel) 2021; 11:271. [PMID: 33578665 PMCID: PMC7916330 DOI: 10.3390/diagnostics11020271] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 12/20/2020] [Accepted: 01/15/2021] [Indexed: 12/11/2022] Open
Abstract
Massive worldwide serological testing for SARS-CoV-2 is needed to determine the extent of virus exposure in a particular region, the ratio of symptomatic to asymptomatic infected persons, and the duration and extent of immunity after infection. To achieve this, the development and production of reliable and cost-effective SARS-CoV-2 antigens is critical. We report the bacterial production of the peptide S-RBDN318-V510, which contains the receptor-binding domain of the SARS-CoV-2 spike protein (region of 193 amino acid residues from asparagine-318 to valine-510) of the SARS-CoV-2 spike protein. We purified this peptide using a straightforward approach involving bacterial lysis, his-tag-mediated affinity chromatography, and imidazole-assisted refolding. The antigen performances of S-RBDN318-V510 and a commercial full-length spike protein were compared in ELISAs. In direct ELISAs, where the antigen was directly bound to the ELISA surface, both antigens discriminated sera from non-exposed and exposed individuals. However, the discriminating resolution was better in ELISAs that used the full-spike antigen than the S-RBDN318-V510. Attachment of the antigens to the ELISA surface using a layer of anti-histidine antibodies gave equivalent resolution for both S-RBDN318-V510 and the full-length spike protein. Results demonstrate that ELISA-functional SARS-CoV-2 antigens can be produced in bacterial cultures, and that S-RBDN318-V510 may represent a cost-effective alternative to the use of structurally more complex antigens in serological COVID-19 testing.
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Affiliation(s)
- Alan Roberto Márquez-Ipiña
- Centro de Biotecnología-FEMSA, Tecnologico de Monterrey, Monterrey CP 64849, NL, Mexico; (A.R.M.-I.); (I.M.L.-M.); (L.A.M.-M.); (J.G.G.-V.)
| | - Everardo González-González
- Departamento de Bioingeniería, Tecnologico de Monterrey, Monterrey CP 64849, NL, Mexico; (E.G.-G.); (M.G.S.-S.)
| | - Iram Pablo Rodríguez-Sánchez
- Laboratorio de Fisiología Molecular y Estructural, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, San Nicolas de los Garza CP 66455, NL, Mexico;
- Alfa Medical Center, Guadalupe CP 67100, NL, Mexico
| | - Itzel Montserrat Lara-Mayorga
- Centro de Biotecnología-FEMSA, Tecnologico de Monterrey, Monterrey CP 64849, NL, Mexico; (A.R.M.-I.); (I.M.L.-M.); (L.A.M.-M.); (J.G.G.-V.)
- Departamento de Ingeniería Mecatrónica y Eléctrica, Tecnologico de Monterrey, Monterrey CP 64849, NL, Mexico
| | - Luis Alberto Mejía-Manzano
- Centro de Biotecnología-FEMSA, Tecnologico de Monterrey, Monterrey CP 64849, NL, Mexico; (A.R.M.-I.); (I.M.L.-M.); (L.A.M.-M.); (J.G.G.-V.)
| | | | - José Guillermo González-Valdez
- Centro de Biotecnología-FEMSA, Tecnologico de Monterrey, Monterrey CP 64849, NL, Mexico; (A.R.M.-I.); (I.M.L.-M.); (L.A.M.-M.); (J.G.G.-V.)
| | - Rocio Ortiz-López
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey CP 64718, NL, Mexico; (R.O.-L.); (A.R.-M.)
| | - Augusto Rojas-Martínez
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey CP 64718, NL, Mexico; (R.O.-L.); (A.R.-M.)
| | - Grissel Trujillo-de Santiago
- Centro de Biotecnología-FEMSA, Tecnologico de Monterrey, Monterrey CP 64849, NL, Mexico; (A.R.M.-I.); (I.M.L.-M.); (L.A.M.-M.); (J.G.G.-V.)
- Departamento de Ingeniería Mecatrónica y Eléctrica, Tecnologico de Monterrey, Monterrey CP 64849, NL, Mexico
| | - Mario Moisés Alvarez
- Centro de Biotecnología-FEMSA, Tecnologico de Monterrey, Monterrey CP 64849, NL, Mexico; (A.R.M.-I.); (I.M.L.-M.); (L.A.M.-M.); (J.G.G.-V.)
- Departamento de Bioingeniería, Tecnologico de Monterrey, Monterrey CP 64849, NL, Mexico; (E.G.-G.); (M.G.S.-S.)
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24
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Azzi L, Maurino V, Baj A, Dani M, d’Aiuto A, Fasano M, Lualdi M, Sessa F, Alberio T. Diagnostic Salivary Tests for SARS-CoV-2. J Dent Res 2021; 100:115-123. [PMID: 33131360 PMCID: PMC7604673 DOI: 10.1177/0022034520969670] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The diagnosis of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection relies on the detection of viral RNA by real-time reverse transcription polymerase chain reaction (rRT-PCR) performed with respiratory specimens, especially nasopharyngeal swabs. However, this procedure requires specialized medical personnel, centralized laboratory facilities, and time to provide results (from several hours up to 1 d). In addition, there is a non-negligible risk of viral transmission for the operator who performs the procedure. For these reasons, several studies have suggested the use of other body fluids, including saliva, for the detection of SARS-CoV-2. The use of saliva as a diagnostic specimen has numerous advantages: it is easily self-collected by the patient with almost no discomfort, it does not require specialized health care personnel for its management, and it reduces the risks for the operator. In the past few months, several scientific papers, media, and companies have announced the development of new salivary tests to detect SARS-CoV-2 infection. Posterior oropharyngeal saliva should be distinguished from oral saliva, since the former is a part of respiratory secretions, while the latter is produced by the salivary glands, which are outside the respiratory tract. Saliva can be analyzed through standard (rRT-PCR) or rapid molecular biology tests (direct rRT-PCR without extraction), although, in a hospital setting, these procedures may be performed only in addition to nasopharyngeal swabs to minimize the incidence of false-negative results. Conversely, the promising role of saliva in the diagnosis of SARS-CoV-2 infection is highlighted by the emergence of point-of-care technologies and, most important, point-of-need devices. Indeed, these devices can be directly used in workplaces, airports, schools, cinemas, and shopping centers. An example is the recently described Rapid Salivary Test, an antigen test based on the lateral flow assay, which detects the presence of the virus by identifying the spike protein in the saliva within a few minutes.
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Affiliation(s)
- L. Azzi
- Unit of Oral Medicine and
Pathology, ASST dei Sette Laghi–Ospedale di Circolo e Fondazione Macchi,
Department of Medicine and Surgery, University of Insubria, Varese,
Italy
| | - V. Maurino
- Unit of Oral Medicine and
Pathology, ASST dei Sette Laghi–Ospedale di Circolo e Fondazione Macchi,
Department of Medicine and Surgery, University of Insubria, Varese,
Italy
| | - A. Baj
- Laboratory of Clinical
Microbiology, ASST dei Sette Laghi–Ospedale di Circolo e Fondazione Macchi,
Department of Medicine and Surgery, University of Insubria, Varese,
Italy
| | - M. Dani
- Unit of Oral Medicine and
Pathology, ASST dei Sette Laghi–Ospedale di Circolo e Fondazione Macchi,
Department of Medicine and Surgery, University of Insubria, Varese,
Italy
| | - A. d’Aiuto
- Unit of Oral Medicine and
Pathology, ASST dei Sette Laghi–Ospedale di Circolo e Fondazione Macchi,
Department of Medicine and Surgery, University of Insubria, Varese,
Italy
| | - M. Fasano
- Laboratory of Biochemistry and
Functional Proteomics, Department of Science and High Technology, Busto
Arsizio (VA), Italy
| | - M. Lualdi
- Laboratory of Biochemistry and
Functional Proteomics, Department of Science and High Technology, Busto
Arsizio (VA), Italy
| | - F. Sessa
- Unit of Pathology, ASST dei Sette
Laghi–Ospedale di Circolo e Fondazione Macchi, Department of Medicine and
Surgery, University of Insubria, Varese, Italy
| | - T. Alberio
- Laboratory of Biochemistry and
Functional Proteomics, Department of Science and High Technology, Busto
Arsizio (VA), Italy
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25
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Wan B, Zhang X, Luo D, Zhang T, Chen X, Yao Y, Zhao X, Lei L, Liu C, Zhao W, Zhou L, Ge Y, Mao H, Liu S, Chen J, Cheng X, Zhao J, Sui G. On-site analysis of COVID-19 on the surfaces in wards. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 753:141758. [PMID: 32898806 PMCID: PMC7434306 DOI: 10.1016/j.scitotenv.2020.141758] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 08/13/2020] [Accepted: 08/15/2020] [Indexed: 05/11/2023]
Abstract
SARS-Cov-2 has erupted across the globe, and confirmed cases of COVID-19 pose a high infection risk. Infected patients typically receive their treatment in specific isolation wards, where they are confined for at least 14 days. The virus may contaminate any surface of the room, especially frequently touched surfaces. Therefore, surface contamination in wards should be monitored for disease control and hygiene purposes. Herein, surface contamination in the ward was detected on-site using an RNA extraction-free rapid method. The whole detection process, from surface sample collection to readout of the detection results, was finished within 45 min. The nucleic acid extraction-free method requires minimal labor. More importantly, the tests were performed on-site and the results were obtained almost in real-time. The test confirmed that 31 patients contaminated seven individual sites. Among the sampled surfaces, the electrocardiogram fingertip presented a 72.7% positive rate, indicating that this surface is an important hygiene site. Meanwhile, the bedrails showed the highest correlation with other surfaces, so should be detected daily. Another surface with high contamination risk was the door handle in the bathroom. To our knowledge, we present the first on-site analysis of COVID-19 surface contamination in wards. The results and applied technique provide a potential further reference for disease control and hygiene suggestions.
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Affiliation(s)
- Bin Wan
- Public Health Clinical Center of Chengdu, No. 377 Jingming Road, Jinjiang District, Chengdu, Sichuan 610066, China
| | - Xinlian Zhang
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP(3)), Department of Environment Science & Engineering, Fudan University, Shanghai 200433, China
| | - Dongxia Luo
- Public Health Clinical Center of Chengdu, No. 377 Jingming Road, Jinjiang District, Chengdu, Sichuan 610066, China
| | - Tong Zhang
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP(3)), Department of Environment Science & Engineering, Fudan University, Shanghai 200433, China
| | - Xi Chen
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP(3)), Department of Environment Science & Engineering, Fudan University, Shanghai 200433, China
| | - Yuhan Yao
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP(3)), Department of Environment Science & Engineering, Fudan University, Shanghai 200433, China
| | - Xia Zhao
- Public Health Clinical Center of Chengdu, No. 377 Jingming Road, Jinjiang District, Chengdu, Sichuan 610066, China
| | - Limei Lei
- Public Health Clinical Center of Chengdu, No. 377 Jingming Road, Jinjiang District, Chengdu, Sichuan 610066, China
| | - Chunmei Liu
- Public Health Clinical Center of Chengdu, No. 377 Jingming Road, Jinjiang District, Chengdu, Sichuan 610066, China
| | - Wang Zhao
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP(3)), Department of Environment Science & Engineering, Fudan University, Shanghai 200433, China
| | - Lin Zhou
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology (SIMIT), Chinese Academy of Sciences, Shanghai 200050, China
| | - Yuqing Ge
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology (SIMIT), Chinese Academy of Sciences, Shanghai 200050, China
| | - Hongju Mao
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology (SIMIT), Chinese Academy of Sciences, Shanghai 200050, China
| | - Sixiu Liu
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP(3)), Department of Environment Science & Engineering, Fudan University, Shanghai 200433, China
| | - Jianmin Chen
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP(3)), Department of Environment Science & Engineering, Fudan University, Shanghai 200433, China; Shanghai Institute of Pollution Control and Ecological Security, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Xunjia Cheng
- Department of Medical Microbiology, Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, School of Basic Medical Sciences, Fudan University, 131 Dongan Road, Shanghai 200032, China
| | - Jianlong Zhao
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology (SIMIT), Chinese Academy of Sciences, Shanghai 200050, China.
| | - Guodong Sui
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP(3)), Department of Environment Science & Engineering, Fudan University, Shanghai 200433, China; Shanghai Institute of Pollution Control and Ecological Security, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China; Department of Medical Microbiology, Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, School of Basic Medical Sciences, Fudan University, 131 Dongan Road, Shanghai 200032, China.
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26
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Jayamohan H, Lambert CJ, Sant HJ, Jafek A, Patel D, Feng H, Beeman M, Mahmood T, Nze U, Gale BK. SARS-CoV-2 pandemic: a review of molecular diagnostic tools including sample collection and commercial response with associated advantages and limitations. Anal Bioanal Chem 2021; 413:49-71. [PMID: 33073312 PMCID: PMC7568947 DOI: 10.1007/s00216-020-02958-1] [Citation(s) in RCA: 86] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 09/03/2020] [Accepted: 09/16/2020] [Indexed: 12/18/2022]
Abstract
The unprecedented global pandemic known as SARS-CoV-2 has exercised to its limits nearly all aspects of modern viral diagnostics. In doing so, it has illuminated both the advantages and limitations of current technologies. Tremendous effort has been put forth to expand our capacity to diagnose this deadly virus. In this work, we put forth key observations in the functionality of current methods for SARS-CoV-2 diagnostic testing. These methods include nucleic acid amplification-, CRISPR-, sequencing-, antigen-, and antibody-based detection methods. Additionally, we include analysis of equally critical aspects of COVID-19 diagnostics, including sample collection and preparation, testing models, and commercial response. We emphasize the integrated nature of assays, wherein issues in sample collection and preparation could impact the overall performance in a clinical setting.
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Affiliation(s)
- Harikrishnan Jayamohan
- Department of Mechanical Engineering, University of Utah, Salt Lake City, UT, 84112, USA.
| | - Christopher J Lambert
- Department of Mechanical Engineering, University of Utah, Salt Lake City, UT, 84112, USA
| | - Himanshu J Sant
- Department of Mechanical Engineering, University of Utah, Salt Lake City, UT, 84112, USA
| | - Alexander Jafek
- Department of Mechanical Engineering, University of Utah, Salt Lake City, UT, 84112, USA
| | - Dhruv Patel
- Department of Mechanical Engineering, University of Utah, Salt Lake City, UT, 84112, USA
| | - Haidong Feng
- Department of Mechanical Engineering, University of Utah, Salt Lake City, UT, 84112, USA
| | - Michael Beeman
- Department of Mechanical Engineering, University of Utah, Salt Lake City, UT, 84112, USA
| | - Tawsif Mahmood
- Department of Mechanical Engineering, University of Utah, Salt Lake City, UT, 84112, USA
| | - Ugochukwu Nze
- Department of Mechanical Engineering, University of Utah, Salt Lake City, UT, 84112, USA
| | - Bruce K Gale
- Department of Mechanical Engineering, University of Utah, Salt Lake City, UT, 84112, USA
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27
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Parihar A, Ranjan P, Sanghi SK, Srivastava AK, Khan R. Point-of-Care Biosensor-Based Diagnosis of COVID-19 Holds Promise to Combat Current and Future Pandemics. ACS APPLIED BIO MATERIALS 2020; 3:7326-7343. [PMID: 35019474 PMCID: PMC7571308 DOI: 10.1021/acsabm.0c01083] [Citation(s) in RCA: 91] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 10/03/2020] [Indexed: 02/08/2023]
Abstract
Efficient and rapid detection of viruses plays an extremely important role in disease prevention, diagnosis, and environmental monitoring. Early screening of viral infection among the population has the potential to combat the spread of infection. However, the traditional methods of virus detection being used currently, such as plate culturing and quantitative RT-PCR, give promising results, but they are time-consuming and require expert analysis and costly equipment and reagents; therefore, they are not affordable by people in low socio-economic groups in developing countries. Further, mass or bulk testing chosen by many governments to tackle the pandemic situation has led to severe shortages of testing kits and reagents and hence are affecting the demand and supply chain drastically. We tried to include all the reported current scenario-based biosensors such as electrochemical, optical, and microfluidics, which have the potential to replace mainstream diagnostic methods and therefore could pave the way to combat COVID-19. Apart from this, we have also provided information on commercially available biosensors for detection of SARS-CoV-2 along with the challenges in development of better diagnostic approaches. It is therefore expected that the content of this review will help researchers to design and develop more sensitive advanced commercial biosensor devices for early diagnosis of viral infection, which can open up avenues for better and more specific therapeutic outcomes.
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Affiliation(s)
- Arpana Parihar
- Department of Genetics,
Barkatullah University, Bhopal,
Madhya Pradesh - 462026, India
| | - Pushpesh Ranjan
- CSIR - Advanced Materials and
Processes Research Institute, CSIR-AMPRI,
Bhopal, Madhya Pradesh - 462026, India
- Academy of Scientific and Innovative
Research (AcSIR), CSIR-AMPRI, Bhopal,
Madhya Pradesh - 462026, India
| | - Sunil K. Sanghi
- CSIR - Advanced Materials and
Processes Research Institute, CSIR-AMPRI,
Bhopal, Madhya Pradesh - 462026, India
| | - Avanish K. Srivastava
- CSIR - Advanced Materials and
Processes Research Institute, CSIR-AMPRI,
Bhopal, Madhya Pradesh - 462026, India
| | - Raju Khan
- CSIR - Advanced Materials and
Processes Research Institute, CSIR-AMPRI,
Bhopal, Madhya Pradesh - 462026, India
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28
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Park GS, Baek SH, Ku K, Kim SJ, Kim SI, Kim BT, Maeng JS. Colorimetric RT-LAMP Methods to Detect Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Bio Protoc 2020; 10:e3804. [PMID: 33659458 DOI: 10.21769/bioprotoc.3804] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 08/18/2020] [Accepted: 08/19/2020] [Indexed: 11/02/2022] Open
Abstract
Standard diagnostic methods of Coronavirus Disease 2019 (COVID-19) rely on RT-qPCR technique which have limited point-of-care test (POCT) potential due to necessity of dedicated equipment and specialized personnel. LAMP, an isothermal nucleic acid amplification test (NAAT), is a promising technique that may substitute RT-qPCR for POCT of genomic materials. Here, we provide a protocol to perform reverse transcription LAMP targeting SARS-CoV-2. We adopted both real-time fluorescence detection and end-point colorimetric detection approaches. Our protocol would be useful for screening diagnosis of COVID-19 and be a baseline for development of improved POCT NAAT.
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Affiliation(s)
- Gun-Soo Park
- Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon, Republic of Korea.,Research Group of Food Processing, Korea Food Research Institute, Wanju-gun, Jeollabuk-do, Republic of Korea
| | - Seung-Hwa Baek
- Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon, Republic of Korea.,Department of Predictive Toxicology, Korea Institute of Toxicology, Daejeon, Republic of Korea
| | - Keunbon Ku
- Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon, Republic of Korea
| | - Seong-Jun Kim
- Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon, Republic of Korea
| | - Seung Il Kim
- Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon, Republic of Korea.,Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Cheongju, Republic of Korea
| | - Bum-Tae Kim
- Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon, Republic of Korea
| | - Jin-Soo Maeng
- Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon, Republic of Korea.,Research Group of Food Processing, Korea Food Research Institute, Wanju-gun, Jeollabuk-do, Republic of Korea
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29
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Zhang Y, Ren G, Buss J, Barry AJ, Patton GC, Tanner NA. Enhancing colorimetric loop-mediated isothermal amplification speed and sensitivity with guanidine chloride. Biotechniques 2020; 69:178-185. [DOI: 10.2144/btn-2020-0078] [Citation(s) in RCA: 102] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Loop-mediated isothermal amplification (LAMP) is a versatile technique for detection of target DNA and RNA, enabling rapid molecular diagnostic assays with minimal equipment. The global SARS-CoV-2 pandemic has presented an urgent need for new and better diagnostic methods, with colorimetric LAMP utilized in numerous studies for SARS-CoV-2 detection. However, the sensitivity of colorimetric LAMP in early reports has been below that of the standard RT-qPCR tests, and we sought to improve performance. Here we report the use of guanidine hydrochloride and combined primer sets to increase speed and sensitivity in colorimetric LAMP, bringing this simple method up to the standards of sophisticated techniques and enabling accurate, high-throughput diagnostics.
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Affiliation(s)
- Yinhua Zhang
- New England Biolabs, Inc. 240 County Road, Ipswich, MA 01938, USA
| | - Guoping Ren
- New England Biolabs, Inc. 240 County Road, Ipswich, MA 01938, USA
| | - Jackson Buss
- New England Biolabs, Inc. 240 County Road, Ipswich, MA 01938, USA
| | - Andrew J Barry
- New England Biolabs, Inc. 240 County Road, Ipswich, MA 01938, USA
| | - Gregory C Patton
- New England Biolabs, Inc. 240 County Road, Ipswich, MA 01938, USA
| | - Nathan A Tanner
- New England Biolabs, Inc. 240 County Road, Ipswich, MA 01938, USA
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30
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Dinnes J, Deeks JJ, Adriano A, Berhane S, Davenport C, Dittrich S, Emperador D, Takwoingi Y, Cunningham J, Beese S, Dretzke J, Ferrante di Ruffano L, Harris IM, Price MJ, Taylor-Phillips S, Hooft L, Leeflang MM, Spijker R, Van den Bruel A. Rapid, point-of-care antigen and molecular-based tests for diagnosis of SARS-CoV-2 infection. Cochrane Database Syst Rev 2020; 8:CD013705. [PMID: 32845525 PMCID: PMC8078202 DOI: 10.1002/14651858.cd013705] [Citation(s) in RCA: 348] [Impact Index Per Article: 87.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
BACKGROUND Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the resulting COVID-19 pandemic present important diagnostic challenges. Several diagnostic strategies are available to identify or rule out current infection, identify people in need of care escalation, or to test for past infection and immune response. Point-of-care antigen and molecular tests to detect current SARS-CoV-2 infection have the potential to allow earlier detection and isolation of confirmed cases compared to laboratory-based diagnostic methods, with the aim of reducing household and community transmission. OBJECTIVES To assess the diagnostic accuracy of point-of-care antigen and molecular-based tests to determine if a person presenting in the community or in primary or secondary care has current SARS-CoV-2 infection. SEARCH METHODS On 25 May 2020 we undertook electronic searches in the Cochrane COVID-19 Study Register and the COVID-19 Living Evidence Database from the University of Bern, which is updated daily with published articles from PubMed and Embase and with preprints from medRxiv and bioRxiv. In addition, we checked repositories of COVID-19 publications. We did not apply any language restrictions. SELECTION CRITERIA We included studies of people with suspected current SARS-CoV-2 infection, known to have, or not to have SARS-CoV-2 infection, or where tests were used to screen for infection. We included test accuracy studies of any design that evaluated antigen or molecular tests suitable for a point-of-care setting (minimal equipment, sample preparation, and biosafety requirements, with results available within two hours of sample collection). We included all reference standards to define the presence or absence of SARS-CoV-2 (including reverse transcription polymerase chain reaction (RT-PCR) tests and established clinical diagnostic criteria). DATA COLLECTION AND ANALYSIS Two review authors independently screened studies and resolved any disagreements by discussion with a third review author. One review author independently extracted study characteristics, which were checked by a second review author. Two review authors independently extracted 2x2 contingency table data and assessed risk of bias and applicability of the studies using the QUADAS-2 tool. We present sensitivity and specificity, with 95% confidence intervals (CIs), for each test using paired forest plots. We pooled data using the bivariate hierarchical model separately for antigen and molecular-based tests, with simplifications when few studies were available. We tabulated available data by test manufacturer. MAIN RESULTS We included 22 publications reporting on a total of 18 study cohorts with 3198 unique samples, of which 1775 had confirmed SARS-CoV-2 infection. Ten studies took place in North America, two in South America, four in Europe, one in China and one was conducted internationally. We identified data for eight commercial tests (four antigen and four molecular) and one in-house antigen test. Five of the studies included were only available as preprints. We did not find any studies at low risk of bias for all quality domains and had concerns about applicability of results across all studies. We judged patient selection to be at high risk of bias in 50% of the studies because of deliberate over-sampling of samples with confirmed COVID-19 infection and unclear in seven out of 18 studies because of poor reporting. Sixteen (89%) studies used only a single, negative RT-PCR to confirm the absence of COVID-19 infection, risking missing infection. There was a lack of information on blinding of index test (n = 11), and around participant exclusions from analyses (n = 10). We did not observe differences in methodological quality between antigen and molecular test evaluations. Antigen tests Sensitivity varied considerably across studies (from 0% to 94%): the average sensitivity was 56.2% (95% CI 29.5 to 79.8%) and average specificity was 99.5% (95% CI 98.1% to 99.9%; based on 8 evaluations in 5 studies on 943 samples). Data for individual antigen tests were limited with no more than two studies for any test. Rapid molecular assays Sensitivity showed less variation compared to antigen tests (from 68% to 100%), average sensitivity was 95.2% (95% CI 86.7% to 98.3%) and specificity 98.9% (95% CI 97.3% to 99.5%) based on 13 evaluations in 11 studies of on 2255 samples. Predicted values based on a hypothetical cohort of 1000 people with suspected COVID-19 infection (with a prevalence of 10%) result in 105 positive test results including 10 false positives (positive predictive value 90%), and 895 negative results including 5 false negatives (negative predictive value 99%). Individual tests We calculated pooled results of individual tests for ID NOW (Abbott Laboratories) (5 evaluations) and Xpert Xpress (Cepheid Inc) (6 evaluations). Summary sensitivity for the Xpert Xpress assay (99.4%, 95% CI 98.0% to 99.8%) was 22.6 (95% CI 18.8 to 26.3) percentage points higher than that of ID NOW (76.8%, (95% CI 72.9% to 80.3%), whilst the specificity of Xpert Xpress (96.8%, 95% CI 90.6% to 99.0%) was marginally lower than ID NOW (99.6%, 95% CI 98.4% to 99.9%; a difference of -2.8% (95% CI -6.4 to 0.8)) AUTHORS' CONCLUSIONS: This review identifies early-stage evaluations of point-of-care tests for detecting SARS-CoV-2 infection, largely based on remnant laboratory samples. The findings currently have limited applicability, as we are uncertain whether tests will perform in the same way in clinical practice, and according to symptoms of COVID-19, duration of symptoms, or in asymptomatic people. Rapid tests have the potential to be used to inform triage of RT-PCR use, allowing earlier detection of those testing positive, but the evidence currently is not strong enough to determine how useful they are in clinical practice. Prospective and comparative evaluations of rapid tests for COVID-19 infection in clinically relevant settings are urgently needed. Studies should recruit consecutive series of eligible participants, including both those presenting for testing due to symptoms and asymptomatic people who may have come into contact with confirmed cases. Studies should clearly describe symptomatic status and document time from symptom onset or time since exposure. Point-of-care tests must be conducted on samples according to manufacturer instructions for use and be conducted at the point of care. Any future research study report should conform to the Standards for Reporting of Diagnostic Accuracy (STARD) guideline.
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Affiliation(s)
- Jacqueline Dinnes
- Test Evaluation Research Group, Institute of Applied Health Research, University of Birmingham, Birmingham, UK
- NIHR Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust and University of Birmingham, Birmingham, UK
| | - Jonathan J Deeks
- Test Evaluation Research Group, Institute of Applied Health Research, University of Birmingham, Birmingham, UK
- NIHR Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust and University of Birmingham, Birmingham, UK
| | - Ada Adriano
- Test Evaluation Research Group, Institute of Applied Health Research, University of Birmingham, Birmingham, UK
| | - Sarah Berhane
- NIHR Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust and University of Birmingham, Birmingham, UK
| | - Clare Davenport
- Test Evaluation Research Group, Institute of Applied Health Research, University of Birmingham, Birmingham, UK
- NIHR Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust and University of Birmingham, Birmingham, UK
| | | | | | - Yemisi Takwoingi
- Test Evaluation Research Group, Institute of Applied Health Research, University of Birmingham, Birmingham, UK
- NIHR Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust and University of Birmingham, Birmingham, UK
| | - Jane Cunningham
- Global Malaria Programme, World Health Organization, Geneva, Switzerland
| | - Sophie Beese
- Test Evaluation Research Group, Institute of Applied Health Research, University of Birmingham, Birmingham, UK
| | - Janine Dretzke
- Test Evaluation Research Group, Institute of Applied Health Research, University of Birmingham, Birmingham, UK
| | - Lavinia Ferrante di Ruffano
- Test Evaluation Research Group, Institute of Applied Health Research, University of Birmingham, Birmingham, UK
| | - Isobel M Harris
- Test Evaluation Research Group, Institute of Applied Health Research, University of Birmingham, Birmingham, UK
| | - Malcolm J Price
- Test Evaluation Research Group, Institute of Applied Health Research, University of Birmingham, Birmingham, UK
| | - Sian Taylor-Phillips
- Division of Health Sciences, Warwick Medical School, University of Warwick, Coventry, UK
| | - Lotty Hooft
- Cochrane Netherlands, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Mariska Mg Leeflang
- Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
- Biomarker and Test Evaluation Programme (BiTE), Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - René Spijker
- Cochrane Netherlands, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
- Medical Library, Amsterdam UMC, University of Amsterdam, Amsterdam Public Health, Amsterdam, Netherlands
| | - Ann Van den Bruel
- Department of Public Health and Primary Care, KU Leuven, Leuven, Belgium
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