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Lim J, Stavins R, Kindratenko V, Baek J, Wang L, White K, Kumar J, Valera E, King WP, Bashir R. Microfluidic point-of-care device for detection of early strains and B.1.1.7 variant of SARS-CoV-2 virus. LAB ON A CHIP 2022; 22:1297-1309. [PMID: 35244660 DOI: 10.1039/d2lc00021k] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Since the beginning of the COVID-19 pandemic, several mutations of the SARS-CoV-2 virus have emerged. Current gold standard detection methods for detecting the virus and its variants are based on PCR-based diagnostics using complex laboratory protocols and time-consuming steps, such as RNA isolation and purification, and thermal cycling. These steps limit the translation of technology to the point-of-care and limit accessibility to under-resourced regions. While PCR-based assays currently offer the possibility of multiplexed gene detection, and commercial products of single gene PCR and isothermal LAMP at point-of-care are also now available, reports of isothermal assays at the point-of-care with detection of multiple genes are lacking. Here, we present a microfluidic assay and device to detect and differentiate the Alpha variant (B.1.1.7) from the SARS-CoV-2 virus early strains in saliva samples. The detection assay, which is based on isothermal RT-LAMP amplification, takes advantage of the S-gene target failure (SGTF) to differentiate the Alpha variant from the SARS-CoV-2 virus early strains using a binary detection system based on spatial separation of the primers specific to the N- and S-genes. We use additively manufactured plastic cartridges in a low-cost optical reader system to successfully detect the SARS-CoV-2 virus from saliva samples (positive amplification is detected with concentration ≥10 copies per μL) within 30 min. We demonstrate that our platform can discriminate the B.1.1.7 variant (USA/CA_CDC_5574/2020 isolate) from SARS-CoV-2 negative samples, but also from the SARS-CoV-2 USA-WA1/2020 isolate. The reliability of the developed point-of-care device was confirmed by testing 38 clinical saliva samples, including 20 samples positive for Alpha variant (sensitivity > 90%, specificity = 100%). This study highlights the current relevance of binary-based testing, as the new Omicron variant also exhibits S-gene target failure and could be tested by adapting the approach presented here.
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Affiliation(s)
- Jongwon Lim
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - Robert Stavins
- Department of Mechanical Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Victoria Kindratenko
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - Janice Baek
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Leyi Wang
- Veterinary Diagnostic Laboratory and Department of Veterinary Clinical Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Karen White
- Department of Biomedical and Translational Sciences, Carle Illinois College of Medicine, Urbana, IL 61801, USA
- Carle Foundation Hospital, Urbana, Illinois 61801, USA
| | - James Kumar
- Department of Biomedical and Translational Sciences, Carle Illinois College of Medicine, Urbana, IL 61801, USA
- Carle Foundation Hospital, Urbana, Illinois 61801, USA
| | - Enrique Valera
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - William Paul King
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
- Department of Mechanical Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Biomedical and Translational Sciences, Carle Illinois College of Medicine, Urbana, IL 61801, USA
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Rashid Bashir
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
- Department of Mechanical Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Biomedical and Translational Sciences, Carle Illinois College of Medicine, Urbana, IL 61801, USA
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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Waheed W, Saylan S, Hassan T, Kannout H, Alsafar H, Alazzam A. A deep learning-driven low-power, accurate, and portable platform for rapid detection of COVID-19 using reverse-transcription loop-mediated isothermal amplification. Sci Rep 2022; 12:4132. [PMID: 35260715 PMCID: PMC8903312 DOI: 10.1038/s41598-022-07954-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 02/28/2022] [Indexed: 12/24/2022] Open
Abstract
This paper presents a deep learning-driven portable, accurate, low-cost, and easy-to-use device to perform Reverse-Transcription Loop-Mediated Isothermal Amplification (RT-LAMP) to facilitate rapid detection of COVID-19. The 3D-printed device-powered using only a 5 Volt AC-DC adapter-can perform 16 simultaneous RT-LAMP reactions and can be used multiple times. Moreover, the experimental protocol is devised to obviate the need for separate, expensive equipment for RNA extraction in addition to eliminating sample evaporation. The entire process from sample preparation to the qualitative assessment of the LAMP amplification takes only 45 min (10 min for pre-heating and 35 min for RT-LAMP reactions). The completion of the amplification reaction yields a fuchsia color for the negative samples and either a yellow or orange color for the positive samples, based on a pH indicator dye. The device is coupled with a novel deep learning system that automatically analyzes the amplification results and pays attention to the pH indicator dye to screen the COVID-19 subjects. The proposed device has been rigorously tested on 250 RT-LAMP clinical samples, where it achieved an overall specificity and sensitivity of 0.9666 and 0.9722, respectively with a recall of 0.9892 for Ct < 30. Also, the proposed system can be widely used as an accurate, sensitive, rapid, and portable tool to detect COVID-19 in settings where access to a lab is difficult, or the results are urgently required.
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Affiliation(s)
- Waqas Waheed
- Department of Mechanical Engineering, Khalifa University, Abu Dhabi, UAE
| | - Sueda Saylan
- System on Chip Center (SOCC), Khalifa University, Abu Dhabi, UAE
- Department of Electrical Engineering and Computer Science, Khalifa University, Abu Dhabi, UAE
| | - Taimur Hassan
- Department of Electrical Engineering and Computer Science, Khalifa University, Abu Dhabi, UAE
- Center for Cyber-Physical Systems (C2PS), EECS Department, Khalifa University, Abu Dhabi, UAE
| | - Hussain Kannout
- Center for Biotechnology (BTC), Khalifa University, Abu Dhabi, UAE
| | - Habiba Alsafar
- Center for Biotechnology (BTC), Khalifa University, Abu Dhabi, UAE
- College of Medicine and Health Sciences, Khalifa University, Abu Dhabi, UAE
| | - Anas Alazzam
- Department of Mechanical Engineering, Khalifa University, Abu Dhabi, UAE.
- System on Chip Center (SOCC), Khalifa University, Abu Dhabi, UAE.
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53
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Shi Y, Kang L, Mu R, Xu M, Duan X, Li Y, Yang C, Ding JW, Wang Q, Li S. CRISPR/Cas12a-Enhanced Loop-Mediated Isothermal Amplification for the Visual Detection of Shigella flexneri. Front Bioeng Biotechnol 2022; 10:845688. [PMID: 35265606 PMCID: PMC8899461 DOI: 10.3389/fbioe.2022.845688] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 01/14/2022] [Indexed: 12/26/2022] Open
Abstract
Shigella flexneri is a serious threat to global public health, and a rapid detection method is urgently needed. The CRISPR/Cas (clustered regularly interspaced short palindromic repeats/CRISPR-associated) system is widely used in gene editing, gene therapy, and in vitro diagnosis. Here, we combined loop-mediated isothermal amplification (LAMP) and CRISPR/Cas12a to develop a novel diagnostic test (CRISPR/Cas12a-E-LAMP) for the diagnosis of S. flexneri. The CRISPR/Cas12a-E-LAMP protocol conducts LAMP reaction for S. flexneri templates followed by CRISPR/Cas12a detection of predefined target sequences. LAMP primers and sgRNAs were designed to the highly conserved gene hypothetical protein (accession: AE014073, region: 4170556–4171,068) of S. flexneri. After the LAMP reaction at 60°C for 20 min, the pre-loaded CRISPR/Cas12a regents were mixed with the LAMP products in one tube at 37°C for 20 min, and the final results can be viewed by naked eyes with a total time of 40 min. The sensitivity of CRISPR/Cas12a-E-LAMP to detect S. flexneri was 4 × 100 copies/μl plasmids and without cross-reaction with other six closely related non-S. flexneri. Therefore, the CRISPR/Cas12a-E-LAMP assay is a useful method for the reliable and quick diagnosis of S. flexneri and may be applied in other pathogen infection detection.
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Affiliation(s)
- Yaoqiang Shi
- Provincial Key Laboratory for Transfusion-Transmitted Infectious Diseases, Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, China
| | - Lan Kang
- Provincial Key Laboratory for Transfusion-Transmitted Infectious Diseases, Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, China
| | - Rongrong Mu
- Provincial Key Laboratory for Transfusion-Transmitted Infectious Diseases, Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, China
| | - Min Xu
- Provincial Key Laboratory for Transfusion-Transmitted Infectious Diseases, Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, China
| | - Xiaoqiong Duan
- Provincial Key Laboratory for Transfusion-Transmitted Infectious Diseases, Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, China
| | - Yujia Li
- Provincial Key Laboratory for Transfusion-Transmitted Infectious Diseases, Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, China
| | - Chunhui Yang
- Provincial Key Laboratory for Transfusion-Transmitted Infectious Diseases, Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, China
| | - Jia-Wei Ding
- Clinical Laboratory Department, Yan’an Hospital Affiliated to Kunming Medical University, Kunming, China
| | - Qinghua Wang
- Department of Emergency, The Traditional Chinese Medicine Hospital of Wenjiang District, Chengdu, China
- *Correspondence: Shilin Li, ; Qinghua Wang,
| | - Shilin Li
- Provincial Key Laboratory for Transfusion-Transmitted Infectious Diseases, Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, China
- *Correspondence: Shilin Li, ; Qinghua Wang,
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54
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De Felice M, De Falco M, Zappi D, Antonacci A, Scognamiglio V. Isothermal amplification-assisted diagnostics for COVID-19. Biosens Bioelectron 2022; 205:114101. [PMID: 35202984 PMCID: PMC8849862 DOI: 10.1016/j.bios.2022.114101] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 02/02/2022] [Accepted: 02/14/2022] [Indexed: 12/12/2022]
Abstract
The scenery of molecular diagnostics for infectious diseases is rapidly evolving to respond to the COVID-19 epidemic. The sensitivity and specificity of diagnostics, along with speed and accuracy, are crucial requirements for effective analytical tools to address the disease spreading around the world. Emerging diagnostic devices combine the latest trends in isothermal amplification methods for nucleic acids with state-of-the-art biosensing systems, intending to bypass roadblocks encountered in the last 2 years of the pandemic. Isothermal nucleic acid amplification is a simple procedure that quickly and efficiently accumulates nucleic acid sequences at a constant temperature, without the need for sophisticated equipment. The integration of isothermal amplification into portable biosensing devices confers high sensitivity and improves screening at the point of need in low-resource settings. This review reports the latest trends reached in this field with the latest examples of isothermal amplification-powered biosensors for detecting SARS-CoV-2, with different configurations, as well as their intrinsic advantages and disadvantages.
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Affiliation(s)
- Mariarita De Felice
- Institute of Bioscience and BioResources, National Research Council, Department of Biology, Agriculture and Food Science, Via P. Castellino 111, 80100, Naples, Italy
| | - Mariarosaria De Falco
- Institute of Bioscience and BioResources, National Research Council, Department of Biology, Agriculture and Food Science, Via P. Castellino 111, 80100, Naples, Italy
| | - Daniele Zappi
- Institute of Crystallography, National Research Council, Department of Chemical Sciences and Materials Technologies, Via Salaria km 29.300, 00015, Monterotondo, Rome, Italy
| | - Amina Antonacci
- Institute of Crystallography, National Research Council, Department of Chemical Sciences and Materials Technologies, Via Salaria km 29.300, 00015, Monterotondo, Rome, Italy
| | - Viviana Scognamiglio
- Institute of Crystallography, National Research Council, Department of Chemical Sciences and Materials Technologies, Via Salaria km 29.300, 00015, Monterotondo, Rome, Italy.
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55
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Li N, Zhao B, Stavins R, Peinetti AS, Chauhan N, Bashir R, Cunningham BT, King WP, Lu Y, Wang X, Valera E. Overcoming the limitations of COVID-19 diagnostics with nanostructures, nucleic acid engineering, and additive manufacturing. CURRENT OPINION IN SOLID STATE & MATERIALS SCIENCE 2022; 26:100966. [PMID: 34840515 PMCID: PMC8604633 DOI: 10.1016/j.cossms.2021.100966] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 11/05/2021] [Accepted: 11/09/2021] [Indexed: 05/04/2023]
Abstract
The COVID-19 pandemic revealed fundamental limitations in the current model for infectious disease diagnosis and serology, based upon complex assay workflows, laboratory-based instrumentation, and expensive materials for managing samples and reagents. The lengthy time delays required to obtain test results, the high cost of gold-standard PCR tests, and poor sensitivity of rapid point-of-care tests contributed directly to society's inability to efficiently identify COVID-19-positive individuals for quarantine, which in turn continues to impact return to normal activities throughout the economy. Over the past year, enormous resources have been invested to develop more effective rapid tests and laboratory tests with greater throughput, yet the vast majority of engineering and chemistry approaches are merely incremental improvements to existing methods for nucleic acid amplification, lateral flow test strips, and enzymatic amplification assays for protein-based biomarkers. Meanwhile, widespread commercial availability of new test kits continues to be hampered by the cost and time required to develop single-use disposable microfluidic plastic cartridges manufactured by injection molding. Through development of novel technologies for sensitive, selective, rapid, and robust viral detection and more efficient approaches for scalable manufacturing of microfluidic devices, we can be much better prepared for future management of infectious pathogen outbreaks. Here, we describe how photonic metamaterials, graphene nanomaterials, designer DNA nanostructures, and polymers amenable to scalable additive manufacturing are being applied towards overcoming the fundamental limitations of currently dominant COVID-19 diagnostic approaches. In this paper, we review how several distinct classes of nanomaterials and nanochemistry enable simple assay workflows, high sensitivity, inexpensive instrumentation, point-of-care sample-to-answer virus diagnosis, and rapidly scaled manufacturing.
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Affiliation(s)
- Nantao Li
- Carle Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, United States
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, United States
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, United States
| | - Bin Zhao
- Carle Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, United States
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, United States
| | - Robert Stavins
- Department of Mechanical Science and Engineering, University of Illinois at Urbana-Champaign, United States
| | - Ana Sol Peinetti
- Department of Chemistry, University of Illinois at Urbana-Champaign, United States
| | - Neha Chauhan
- Carle Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, United States
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, United States
| | - Rashid Bashir
- Carle Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, United States
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, United States
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, United States
- Department of Bioengineering, University of Illinois at Urbana-Champaign, United States
| | - Brian T Cunningham
- Carle Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, United States
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, United States
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, United States
- Department of Bioengineering, University of Illinois at Urbana-Champaign, United States
| | - William P King
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, United States
- Department of Mechanical Science and Engineering, University of Illinois at Urbana-Champaign, United States
| | - Yi Lu
- Carle Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, United States
- Department of Chemistry, University of Illinois at Urbana-Champaign, United States
| | - Xing Wang
- Carle Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, United States
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, United States
- Department of Chemistry, University of Illinois at Urbana-Champaign, United States
| | - Enrique Valera
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, United States
- Department of Bioengineering, University of Illinois at Urbana-Champaign, United States
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56
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Tng DJH, Yin BCY, Cao J, Ko KKK, Goh KCM, Chua DXW, Zhang Y, Chua MLK, Low JGH, Ooi EE, Soo KC. Amplified parallel antigen rapid test for point-of-care salivary detection of SARS-CoV-2 with improved sensitivity. Mikrochim Acta 2022; 189:14. [PMID: 34870771 PMCID: PMC8646336 DOI: 10.1007/s00604-021-05113-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 11/23/2021] [Indexed: 01/11/2023]
Abstract
In the ongoing COVID-19 pandemic, simple, rapid, point-of-care tests not requiring trained personnel for primary care testing are essential. Saliva-based antigen rapid tests (ARTs) can fulfil this need, but these tests require overnight-fasted samples; without which independent studies have demonstrated sensitivities of only 11.7 to 23.1%. Herein, we report an Amplified Parallel ART (AP-ART) with sensitivity above 90%, even with non-fasted samples. The virus was captured multimodally, using both anti-spike protein antibodies and Angiotensin Converting Enzyme 2 (ACE2) protein. It also featured two parallel flow channels. The first contained spike protein binding gold nanoparticles which produced a visible red line upon encountering the virus. The second contained signal amplifying nanoparticles that complex with the former and amplify the signal without any linker. Compared to existing dual gold amplification techniques, a limit of detection of one order of magnitude lower was achieved (0.0064 ng·mL-1). AP-ART performance in detecting SARS-CoV-2 in saliva of COVID-19 patients was investigated using a case-control study (139 participants enrolled and 162 saliva samples tested). Unlike commercially available ARTs, the sensitivity of AP-ART was maintained even when non-fasting saliva was used. Compared to the gold standard reverse transcription-polymerase chain reaction testing on nasopharyngeal samples, non-fasting saliva tested on AP-ART showed a sensitivity of 97.0% (95% CI: 84.7-99.8); without amplification, the sensitivity was 72.7% (95% CI: 83.7-94.8). Thus, AP-ART has the potential to be developed for point-of-care testing, which may be particularly important in resource-limited settings, and for early diagnosis to initiate newly approved therapies to reduce COVID-19 severity.
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Affiliation(s)
- Danny Jian Hang Tng
- Department of Infectious Diseases, Singapore General Hospital, 20 College Road, Singapore, 169856 Singapore
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, Singapore, 169857 Singapore
- Department of Head and Neck and Thoracic Cancers, Division of Radiation Oncology, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore, 169610 Singapore
| | - Bryan Chu Yang Yin
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, Singapore, 169857 Singapore
| | - Jing Cao
- Department of Biomedical Engineering, National University Singapore, 4 Engineering Drive 3, Engineering Block 4, Singapore, 117583 Singapore
- State Key Laboratory for Oncogenes and Related Genes, School of Biomedical Engineering and Institute of Medical Robotics, Shanghai Jiao Tong University, Shanghai, 200030 People’s Republic of China
| | - Kwan Ki Karrie Ko
- Department of Microbiology, Singapore General Hospital, 20 College Road, Singapore, 169856 Singapore
| | - Kenneth Choon Meng Goh
- Department of Microbiology, Singapore General Hospital, 20 College Road, Singapore, 169856 Singapore
| | - Delia Xue Wen Chua
- Department of Biomedical Engineering, National University Singapore, 4 Engineering Drive 3, Engineering Block 4, Singapore, 117583 Singapore
| | - Yong Zhang
- Department of Biomedical Engineering, National University Singapore, 4 Engineering Drive 3, Engineering Block 4, Singapore, 117583 Singapore
| | - Melvin Lee Kiang Chua
- Department of Head and Neck and Thoracic Cancers, Division of Radiation Oncology, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore, 169610 Singapore
- Division of Medical Sciences, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore, 169610 Singapore
- Oncology Academic Programme, Duke-NUS Medical School, 8 College Road, Singapore, 169857 Singapore
| | - Jenny Guek Hong Low
- Department of Infectious Diseases, Singapore General Hospital, 20 College Road, Singapore, 169856 Singapore
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, Singapore, 169857 Singapore
| | - Eng Eong Ooi
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, Singapore, 169857 Singapore
| | - Khee Chee Soo
- Division of Medical Sciences, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore, 169610 Singapore
- Oncology Academic Programme, Duke-NUS Medical School, 8 College Road, Singapore, 169857 Singapore
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Malpartida-Cardenas K, Miglietta L, Peng T, Moniri A, Holmes A, Georgiou P, Rodriguez-Manzano J. Single-channel digital LAMP multiplexing using amplification curve analysis. SENSORS & DIAGNOSTICS 2022; 1:465-468. [PMID: 37034965 PMCID: PMC7614402 DOI: 10.1039/d2sd00038e] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We demonstrate LAMP multiplexing (5-plex) in a single reaction with a single fluorescent channel using the machine learning-based method amplification curve analysis, showing a classification accuracy of 91.33% for detection of respiratory pathogens.
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Affiliation(s)
- Kenny Malpartida-Cardenas
- Department of Infectious Disease, Imperial College London, London W12 0NN, UK
- Department of Electrical and Electronic Engineering, Imperial College London, London SW7 2AZ, UK
| | - Luca Miglietta
- Department of Infectious Disease, Imperial College London, London W12 0NN, UK
- Department of Electrical and Electronic Engineering, Imperial College London, London SW7 2AZ, UK
| | - Tianyi Peng
- Department of Infectious Disease, Imperial College London, London W12 0NN, UK
| | - Ahmad Moniri
- Department of Electrical and Electronic Engineering, Imperial College London, London SW7 2AZ, UK
| | - Alison Holmes
- Department of Infectious Disease, Imperial College London, London W12 0NN, UK
| | - Pantelis Georgiou
- Department of Electrical and Electronic Engineering, Imperial College London, London SW7 2AZ, UK
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58
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Panpradist N, Kline EC, Atkinson RG, Roller M, Wang Q, Hull IT, Kotnik JH, Oreskovic AK, Bennett C, Leon D, Lyon V, Gilligan-Steinberg SD, Han PD, Drain PK, Starita LM, Thompson MJ, Lutz BR. Harmony COVID-19: A ready-to-use kit, low-cost detector, and smartphone app for point-of-care SARS-CoV-2 RNA detection. SCIENCE ADVANCES 2021; 7:eabj1281. [PMID: 34910507 PMCID: PMC8673764 DOI: 10.1126/sciadv.abj1281] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 10/26/2021] [Indexed: 05/22/2023]
Abstract
RNA amplification tests sensitively detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, but their complexity and cost are prohibitive for expanding coronavirus disease 2019 (COVID-19) testing. We developed “Harmony COVID-19,” a point-of-care test using inexpensive consumables, ready-to-use reagents, and a simple device. Our ready-to-use, multiplexed reverse transcription, loop-mediated isothermal amplification (RT-LAMP) can detect down to 0.38 SARS-CoV-2 RNA copies/μl and can report in 17 min for high–viral load samples (5000 copies/μl). Harmony detected 97 or 83% of contrived samples with ≥0.5 viral particles/μl in nasal matrix or saliva, respectively. Evaluation in clinical nasal specimens (n = 101) showed 100% detection of RNA extracted from specimens with ≥0.5 SARS-CoV-2 RNA copies/μl, with 100% specificity in specimens positive for other respiratory pathogens. Extraction-free analysis (n = 29) had 95% success in specimens with ≥1 RNA copies/μl. Usability testing performed first time by health care workers showed 95% accuracy.
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Affiliation(s)
- Nuttada Panpradist
- Department of Bioengineering, University of Washington, Seattle, WA, USA
- Global Health for Women, Adolescents, and Children, School of Public Health, University of Washington, Seattle, WA, USA
| | - Enos C. Kline
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Robert G. Atkinson
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Michael Roller
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Qin Wang
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Ian T. Hull
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Jack H. Kotnik
- Department of Bioengineering, University of Washington, Seattle, WA, USA
- Department of Family Medicine, University of Washington, Seattle, WA, USA
| | - Amy K. Oreskovic
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Crissa Bennett
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Daniel Leon
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Victoria Lyon
- Department of Family Medicine, University of Washington, Seattle, WA, USA
| | | | - Peter D. Han
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Paul K. Drain
- Departments of Global Health, Medicine, and Epidemiology, University of Washington, Seattle, WA, USA
| | - Lea M. Starita
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | | | - Barry R. Lutz
- Department of Bioengineering, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
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59
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Shojaei Baghini M, Vilouras A, Douthwaite M, Georgiou P, Dahiya R. Ultra‐thin ISFET‐based sensing systems. ELECTROCHEMICAL SCIENCE ADVANCES 2021. [DOI: 10.1002/elsa.202100202] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Affiliation(s)
- Mahdieh Shojaei Baghini
- Bendable Electronics and Sensing Technologies (BEST) Group School of Engineering University of Glasgow Glasgow UK
| | - Anastasios Vilouras
- Bendable Electronics and Sensing Technologies (BEST) Group School of Engineering University of Glasgow Glasgow UK
| | - Matthew Douthwaite
- Centre for Bio‐Inspired Technology Department of Electrical and Electronic Engineering Imperial College London London UK
| | - Pantelis Georgiou
- Centre for Bio‐Inspired Technology Department of Electrical and Electronic Engineering Imperial College London London UK
| | - Ravinder Dahiya
- Bendable Electronics and Sensing Technologies (BEST) Group School of Engineering University of Glasgow Glasgow UK
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60
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Manzanas C, Alam MM, Loeb JC, Lednicky JA, Wu CY, Fan ZH. A Valve-Enabled Sample Preparation Device with Isothermal Amplification for Multiplexed Virus Detection at the Point-of-Care. ACS Sens 2021; 6:4176-4184. [PMID: 34767357 PMCID: PMC8609915 DOI: 10.1021/acssensors.1c01718] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Early and accurate detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and influenza viruses at the point-of-care is crucial for reducing disease transmission during the current pandemic and future flu seasons. To prepare for potential cocirculation of these two viruses, we report a valve-enabled, paper-based sample preparation device integrated with isothermal amplification for their simultaneous detection. The device incorporates (1) virus lysis and RNA enrichment, enabled by ball-based valves for sequential delivery of reagents with no pipet requirement, (2) reverse transcription loop-mediated isothermal amplification, carried out in a coffee mug, and (3) colorimetric detection. We have used the device for simultaneously detecting inactivated SARS-CoV-2 and influenza A H1N1 viruses in 50 min, with limits of detection at 2 and 6 genome equivalents, respectively. The device was further demonstrated to detect both viruses in environmental samples.
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Affiliation(s)
- Carlos Manzanas
- Interdisciplinary Microsystems Group, Department of Mechanical and Aerospace Engineering, University of Florida, P. O. Box 116250, Gainesville, Florida 32611, United States
| | - Md Mahbubul Alam
- Department of Environmental and Global Health, University of Florida, Gainesville, Florida 32610, United States
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida 32610, United States
| | - Julia C Loeb
- Department of Environmental and Global Health, University of Florida, Gainesville, Florida 32610, United States
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida 32610, United States
| | - John A Lednicky
- Department of Environmental and Global Health, University of Florida, Gainesville, Florida 32610, United States
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida 32610, United States
| | - Chang-Yu Wu
- Department of Environmental Engineering Sciences, University of Florida, Gainesville, Florida 32611, United States
| | - Z Hugh Fan
- Interdisciplinary Microsystems Group, Department of Mechanical and Aerospace Engineering, University of Florida, P. O. Box 116250, Gainesville, Florida 32611, United States
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, Florida 32611, United States
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Tang Z, Nouri R, Dong M, Yang J, Greene W, Zhu Y, Yon M, Nair MS, Kuchipudi SV, Guan W. Rapid detection of novel coronavirus SARS-CoV-2 by RT-LAMP coupled solid-state nanopores. Biosens Bioelectron 2021; 197:113759. [PMID: 34741956 PMCID: PMC8560184 DOI: 10.1016/j.bios.2021.113759] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 09/25/2021] [Accepted: 10/29/2021] [Indexed: 12/15/2022]
Abstract
The current pandemic of COVID-19 caused by SARS-CoV-2 (severe acute respiratory syndrome coronavirus-2) has raised significant public health concerns. Rapid and accurate testing of SARS-CoV-2 is urgently needed for early detection and control of the disease spread. Here, we present an RT-LAMP coupled glass nanopore digital counting method for rapid detection of SARS-CoV-2. We validated and compared two one-pot RT-LAMP assays targeting nucleocapsid (N) and envelop (E) genes. The nucleocapsid assay was adopted due to its quick time to positive and better copy number sensitivity. For qualitative positive/negative classification of a testing sample, we used the glass nanopore to digitally count the RT-LAMP amplicons and benchmarked the event rate with a threshold. Due to its intrinsic single molecule sensitivity, nanopore sensors could capture the amplification dynamics more rapidly (quick time to positive). We validated our RT-LAMP coupled glass nanopore digital counting method for SARS-CoV-2 detection by using both spiked saliva samples and COVID-19 clinical nasopharyngeal swab samples. The results obtained showed excellent agreement with the gold standard RT-PCR assay. With its integration capability, the electronic nanopore digital counting platform has significant potential to provide a rapid, sensitive, and specific point-of-care assay for SARS-CoV-2.
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Affiliation(s)
- Zifan Tang
- Department of Electrical Engineering, Pennsylvania State University, University Park, PA, 16802, United States
| | - Reza Nouri
- Department of Electrical Engineering, Pennsylvania State University, University Park, PA, 16802, United States
| | - Ming Dong
- Department of Electrical Engineering, Pennsylvania State University, University Park, PA, 16802, United States
| | - Jianbo Yang
- Department of Pathology and Laboratory Medicine, Penn State Hershey Medical, Hershey, PA, 17033, United States
| | - Wallace Greene
- Department of Pathology and Laboratory Medicine, Penn State Hershey Medical, Hershey, PA, 17033, United States
| | - Yusheng Zhu
- Department of Pathology and Laboratory Medicine, Penn State Hershey Medical, Hershey, PA, 17033, United States
| | - Michele Yon
- Animal Diagnostic Laboratory, Pennsylvania State University, University Park, PA, 16802, United States
| | - Meera Surendran Nair
- Animal Diagnostic Laboratory, Pennsylvania State University, University Park, PA, 16802, United States
| | - Suresh V Kuchipudi
- Animal Diagnostic Laboratory, Pennsylvania State University, University Park, PA, 16802, United States; Center for Infectious Disease Dynamic, Pennsylvania State University, University Park, PA, 16802, United States
| | - Weihua Guan
- Department of Electrical Engineering, Pennsylvania State University, University Park, PA, 16802, United States; Department of Biomedical Engineering, Pennsylvania State University, University Park, PA, 16802, United States.
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62
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Wormald B, Rodriguez-Manzano J, Moser N, Pennisi I, Ind TEJ, Vroobel K, Attygalle A, Georgiou P, deSouza NM. Loop-Mediated Isothermal Amplification Assay for Detecting Tumor Markers and Human Papillomavirus: Accuracy and Supplemental Diagnostic Value to Endovaginal MRI in Cervical Cancer. Front Oncol 2021; 11:747614. [PMID: 34790573 PMCID: PMC8591099 DOI: 10.3389/fonc.2021.747614] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 10/13/2021] [Indexed: 11/18/2022] Open
Abstract
OBJECTIVE To establish the sensitivity and specificity of a human papillomavirus (HPV) and tumor marker DNA/mRNA assay for detecting cervical cancer that is transferrable to a Lab-on-a-chip platform and determine its diagnostic benefit in early stage disease when used in conjunction with high-resolution endovaginal magnetic resonance imaging (MRI). METHODS Forty-one patients (27 with Stage1 cervical cancer [Group1] and 14 non-cancer HPV negative controls [Group2]) had DNA and RNA extracted from cervical cytology swab samples. HPV16, HPV18, hTERT, TERC/GAPDH and MYC/GAPDH concentration was established using a loop mediated isothermal amplification (LAMP) assay. Thresholds for tumor marker detection for Group1 were set from Group2 analysis (any hTERT, TERC/GAPDH 3.12, MYC/GAPDH 0.155). Group 1 participants underwent endovaginal MRI. Sensitivity and specificity for cancer detection by LAMP and MRI individually and combined was documented by comparison to pathology. RESULTS Sensitivity and specificity for cancer detection was 68.8% and 77.8% if any tumor marker was positive regardless of HPV status (scenario1), and 93.8% and 55.8% if tumor marker or HPV were positive (scenario 2). Adding endovaginal MRI improved specificity to 88.9% in scenario 1 (sensitivity 68.8%) and to 77.8%% in scenario2 (sensitivity 93.8%). CONCLUSION Specificity for cervical cancer detection using a LAMP assay is superior with tumor markers; low sensitivity is improved by HPV detection. Accuracy for early stage cervical cancer detection is optimal using a spatially multiplexed tumor marker/HPV LAMP assay together with endovaginal MRI.
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Affiliation(s)
- Benjamin Wormald
- Cancer Research UK Cancer Imaging Centre, Division of Radiotherapy and Imaging, The Institute of Cancer Research, London, United Kingdom
| | - Jesus Rodriguez-Manzano
- Department of Infectious Disease, Faculty of Medicine, Imperial College, London, United Kingdom
| | - Nicolas Moser
- Department of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College London, London, United Kingdom
| | - Ivana Pennisi
- Department of Infectious Disease, Faculty of Medicine, Imperial College, London, United Kingdom
| | - Thomas E. J. Ind
- Departmentof Surgical Oncology, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Katherine Vroobel
- Department of Histopathology, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Ayoma Attygalle
- Department of Histopathology, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Pantelis Georgiou
- Department of Electrical and Electronic Engineering, Faculty of Engineering, Imperial College London, London, United Kingdom
| | - Nandita M. deSouza
- Cancer Research UK Cancer Imaging Centre, Division of Radiotherapy and Imaging, The Institute of Cancer Research, London, United Kingdom
- MRI Unit, Royal Marsden NHS Foundation Trust, Sutton, United Kingdom
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Saki EF, Setiawan SA, Wicaksono DHB. Portable Tools for COVID-19 Point-of-Care Detection: A Review. IEEE SENSORS JOURNAL 2021; 21:23737-23750. [PMID: 35582343 PMCID: PMC8864949 DOI: 10.1109/jsen.2021.3110857] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 08/22/2021] [Accepted: 08/26/2021] [Indexed: 06/12/2023]
Abstract
Recently, several methods for SARS-CoV-2 detection have been developed to obtain rapid, portable, cheap, and easy-to-use diagnostic tools. This review paper summarizes and discusses studies on the development of point-of-care devices for SARS-CoV-2 diagnosis with comparisons between them from several aspects. Various detection methods of the recently developed portable COVID-19 biosensor will be presented in this review. The discussion is divided into four major classifications based on the target biomarkers of SARS-CoV-2, such as antibodies, nucleic acids, antigens, and metabolic products. An overview of the potential development for future study is also provided. Moreover, basic knowledge of biosensors is also explained for tutoring the implementation of theory into the research of COVID-19 biosensors. This review paper is aimed to provide a tutorial by collecting the information on the development of a point-of-care device for SARS-CoV-2 detection to provide information for further research and propose the new COVID-19 portable diagnostic tool.
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Affiliation(s)
- Elga F. Saki
- Department of Biomedical EngineeringFaculty of Life Sciences and TechnologySwiss German University (SGU)Tangerang15143Indonesia
| | | | - Dedy H. B. Wicaksono
- Department of Biomedical EngineeringFaculty of Life Sciences and TechnologySwiss German University (SGU)Tangerang15143Indonesia
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64
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Alvarez MM, Bravo-González S, González-González E, Trujillo-de Santiago G. Portable and Label-Free Quantitative Loop-Mediated Isothermal Amplification (LF-qLamp) for Reliable COVID-19 Diagnostics in Three Minutes of Reaction Time: Arduino-Based Detection System Assisted by a pH Microelectrode. BIOSENSORS 2021; 11:386. [PMID: 34677342 PMCID: PMC8533988 DOI: 10.3390/bios11100386] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 10/02/2021] [Accepted: 10/07/2021] [Indexed: 11/16/2022]
Abstract
Loop-mediated isothermal amplification (LAMP) has been recently studied as an alternative method for cost-effective diagnostics in the context of the current COVID-19 pandemic. Recent reports document that LAMP-based diagnostic methods have a comparable sensitivity and specificity to that of RT-qPCR. We report the use of a portable Arduino-based LAMP-based amplification system assisted by pH microelectrodes for the accurate and reliable diagnosis of SARS-CoV-2 during the first 3 min of the amplification reaction. We show that this simple system enables a straightforward discrimination between samples containing or not containing artificial SARS-CoV-2 genetic material in the range of 10 to 10,000 copies per 50 µL of reaction mix. We also spiked saliva samples with SARS-CoV-2 synthetic material and corroborated that the LAMP reaction can be successfully monitored in real time using microelectrodes in saliva samples as well. These results may have profound implications for the design of real-time and portable quantitative systems for the reliable detection of viral pathogens including SARS-CoV-2.
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Affiliation(s)
- Mario Moisés Alvarez
- Centro de Biotecnología-FEMSA, Tecnologico de Monterrey, Monterrey 64849, Mexico; (S.B.-G.); (E.G.-G.)
- Departamento de Bioingeniería, Tecnologico de Monterrey, Monterrey 64849, Mexico
| | - Sergio Bravo-González
- Centro de Biotecnología-FEMSA, Tecnologico de Monterrey, Monterrey 64849, Mexico; (S.B.-G.); (E.G.-G.)
- Departamento de Bioingeniería, Tecnologico de Monterrey, Monterrey 64849, Mexico
| | - Everardo González-González
- Centro de Biotecnología-FEMSA, Tecnologico de Monterrey, Monterrey 64849, Mexico; (S.B.-G.); (E.G.-G.)
- Departamento de Bioingeniería, Tecnologico de Monterrey, Monterrey 64849, Mexico
| | - Grissel Trujillo-de Santiago
- Centro de Biotecnología-FEMSA, Tecnologico de Monterrey, Monterrey 64849, Mexico; (S.B.-G.); (E.G.-G.)
- Departamento de Ingeniería Mecatrónica y Eléctrica, Tecnologico de Monterrey, Monterrey 64849, Mexico
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65
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Krokhine S, Torabi H, Doostmohammadi A, Rezai P. Conventional and microfluidic methods for airborne virus isolation and detection. Colloids Surf B Biointerfaces 2021; 206:111962. [PMID: 34352699 PMCID: PMC8249716 DOI: 10.1016/j.colsurfb.2021.111962] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 06/22/2021] [Accepted: 06/29/2021] [Indexed: 12/23/2022]
Abstract
With the COVID-19 pandemic, the threat of infectious diseases to public health and safety has become much more apparent. Viral, bacterial and fungal diseases have led to the loss of millions of lives, especially in the developing world. Diseases caused by airborne viruses like SARS-CoV-2 are difficult to control, as these viruses are easily transmissible and can circulate in the air for hours. To contain outbreaks of viruses such as SARS-CoV-2 and institute targeted precautions, it is important to detect them in air and understand how they infect their targets. Point-of-care (PoC) diagnostics and point-of-need (PoN) detection methods are necessary to rapidly test patient and environmental samples, so precautions can immediately be applied. Traditional benchtop detection methods such as ELISA, PCR and culture are not suitable for PoC and PoN monitoring, because they can take hours to days and require specialized equipment. Microfluidic devices can be made at low cost to perform such assays rapidly and at the PoN. They can also be integrated with air- and liquid-based sampling technologies to capture and analyze viruses from air and body fluids. Here, conventional and microfluidic virus detection methods are reviewed and compared. The use of air sampling devices to capture and concentrate viruses is discussed first, followed by a review of analysis methods such as immunoassays, RT-PCR and isothermal amplification in conventional and microfluidic platforms. This review provides an overview of the capabilities of microfluidics in virus handling and detection, which will be useful to infectious disease researchers, biomedical engineers, and public health agencies.
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Affiliation(s)
- Sophie Krokhine
- Faculty of Science, McMaster University, Burke Science Building, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada.
| | - Hadis Torabi
- Department of Biomedical Engineering, University of Isfahan, Iran.
| | | | - Pouya Rezai
- Department of Mechanical Engineering, York University, ON, Canada.
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66
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Hepp C, Shiaelis N, Robb NC, Vaughan A, Matthews PC, Stoesser N, Crook D, Kapanidis AN. Viral detection and identification in 20 min by rapid single-particle fluorescence in-situ hybridization of viral RNA. Sci Rep 2021; 11:19579. [PMID: 34599242 PMCID: PMC8486776 DOI: 10.1038/s41598-021-98972-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 09/09/2021] [Indexed: 12/24/2022] Open
Abstract
The increasing risk from viral outbreaks such as the ongoing COVID-19 pandemic exacerbates the need for rapid, affordable and sensitive methods for virus detection, identification and quantification; however, existing methods for detecting virus particles in biological samples usually depend on multistep protocols that take considerable time to yield a result. Here, we introduce a rapid fluorescence in situ hybridization (FISH) protocol capable of detecting influenza virus, avian infectious bronchitis virus and SARS-CoV-2 specifically and quantitatively in approximately 20 min, in virus cultures, combined nasal and throat swabs with added virus and likely patient samples without previous purification. This fast and facile workflow can be adapted both as a lab technique and a future diagnostic tool in enveloped viruses with an accessible genome.
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Affiliation(s)
- Christof Hepp
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, OX1 3PU, UK.
| | - Nicolas Shiaelis
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, OX1 3PU, UK
| | - Nicole C Robb
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, OX1 3PU, UK
- Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
| | - Alison Vaughan
- Nuffield Department for Medicine, University of Oxford, Oxford, OX3 9DU, UK
| | | | - Nicole Stoesser
- Nuffield Department for Medicine, University of Oxford, Oxford, OX3 9DU, UK
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at the University of Oxford in Partnership With Public Health England, University of Oxford, Oxford, UK
| | - Derrick Crook
- Nuffield Department for Medicine, University of Oxford, Oxford, OX3 9DU, UK
- NIHR Biomedical Research Centre, University of Oxford, Oxford, UK
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at the University of Oxford in Partnership With Public Health England, University of Oxford, Oxford, UK
| | - Achillefs N Kapanidis
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, OX1 3PU, UK.
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Lee D, Chu CH, Sarioglu AF. Point-of-Care Toolkit for Multiplex Molecular Diagnosis of SARS-CoV-2 and Influenza A and B Viruses. ACS Sens 2021; 6:3204-3213. [PMID: 34523904 PMCID: PMC8456773 DOI: 10.1021/acssensors.1c00702] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 08/24/2021] [Indexed: 12/23/2022]
Abstract
Severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) is still spreading around the globe causing immense public health and socioeconomic problems. As the infection can progress with mild symptoms that can be misinterpreted as the flu, self-testing methods that can positively identify SARS-CoV-2 are needed to effectively track and prevent the transmission of the virus. In this work, we report a point-of-care toolkit for multiplex molecular diagnosis of SARS-CoV-2 and influenza A and B viruses in saliva samples. Our assay is physically programmed to run a sequence of chemical reactions on a paper substrate and internally generate heat to drive these reactions for an autonomous extraction, purification, and amplification of the viral RNA. Using our assay, we could reliably detect SARS-CoV-2 and influenza viruses at concentrations as low as 50 copies/μL visually from a colorimetric analysis. The capability to autonomously perform a traditionally labor-intensive genetic assay on a disposable platform will enable frequent, on-demand self-testing, a critical need to track and contain this and future outbreaks.
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Affiliation(s)
- Dohwan Lee
- School
of Electrical and Computer Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Chia-Heng Chu
- School
of Electrical and Computer Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - A. Fatih Sarioglu
- School
of Electrical and Computer Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
- Parker
H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
- Institute
for Electronics and Nanotechnology, Georgia
Institute of Technology, Atlanta, Georgia 30332, United States
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68
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Li F, He P, Xiong D, Lou Y, Pu Q, Zhang H, Zhang H, Yu J. A Reverse Transcription Recombinase-Aided Amplification Method for Rapid and Point-of-Care Detection of SARS-CoV-2, including Variants. Viruses 2021; 13:1875. [PMID: 34578456 PMCID: PMC8472806 DOI: 10.3390/v13091875] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 09/08/2021] [Accepted: 09/17/2021] [Indexed: 12/23/2022] Open
Abstract
The worldwide pandemic caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and its emergence of variants needs rapid and point-of-care testing methods for a broad diagnosis. The regular RT-qPCR is time-consuming and limited in central laboratories, so a broad and large-scale screening requirement calls for rapid and in situ methods. In this regard, a reverse transcription recombinase-aided amplification (RT-RAA) is proposed here for the rapid and point-of-care detection of SARS-CoV-2. A set of highly conserved primers and probes targeting more than 98% of SARS-CoV-2 strains, including currently circulating variants (four variants of concerns (VOCs) and three variants of interest (VOIs)), was used in this study. With the preferred primers, the RT-RAA assay showed a 100% specificity to SARS-CoV-2 from eight other respiratory RNA viruses. Moreover, the assay here is of a high sensitivity and 0.48 copies/μL can be detected within 25 min at a constant temperature (42 °C), which can be realized on portable equipment. Furthermore, the RT-RAA assay demonstrated its high agreement for the detection of SARS-CoV-2 in clinical specimens compared with RT-qPCR. The rapid, simple and point-of-care RT-RAA method is expected to be an appealing detection tool to detect SARS-CoV-2, including variants, in clinical diagnostic applications.
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Affiliation(s)
- Fengyun Li
- State Key Laboratory of Applied Organic Chemistry, Key Laboratory of Nonferrous Metals Chemistry and Resources Utilization of Gansu Province, Department of Chemistry, Lanzhou University, Lanzhou 730000, China; (F.L.); (Q.P.); (H.Z.); (H.Z.)
| | - Ping He
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; (P.H.); (D.X.)
- College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dongyan Xiong
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; (P.H.); (D.X.)
- College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yakun Lou
- Zhengzhou Zhongdao Biotechnology Co., Ltd., Zhengzhou 450000, China;
| | - Qiaosheng Pu
- State Key Laboratory of Applied Organic Chemistry, Key Laboratory of Nonferrous Metals Chemistry and Resources Utilization of Gansu Province, Department of Chemistry, Lanzhou University, Lanzhou 730000, China; (F.L.); (Q.P.); (H.Z.); (H.Z.)
| | - Haixia Zhang
- State Key Laboratory of Applied Organic Chemistry, Key Laboratory of Nonferrous Metals Chemistry and Resources Utilization of Gansu Province, Department of Chemistry, Lanzhou University, Lanzhou 730000, China; (F.L.); (Q.P.); (H.Z.); (H.Z.)
| | - Huige Zhang
- State Key Laboratory of Applied Organic Chemistry, Key Laboratory of Nonferrous Metals Chemistry and Resources Utilization of Gansu Province, Department of Chemistry, Lanzhou University, Lanzhou 730000, China; (F.L.); (Q.P.); (H.Z.); (H.Z.)
| | - Junping Yu
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; (P.H.); (D.X.)
- College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
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Moore KJM, Cahill J, Aidelberg G, Aronoff R, Bektaş A, Bezdan D, Butler DJ, Chittur SV, Codyre M, Federici F, Tanner NA, Tighe SW, True R, Ware SB, Wyllie AL, Afshin EE, Bendesky A, Chang CB, Dela Rosa R, Elhaik E, Erickson D, Goldsborough AS, Grills G, Hadasch K, Hayden A, Her SY, Karl JA, Kim CH, Kriegel AJ, Kunstman T, Landau Z, Land K, Langhorst BW, Lindner AB, Mayer BE, McLaughlin LA, McLaughlin MT, Molloy J, Mozsary C, Nadler JL, D'Silva M, Ng D, O'Connor DH, Ongerth JE, Osuolale O, Pinharanda A, Plenker D, Ranjan R, Rosbash M, Rotem A, Segarra J, Schürer S, Sherrill-Mix S, Solo-Gabriele H, To S, Vogt MC, Yu AD, Mason CE. Loop-Mediated Isothermal Amplification Detection of SARS-CoV-2 and Myriad Other Applications. J Biomol Tech 2021; 32:228-275. [PMID: 35136384 PMCID: PMC8802757 DOI: 10.7171/jbt.21-3203-017] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
As the second year of the COVID-19 pandemic begins, it remains clear that a massive increase in the ability to test for SARS-CoV-2 infections in a myriad of settings is critical to controlling the pandemic and to preparing for future outbreaks. The current gold standard for molecular diagnostics is the polymerase chain reaction (PCR), but the extraordinary and unmet demand for testing in a variety of environments means that both complementary and supplementary testing solutions are still needed. This review highlights the role that loop-mediated isothermal amplification (LAMP) has had in filling this global testing need, providing a faster and easier means of testing, and what it can do for future applications, pathogens, and the preparation for future outbreaks. This review describes the current state of the art for research of LAMP-based SARS-CoV-2 testing, as well as its implications for other pathogens and testing. The authors represent the global LAMP (gLAMP) Consortium, an international research collective, which has regularly met to share their experiences on LAMP deployment and best practices; sections are devoted to all aspects of LAMP testing, including preanalytic sample processing, target amplification, and amplicon detection, then the hardware and software required for deployment are discussed, and finally, a summary of the current regulatory landscape is provided. Included as well are a series of first-person accounts of LAMP method development and deployment. The final discussion section provides the reader with a distillation of the most validated testing methods and their paths to implementation. This review also aims to provide practical information and insight for a range of audiences: for a research audience, to help accelerate research through sharing of best practices; for an implementation audience, to help get testing up and running quickly; and for a public health, clinical, and policy audience, to help convey the breadth of the effect that LAMP methods have to offer.
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Affiliation(s)
- Keith J M Moore
- School of Science and Engineering, Ateneo de Manila University, Quezon City 1108, Philippines
| | | | - Guy Aidelberg
- Université de Paris, INSERM U1284, Center for Research and Interdisciplinarity (CRI), 75006 Paris, France
- Just One Giant Lab, Centre de Recherches Interdisciplinaires (CRI), 75004 Paris, France
| | - Rachel Aronoff
- Just One Giant Lab, Centre de Recherches Interdisciplinaires (CRI), 75004 Paris, France
- Action for Genomic Integrity Through Research! (AGiR!), Lausanne, Switzerland
- Association Hackuarium, Lausanne, Switzerland
| | - Ali Bektaş
- Oakland Genomics Center, Oakland, CA 94609, USA
| | - Daniela Bezdan
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tübingen, Germany
- NGS Competence Center Tübingen (NCCT), University of Tübingen, 72076 Tübingen, Germany
- Poppy Health, Inc, San Francisco, CA 94158, USA
- Institute of Medical Virology and Epidemiology of Viral Diseases, University Hospital, 72076 Tübingen, Germany
| | - Daniel J Butler
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Sridar V Chittur
- Center for Functional Genomics, Department of Biomedical Sciences, School of Public Health, University at Albany, State University of New York, Rensselaer, 12222, USA
| | - Martin Codyre
- GiantLeap Biotechnology Ltd, Wicklow A63 Kv91, Ireland
| | - Fernan Federici
- ANID, Millennium Science Initiative Program, Millennium Institute for Integrative Biology (iBio), Institute for Biological and Medical Engineering, Schools of Engineering, Biology and Medicine, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
| | | | | | - Randy True
- FloodLAMP Biotechnologies, San Carlos, CA 94070, USA
| | - Sarah B Ware
- Just One Giant Lab, Centre de Recherches Interdisciplinaires (CRI), 75004 Paris, France
- BioBlaze Community Bio Lab, 1800 W Hawthorne Ln, Ste J-1, West Chicago, IL 60185, USA
- Blossom Bio Lab, 1800 W Hawthorne Ln, Ste K-2, West Chicago, IL 60185, USA
| | - Anne L Wyllie
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Evan E Afshin
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY 10065, USA
| | - Andres Bendesky
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY 10027, USA
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Connie B Chang
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, 59717, USA
- Center for Biofilm Engineering, Montana State University, Bozeman, 59717, USA
| | - Richard Dela Rosa
- School of Science and Engineering, Ateneo de Manila University, Quezon City 1108, Philippines
| | - Eran Elhaik
- Department of Biology, Lund University, Sölvegatan 35, Lund, Sweden
| | - David Erickson
- Sibley School of Mechanical and Aerospace Engineering, Cornell University, Ithaca, NY 14850, USA
| | | | - George Grills
- Department of Microbiology, University of Pennsylvania, Philadelphia, 19104, USA
| | - Kathrin Hadasch
- Université de Paris, INSERM U1284, Center for Research and Interdisciplinarity (CRI), 75006 Paris, France
- Department of Biology, Membrane Biophysics, Technische Universität Darmstadt, 64289 Darmstadt, Germany
- Lab3 eV, Labspace Darmstadt, 64295 Darmstadt, Germany
- IANUS Verein für Friedensorientierte Technikgestaltung eV, 64289 Darmstadt, Germany
| | - Andrew Hayden
- Center for Functional Genomics, Department of Biomedical Sciences, School of Public Health, University at Albany, State University of New York, Rensselaer, 12222, USA
| | | | - Julie A Karl
- Department of Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin, Madison, Madison 53705, USA
| | | | | | | | - Zeph Landau
- Department of Computer Science, University of California, Berkeley, Berkeley, 94720, USA
| | - Kevin Land
- Mologic, Centre for Advanced Rapid Diagnostics, (CARD), Bedford Technology Park, Thurleigh MK44 2YA, England
- Department of Electrical, Electronic and Computer Engineering, University of Pretoria, 0028 Pretoria, South Africa
| | | | - Ariel B Lindner
- Université de Paris, INSERM U1284, Center for Research and Interdisciplinarity (CRI), 75006 Paris, France
| | - Benjamin E Mayer
- Department of Biology, Membrane Biophysics, Technische Universität Darmstadt, 64289 Darmstadt, Germany
- Lab3 eV, Labspace Darmstadt, 64295 Darmstadt, Germany
| | | | - Matthew T McLaughlin
- Department of Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin, Madison, Madison 53705, USA
| | - Jenny Molloy
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB3 0AS, England
| | - Christopher Mozsary
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Jerry L Nadler
- Department of Pharmacology, New York Medical College, Valhalla, 10595, USA
| | - Melinee D'Silva
- Department of Pharmacology, New York Medical College, Valhalla, 10595, USA
| | - David Ng
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
| | - David H O'Connor
- Department of Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin, Madison, Madison 53705, USA
| | - Jerry E Ongerth
- University of Wollongong, Environmental Engineering, Wollongong NSW 2522, Australia
| | - Olayinka Osuolale
- Applied Environmental Metagenomics and Infectious Diseases Research (AEMIDR), Department of Biological Sciences, Elizade University, Ilara Mokin, Nigeria
| | - Ana Pinharanda
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Dennis Plenker
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Ravi Ranjan
- Genomics Resource Laboratory, Institute for Applied Life Sciences, University of Massachusetts, Amherst, 01003, USA
| | - Michael Rosbash
- Howard Hughes Medical Institute and Department of Biology, Brandeis University, Waltham, MA 02453, USA
| | | | | | | | - Scott Sherrill-Mix
- Department of Microbiology, University of Pennsylvania, Philadelphia, 19104, USA
| | | | - Shaina To
- School of Science and Engineering, Ateneo de Manila University, Quezon City 1108, Philippines
| | - Merly C Vogt
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Albert D Yu
- Howard Hughes Medical Institute and Department of Biology, Brandeis University, Waltham, MA 02453, USA
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY 10065, USA
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY 10065, USA
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70
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Toropov N, Osborne E, Joshi LT, Davidson J, Morgan C, Page J, Pepperell J, Vollmer F. SARS-CoV-2 Tests: Bridging the Gap between Laboratory Sensors and Clinical Applications. ACS Sens 2021; 6:2815-2837. [PMID: 34392681 PMCID: PMC8386036 DOI: 10.1021/acssensors.1c00612] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 07/28/2021] [Indexed: 12/15/2022]
Abstract
This review covers emerging biosensors for SARS-CoV-2 detection together with a review of the biochemical and clinical assays that are in use in hospitals and clinical laboratories. We discuss the gap in bridging the current practice of testing laboratories with nucleic acid amplification methods, and the robustness of assays the laboratories seek, and what emerging SARS-CoV-2 sensors have currently addressed in the literature. Together with the established nucleic acid and biochemical tests, we review emerging technology and antibody tests to determine the effectiveness of vaccines on individuals.
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Affiliation(s)
- Nikita Toropov
- Living
Systems Institute, University of Exeter, Exeter EX4 4QD, United Kingdom
| | - Eleanor Osborne
- Living
Systems Institute, University of Exeter, Exeter EX4 4QD, United Kingdom
| | | | - James Davidson
- Somerset
Lung Centre, Musgrove Park Hospital, Parkfield Drive, Taunton TA1 5DA, United Kingdom
| | - Caitlin Morgan
- Somerset
Lung Centre, Musgrove Park Hospital, Parkfield Drive, Taunton TA1 5DA, United Kingdom
| | - Joseph Page
- Somerset
Lung Centre, Musgrove Park Hospital, Parkfield Drive, Taunton TA1 5DA, United Kingdom
| | - Justin Pepperell
- Somerset
Lung Centre, Musgrove Park Hospital, Parkfield Drive, Taunton TA1 5DA, United Kingdom
| | - Frank Vollmer
- Living
Systems Institute, University of Exeter, Exeter EX4 4QD, United Kingdom
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71
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Li HK, Kaforou M, Rodriguez-Manzano J, Channon-Wells S, Moniri A, Habgood-Coote D, Gupta RK, Mills EA, Arancon D, Lin J, Chiu YH, Pennisi I, Miglietta L, Mehta R, Obaray N, Herberg JA, Wright VJ, Georgiou P, Shallcross LJ, Mentzer AJ, Levin M, Cooke GS, Noursadeghi M, Sriskandan S. Discovery and validation of a three-gene signature to distinguish COVID-19 and other viral infections in emergency infectious disease presentations: a case-control and observational cohort study. LANCET MICROBE 2021; 2:e594-e603. [PMID: 34423323 PMCID: PMC8367196 DOI: 10.1016/s2666-5247(21)00145-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Background Emergency admissions for infection often lack initial diagnostic certainty. COVID-19 has highlighted a need for novel diagnostic approaches to indicate likelihood of viral infection in a pandemic setting. We aimed to derive and validate a blood transcriptional signature to detect viral infections, including COVID-19, among adults with suspected infection who presented to the emergency department. Methods Individuals (aged ≥18 years) presenting with suspected infection to an emergency department at a major teaching hospital in the UK were prospectively recruited as part of the Bioresource in Adult Infectious Diseases (BioAID) discovery cohort. Whole-blood RNA sequencing was done on samples from participants with subsequently confirmed viral, bacterial, or no infection diagnoses. Differentially expressed host genes that met additional filtering criteria were subjected to feature selection to derive the most parsimonious discriminating signature. We validated the signature via RT-qPCR in a prospective validation cohort of participants who presented to an emergency department with undifferentiated fever, and a second case-control validation cohort of emergency department participants with PCR-positive COVID-19 or bacterial infection. We assessed signature performance by calculating the area under receiver operating characteristic curves (AUROCs), sensitivities, and specificities. Findings A three-gene transcript signature, comprising HERC6, IGF1R, and NAGK, was derived from the discovery cohort of 56 participants with bacterial infections and 27 with viral infections. In the validation cohort of 200 participants, the signature differentiated bacterial from viral infections with an AUROC of 0·976 (95% CI 0·919−1·000), sensitivity of 97·3% (85·8−99·9), and specificity of 100% (63·1−100). The AUROC for C-reactive protein (CRP) was 0·833 (0·694−0·944) and for leukocyte count was 0·938 (0·840−0·986). The signature achieved higher net benefit in decision curve analysis than either CRP or leukocyte count for discriminating viral infections from all other infections. In the second validation analysis, which included SARS-CoV-2-positive participants, the signature discriminated 35 bacterial infections from 34 SARS-CoV-2-positive COVID-19 infections with AUROC of 0·953 (0·893−0·992), sensitivity 88·6%, and specificity of 94·1%. Interpretation This novel three-gene signature discriminates viral infections, including COVID-19, from other emergency infection presentations in adults, outperforming both leukocyte count and CRP, thus potentially providing substantial clinical utility in managing acute presentations with infection. Funding National Institute for Health Research, Medical Research Council, Wellcome Trust, and EU-FP7.
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Affiliation(s)
- Ho Kwong Li
- Department of Infectious Disease, Imperial College London, London, UK
- Medical Research Council Centre for Molecular Bacteriology & Infection, Imperial College London, London, UK
| | - Myrsini Kaforou
- Department of Infectious Disease, Imperial College London, London, UK
| | - Jesus Rodriguez-Manzano
- Department of Infectious Disease, Imperial College London, London, UK
- National Institute for Health Research Health Protection Research Unit in Healthcare-associated Infection & Antimicrobial Resistance, Imperial College London, London, UK
| | | | - Ahmad Moniri
- Department of Electrical & Electronic Engineering, Imperial College London, London, UK
| | | | - Rishi K Gupta
- Institute of Global Health, University College London, London, UK
| | - Ewurabena A Mills
- Department of Infectious Disease, Imperial College London, London, UK
| | | | - Jessica Lin
- Department of Infectious Disease, Imperial College London, London, UK
| | - Yueh-Ho Chiu
- Department of Infectious Disease, Imperial College London, London, UK
| | - Ivana Pennisi
- Department of Infectious Disease, Imperial College London, London, UK
| | - Luca Miglietta
- Department of Infectious Disease, Imperial College London, London, UK
- Department of Electrical & Electronic Engineering, Imperial College London, London, UK
| | - Ravi Mehta
- Department of Infectious Disease, Imperial College London, London, UK
| | - Nelofar Obaray
- Department of Infectious Disease, Imperial College London, London, UK
| | - Jethro A Herberg
- Department of Infectious Disease, Imperial College London, London, UK
| | - Victoria J Wright
- Department of Infectious Disease, Imperial College London, London, UK
| | - Pantelis Georgiou
- Department of Electrical & Electronic Engineering, Imperial College London, London, UK
- Centre for Bio-Inspired Technology, Imperial College London, London, UK
| | | | | | - Michael Levin
- Department of Infectious Disease, Imperial College London, London, UK
| | - Graham S Cooke
- Department of Infectious Disease, Imperial College London, London, UK
| | - Mahdad Noursadeghi
- Division of Infection and Immunity, University College London, London, UK
| | - Shiranee Sriskandan
- Department of Infectious Disease, Imperial College London, London, UK
- Medical Research Council Centre for Molecular Bacteriology & Infection, Imperial College London, London, UK
- National Institute for Health Research Health Protection Research Unit in Healthcare-associated Infection & Antimicrobial Resistance, Imperial College London, London, UK
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72
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Biochemical composition, transmission and diagnosis of SARS-CoV-2. Biosci Rep 2021; 41:229295. [PMID: 34291285 PMCID: PMC8350435 DOI: 10.1042/bsr20211238] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 07/19/2021] [Accepted: 07/21/2021] [Indexed: 01/08/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) is a life-threatening respiratory infection caused by severe acute respiratory syndrome virus (SARS-CoV-2), a novel human coronavirus. COVID-19 was declared a pandemic by World Health Organization in March 2020 for its continuous and rapid spread worldwide. Rapidly emerging COVID-19 epicenters and mutants of concerns have created mammoth chaos in healthcare sectors across the globe. With over 185 million infections and approximately 4 million deaths globally, COVID-19 continues its unchecked spread despite all mitigation measures. Until effective and affordable antiretroviral drugs are made available and the population at large is vaccinated, timely diagnosis of the infection and adoption of COVID-appropriate behavior remains major tool available to curtail the still escalating COVID-19 pandemic. This review provides an updated overview of various techniques of COVID-19 testing in human samples and also discusses, in brief, the biochemical composition and mode of transmission of the SARS-CoV-2. Technological advancement in various molecular, serological and immunological techniques including mainly the reverse-transcription polymerase chain reaction (RT-PCR), CRISPR, lateral flow assays (LFAs), and immunosensors are reviewed.
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73
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Zeng J, Kuang L, Cacho-Soblechero M, Georgiou P. An Ultra-High Frame Rate Ion Imaging Platform Using ISFET Arrays With Real-Time Compression. IEEE TRANSACTIONS ON BIOMEDICAL CIRCUITS AND SYSTEMS 2021; 15:820-833. [PMID: 34406947 DOI: 10.1109/tbcas.2021.3105328] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
In this paper, a Lab-on-Chip platform with ultra-high throughput and real-time image compression for high speed ion imaging is presented. The sensing front-end comprises of a CMOS ISFET array with sensors biased in velocity saturation for a linear pH-to-current conversion and high spatial and temporal resolution. An array of 128 × 128 pixels is designed with a pixel size of 13.5 μm × 10.5 μm. In-pixel reset switches are applied for offset compensation, by asynchronously resetting the floating gate of the ISFET to a known fixed potential. Additionally, each row of pixels is processed by a current mode signal pipeline with auto zeroing functionality to remove fixed pattern noise, followed by an on-chip 1 MS/s 8-bit row-parallel single slope ADC. Fabricated in standard TSMC 180 nm BCD process, the entire system-on-chip occupies a silicon area of 2 mm × 2 mm, and achieves a frame rate of 6100 fps (7800 fps from simulation). A high speed 25 ms-latency readout platform based on a USB 3.0 interface and standard JPEG is presented for real-time ion imaging and image compression respectively, while an optimised JPEG algorithm is also designed and verified for a higher compression ratio without sacrificing image quality. We demonstrate real-time ion image visualisation by sensing high speed ion diffusion at 6100 fps, which is more than two times faster than the current state-of-the-art.
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Takemura K. Surface Plasmon Resonance (SPR)- and Localized SPR (LSPR)-Based Virus Sensing Systems: Optical Vibration of Nano- and Micro-Metallic Materials for the Development of Next-Generation Virus Detection Technology. BIOSENSORS 2021; 11:250. [PMID: 34436053 PMCID: PMC8391291 DOI: 10.3390/bios11080250] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 07/13/2021] [Accepted: 07/23/2021] [Indexed: 01/04/2023]
Abstract
The global damage that a widespread viral infection can cause is evident from the ongoing COVID-19 pandemic. The importance of virus detection to prevent the spread of viruses has been reaffirmed by the pandemic and the associated social and economic damage. Surface plasmon resonance (SPR) in microscale and localized SPR (LSPR) in nanoscale virus sensing systems are thought to be useful as next-generation detection methods. Many studies have been conducted on ultra-sensitive technologies, especially those based on signal amplification. In some cases, it has been reported that even a low viral load can be measured, indicating that the virus can be detected in patients even in the early stages of the viral infection. These findings corroborate that SPR and LSPR are effective in minimizing false-positives and false-negatives that are prevalent in the existing virus detection techniques. In this review, the methods and signal responses of SPR and LSPR-based virus detection technologies are summarized. Furthermore, this review surveys some of the recent developments reported and discusses the limitations of SPR and LSPR-based virus detection as the next-generation detection technologies.
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Affiliation(s)
- Kenshin Takemura
- Sensing System Research Center, The National Institute of Advanced Industrial Science and Technology, 07-1 Shuku-Machi, Tosu 841-0052, Japan
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75
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Silva LDC, Dos Santos CA, Mendes GDM, Oliveira KGD, de Souza Júnior MN, Estrela PFN, Costa SHN, Silveira-Lacerda EDP, Duarte GRM. Can a field molecular diagnosis be accurate? A performance evaluation of colorimetric RT-LAMP for the detection of SARS-CoV-2 in a hospital setting. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2021; 13:2898-2907. [PMID: 34109949 DOI: 10.1039/d1ay00481f] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
SARS-CoV-2 currently represents a serious global public health problem. Non-pharmaceutical intervention measures (NPIs) have been widely adopted, and the testing strategy since the beginning of the infection is the most effective tool for tracking, isolating, and minimizing transmission. The high operating costs and the need for sophisticated instrumentation related to gold standard diagnostic for COVID-19, Reverse Transcription quantitative Polymerase Chain Reaction (RT-qPCR), have highlighted the urgency and importance of developing and applying new diagnostic techniques, especially in places with scarce resources. Thus, alternative molecular tests, such as Reverse Transcription Loop-Mediated Isothermal Amplification (RT-LAMP), based on isothermal amplification have been used to detect SARS-CoV-2 using different protocols. The potential for field application of RT-LAMP is due to the lower cost and time and not requiring high-cost instrumentation. Here, we evaluate the colorimetric RT-LAMP to detect SARS-CoV-2 in a hospital environment and correlate its performance with tests performed in a reference laboratory. The analysis performed at the hospital showed high sensitivity (88.89%), specificity (98.55%), accuracy (95.83%), and a Cohen's kappa of 0.895. However, we achieved 100% of agreement when comparing the RT-LAMP results with the gold standard (qRT-PCR) results for samples with Ct < 30 in the hospital-based test. In addition, a similar performance was found in the field compared to the reference laboratory, corroborating the proposal to apply the test directly at point-of-care.
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Affiliation(s)
- Lívia do Carmo Silva
- Instituto de Química, Universidade Federal de Goiás, Campus Samambaia, Goiânia-GO 74690-900, Brazil.
| | | | - Geovana de Melo Mendes
- Instituto de Química, Universidade Federal de Goiás, Campus Samambaia, Goiânia-GO 74690-900, Brazil.
| | - Kézia Gomes de Oliveira
- Instituto de Química, Universidade Federal de Goiás, Campus Samambaia, Goiânia-GO 74690-900, Brazil.
| | | | | | - Sérgio Henrique Nascente Costa
- Hospital do Policial Militar, Goiânia-GO, Brazil and Facudade da Polícia Militar, Goiânia-GO, Brazil and Faculdade de Farmácia, Universidade Federal de Goiás, Goiânia-GO, Brazil
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76
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Dahiya UR, Gupt GD, Dhaka RS, Kalyanasundaram D. Functionalized Co 2FeAl Nanoparticles for Detection of SARS CoV-2 Based on Reverse Transcriptase Loop-Mediated Isothermal Amplification. ACS APPLIED NANO MATERIALS 2021; 4:5871-5882. [PMID: 37556288 PMCID: PMC8147461 DOI: 10.1021/acsanm.1c00782] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 05/08/2021] [Indexed: 05/12/2023]
Abstract
Loop-mediated isothermal amplification (LAMP) is a sensitive, efficient, and rapid nucleic acid amplification technique resulting in a large number of amplicons; however, it suffers from a high incidence of false positives due to carry-over and aerosol. Herein, we report a 10 min nano-capture system that is used in conjunction with a modified reverse transcriptase-LAMP (RT-LAMP) assay for the accurate detection of SARS CoV-2 virus. The nano-capture system employs in-house-designed probe-functionalized magnetic nanoparticles Co2FeAl (cobalt-based Heusler alloy) for efficient capture of contaminating amplicons from the reaction mixture preceding RT-LAMP. The nano-cleaned RT-LAMP assay along with engineered primers successfully detected the presence of 10 copies of SARS CoV-2 virus while completely eliminating the incidence of false positives. The presented contaminant-capture method has been compared with other approaches for elimination of contaminants and was found to be more effective. The insight brought in this work is the design of a rapid nano-capture system that hybridizes with contaminating amplicons (carry-over) with high specificity to enable easy removal from the assay for elimination of false positives. The method has been proven to be successful for RT-LAMP assays in the rapid and highly specific detection of SARS CoV-2, which is currently a major challenge for global health. To the best of our knowledge, this is the first work involving a nano-based cleaning strategy for reliable and rapid diagnosis using isothermal amplification approaches.
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Affiliation(s)
- Ujjwal Ranjan Dahiya
- Centre for Biomedical Engineering, Indian
Institute of Technology Delhi, New Delhi 110016,
India
| | - Guru Dutt Gupt
- Department of Physics, Indian Institute
of Technology Delhi, New Delhi 110016, India
| | - Rajendra S. Dhaka
- Department of Physics, Indian Institute
of Technology Delhi, New Delhi 110016, India
| | - Dinesh Kalyanasundaram
- Centre for Biomedical Engineering, Indian
Institute of Technology Delhi, New Delhi 110016,
India
- Department of Biomedical Engineering, All
India Institute of Medical Sciences, New Delhi 110029,
India
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77
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Zhang Y, Malekjahani A, Udugama BN, Kadhiresan P, Chen H, Osborne M, Franz M, Kucera M, Plenderleith S, Yip L, Bader GD, Tran V, Gubbay JB, McGeer A, Mubareka S, Chan WCW. Surveilling and Tracking COVID-19 Patients Using a Portable Quantum Dot Smartphone Device. NANO LETTERS 2021; 21:5209-5216. [PMID: 34110166 DOI: 10.1021/acs.nanolett.1c01280] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The ability to rapidly diagnose, track, and disseminate information for SARS-CoV-2 is critical to minimize its spread. Here, we engineered a portable smartphone-based quantum barcode serological assay device for real-time surveillance of patients infected with SARS-CoV-2. Our device achieved a clinical sensitivity of 90% and specificity of 100% for SARS-CoV-2, as compared to 34% and 100%, respectively, for lateral flow assays in a head-to-head comparison. The lateral flow assay misdiagnosed ∼2 out of 3 SARS-CoV-2 positive patients. Our quantum dot barcode device has ∼3 times greater clinical sensitivity because it is ∼140 times more analytically sensitive than lateral flow assays. Our device can diagnose SARS-CoV-2 at different sampling dates and infectious severity. We developed a databasing app to provide instantaneous results to inform patients, physicians, and public health agencies. This assay and device enable real-time surveillance of SARS-CoV-2 seroprevalence and potential immunity.
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Affiliation(s)
- Yuwei Zhang
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Ayden Malekjahani
- Institute of Biomedical Engineering, University of Toronto, 164 College Street, Toronto, Ontario M5S 3G9, Canada
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Buddhisha N Udugama
- Institute of Biomedical Engineering, University of Toronto, 164 College Street, Toronto, Ontario M5S 3G9, Canada
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Pranav Kadhiresan
- Institute of Biomedical Engineering, University of Toronto, 164 College Street, Toronto, Ontario M5S 3G9, Canada
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Hongmin Chen
- Institute of Biomedical Engineering, University of Toronto, 164 College Street, Toronto, Ontario M5S 3G9, Canada
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Matthew Osborne
- Institute of Biomedical Engineering, University of Toronto, 164 College Street, Toronto, Ontario M5S 3G9, Canada
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Max Franz
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Mike Kucera
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Simon Plenderleith
- Biological Sciences, Sunnybrook Research Institute, Toronto, Ontario M4N 3M5, Canada
| | - Lily Yip
- Biological Sciences, Sunnybrook Research Institute, Toronto, Ontario M4N 3M5, Canada
| | - Gary D Bader
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health System, Toronto, Ontario M5G 1X5, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5G 1A8, Canada
- Department of Computer Science, University of Toronto, Toronto, Ontario, M5S 2E4, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, M5G 2C1, Canada
| | - Vanessa Tran
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Public Health Ontario, Toronto, Ontario M5G 1M1, Canada
| | - Jonathan B Gubbay
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Public Health Ontario, Toronto, Ontario M5G 1M1, Canada
| | - Allison McGeer
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health System, Toronto, Ontario M5G 1X5, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario M5T 3M7, Canada
- Department of Microbiology, Mount Sinai Hospital, Sinai Health System, Toronto, Ontario M5G 1X5, Canada
| | - Samira Mubareka
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Biological Sciences, Sunnybrook Research Institute, Toronto, Ontario M4N 3M5, Canada
| | - Warren C W Chan
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
- Institute of Biomedical Engineering, University of Toronto, 164 College Street, Toronto, Ontario M5S 3G9, Canada
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
- Department of Chemical Engineering, University of Toronto, 200 College Street, Toronto, Ontario M5S 3E5, Canada
- Department of Materials Science and Engineering, University of Toronto, 184 College Street, Toronto, Ontario M5S 3E1, Canada
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Duan M, Zhong X, Zhao X, El-Agnaf OM, Lee YK, Bermak A. An Optical and Temperature Assisted CMOS ISFET Sensor Array for Robust E. Coli Detection. IEEE TRANSACTIONS ON BIOMEDICAL CIRCUITS AND SYSTEMS 2021; 15:497-508. [PMID: 34043514 DOI: 10.1109/tbcas.2021.3084540] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Both bacterial viability and concentration are significant metrics for bacterial detection. Existing miniaturized and cost-effective single-mode sensor, pH or optical, can only be skilled at detecting single information viability or concentration. This paper presents an inverter-based CMOS ion-sensitive-field-effect-transistor (ISFET) sensor array, featuring bacterial pH detection which is an indicator of viability. The proposed design realizes pH detection using the native passivation layer of CMOS process as a sensing layer and configuring an inverter-based front-end as a capacitive feedback amplifier. This sensor array is assisted by temperature sensing and optical detection which reveals bacterial concentration. The optical detection is enabled using the leakage current of a reset switch as a response to a light source. While in reset mode, the inverter-based amplifier works as a temperature sensor that could help to reduce temperature influences on pH and optical detection. All the functionalities are realized using one single inverter-based amplifier, resulting in a compact pixel structure and largely relaxed design complexity for the sensor system. Fabricated in 0.18 μm standard CMOS process, the proposed CMOS sensor array system achieves an amplified pH sensitivity of 221 mV/pH, an improved sensor resolution of 0.03 pH through systematic noise optimization, a linear optical response, and a maximum temperature error of 0.69 °C. The sensing capabilities of the proposed design are demonstrated through on-chip Escherichia coli (E. coli) detection. This study may be extended to a rapid and cost-effective platform that renders multiple information of bacterial samples.
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Diagnosis of SARS-CoV-2 Infection with LamPORE, a High-Throughput Platform Combining Loop-Mediated Isothermal Amplification and Nanopore Sequencing. J Clin Microbiol 2021; 59:JCM.03271-20. [PMID: 33782112 PMCID: PMC8315953 DOI: 10.1128/jcm.03271-20] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 03/23/2021] [Indexed: 12/17/2022] Open
Abstract
LamPORE is a novel diagnostic platform for the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA combining loop-mediated isothermal amplification with nanopore sequencing, which could potentially be used to analyze thousands of samples per day on a single instrument. We evaluated the performance of LamPORE against reverse transcriptase PCR (RT-PCR) using RNA extracted from spiked respiratory samples and stored nose and throat swabs collected at two UK hospitals. The limit of detection of LamPORE was 10 genome copies/μl of extracted RNA, which is above the limit achievable by RT-PCR, but was not associated with a significant reduction of sensitivity in clinical samples. Positive clinical specimens came mostly from patients with acute symptomatic infection, and among them, LamPORE had a diagnostic sensitivity of 99.1% (226/228; 95% confidence interval [CI], 96.9% to 99.9%). Among negative clinical specimens, including 153 with other respiratory pathogens detected, LamPORE had a diagnostic specificity of 99.6% (278/279; 98.0% to 100.0%). Overall, 1.4% (7/514; 0.5% to 2.9%) of samples produced an indeterminate result on first testing, and repeat LamPORE testing on the same RNA extract had a reproducibility of 96.8% (478/494; 94.8% to 98.1%). LamPORE has a similar performance as RT-PCR for the diagnosis of SARS-CoV-2 infection in symptomatic patients and offers a promising approach to high-throughput testing.
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Ramesh A, Potdar R, Bhandary R. Oral Fluids—A Diagnostic Tool for COVID-19: A Review. JOURNAL OF HEALTH AND ALLIED SCIENCES NU 2021. [DOI: 10.1055/s-0041-1726683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
AbstractGlobal outbreak of coronavirus disease 2019 (COVID-19) in December 2019 has affected millions of people around the world. This virus binds to angiotensin-converting enzyme-2 receptors present in the pharynx, nose, oral cavity, salivary glands, tongue, etc. Saliva has been shown to have viral loads of COVID-19 as it reported to be 2019-novel-coronavirus nucleic acid positive. This article is based on the association of oral fluids and their role in diagnosis of coronavirus infection.
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Affiliation(s)
- Amitha Ramesh
- A.B. Shetty Memorial Institute of Dental Sciences, NITTE (deemed to be) University, Mangalore, Karnataka, India
| | - Raksha Potdar
- A.B. Shetty Memorial Institute of Dental Sciences, NITTE (deemed to be) University, Mangalore, Karnataka, India
| | - Rahul Bhandary
- A.B. Shetty Memorial Institute of Dental Sciences, NITTE (deemed to be) University, Mangalore, Karnataka, India
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Khan AH, Tirth V, Fawzy M, Mahmoud AED, Khan NA, Ahmed S, Ali SS, Akram M, Hameed L, Islam S, Das G, Roy S, Dehghani MH. COVID-19 transmission, vulnerability, persistence and nanotherapy: a review. ENVIRONMENTAL CHEMISTRY LETTERS 2021; 19:2773-2787. [PMID: 33846683 PMCID: PMC8026094 DOI: 10.1007/s10311-021-01229-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 03/16/2021] [Indexed: 05/09/2023]
Abstract
End 2019, the zoonotic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), named COVID-19 for coronavirus disease 2019, is the third adaptation of a contagious virus following the severe acute respiratory syndrome coronavirus in 2002, SARS-CoV, and the Middle East respiratory syndrome virus in 2012, MERS-CoV. COVID-19 is highly infectious and virulent compared to previous outbreaks. We review sources, contagious routes, preventive measures, pandemic, outbreak, epidemiology of SARS-CoV, MERS-CoV and SARS-CoV-2 from 2002 to 2020 using a Medline search. We discuss the chronology of the three coronaviruses, the vulnerability of healthcare workers, coronaviruses on surface and in wastewater, diagnostics and cures, and measures to prevent spreading.
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Affiliation(s)
- Afzal Husain Khan
- Civil Engineering Department, Jazan University, Jazan, 114 Saudi Arabia
| | - Vineet Tirth
- Department of Mechanical Engineering, King Khalid University, Abha, 61413 Saudi Arabia
| | - Manal Fawzy
- Environmental Sciences Department, Faculty of Science, Alexandria University, Alexandria, 21511 Egypt
| | - Alaa El Din Mahmoud
- Environmental Sciences Department, Faculty of Science, Alexandria University, Alexandria, 21511 Egypt
| | - Nadeem A. Khan
- Civil Engineering Department, Jamia Millia Islamia (A Central University), New Delhi, 110025 India
| | - Sirajuddin Ahmed
- Civil Engineering Department, Jamia Millia Islamia (A Central University), New Delhi, 110025 India
| | - Syed Sadat Ali
- Department of Physiology, Faculty of Medicine, Jazan University, Jazan, 114 Saudi Arabia
| | - Muhammad Akram
- Department of Eastern Medicine, Government College University, Faisalabad, Pakistan
| | - Leena Hameed
- Faculty of Eastern Medicine, Hamdard University, Karachi, Pakistan
| | - Saiful Islam
- Civil Engineering Department, College of Engineering, King Khalid University, Abha, Kingdom of Saudi Arabia
| | - Gotam Das
- Department of Prosthodontics, College of Dentistry, King Khalid University, Abha, 61413 Saudi Arabia
| | - Sharmili Roy
- Division of Oncology, School of Medicine, Stanford University, Stanford, CA 94305 USA
| | - Mohammad Hadi Dehghani
- Department of Environmental Health Engineering, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
- Center for Solid Waste Research, Institute for Environmental Research, Tehran University of Medical Sciences, Tehran, Iran
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Abdelhamid HN, Badr G. Nanobiotechnology as a platform for the diagnosis of COVID-19: a review. NANOTECHNOLOGY FOR ENVIRONMENTAL ENGINEERING 2021. [PMCID: PMC7988262 DOI: 10.1007/s41204-021-00109-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A sensitive method for diagnosing coronavirus disease 2019 (COVID-19) is highly required to fight the current and future global health threats due to severe acute respiratory syndrome coronavirus 2 (SARS-CoV 2). However, most of the current methods exhibited high false‐negative rates, resulting in patient misdiagnosis and impeding early treatment. Nanoparticles show promising performance and great potential to serve as a platform for diagnosing viral infection in a short time and with high sensitivity. This review highlighted the potential of nanoparticles as platforms for the diagnosis of COVID-19. Nanoparticles such as gold nanoparticles, magnetic nanoparticles, and graphene (G) were applied to detect SARS-CoV 2. They have been used for molecular-based diagnosis methods and serological methods. Nanoparticles improved specificity and shorten the time required for the diagnosis. They may be implemented into small devices that facilitate the self-diagnosis at home or in places such as airports and shops. Nanoparticles-based methods can be used for the analysis of virus-contaminated samples from a patient, surface, and air. The advantages and challenges were discussed to introduce useful information for designing a sensitive, fast, and low-cost diagnostic method. This review aims to present a helpful survey for the lesson learned from handling this outbreak to prepare ourself for future pandemic.
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Affiliation(s)
- Hani Nasser Abdelhamid
- Advanced Multifunctional Materials Laboratory, Department of Chemistry, Faculty of Science, Assiut University, Assiut, Egypt
| | - Gamal Badr
- Laboratory of Immunology, Zoology Department, Faculty of Science, Assiut University, Assiut, Egypt
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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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Erdem Ö, Derin E, Sagdic K, Yilmaz EG, Inci F. Smart materials-integrated sensor technologies for COVID-19 diagnosis. EMERGENT MATERIALS 2021; 4:169-185. [PMID: 33495747 PMCID: PMC7817967 DOI: 10.1007/s42247-020-00150-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 12/01/2020] [Indexed: 05/05/2023]
Abstract
After the first case has appeared in China, the COVID-19 pandemic continues to pose an omnipresent threat to global health, affecting more than 70 million patients and leading to around 1.6 million deaths. To implement rapid and effective clinical management, early diagnosis is the mainstay. Today, real-time reverse transcriptase (RT)-PCR test is the major diagnostic practice as a gold standard method for accurate diagnosis of this disease. On the other side, serological assays are easy to be implemented for the disease screening. Considering the limitations of today's tests including lengthy assay time, cost, the need for skilled personnel, and specialized infrastructure, both strategies, however, have impediments to be applied to the resource-scarce settings. Therefore, there is an urgent need to democratize all these practices to be applicable across the globe, specifically to the locations comprising of very limited infrastructure. In this regard, sensor systems have been utilized in clinical diagnostics largely, holding great potential to have pivotal roles as an alternative or complementary options to these current tests, providing crucial fashions such as being suitable for point-of-care settings, cost-effective, and having short turnover time. In particular, the integration of smart materials into sensor technologies leverages their analytical performances, including sensitivity, linear dynamic range, and specificity. Herein, we comprehensively review major smart materials such as nanomaterials, photosensitive materials, electrically sensitive materials, their integration with sensor platforms, and applications as wearable tools within the scope of the COVID-19 diagnosis.
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Affiliation(s)
- Özgecan Erdem
- UNAM-National Nanotechnology Research Center, Bilkent University, 06800 Ankara, Turkey
| | - Esma Derin
- UNAM-National Nanotechnology Research Center, Bilkent University, 06800 Ankara, Turkey
- Institute of Materials Science and Nanotechnology, Bilkent University, 06800 Ankara, Turkey
| | - Kutay Sagdic
- UNAM-National Nanotechnology Research Center, Bilkent University, 06800 Ankara, Turkey
- Institute of Materials Science and Nanotechnology, Bilkent University, 06800 Ankara, Turkey
| | - Eylul Gulsen Yilmaz
- UNAM-National Nanotechnology Research Center, Bilkent University, 06800 Ankara, Turkey
- Institute of Materials Science and Nanotechnology, Bilkent University, 06800 Ankara, Turkey
| | - Fatih Inci
- UNAM-National Nanotechnology Research Center, Bilkent University, 06800 Ankara, Turkey
- Institute of Materials Science and Nanotechnology, Bilkent University, 06800 Ankara, Turkey
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