1
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Yigci D, Atçeken N, Yetisen AK, Tasoglu S. Loop-Mediated Isothermal Amplification-Integrated CRISPR Methods for Infectious Disease Diagnosis at Point of Care. ACS OMEGA 2023; 8:43357-43373. [PMID: 38027359 PMCID: PMC10666231 DOI: 10.1021/acsomega.3c04422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 09/26/2023] [Indexed: 12/01/2023]
Abstract
Infectious diseases continue to pose an imminent threat to global public health, leading to high numbers of deaths every year and disproportionately impacting developing countries where access to healthcare is limited. Biological, environmental, and social phenomena, including climate change, globalization, increased population density, and social inequity, contribute to the emergence of novel communicable diseases. Rapid and accurate diagnoses of infectious diseases are essential to preventing the transmission of infectious diseases. Although some commonly used diagnostic technologies provide highly sensitive and specific measurements, limitations including the requirement for complex equipment/infrastructure and refrigeration, the need for trained personnel, long sample processing times, and high cost remain unresolved. To ensure global access to affordable diagnostic methods, loop-mediated isothermal amplification (LAMP) integrated clustered regularly interspaced short palindromic repeat (CRISPR) based pathogen detection has emerged as a promising technology. Here, LAMP-integrated CRISPR-based nucleic acid detection methods are discussed in point-of-care (PoC) pathogen detection platforms, and current limitations and future directions are also identified.
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Affiliation(s)
- Defne Yigci
- School
of Medicine, Koç University, Istanbul 34450, Turkey
| | - Nazente Atçeken
- Koç
University Translational Medicine Research Center (KUTTAM), Koç University, Istanbul 34450, Turkey
| | - Ali K. Yetisen
- Department
of Chemical Engineering, Imperial College
London, London SW7 2AZ, U.K.
| | - Savas Tasoglu
- Koç
University Translational Medicine Research Center (KUTTAM), Koç University, Istanbul 34450, Turkey
- Boğaziçi
Institute of Biomedical Engineering, Boğaziçi
University, Istanbul 34684, Turkey
- Koç
University Arçelik Research Center for Creative Industries
(KUAR), Koç University, Istanbul 34450, Turkey
- Physical
Intelligence Department, Max Planck Institute
for Intelligent Systems, Stuttgart 70569, Germany
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2
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Poirier AC, Riaño Moreno RD, Takaindisa L, Carpenter J, Mehat JW, Haddon A, Rohaim MA, Williams C, Burkhart P, Conlon C, Wilson M, McClumpha M, Stedman A, Cordoni G, Branavan M, Tharmakulasingam M, Chaudhry NS, Locker N, Fernando A, Balachandran W, Bullen M, Collins N, Rimer D, Horton DL, Munir M, La Ragione RM. VIDIIA Hunter diagnostic platform: a low-cost, smartphone connected, artificial intelligence-assisted COVID-19 rapid diagnostics approved for medical use in the UK. Front Mol Biosci 2023; 10:1144001. [PMID: 37842636 PMCID: PMC10572354 DOI: 10.3389/fmolb.2023.1144001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 09/12/2023] [Indexed: 10/17/2023] Open
Abstract
Introduction: Accurate and rapid diagnostics paired with effective tracking and tracing systems are key to halting the spread of infectious diseases, limiting the emergence of new variants and to monitor vaccine efficacy. The current gold standard test (RT-qPCR) for COVID-19 is highly accurate and sensitive, but is time-consuming, and requires expensive specialised, lab-based equipment. Methods: Herein, we report on the development of a SARS-CoV-2 (COVID-19) rapid and inexpensive diagnostic platform that relies on a reverse-transcription loop-mediated isothermal amplification (RT-LAMP) assay and a portable smart diagnostic device. Automated image acquisition and an Artificial Intelligence (AI) deep learning model embedded in the Virus Hunter 6 (VH6) device allow to remove any subjectivity in the interpretation of results. The VH6 device is also linked to a smartphone companion application that registers patients for swab collection and manages the entire process, thus ensuring tests are traced and data securely stored. Results: Our designed AI-implemented diagnostic platform recognises the nucleocapsid protein gene of SARS-CoV-2 with high analytical sensitivity and specificity. A total of 752 NHS patient samples, 367 confirmed positives for coronavirus disease (COVID-19) and 385 negatives, were used for the development and validation of the test and the AI-assisted platform. The smart diagnostic platform was then used to test 150 positive clinical samples covering a dynamic range of clinically meaningful viral loads and 250 negative samples. When compared to RT-qPCR, our AI-assisted diagnostics platform was shown to be reliable, highly specific (100%) and sensitive (98-100% depending on viral load) with a limit of detection of 1.4 copies of RNA per µL in 30 min. Using this data, our CE-IVD and MHRA approved test and associated diagnostic platform has been approved for medical use in the United Kingdom under the UK Health Security Agency's Medical Devices (Coronavirus Test Device Approvals, CTDA) Regulations 2022. Laboratory and in-silico data presented here also indicates that the VIDIIA diagnostic platform is able to detect the main variants of concern in the United Kingdom (September 2023). Discussion: This system could provide an efficient, time and cost-effective platform to diagnose SARS-CoV-2 and other infectious diseases in resource-limited settings.
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Affiliation(s)
- Aurore C. Poirier
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, University of Surrey, Guildford, United Kingdom
| | | | - Leona Takaindisa
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, University of Surrey, Guildford, United Kingdom
| | - Jessie Carpenter
- VIDIIA Ltd., Surrey Technology Centre, Guildford, United Kingdom
| | - Jai W. Mehat
- Department of Microbial Sciences, School of Biosciences, University of Surrey, Guildford, United Kingdom
| | - Abi Haddon
- Berkshire and Surrey Pathology Services, Molecular Diagnostics, Royal Surrey County Hospital, Guildford, United Kingdom
| | - Mohammed A. Rohaim
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, The Lancaster University, Lancaster, United Kingdom
| | - Craig Williams
- The Royal Lancaster Infirmary, University Hospitals of Morecambe Bay NHS Foundation Trust, Kendal, United Kingdom
| | - Peter Burkhart
- The Royal Lancaster Infirmary, University Hospitals of Morecambe Bay NHS Foundation Trust, Kendal, United Kingdom
| | - Chris Conlon
- GB Electronics (UK) Ltd, Worthing, United Kingdom
| | | | | | - Anna Stedman
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, University of Surrey, Guildford, United Kingdom
| | - Guido Cordoni
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, University of Surrey, Guildford, United Kingdom
| | - Manoharanehru Branavan
- College of Engineering, Design and Physical Sciences, Brunel University London, Uxbridge, United Kingdom
| | | | - Nouman S. Chaudhry
- Centre for Vision, Speech and Signal Processing, University of Surrey, Guildford, United Kingdom
| | - Nicolas Locker
- Department of Microbial Sciences, School of Biosciences, University of Surrey, Guildford, United Kingdom
| | - Anil Fernando
- Centre for Vision, Speech and Signal Processing, University of Surrey, Guildford, United Kingdom
| | - Wamadeva Balachandran
- College of Engineering, Design and Physical Sciences, Brunel University London, Uxbridge, United Kingdom
| | - Mark Bullen
- GB Electronics (UK) Ltd, Worthing, United Kingdom
| | - Nadine Collins
- Berkshire and Surrey Pathology Services, Molecular Diagnostics, Royal Surrey County Hospital, Guildford, United Kingdom
| | - David Rimer
- VIDIIA Ltd., Surrey Technology Centre, Guildford, United Kingdom
| | - Daniel L. Horton
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, University of Surrey, Guildford, United Kingdom
| | - Muhammad Munir
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, The Lancaster University, Lancaster, United Kingdom
| | - Roberto M. La Ragione
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, University of Surrey, Guildford, United Kingdom
- Department of Microbial Sciences, School of Biosciences, University of Surrey, Guildford, United Kingdom
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3
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Lamothe G, Carbonneau J, Joly Beauparlant C, Vincent T, Quessy P, Guedon A, Kobinger G, Lemay JF, Boivin G, Droit A, Turgeon N, Tremblay JP. Rapid and Technically Simple Detection of SARS-CoV-2 Variants Using CRISPR Cas12 and Cas13. CRISPR J 2023; 6:369-385. [PMID: 37347931 DOI: 10.1089/crispr.2023.0007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/24/2023] Open
Abstract
The worldwide proliferation of the SARS-CoV-2 virus in the past 3 years has allowed the virus to accumulate numerous mutations. Dangerous lineages have emerged one after another, each leading to a new wave of the pandemic. In this study, we have developed the THRASOS pipeline to rapidly discover lineage-specific mutation signatures and thus advise the development of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-based diagnostic tests. We also optimized a strategy to modify loop-mediated isothermal amplification amplicons for downstream use with Cas12 and Cas13 for future multiplexing. The close ancestry of the BA.1 and BA.2 variants of SARS-CoV-2 (Omicron) made these excellent candidates for the development of a first test using this workflow. With a quick turnaround time and low requirements for laboratory equipment, the test we have created is ideally suited for settings such as mobile clinics lacking equipment such as Next-Generation Sequencers or Sanger Sequencers and the personnel to run these devices.
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Affiliation(s)
- Gabriel Lamothe
- Centre de recherche du CHU de Québec, Québec, Québec, Canada; Québec, Québec, Canada
- Department of Molecular Medicine, Faculty of Medicine, Laval University, Québec, Québec, Canada; Québec, Québec, Canada
| | - Julie Carbonneau
- Centre de recherche du CHU de Québec, Québec, Québec, Canada; Québec, Québec, Canada
- Infectiology Research Center, CHU de Québec-Université Laval, Québec, Québec, Canada; Québec, Québec, Canada
- Department of Pediatrics, Faculty of Medicine, Université Laval, Québec, Québec, Canada; Québec, Québec, Canada
| | - Charles Joly Beauparlant
- Centre de recherche du CHU de Québec, Québec, Québec, Canada; Québec, Québec, Canada
- Department of Molecular Medicine, Faculty of Medicine, Laval University, Québec, Québec, Canada; Québec, Québec, Canada
| | - Thierry Vincent
- Centre de Recherche sur la fonction, la structure et l'ingénierie des protéines, Québec, Québec, Canada; Québec, Québec, Canada
- Département de Génie chimique, Faculté des Sciences, Université Laval, Québec, Québec, Canada; Québec, Québec, Canada
| | - Patrik Quessy
- CNETE, Shawinigan, Québec, Canada; Québec, Québec, Canada
- PROTEO, Québec, Québec, Canada; Québec, Québec, Canada
| | - Anthony Guedon
- CNETE, Shawinigan, Québec, Canada; Québec, Québec, Canada
- PROTEO, Québec, Québec, Canada; Québec, Québec, Canada
| | - Gary Kobinger
- Galveston National Laboratory, University of Texas Medical Branch, Galveston, Texas, USA; and Québec, Québec, Canada
| | - Jean-Francois Lemay
- CNETE, Shawinigan, Québec, Canada; Québec, Québec, Canada
- PROTEO, Québec, Québec, Canada; Québec, Québec, Canada
| | - Guy Boivin
- Centre de recherche du CHU de Québec, Québec, Québec, Canada; Québec, Québec, Canada
- Infectiology Research Center, CHU de Québec-Université Laval, Québec, Québec, Canada; Québec, Québec, Canada
- Department of Pediatrics, Faculty of Medicine, Université Laval, Québec, Québec, Canada; Québec, Québec, Canada
| | - Arnaud Droit
- Centre de recherche du CHU de Québec, Québec, Québec, Canada; Québec, Québec, Canada
- Department of Molecular Medicine, Faculty of Medicine, Laval University, Québec, Québec, Canada; Québec, Québec, Canada
| | - Nathalie Turgeon
- Centre de recherche du CHU de Québec, Québec, Québec, Canada; Québec, Québec, Canada
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Québec, Québec, Canada
| | - Jacques P Tremblay
- Centre de recherche du CHU de Québec, Québec, Québec, Canada; Québec, Québec, Canada
- Department of Molecular Medicine, Faculty of Medicine, Laval University, Québec, Québec, Canada; Québec, Québec, Canada
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4
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Sritong N, Sala de Medeiros M, Basing LA, Linnes JC. Promise and perils of paper-based point-of-care nucleic acid detection for endemic and pandemic pathogens. LAB ON A CHIP 2023; 23:888-912. [PMID: 36688463 PMCID: PMC10028599 DOI: 10.1039/d2lc00554a] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
From HIV and influenza to emerging pathogens like COVID-19, each new infectious disease outbreak has highlighted the need for massively-scalable testing that can be performed outside centralized laboratory settings at the point-of-care (POC) in order to prevent, track, and monitor endemic and pandemic threats. Nucleic acid amplification tests (NAATs) are highly sensitive and can be developed and scaled within weeks while protein-based rapid tests require months for production. Combining NAATs with paper-based detection platforms are promising due to the manufacturability, scalability, and simplicity of each of these components. Typically, paper-based NAATs consist of three sequential steps: sample collection and preparation, amplification of DNA or RNA from pathogens of interest, and detection. However, these exist within a larger ecosystem of sample collection and interpretation workflow, usability, and manufacturability which can be vastly perturbed during a pandemic emergence. This review aims to explore the challenges of paper-based NAATs covering sample-to-answer procedures along with three main types of clinical samples; blood, urine, and saliva, as well as broader operational, scale up, and regulatory aspects of device development and implementation. To fill the technological gaps in paper-based NAATs, a sample-in-result-out system that incorporates the integrated sample collection, sample preparation, and integrated internal amplification control while also balancing needs of users and manufacturability upfront in the early design process is required.
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Affiliation(s)
- Navaporn Sritong
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA.
| | | | - Laud Anthony Basing
- Department of Medical Diagnostics, Kwame Nkrumah University of Science and Technology, Kumasi, Ashanti, Ghana
| | - Jacqueline C Linnes
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA.
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5
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Zhang L, Wang X, Liu D, Wu Y, Feng L, Han C, Liu J, Lu Y, Sotnikov DV, Xu Y, Cheng J. SMART: A Swing-Assisted Multiplexed Analyzer for Point-of-Care Respiratory Tract Infection Testing. BIOSENSORS 2023; 13:228. [PMID: 36831994 PMCID: PMC9954503 DOI: 10.3390/bios13020228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 01/26/2023] [Accepted: 02/02/2023] [Indexed: 06/18/2023]
Abstract
Respiratory tract infections such as the ongoing coronavirus disease 2019 (COVID-19) has seriously threatened public health in the last decades. The experience of fighting against the epidemic highlights the importance of user-friendly and accessible point-of-care systems for nucleic acid (NA) detection. To realize low-cost and multiplexed point-of-care NA detection, a swing-assisted multiplexed analyzer for point-of-care respiratory tract infection testing (SMART) was proposed to detect multiple respiratory tract pathogens using visible loop-mediated isothermal amplification. By performing hand-swing movements to generate acceleration force to distribute samples into reaction chambers, the design of the SMART system was greatly simplified. By using different format of chips and integrating into a suitcase, this system can be applied to on-site multitarget and multi-sample testing. Three targets including the N and Orf genes of SARS-CoV-2 and the internal control were simultaneously analyzed (limit of detection: 2000 copies/mL for raw sample; 200 copies/mL for extracted sample). Twenty-three clinical samples with eight types of respiratory bacteria and twelve COVID-19 clinical samples were successfully detected. These results indicate that the SMART system has the potential to be further developed as a versatile tool in the diagnosis of respiratory tract infection.
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Affiliation(s)
- Li Zhang
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Xu Wang
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Dongchen Liu
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Yu Wu
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Li Feng
- CapitalBiotech Technology, Beijing 101111, China
| | - Chunyan Han
- CapitalBiotech Technology, Beijing 101111, China
| | - Jiajia Liu
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Ying Lu
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China
- National Engineering Research Center for Beijing Biochip Technology, Beijing 102200, China
| | - Dmitriy V. Sotnikov
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prospect 33, 119071 Moscow, Russia
| | - Youchun Xu
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China
- National Engineering Research Center for Beijing Biochip Technology, Beijing 102200, China
| | - Jing Cheng
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China
- National Engineering Research Center for Beijing Biochip Technology, Beijing 102200, China
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6
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CRISPR/Cas12a-based assay for the rapid and high-sensitivity detection of Streptococcus agalactiae colonization in pregnant women with premature rupture of membrane. Ann Clin Microbiol Antimicrob 2023; 22:8. [PMID: 36658599 PMCID: PMC9854146 DOI: 10.1186/s12941-023-00558-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Accepted: 01/10/2023] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Streptococcus agalactiae or group B Streptococcus (GBS) is a leading infectious cause of neonatal morbidity and mortality. It is essential to establish a robust method for the rapid and ultra-sensitive detection of GBS in pregnant women with premature rupture of membrane (PROM). METHODS This study developed a CRISPR-GBS assay that combined the advantages of the recombinase polymerase amplification (RPA) and CRISPR/Cas12a system for GBS detection. The clinical performance of the CRISPR-GBS assay was assessed using vaginal or cervical swabs that were collected from 179 pregnant women with PROM, compared in parallel to culture-based matrix-assisted laser desorption ionization time-of-flight mass spectrometry (culture-MS) method and real-time quantitative polymerase chain reaction (qPCR) assay. RESULTS The CRISPR-GBS assay can be completed within 35 min and the limit of detection was as low as 5 copies μL-1. Compared with the culture-MS, the CRISPR-GBS assay demonstrated a sensitivity of 96.64% (144/149, 95% confidence interval [CI] 92.39-98.56%) and a specificity of 100% (30/30, 95% CI 88.65-100%). It also had a high concordance rate of 98.88% with the qPCR assay. CONCLUSIONS The established CRISPR-GBS platform can detect GBS in a rapid, accurate, easy-to-operate, and cost-efficient manner. It offered a promising tool for the intrapartum screening of GBS colonization.
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Abstract
INTRODUCTION The SARS-CoV-2 pandemic, and the subsequent limitations on standard diagnostics, has vastly expanded the user base of Reverse Transcription Loop-mediated isothermal Amplification (RT-LAMP) in fundamental research and development. RT-LAMP has also penetrated commercial markets, with emergency use authorizations for clinical diagnosis. AREAS COVERED This review discusses the role of RT-LAMP within the context of other technologies like RT-qPCR and rapid antigen tests, progress in sample preparation strategies to enable simplified workflow for RT-LAMP directly from clinical specimens, new challenges with primer and assay design for the evolving pandemic, prominent detection modalities including colorimetric and CRISPR-mediated methods, and translational research and commercial development of RT-LAMP for clinical applications. EXPERT OPINION RT-LAMP occupies a middle ground between RT-qPCR and rapid antigen tests. The simplicity approaches that of rapid antigen tests, making it suitable for point-of-care use, but the sensitivity nears that of RT-qPCR. RT-LAMP still lags RT-qPCR in fundamental understanding of the mechanism, and the interplay between sample preparation and assay performance. Industry is now beginning to address issues around scalability and usability, which could finally enable LAMP and RT-LAMP to find future widespread application as a diagnostic for other conditions, including other pathogens with pandemic potential.
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Affiliation(s)
- Gihoon Choi
- Biotechnology & Bioengineering Department, Sandia National Laboratories, Livermore, CA, USA
| | - Taylor J Moehling
- Biotechnology & Bioengineering Department, Sandia National Laboratories, Livermore, CA, USA
| | - Robert J Meagher
- Biotechnology & Bioengineering Department, Sandia National Laboratories, Livermore, CA, USA
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8
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Roychoudhury A, Allen RJ, Curk T, Farrell J, McAllister G, Templeton K, Bachmann TT. Amplification Free Detection of SARS-CoV-2 Using Multi-Valent Binding. ACS Sens 2022; 7:3692-3699. [PMID: 36482673 PMCID: PMC9743695 DOI: 10.1021/acssensors.2c01340] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We present the development of electrochemical impedance spectroscopy (EIS)-based biosensors for sensitive detection of SARS-CoV-2 RNA using multi-valent binding. By increasing the number of probe-target binding events per target molecule, multi-valent binding is a viable strategy for improving the biosensor performance. As EIS can provide sensitive and label-free measurements of nucleic acid targets during probe-target hybridization, we used multi-valent binding to build EIS biosensors for targeting SARS-CoV-2 RNA. For developing the biosensor, we explored two different approaches including probe combinations that individually bind in a single-valent fashion and the probes that bind in a multi-valent manner on their own. While we found excellent biosensor performance using probe combinations, we also discovered unexpected signal suppression. We explained the signal suppression theoretically using inter- and intra-probe hybridizations which confirmed our experimental findings. With our best probe combination, we achieved a LOD of 182 copies/μL (303 aM) of SARS-CoV-2 RNA and used these for successful evaluation of patient samples for COVID-19 diagnostics. We were also able to show the concept of multi-valent binding with shorter probes in the second approach. Here, a 13-nt-long probe has shown the best performance during SARS-CoV-2 RNA binding. Therefore, multi-valent binding approaches using EIS have high utility for direct detection of nucleic acid targets and for point-of-care diagnostics.
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Affiliation(s)
- Appan Roychoudhury
- Infection
Medicine, Edinburgh Medical School: Biomedical Sciences, University of Edinburgh, Chancellor’s Building, 49 Little France
Crescent, Edinburgh, EH16
4SB, United Kingdom
| | - Rosalind J. Allen
- School
of Physics and Astronomy, University of
Edinburgh, Edinburgh, EH9 3FD, United Kingdom
| | - Tine Curk
- Department
of Materials Science and Engineering, Northwestern
University, Evanston, Illinois 60208, United
States
| | - James Farrell
- Institute
of Physics, Chinese Academy of Sciences, Beijing, 100190, China,School
of Physical Sciences, University of Chinese
Academy of Sciences, Beijing, 100049, China
| | - Gina McAllister
- Department
of Laboratory Medicine, Royal Infirmary
of Edinburgh, Edinburgh, EH16 4SA, United Kingdom
| | - Kate Templeton
- Department
of Laboratory Medicine, Royal Infirmary
of Edinburgh, Edinburgh, EH16 4SA, United Kingdom
| | - Till T. Bachmann
- Infection
Medicine, Edinburgh Medical School: Biomedical Sciences, University of Edinburgh, Chancellor’s Building, 49 Little France
Crescent, Edinburgh, EH16
4SB, United Kingdom,E-mail:
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9
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Donia A, Furqan Shahid M, Hassan SU, Shahid R, Ahmad A, Javed A, Nawaz M, Yaqub T, Bokhari H. Integration of RT-LAMP and Microfluidic Technology for Detection of SARS-CoV-2 in Wastewater as an Advanced Point-of-Care Platform. FOOD AND ENVIRONMENTAL VIROLOGY 2022; 14:364-373. [PMID: 35508752 PMCID: PMC9067896 DOI: 10.1007/s12560-022-09522-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 04/04/2022] [Indexed: 05/21/2023]
Abstract
Development of lab-on-a-chip (LOC) system based on integration of reverse transcription loop-mediated isothermal amplification (RT-LAMP) and microfluidic technology is expected to speed up SARS-CoV-2 diagnostics allowing early intervention. In the current work, reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) and RT-LAMP assays were performed on extracted RNA of seven wastewater samples from COVID-19 hotspots. RT‑LAMP assay was also performed on wastewater samples without RNA extraction. Current detection of SARS-CoV-2 is mainly by RT-qPCR of ORF (ORF1ab) and N genes so we targeted both to find the best target gene for SARS-CoV-2 detection. We also performed RT-LAMP with/without RNA extraction inside microfluidic device to target both genes. Positivity rates of RT-qPCR and RT-LAMP performed on extracted RNA were 100.0% (7/7) and 85.7% (6/7), respectively. RT-qPCR results revealed that all 7 wastewater samples were positive for N gene (Ct range 37-39), and negative for ORF1ab, suggesting that N gene could be the best target gene for SARS-CoV-2 detection. RT-LAMP of N and ORF (ORF1a) genes performed on wastewater samples without RNA extraction indicated that all 7 samples remains pink (negative). The color remains pink in all microchannels except microchannels which subjected to RT-LAMP for targeting N region after RNA extraction (yellow color) in 6 out of 7 samples. This study shows that SARS-CoV-2 was successfully detected from wastewater samples using RT-LAMP in microfluidic chips. This study brings the novelty involving the use of wastewater samples for detection of SARS-CoV-2 without previous virus concentration and with/without RNA extraction.
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Affiliation(s)
- Ahmed Donia
- Department of Biosciences, Faculty of Science, COMSATS University Islamabad, Islamabad, Pakistan
| | - Muhammad Furqan Shahid
- Institute of Microbiology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Sammer-ul Hassan
- Department of Mechanical Engineering, University of Hong Kong, Pok Fu Lam, Hong Kong, Hong Kong
| | - Ramla Shahid
- Department of Biosciences, Faculty of Science, COMSATS University Islamabad, Islamabad, Pakistan
| | | | - Aneela Javed
- Healthcare Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Science and Technology, Islamabad, Pakistan
| | - Muhammad Nawaz
- Institute of Microbiology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Tahir Yaqub
- Institute of Microbiology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Habib Bokhari
- Department of Biosciences, Faculty of Science, COMSATS University Islamabad, Islamabad, Pakistan
- Kohsar University Murree, Murree, Pakistan
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10
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Atçeken N, Yigci D, Ozdalgic B, Tasoglu S. CRISPR-Cas-Integrated LAMP. BIOSENSORS 2022; 12:1035. [PMID: 36421156 PMCID: PMC9688180 DOI: 10.3390/bios12111035] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 10/10/2022] [Accepted: 11/14/2022] [Indexed: 06/16/2023]
Abstract
Pathogen-specific point-of-care (PoC) diagnostic tests have become an important need in the fight against infectious diseases and epidemics in recent years. PoC diagnostic tests are designed with the following parameters in mind: rapidity, accuracy, sensitivity, specificity, and ease of use. Molecular techniques are the gold standard for pathogen detection due to their accuracy and specificity. There are various limitations in adapting molecular diagnostic methods to PoC diagnostic tests. Efforts to overcome limitations are focused on the development of integrated molecular diagnostics by utilizing the latest technologies available to create the most successful PoC diagnostic platforms. With this point of view, a new generation technology was developed by combining loop-mediated isothermal amplification (LAMP) technology with clustered regularly interspaced short palindromic repeat (CRISPR)-associated (CRISPR-Cas) technology. This integrated approach benefits from the properties of LAMP technology, namely its high efficiency, short turnaround time, and the lack of need for a complex device. It also makes use of the programmable function of CRISPR-Cas technology and the collateral cleavage activity of certain Cas proteins that allow for convenient reporter detection. Thus, this combined technology enables the development of PoC diagnostic tests with high sensitivity, specificity, and ease of use without the need for complicated devices. In this review, we discuss the advantages and limitations of the CRISPR/Cas combined LAMP technology. We review current limitations to convert CRISPR combined LAMP into pathogen-specific PoC platforms. Furthermore, we point out the need to design more useful PoC platforms using microfabrication technologies by developing strategies that overcome the limitations of this new technology, reduce its complexity, and reduce the risk of contamination.
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Affiliation(s)
- Nazente Atçeken
- Koç University Translational Medicine Research Center (KUTTAM), Koç University, Istanbul 34450, Turkey
| | - Defne Yigci
- School of Medicine, Koç University, Istanbul 34450, Turkey
| | - Berin Ozdalgic
- Koç University Translational Medicine Research Center (KUTTAM), Koç University, Istanbul 34450, Turkey
- Department of Mechanical Engineering, Engineering Faculty, Koç University, Istanbul 34450, Turkey
- School of Medical Services & Techniques, Dogus University, Istanbul 34775, Turkey
| | - Savas Tasoglu
- Koç University Translational Medicine Research Center (KUTTAM), Koç University, Istanbul 34450, Turkey
- Department of Mechanical Engineering, Engineering Faculty, Koç University, Istanbul 34450, Turkey
- Boğaziçi Institute of Biomedical Engineering, Boğaziçi University, Istanbul 34684, Turkey
- Koç University Arçelik Research Center for Creative Industries (KUAR), Koç University, Istanbul 34450, Turkey
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11
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In Silico Evaluation of CRISPR-Based Assays for Effective Detection of SARS-CoV-2. Pathogens 2022; 11:pathogens11090968. [PMID: 36145402 PMCID: PMC9506389 DOI: 10.3390/pathogens11090968] [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: 07/19/2022] [Revised: 08/22/2022] [Accepted: 08/23/2022] [Indexed: 12/02/2022] Open
Abstract
Coronavirus disease (COVID-19) caused by the SARS-CoV-2 has been an outbreak since late 2019 up to now. This pandemic causes rapid development in molecular detection technologies to diagnose viral infection for epidemic prevention. In addition to antigen test kit (ATK) and polymerase chain reaction (PCR), CRISPR-based assays for detection of SARS-CoV-2 have gained attention because it has a simple setup but still maintain high specificity and sensitivity. However, the SARS-CoV-2 has been continuing mutating over the past few years. Thus, molecular tools that rely on matching at the nucleotide level need to be reevaluated to preserve their specificity and sensitivity. Here, we analyzed how mutations in different variants of concern (VOC), including Alpha, Beta, Gamma, Delta, and Omicron strains, could introduce mismatches to the previously reported primers and crRNAs used in the CRISPR-Cas system. Over 40% of the primer sets and 15% of the crRNAs contain mismatches. Hence, primers and crRNAs in nucleic acid-based assays must be chosen carefully to pair up with SARS-CoV-2 variants. In conclusion, the data obtained from this study could be useful in selecting the conserved primers and crRNAs for effective detections against the VOC of SARS-CoV-2.
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12
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Li X, Zhang H, Zhang J, Song Y, Shi X, Zhao C, Wang J. Diagnostic accuracy of CRISPR technology for detecting SARS-CoV-2: a systematic review and meta-analysis. Expert Rev Mol Diagn 2022; 22:655-663. [PMID: 35902079 DOI: 10.1080/14737159.2022.2107425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
OBJECTIVE To evaluate the diagnostic accuracy of CRISPR-Cas technology for SARS-CoV-2. METHODS In our study, RT-qPCR is defined as the reference standard. Data was collected independently and assessed by Quality Assessment of Diagnostic Accuracy Studies (QUADAS)-2 tool. A bivariate model for pooling was employed to estimates of sensitivity and specificity and subgroups analysis was used to explore heterogeneity. RESULTS 2264 samples and 6 countries from 28 articles were extracted for evaluating the accuracy of CRISPR technology for diagnosing SARS-CoV-2. The overall pooled sensitivity and specificity of CRISPR technology were 0.98 (95% CI: 0.95-0.99) and 1.0 (95% CI: 0.98-1.00), respectively. As for literature quality assessment, high risks in patient selection bias and unclear risk of index test bias may affect accuracy. Subgroup analysis draws significant conclusions. CRISPR-Cas12 is more applicable for molecular diagnostics for its active editing characteristics. RT-LAMP and RT-RPA are usually used for pre-amplification and combined with fluorescence detection to output results quantitatively. Nasopharyngeal swabs and dual-genes perform greatly in our study. CONCLUSION The results concluded from all studies showed that CRISPR technology is a promising and accurate molecular method for detecting SARS-CoV-2. Standard methods including comparable sample material, patient selection, operating procedure and operators should be established.
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Affiliation(s)
- Xin Li
- School of Public Health, Jilin University, Changchun 130021, China
| | - Huiling Zhang
- School of Public Health, Jilin University, Changchun 130021, China
| | - Jing Zhang
- School of Public Health, Jilin University, Changchun 130021, China
| | - Yang Song
- School of Public Health, Jilin University, Changchun 130021, China
| | - Xuening Shi
- School of Public Health, Jilin University, Changchun 130021, China
| | - Chao Zhao
- School of Public Health, Jilin University, Changchun 130021, China
| | - Juan Wang
- School of Public Health, Jilin University, Changchun 130021, China
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13
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Misra CS, Rangu SS, Phulsundar RD, Bindal G, Singh M, Shashidhar R, Saha TK, Rao AVSSN, Rath D. An improved, simple and field deployable CRISPR-Cas12a assay for detection of SARS-CoV-2. J Appl Microbiol 2022; 133:2668-2677. [PMID: 35882427 DOI: 10.1111/jam.15737] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 07/21/2022] [Accepted: 07/22/2022] [Indexed: 11/29/2022]
Abstract
AIMS The RT-PCR is the most popular confirmatory test for SARS-CoV-2. It is sensitive, but high instrumentation cost makes it difficult for use outside routine clinical setup. This has necessitated development of alternative methods such as CRISPR-based DETECTR method which uses lateral flow technology. Though accurate and sensitive, this method is limited by complex steps and recurrent cost of high quality lateral flow strips. The main goal of this study was to improve the Cas12a-based SARS-CoV-2 DETECTR method and develop a portable and field deployable system to reduce the recurring consumable cost. METHODS AND RESULTS Specific regions of N and E genes from SARS-CoV-2 virus and human RNase P (internal control) were reverse transcribed (RT) and amplified by loop-mediated isothermal amplification (LAMP). The amplified products were detected by a Cas12a-based trans-cleavage reaction that generated a fluorescent signal which could be easily visualised by naked eye. Detection of internal control, RNase P gene was improved and optimised by re-designing RT-LAMP primers. Number of steps were reduced by combining the reagents related to detection of Cas12a trans-cleavage reaction into a single ready-to-use mix. A portable, cost-effective battery-operated instrument, CRISPR-CUBE was developed to run the assay and visualise the outcome. The method and instrument were validated using both contrived and patient samples. CONCLUSIONS The simplified CRISPR-based SARS-CoV-2 detection and instrument developed in this study, along with improved design for internal control detection allows for easier, more definitive viral detection requiring only reagents, consumables and the battery operable CRISPR-CUBE. SIGNIFICANCE AND IMPACT OF STUDY Significant improvement in Cas12 method, coupled with simple visualisation of end-point makes the method and instrument deployable at the point of care for SARS-CoV-2 detection, without any recurrent cost for the lateral flow strips which is used in other POC methods.
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Affiliation(s)
- Chitra S Misra
- Applied Genomics Section, Bio-Science Group, Bhabha Atomic Research Centre, Mumbai, Maharashtra, India
| | - Shyam Sunder Rangu
- Applied Genomics Section, Bio-Science Group, Bhabha Atomic Research Centre, Mumbai, Maharashtra, India
| | - Ravindra D Phulsundar
- Electromagnetic Application and Instrumentation Division, Bhabha Atomic Research Centre, Mumbai, Maharashtra, India
| | - Gargi Bindal
- Applied Genomics Section, Bio-Science Group, Bhabha Atomic Research Centre, Mumbai, Maharashtra, India.,Homi Bhabha National Institute, Anushaktinagar, Mumbai, Maharashtra, India
| | - Mandeep Singh
- Applied Genomics Section, Bio-Science Group, Bhabha Atomic Research Centre, Mumbai, Maharashtra, India
| | - R Shashidhar
- Food Technology Division, Bhabha Atomic Research Centre, Mumbai, Maharashtra, India.,Homi Bhabha National Institute, Anushaktinagar, Mumbai, Maharashtra, India
| | - T K Saha
- Electromagnetic Application and Instrumentation Division, Bhabha Atomic Research Centre, Mumbai, Maharashtra, India
| | - A V S S N Rao
- Applied Genomics Section, Bio-Science Group, Bhabha Atomic Research Centre, Mumbai, Maharashtra, India
| | - Devashish Rath
- Applied Genomics Section, Bio-Science Group, Bhabha Atomic Research Centre, Mumbai, Maharashtra, India.,Homi Bhabha National Institute, Anushaktinagar, Mumbai, Maharashtra, India
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14
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Yu Y, Zhou JXY, Li B, Ji M, Wang Y, Carnaby E, Andersson MI, Huang WE, Cui Z. A quantitative RT-qLAMP for the detection of SARS-CoV-2 and human gene in clinical application. Microb Biotechnol 2022; 15:2619-2630. [PMID: 35830452 PMCID: PMC9349938 DOI: 10.1111/1751-7915.14112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 06/11/2022] [Accepted: 06/16/2022] [Indexed: 11/30/2022] Open
Abstract
Reverse transcription (RT) - loop-mediated isothermal amplification (LAMP) assay is a rapid and one-step method to detect SARS-CoV-2 in the pandemic. Quantitative estimation of the viral load of SARS-CoV-2 in patient samples could help physicians make decisions on clinical treatment and patient management. Here, we propose to use a quantitative LAMP (qLAMP) method to evaluate the viral load of SARS-CoV-2 in samples. We used threshold time (TT) values of qLAMP, the isothermal incubation time required for the fluorescent or colorimetric signal to reach the threshold, to indicate the viral load of clinical samples. Similar to the cycle threshold (Ct ) values in conventional qPCR, TT values of qLAMP show a linear relationship to the copy numbers of SARS-CoV-2. The higher the viral loadings, the lower qLAMP TT values are. The RT-qLAMP assay was demonstrated to quantify the viral loads of synthesized full-length RNA, inactivated viral particles (BBIBP-CorV), and clinical samples within 15 min by fluorescent reading and 25 min by colorimetric reading. The RT-qLAMP has been applied to detect Alpha, Beta, Kappa, Delta, and Omicron variants of SARS-CoV-2, as well as the human beta-actin gene, and their TT values showed the linear patterns. The RT-qLAMP assays were evaluated by 64 clinical samples (25 positives and 39 negatives) for the assessment of viral loads, and it was also used to quantify the human beta-actin gene, which was used as a control and an indicator of sampling quality in clinical swab samples. The result of RT-qLAMP was in good agreement with the result of RT-qPCR. The RT-qLAMP assay detected all clinical samples, including those with Ct = 35, within 10 min using fluorescent reading.
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Affiliation(s)
- Yejiong Yu
- Department of Engineering Science, Institute of Biomedical Engineering, University of Oxford, Oxford, UK
| | - Johnny X Y Zhou
- Department of Engineering Science, Institute of Biomedical Engineering, University of Oxford, Oxford, UK
| | - Binbin Li
- Oxford Suzhou Centre for Advanced Research (OSCAR), University of Oxford, Suzhou, China
| | - Mengmeng Ji
- Oxford Suzhou Centre for Advanced Research (OSCAR), University of Oxford, Suzhou, China
| | - Yun Wang
- Oxford Suzhou Centre for Advanced Research (OSCAR), University of Oxford, Suzhou, China
| | - Emma Carnaby
- Department of Microbiology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Monique I Andersson
- Department of Microbiology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK.,Nuffield Division of Clinical Laboratory Science, University of Oxford, Oxford, UK
| | - Wei E Huang
- Department of Engineering Science, Institute of Biomedical Engineering, University of Oxford, Oxford, UK.,Oxford Suzhou Centre for Advanced Research (OSCAR), University of Oxford, Suzhou, China
| | - Zhanfeng Cui
- Department of Engineering Science, Institute of Biomedical Engineering, University of Oxford, Oxford, UK.,Oxford Suzhou Centre for Advanced Research (OSCAR), University of Oxford, Suzhou, China
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15
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Tobik ER, Kitfield-Vernon LB, Thomas RJ, Steel SA, Tan SH, Allicock OM, Choate BL, Akbarzada S, Wyllie AL. Saliva as a sample type for SARS-CoV-2 detection: implementation successes and opportunities around the globe. Expert Rev Mol Diagn 2022; 22:519-535. [PMID: 35763281 DOI: 10.1080/14737159.2022.2094250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION Symptomatic testing and asymptomatic screening for SARS-CoV-2 continue to be essential tools for mitigating virus transmission. Though COVID-19 diagnostics initially defaulted to oropharyngeal or nasopharyngeal sampling, the worldwide urgency to expand testing efforts spurred innovative approaches and increased diversity of detection methods. Strengthening innovation and facilitating widespread testing remains critical for global health, especially as additional variants emerge and other mitigation strategies are recalibrated. AREAS COVERED A growing body of evidence reflects the need to expand testing efforts and further investigate the efficiency, sensitivity, and acceptability of saliva samples for SARS-CoV-2 detection. Countries have made pandemic response decisions based on resources, costs, procedures, and regional acceptability - the adoption and integration of saliva-based testing among them. Saliva has demonstrated high sensitivity and specificity while being less invasive relative to nasopharyngeal swabs, securing saliva's position as a more acceptable sample type. EXPERT OPINION Despite the accessibility and utility of saliva sampling, global implementation remains low compared to swab-based approaches. In some cases, countries have validated saliva-based methods but face challenges with testing implementation or expansion. Here, we review the localities that have demonstrated success with saliva-based SARS-CoV-2 testing approaches and can serve as models for transforming concepts into globally-implemented best practices.
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Affiliation(s)
- Emily R Tobik
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - Lily B Kitfield-Vernon
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - Russell J Thomas
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - Sydney A Steel
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - Steph H Tan
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA.,Department of Health Policy and Management, Yale School of Public Health, New Haven, Connecticut, USA
| | - Orchid M Allicock
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - Brittany L Choate
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - Sumaira Akbarzada
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - Anne L Wyllie
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
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16
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Hernandez-Garcia A, Morales-Moreno MD, Valdés-Galindo EG, Jimenez-Nieto EP, Quezada A. Diagnostics of COVID-19 Based on CRISPR-Cas Coupled to Isothermal Amplification: A Comparative Analysis and Update. Diagnostics (Basel) 2022; 12:1434. [PMID: 35741243 PMCID: PMC9222122 DOI: 10.3390/diagnostics12061434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 04/05/2022] [Accepted: 04/18/2022] [Indexed: 11/20/2022] Open
Abstract
The emergence of the COVID-19 pandemic prompted fast development of novel diagnostic methods of the etiologic virus SARS-CoV-2. Methods based on CRISPR-Cas systems have been particularly promising because they can achieve a similar sensitivity and specificity to the benchmark RT-qPCR, especially when coupled to an isothermal pre-amplification step. Furthermore, they have also solved inherent limitations of RT-qPCR that impede its decentralized use and deployment in the field, such as the need for expensive equipment, high cost per reaction, and delivery of results in hours, among others. In this review, we evaluate publicly available methods to detect SARS-CoV-2 that are based on CRISPR-Cas and isothermal amplification. We critically analyze the steps required to obtain a successful result from clinical samples and pinpoint key experimental conditions and parameters that could be optimized or modified to improve clinical and analytical outputs. The COVID outbreak has propelled intensive research in a short time, which is paving the way to develop effective and very promising CRISPR-Cas systems for the precise detection of SARS-CoV-2. This review could also serve as an introductory guide to new labs delving into this technology.
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Affiliation(s)
- Armando Hernandez-Garcia
- Laboratory of Biomolecular Engineering and Bionanotechnology, Department of Chemistry of Biomacromolecules, Institute of Chemistry, National Autonomous University of Mexico, Circuito Exterior, Ciudad Universitaria, Coyoacan, Ciudad de Mexico C.P. 04510, Mexico; (M.D.M.-M.); (E.G.V.-G.); (E.P.J.-N.); (A.Q.)
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17
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Bhatt A, Fatima Z, Ruwali M, Misra CS, Rangu SS, Rath D, Rattan A, Hameed S. CLEVER assay: A visual and rapid RNA extraction free detection of SARS-CoV-2 based on CRISPR-Cas integrated RT-LAMP technology. J Appl Microbiol 2022; 133:410-421. [PMID: 35396760 PMCID: PMC9111511 DOI: 10.1111/jam.15571] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 04/05/2022] [Accepted: 04/06/2022] [Indexed: 11/28/2022]
Abstract
Aim The current scenario of COVID‐19 pandemic has presented an almost insurmountable challenge even for the most sophisticated hospitals equipped with modern biomedical technology. There is an urgency to develop simple, fast and highly accurate methods for the rapid identification and isolation of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) infected patients. To address the ongoing challenge, the present study offers a CLEVER assay (CRISPR‐Cas integrated RT‐LAMP Easy, Visual and Extraction‐free RNA) which will allow RNA extraction‐free method to visually diagnose COVID‐19. RNA extraction is a major hurdle in preventing rapid and large‐scale screening of samples particularly in low‐resource regions because of the logistics and costs involved. Method and Result Herein, the visual SARS‐CoV‐2 detection method consists of RNA extraction‐free method directly utilizing the patient's nasopharyngeal and oropharyngeal samples for reverse transcription loop‐mediated isothermal amplification (RT‐LAMP). Additionally, the assay also utilizes the integration of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)‐Cas12‐based system using different guide RNAs of N, E and an internal control POP7 (human RNase P) genes along with visual detection via lateral flow readout‐based dip sticks with unaided eye (~100 min). Overall, the clinical sensitivity and specificity of the CLEVER assay were 89.6% and 100%, respectively. Conclusion Together, our CLEVER assay offers a point‐of‐care tool with no equipment dependency and minimum technical expertise requirement for COVID‐19 diagnosis. Significance and Impact of the Study To address the challenges associated with COVID‐19 diagnosis, we need a faster, direct and more versatile detection method for an efficient epidemiological management of the COVID‐19 outbreak. The present study involves developing a method for detection of SARS‐CoV‐2 in human body without RNA isolation step that can visually be detected with unaided eye. Taken together, our assay offers to overcome one major defect of the prior art, that is, RNA extraction step, which could limit the deployment of the previous assays in a testing site having limited lab infrastructure.
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Affiliation(s)
- Akansha Bhatt
- Amity Institute of Biotechnology, Amity University Haryana, Gurugram (Manesar), Haryana, India
| | - Zeeshan Fatima
- Amity Institute of Biotechnology, Amity University Haryana, Gurugram (Manesar), Haryana, India
| | - Munindra Ruwali
- Amity Institute of Biotechnology, Amity University Haryana, Gurugram (Manesar), Haryana, India
| | - Chitra Seetharam Misra
- CRISPR Biology Group, Applied Genomics Section, Bhabha Atomic Research Centre, Mumbai, Maharashtra, India
| | - Shyam Sunder Rangu
- CRISPR Biology Group, Applied Genomics Section, Bhabha Atomic Research Centre, Mumbai, Maharashtra, India
| | - Devashish Rath
- CRISPR Biology Group, Applied Genomics Section, Bhabha Atomic Research Centre, Mumbai, Maharashtra, India
| | | | - Saif Hameed
- Amity Institute of Biotechnology, Amity University Haryana, Gurugram (Manesar), Haryana, India
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18
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Nouri R, Dong M, Politza AJ, Guan W. Figure of Merit for CRISPR-Based Nucleic Acid-Sensing Systems: Improvement Strategies and Performance Comparison. ACS Sens 2022; 7:900-911. [PMID: 35238530 PMCID: PMC9191621 DOI: 10.1021/acssensors.2c00024] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)-based nucleic acid-sensing systems have grown rapidly in the past few years. Nevertheless, an objective approach to benchmark the performances of different CRISPR sensing systems is lacking due to the heterogeneous experimental setup. Here, we developed a quantitative CRISPR sensing figure of merit (FOM) to compare different CRISPR methods and explore performance improvement strategies. The CRISPR sensing FOM is defined as the product of the limit of detection (LOD) and the associated CRISPR reaction time (T). A smaller FOM means that the method can detect smaller target quantities faster. We found that there is a tradeoff between the LOD of the assay and the required reaction time. With the proposed CRISPR sensing FOM, we evaluated five strategies to improve the CRISPR-based sensing: preamplification, enzymes of higher catalytic efficiency, multiple crRNAs, digitalization, and sensitive readout systems. We benchmarked the FOM performances of 57 existing studies and found that the effectiveness of these strategies on improving the FOM is consistent with the model prediction. In particular, we found that digitalization is the most promising amplification-free method for achieving comparable FOM performances (∼1 fM·min) as those using preamplification. The findings here would have broad implications for further optimization of the CRISPR-based sensing.
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Affiliation(s)
- Reza Nouri
- Department of Electrical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Ming Dong
- Department of Electrical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Anthony J. Politza
- Department of Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Weihua Guan
- Department of Electrical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department of Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
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19
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Wang S, Hu J, Sui C, He G, Qu Z, Chen X, Wang Y, Guo D, Liu X. Accuracy of clustered regularly interspaced short palindromic repeats (CRISPR) to diagnose COVID-19, a meta-analysis. Microb Pathog 2022; 165:105498. [PMID: 35341958 PMCID: PMC8949659 DOI: 10.1016/j.micpath.2022.105498] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 02/26/2022] [Accepted: 03/19/2022] [Indexed: 02/06/2023]
Abstract
Objective To estimate the accuracy of clustered regularly interspaced short palindromic repeats (CRISPR) in determining coronavirus disease-19 (COVID-19). Methods As of January 31, 2022, PubMed, Web of Science, Embase, Science Direct, Wiley and Springer Link were searched. Sensitivity, specificity, likelihood ratio (LR), diagnostic odds ratio (DOR) and area under the summary receiver-operating characteristic (AUC) curve were used to assess the accuracy of CRISPR. Results According to the inclusion criteria, 5857 patients from 54 studies were included in this meta-analysis. The pooled sensitivity, specificity and AUC were 0.98, 1.00 and 1.00, respectively. For CRISPR-associated (Cas) proteins-12, the sensitivity, specificity was 0.96, 1.00, respectively. For Cas-13, the sensitivity and specificity were 0.99 and 0.99. Conclusion This meta-analysis showed that the diagnostic performance of CRISPR is close to the gold standard, and it is expected to meet the Point of care requirements in resource poor areas.
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Affiliation(s)
- Song Wang
- Department of Epidemiology and Statistics, School of Public Health, Jilin University, Changchun, Jilin, China
| | - Jiayi Hu
- Department of Epidemiology and Statistics, School of Public Health, Jilin University, Changchun, Jilin, China
| | - Chuanying Sui
- Department of Epidemiology and Statistics, School of Public Health, Jilin University, Changchun, Jilin, China
| | - Guangliang He
- Department of Epidemiology and Statistics, School of Public Health, Jilin University, Changchun, Jilin, China
| | - Zihan Qu
- Department of Epidemiology and Statistics, School of Public Health, Jilin University, Changchun, Jilin, China
| | - Xiaofei Chen
- Department of Epidemiology and Statistics, School of Public Health, Jilin University, Changchun, Jilin, China
| | - Yashan Wang
- Department of Epidemiology and Statistics, School of Public Health, Jilin University, Changchun, Jilin, China
| | - Dingjie Guo
- Department of Epidemiology and Statistics, School of Public Health, Jilin University, Changchun, Jilin, China
| | - Xin Liu
- Department of Epidemiology and Statistics, School of Public Health, Jilin University, Changchun, Jilin, China.
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20
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Ning B, Youngquist BM, Li DD, Lyon CJ, Zelazny A, Maness NJ, Tian D, Hu TY. Rapid detection of multiple SARS-CoV-2 variants of concern by PAM-targeting mutations. CELL REPORTS METHODS 2022; 2:100173. [PMID: 35156077 PMCID: PMC8818353 DOI: 10.1016/j.crmeth.2022.100173] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 10/26/2021] [Accepted: 01/31/2022] [Indexed: 12/02/2022]
Abstract
SARS-CoV-2 variants of concern (VOCs) that increase transmission or disease severity or reduce diagnostic or vaccine efficacy continue to emerge across the world. Current methods available to rapidly detect these can be resource intensive and thus sub-optimal for large-scale deployment needed during a pandemic response. Here, we describe a CRISPR-based assay that detects mutations in spike gene CRISPR PAM motif or seed regions to identify a pan-specific VOC single-nucleotide polymorphism (SNP)) ((D614G) and Alpha- and Delta-specific (S982A and D950N) SNPs. This assay exhibits good diagnostic sensitivity and strain specificity with nasal swabs and is designed for use in laboratory and point-of-care settings. This should enable rapid, high-throughput VOC identification required for surveillance and characterization efforts to inform clinical and public health decisions. Furthermore, the assay can be adapted to target similar SNPs associated with emerging SARS-CoV-2 VOCs, or other rapidly evolving viruses.
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Affiliation(s)
- Bo Ning
- Center for Cellular and Molecular Diagnostics, Tulane University School of Medicine, New Orleans, LA, USA
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA, USA
| | - Brady M. Youngquist
- Center for Cellular and Molecular Diagnostics, Tulane University School of Medicine, New Orleans, LA, USA
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA, USA
| | - Diane D. Li
- Center for Cellular and Molecular Diagnostics, Tulane University School of Medicine, New Orleans, LA, USA
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA, USA
| | - Christopher J. Lyon
- Center for Cellular and Molecular Diagnostics, Tulane University School of Medicine, New Orleans, LA, USA
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA, USA
| | - Adrian Zelazny
- Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, MD, USA
| | | | - Di Tian
- The Molecular Pathology Laboratory, Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, New Orleans, LA, USA
| | - Tony Y. Hu
- Center for Cellular and Molecular Diagnostics, Tulane University School of Medicine, New Orleans, LA, USA
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA, USA
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21
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You H, Gordon CA, MacGregor SR, Cai P, McManus DP. Potential of the CRISPR-Cas system for improved parasite diagnosis: CRISPR-Cas mediated diagnosis in parasitic infections: CRISPR-Cas mediated diagnosis in parasitic infections. Bioessays 2022; 44:e2100286. [PMID: 35142378 DOI: 10.1002/bies.202100286] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/26/2022] [Accepted: 01/27/2022] [Indexed: 12/26/2022]
Abstract
CRISPR-Cas technology accelerates development of fast, accurate, and portable diagnostic tools, typified by recent applications in COVID-19 diagnosis. Parasitic helminths cause devastating diseases afflicting 1.5 billion people globally, representing a significant public health and economic burden, especially in developing countries. Currently available diagnostic tests for worm infection are neither sufficiently sensitive nor field-friendly for use in low-endemic or resource-poor settings, leading to underestimation of true prevalence rates. Mass drug administration programs are unsustainable long-term, and diagnostic tools - required to be rapid, specific, sensitive, cost-effective, and user-friendly without specialized equipment and expertise - are urgently needed for rapid mapping of helminthic diseases and monitoring control programs. We describe the key features of the CRISPR-Cas12/13 system and emphasise its potential for the development of effective tools for the diagnosis of parasitic and other neglected tropical diseases (NTDs), a key recommendation of the NTDs 2021-2030 roadmap released by the World Health Organization.
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Affiliation(s)
- Hong You
- Immunology Department, QIMR Berghofer Medical Research Institute, Queensland, Australia
| | - Catherine A Gordon
- Immunology Department, QIMR Berghofer Medical Research Institute, Queensland, Australia
| | - Skye R MacGregor
- Immunology Department, QIMR Berghofer Medical Research Institute, Queensland, Australia
| | - Pengfei Cai
- Immunology Department, QIMR Berghofer Medical Research Institute, Queensland, Australia
| | - Donald P McManus
- Immunology Department, QIMR Berghofer Medical Research Institute, Queensland, Australia
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22
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Abstract
A big challenge for the control of COVID-19 pandemic is the emergence of variants of concern (VOCs) or variants of interest (VOIs) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which may be more transmissible and/or more virulent and could escape immunity obtained through infection or vaccination. A simple and rapid test for SARS-CoV-2 variants is an unmet need and is of great public health importance. In this study, we designed and analytically validated a CRISPR-Cas12a system for direct detection of SARS-CoV-2 VOCs. We further evaluated the combination of ordinary reverse transcription-PCR (RT-PCR) and CRISPR-Cas12a to improve the detection sensitivity and developed a universal system by introducing a protospacer adjacent motif (PAM) near the target mutation sites through PCR primer design to detect mutations without PAM. Our results indicated that the CRISPR-Cas12a assay could readily detect the signature spike protein mutations (K417N/T, L452R/Q, T478K, E484K/Q, N501Y, and D614G) to distinguish alpha, beta, gamma, delta, kappa, lambda, and epsilon variants of SARS-CoV-2. In addition, the open reading frame 8 (ORF8) mutations (T/C substitution at nt28144 and the corresponding change of amino acid L/S) could differentiate L and S lineages of SARS-CoV-2. The low limit of detection could reach 10 copies/reaction. Our assay successfully distinguished 4 SARS-CoV-2 strains of wild type and alpha (B.1.1.7), beta (B.1.351), and delta (B.1.617.2) variants. By testing 32 SARS-CoV-2-positive clinical samples infected with the wild type (n = 5) and alpha (n = 11), beta (n = 8), and delta variants (n = 8), the concordance between our assay and sequencing was 100%. The CRISPR-based approach is rapid and robust and can be adapted for screening the emerging mutations and immediately implemented in laboratories already performing nucleic acid amplification tests or in resource-limited settings. IMPORTANCE We described CRISPR-Cas12-based multiplex allele-specific assay for rapid SARS-CoV-2 variant genotyping. The new system has the potential to be quickly developed, continuously updated, and easily implemented for screening of SARS-CoV-2 variants in resource-limited settings. This approach can be adapted for emerging mutations and implemented in laboratories already conducting SARS-CoV-2 nucleic acid amplification tests using existing resources and extracted nucleic acid.
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23
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Zhou Y, Wu Y, Ding L, Huang X, Xiong Y. Point-of-care COVID-19 diagnostics powered by lateral flow assay. Trends Analyt Chem 2021; 145:116452. [PMID: 34629572 PMCID: PMC8487324 DOI: 10.1016/j.trac.2021.116452] [Citation(s) in RCA: 82] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Since its first discovery in December 2019, the global coronavirus disease 2019 (COVID-19) pandemic caused by the novel coronavirus (SARS-CoV-2) has been posing a serious threat to human life and health. Diagnostic testing is critical for the control and management of the COVID-19 pandemic. In particular, diagnostic testing at the point of care (POC) has been widely accepted as part of the post restriction COVID-19 control strategy. Lateral flow assay (LFA) is a popular POC diagnostic platform that plays an important role in controlling the COVID-19 pandemic in industrialized countries and resource-limited settings. Numerous pioneering studies on the design and development of diverse LFA-based diagnostic technologies for the rapid diagnosis of COVID-19 have been done and reported by researchers. Hundreds of LFA-based diagnostic prototypes have sprung up, some of which have been developed into commercial test kits for the rapid diagnosis of COVID-19. In this review, we summarize the crucial role of rapid diagnostic tests using LFA in targeting SARS-CoV-2-specific RNA, antibodies, antigens, and whole virus. Then, we discuss the design principle and working mechanisms of these available LFA methods, emphasizing their clinical diagnostic efficiency. Ultimately, we elaborate the challenges of current LFA diagnostics for COVID-19 and highlight the need for continuous improvement in rapid diagnostic tests.
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Affiliation(s)
- Yaofeng Zhou
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, 330047, PR China
- School of Food Science and Technology, Nanchang University, Nanchang, 330047, PR China
| | - Yuhao Wu
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, 330047, PR China
- School of Food Science and Technology, Nanchang University, Nanchang, 330047, PR China
| | - Lu Ding
- Hypertension Research Institute of Jiangxi Province, Department of Cardiology, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, 330006, PR China
| | - Xiaolin Huang
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, 330047, PR China
- School of Food Science and Technology, Nanchang University, Nanchang, 330047, PR China
| | - Yonghua Xiong
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, 330047, PR China
- School of Food Science and Technology, Nanchang University, Nanchang, 330047, PR China
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24
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Chan KG, Ang GY, Yu CY, Yean CY. Harnessing CRISPR-Cas to Combat COVID-19: From Diagnostics to Therapeutics. Life (Basel) 2021; 11:1210. [PMID: 34833086 PMCID: PMC8623262 DOI: 10.3390/life11111210] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Revised: 10/31/2021] [Accepted: 11/03/2021] [Indexed: 12/24/2022] Open
Abstract
The coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), remains a global threat with an ever-increasing death toll even after a year on. Hence, the rapid identification of infected individuals with diagnostic tests continues to be crucial in the on-going effort to combat the spread of COVID-19. Viral nucleic acid detection via real-time reverse transcription polymerase chain reaction (rRT-PCR) or sequencing is regarded as the gold standard for COVID-19 diagnosis, but these technically intricate molecular tests are limited to centralized laboratories due to the highly specialized instrument and skilled personnel requirements. Based on the current development in the field of diagnostics, the programmable clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated proteins (Cas) system appears to be a promising technology that can be further explored to create rapid, cost-effective, sensitive, and specific diagnostic tools for both laboratory and point-of-care (POC) testing. Other than diagnostics, the potential application of the CRISPR-Cas system as an antiviral agent has also been gaining attention. In this review, we highlight the recent advances in CRISPR-Cas-based nucleic acid detection strategies and the application of CRISPR-Cas as a potential antiviral agent in the context of COVID-19.
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Affiliation(s)
- Kok Gan Chan
- International Genome Centre, Jiangsu University, Zhenjiang 212013, China;
- Institute of Marine Sciences, Shantou University, Shantou 515063, China
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia
| | - Geik Yong Ang
- Faculty of Sports Science and Recreation, Universiti Teknologi MARA, Shah Alam 40450, Malaysia
| | - Choo Yee Yu
- Laboratory of Vaccine and Biomolecules, Institute of Bioscience, Universiti Putra Malaysia, Serdang 43400, Malaysia
| | - Chan Yean Yean
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Kota Bharu 16150, Malaysia
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25
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Selvam K, Najib MA, Khalid MF, Mohamad S, Palaz F, Ozsoz M, Aziah I. RT-LAMP CRISPR-Cas12/13-Based SARS-CoV-2 Detection Methods. Diagnostics (Basel) 2021; 11:diagnostics11091646. [PMID: 34573987 PMCID: PMC8467512 DOI: 10.3390/diagnostics11091646] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 08/30/2021] [Accepted: 09/06/2021] [Indexed: 12/26/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19), which is caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), has attracted public attention. The gold standard for diagnosing COVID-19 is reverse transcription–quantitative polymerase chain reaction (RT-qPCR). However, RT-qPCR can only be performed in centralized laboratories due to the requirement for advanced laboratory equipment and qualified workers. In the last decade, clustered regularly interspaced short palindromic repeats (CRISPR) technology has shown considerable promise in the development of rapid, highly sensitive, and specific molecular diagnostic methods that do not require complicated instrumentation. During the current COVID-19 pandemic, there has been growing interest in using CRISPR-based diagnostic techniques to develop rapid and accurate assays for detecting SARS-CoV-2. In this work, we review and summarize reverse-transcription loop-mediated isothermal amplification (RT-LAMP) CRISPR-based diagnostic techniques for detecting SARS-CoV-2.
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Affiliation(s)
- Kasturi Selvam
- Institute for Research in Molecular Medicine (INFORMM), Health Campus, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia; (K.S.); (M.A.N.); (M.F.K.)
| | - Mohamad Ahmad Najib
- Institute for Research in Molecular Medicine (INFORMM), Health Campus, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia; (K.S.); (M.A.N.); (M.F.K.)
| | - Muhammad Fazli Khalid
- Institute for Research in Molecular Medicine (INFORMM), Health Campus, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia; (K.S.); (M.A.N.); (M.F.K.)
| | - Suharni Mohamad
- School of Dental Sciences, Health Campus, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia;
| | - Fahreddin Palaz
- Faculty of Medicine, Hacettepe University, Ankara 06100, Turkey;
| | - Mehmet Ozsoz
- Institute for Research in Molecular Medicine (INFORMM), Health Campus, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia; (K.S.); (M.A.N.); (M.F.K.)
- Department of Biomedical Engineering, Near East University, Nicosia 99138, Turkey
- Correspondence: (M.O.); (I.A.)
| | - Ismail Aziah
- Institute for Research in Molecular Medicine (INFORMM), Health Campus, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia; (K.S.); (M.A.N.); (M.F.K.)
- Correspondence: (M.O.); (I.A.)
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26
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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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27
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Morehouse ZP, Samikwa L, Proctor CM, Meleke H, Kamdolozi M, Ryan GL, Chaima D, Ho A, Nash RJ, Nyirenda TS. Validation of a direct-to-PCR COVID-19 detection protocol utilizing mechanical homogenization: A model for reducing resources needed for accurate testing. PLoS One 2021; 16:e0256316. [PMID: 34407126 PMCID: PMC8372900 DOI: 10.1371/journal.pone.0256316] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 08/03/2021] [Indexed: 12/18/2022] Open
Abstract
Efficient and effective viral detection methodologies are a critical piece in the global response to COVID-19, with PCR-based nasopharyngeal and oropharyngeal swab testing serving as the current gold standard. With over 100 million confirmed cases globally, the supply chains supporting these PCR testing efforts are under a tremendous amount of stress, driving the need for innovative and accurate diagnostic solutions. Herein, the utility of a direct-to-PCR method of SARS-CoV-2 detection grounded in mechanical homogenization is examined for reducing resources needed for testing while maintaining a comparable sensitivity to the current gold standard workflow of nasopharyngeal and oropharyngeal swab testing. In a head-to-head comparison of 30 patient samples, this initial clinical validation study of the proposed homogenization-based workflow demonstrated significant agreeability with the current extraction-based method utilized while cutting the total resources needed in half.
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Affiliation(s)
- Zachary P. Morehouse
- Michigan State University College of Osteopathic Medicine, East Lansing, Michigan, United States of America
- Omni International Inc, A PerkinElmer Company, Kennesaw, Georgia, United States of America
- Jeevan BioSciences, Tucker, Georgia, United States of America
| | - Lyson Samikwa
- Department of Pathology, College of Medicine, University of Malawi, Blantyre, Malawi
| | - Caleb M. Proctor
- Omni International Inc, A PerkinElmer Company, Kennesaw, Georgia, United States of America
| | - Harry Meleke
- Department of Pathology, College of Medicine, University of Malawi, Blantyre, Malawi
| | - Mercy Kamdolozi
- Department of Pathology, College of Medicine, University of Malawi, Blantyre, Malawi
| | - Gabriella L. Ryan
- Omni International Inc, A PerkinElmer Company, Kennesaw, Georgia, United States of America
| | - David Chaima
- Department of Pathology, College of Medicine, University of Malawi, Blantyre, Malawi
| | - Antonia Ho
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Rodney J. Nash
- Omni International Inc, A PerkinElmer Company, Kennesaw, Georgia, United States of America
- Jeevan BioSciences, Tucker, Georgia, United States of America
- Department of Biology, Georgia State University, Atlanta, Georgia, United States of America
| | - Tonney S. Nyirenda
- Department of Pathology, College of Medicine, University of Malawi, Blantyre, Malawi
- * E-mail:
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