51
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Yang T, Li D, Yan Y, Ettoumi FE, Wu RA, Luo Z, Yu H, Lin X. Ultrafast and absolute quantification of SARS-CoV-2 on food using hydrogel RT-LAMP without pre-lysis. JOURNAL OF HAZARDOUS MATERIALS 2023; 442:130050. [PMID: 36182888 PMCID: PMC9507997 DOI: 10.1016/j.jhazmat.2022.130050] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 09/12/2022] [Accepted: 09/21/2022] [Indexed: 05/13/2023]
Abstract
With rapid growing of environmental contact infection, more and more attentions are focused on the precise and absolute quantification of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus on cold chain foods via point-of-care test (POCT). In this work, we propose a hydrogel-mediated reverse transcription loop-mediated isothermal amplification (RT-LAMP) for ultrafast and absolute quantification of SARS-CoV-2. Cross-linked hydrogel offers opportunities for digital single molecule amplification in nanoconfined spaces, facilitating the virus lysis, RNA reverse transcription and amplification process, which is about 3.4-fold faster than conventional bulk RT-LAMP. Ultrafast quantification of SARS-CoV-2 is accomplished in 15 min without virus pre-lysis and RNA extraction. The sensitivity can accurately quantify SARS-CoV-2 down to 0.5 copy/μL. Furthermore, the integrated system has an excellent specificity, reproducibility and storage stability, which can be also used to test SARS-CoV-2 on various cold chain fruits. The developed ultrafast and simple hydrogel RT-LAMP will be an enormous potential for surveillance of virus or other hazardous microbes in environmental, agricultural and food industry.
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Affiliation(s)
- Tao Yang
- College of Biosystems Engineering & Food Science, State Key Laboratory of Fluid Power and Mechatronic Systems, Zhejiang University, 310058, China
| | - Dong Li
- College of Biosystems Engineering & Food Science, State Key Laboratory of Fluid Power and Mechatronic Systems, Zhejiang University, 310058, China
| | - Yuhua Yan
- College of Biosystems Engineering & Food Science, State Key Laboratory of Fluid Power and Mechatronic Systems, Zhejiang University, 310058, China
| | - Fatima-Ezzahra Ettoumi
- College of Biosystems Engineering & Food Science, State Key Laboratory of Fluid Power and Mechatronic Systems, Zhejiang University, 310058, China
| | - Ricardo A Wu
- College of Biosystems Engineering & Food Science, State Key Laboratory of Fluid Power and Mechatronic Systems, Zhejiang University, 310058, China
| | - Zisheng Luo
- College of Biosystems Engineering & Food Science, State Key Laboratory of Fluid Power and Mechatronic Systems, Zhejiang University, 310058, China; Ningbo Research Institute, Zhejiang University, 310058, China
| | - Hanry Yu
- Critical Analytics for Manufacturing Personalized Medicine Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, 138602, Singapore
| | - Xingyu Lin
- College of Biosystems Engineering & Food Science, State Key Laboratory of Fluid Power and Mechatronic Systems, Zhejiang University, 310058, China; Ningbo Research Institute, Zhejiang University, 310058, China.
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52
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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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53
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Li Y, Kim H, Ju Y, Park Y, Kang T, Yong D, Park HG. Ultrasensitive Isothermal Detection of SARS-CoV-2 Based on Self-Priming Hairpin-Utilized Amplification of the G-Rich Sequence. Anal Chem 2022; 94:17448-17455. [PMID: 36480911 PMCID: PMC9743493 DOI: 10.1021/acs.analchem.2c03442] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 11/28/2022] [Indexed: 12/13/2022]
Abstract
The outbreak of the novel coronavirus disease 2019 (COVID-19) pandemic induced by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused millions of fatalities all over the world. Unquestionably, the effective and timely testing for infected individuals is the most imperative for the prevention of the ongoing pandemic. Herein, a new method was established for detecting SARS-CoV-2 based on the self-priming hairpin-utilized isothermal amplification of the G-rich sequence (SHIAG). In this strategy, the target RNA binding to the hairpin probe (HP) was uniquely devised to lead to the self-priming-mediated extension followed by the continuously repeated nicking and extension reactions, consequently generating abundant G-rich sequences from the intended reaction capable of producing fluorescence signals upon specifically interacting with thioflavin T (ThT). Based on the unique isothermal design concept, we successfully identified SARS-CoV-2 genomic RNA (gRNA) as low as 0.19 fM with excellent selectivity by applying only a single HP and further verified its practical diagnostic capability by reliably testing a total of 100 clinical specimens for COVID-19 with 100% clinical sensitivity and specificity. This study would provide notable insights into the design and evolution of new isothermal strategies for the sensitive and facile detection of SARS-CoV-2 under resource constraints.
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Affiliation(s)
- Yan Li
- Department of Chemical and Biomolecular Engineering
(BK21 Four), Korea Advanced Institute of Science and Technology
(KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon34141, Republic of
Korea
| | - Hansol Kim
- Department of Chemical and Biomolecular Engineering
(BK21 Four), Korea Advanced Institute of Science and Technology
(KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon34141, Republic of
Korea
| | - Yong Ju
- Department of Chemical and Biomolecular Engineering
(BK21 Four), Korea Advanced Institute of Science and Technology
(KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon34141, Republic of
Korea
| | - Yeonkyung Park
- Department of Chemical and Biomolecular Engineering
(BK21 Four), Korea Advanced Institute of Science and Technology
(KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon34141, Republic of
Korea
| | - Taejoon Kang
- Bionanotechnology Research Center, Korea
Research Institute of Bioscience and Biotechnology (KRIBB), Yuseong-gu,
Daejeon34141, Republic of Korea
- School of Pharmacy, Sungkyunkwan
University, 2066 Seobu-ro, Jangan-gu, Suwon, Gyeonggi-do16419,
Republic of Korea
| | - Dongeun Yong
- Department of Laboratory Medicine and
Research Institute of Bacterial Resistance, Yonsei University College of
Medicine, Seoul03722, Republic of Korea
| | - Hyun Gyu Park
- Department of Chemical and Biomolecular Engineering
(BK21 Four), Korea Advanced Institute of Science and Technology
(KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon34141, Republic of
Korea
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54
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Blackmore C, Hall GW, Allsopp RC, Hansell AL, Cowley CM, Barber RC, Holmes CW, Tobin MD, Shaw JA, Brunskill NJ, Baker PN. How to design and implement a university-based COVID-19 testing programme? An evaluation of a novel RT-LAMP COVID-19 testing programme in a UK university. BMC Health Serv Res 2022; 22:1502. [PMID: 36494675 PMCID: PMC9733160 DOI: 10.1186/s12913-022-08717-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 10/21/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Little is known about how asymptomatic testing as a method to control transmission of COVID-19 can be implemented, and the prevalence of asymptomatic infection within university populations. The objective of this study was to investigate how to effectively set-up and implement a COVID-19 testing programme using novel reverse transcriptase loop-mediated isothermal amplification (RT-LAMP) technology and to quantify the scale of asymptomatic infection on a university campus. METHODS An observational study to describe the set-up and implementation of a novel COVID-19 testing programme on a UK university campus between September and December 2020. RT-LAMP testing was used to identify asymptomatic cases. RESULTS A total of 1,673 tests were performed using RT-LAMP during the study period, of which 9 were positive for COVID-19, giving an overall positivity rate of 0.54%, equivalent to a rate in the tested population of 538 cases per 100,000 over the duration of testing. All positive tests were found to be positive on RT-PCR testing, giving a false positive rate of 0%. CONCLUSIONS This study shows that it is possible to rapidly setup a universal university testing programme for COVID-19 in collaboration with local healthcare providers using RT-LAMP testing. Positive results were comparable to those in the local population, though with a different peak of infection. Further research to inform the design of the testing programme includes focus groups of those who underwent testing and further interrogation of the demographics of those opting to be tested to identify potential access problems or inequalities.
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Affiliation(s)
- Claire Blackmore
- Centre for Environmental Health and Sustainability, University of Leicester, University Road, Leicester, LE1 7RH, UK.
| | - Gareth W Hall
- College of Life Sciences, University of Leicester, Leicester, UK
| | - Rebecca C Allsopp
- Department of Genetics and Genome Biology, Leicester Cancer Research Centre, University of Leicester, Leicester, UK
| | - Anna L Hansell
- Centre for Environmental Health and Sustainability, University of Leicester, University Road, Leicester, LE1 7RH, UK
- NIHR Health Protection Research Unit (HPRU) in Environmental Exposures and Health, University of Leicester, Leicester, UK
| | - Caroline M Cowley
- Leicester Molecular Diagnostics, Leicester Cancer Research Centre, University of Leicester, Leicester, UK
| | - Ruth C Barber
- Leicester Precision Medicine Institute, University of Leicester, Leicester, UK
| | - Christopher W Holmes
- University Hospitals of Leicester NHS Trust, Leicester, UK
- Department of Respiratory Sciences, University of Leicester, Leicester, UK
| | - Martin D Tobin
- Genetic Epidemiology and Public Health, Department of Health Sciences, University of Leicester, Leicester, UK
- Leicester NIHR Biomedical Research Centre, Leicester, UK
| | - Jacqui A Shaw
- Department of Genetics and Genome Biology, Leicester Cancer Research Centre, Translational Cancer Genetics, University of Leicester, Leicester, UK
| | - Nigel J Brunskill
- Department of Cardiovascular Sciences, University of Leicester, Leicester, UK
| | - Philip N Baker
- Research & Enterprise, Fielding Johnson Building, University of Leicester, Leicester, UK
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55
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Akarapipad P, Bertelson E, Pessell A, Wang TH, Hsieh K. Emerging Multiplex Nucleic Acid Diagnostic Tests for Combating COVID-19. BIOSENSORS 2022; 12:bios12110978. [PMID: 36354487 PMCID: PMC9688249 DOI: 10.3390/bios12110978] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Revised: 10/26/2022] [Accepted: 10/31/2022] [Indexed: 05/29/2023]
Abstract
The COVID-19 pandemic caused by SARS-CoV-2 has drawn attention to the need for fast and accurate diagnostic testing. Concerns from emerging SARS-CoV-2 variants and other circulating respiratory viral pathogens further underscore the importance of expanding diagnostic testing to multiplex detection, as single-plex diagnostic testing may fail to detect emerging variants and other viruses, while sequencing can be too slow and too expensive as a diagnostic tool. As a result, there have been significant advances in multiplex nucleic-acid-based virus diagnostic testing, creating a need for a timely review. This review first introduces frequent nucleic acid targets for multiplex virus diagnostic tests, then proceeds to a comprehensive and up-to-date overview of multiplex assays that incorporate various detection reactions and readout modalities. The performances, advantages, and disadvantages of these assays are discussed, followed by highlights of platforms that are amenable for point-of-care use. Finally, this review points out the remaining technical challenges and shares perspectives on future research and development. By examining the state of the art and synthesizing existing development in multiplex nucleic acid diagnostic tests, this review can provide a useful resource for facilitating future research and ultimately combating COVID-19.
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Affiliation(s)
- Patarajarin Akarapipad
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Elizabeth Bertelson
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Alexander Pessell
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Tza-Huei Wang
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Kuangwen Hsieh
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
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56
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Park S, Su Jeon C, Choi N, Moon JI, Min Lee K, Hyun Pyun S, Kang T, Choo J. Sensitive and reproducible detection of SARS-CoV-2 using SERS-based microdroplet sensor. CHEMICAL ENGINEERING JOURNAL (LAUSANNE, SWITZERLAND : 1996) 2022; 446:137085. [PMID: 35611066 PMCID: PMC9121656 DOI: 10.1016/j.cej.2022.137085] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 05/13/2022] [Accepted: 05/17/2022] [Indexed: 05/08/2023]
Abstract
Surface-enhanced Raman scattering (SERS)-based assays have been recently developed to overcome the low detection sensitivity of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). SERS-based assays using magnetic beads in microtubes slightly improved the limit of detection (LoD) for SARS-CoV-2. However, the sensitivity and reproducibility of the method are still insufficient for reliable SARS-CoV-2 detection. In this study, we developed a SERS-based microdroplet sensor to dramatically improve the LoD and reproducibility of SARS-CoV-2 detection. Raman signals were measured for SERS nanotags in 140 droplets passing through a laser focal volume fixed at the center of the channel for 15 s. A comparison of the Raman signals of SERS nanotags measured in a microtube with those measured for multiple droplets in the microfluidic channel revealed that the LoD and coefficient of variation significantly improved from 36 to 0.22 PFU/mL and 21.2% to 1.79%, respectively. This improvement resulted from the ensemble average effects because the signals were measured for SERS nanotags in multiple droplets. Moreover, the total assay time decreased from 30 to 10 min. A clinical test was performed on patient samples to evaluate the clinical efficacy of the SERS-based microdroplet sensor. The assay results agreed well with those measured by the reverse transcription-polymerase chain reaction (RT-PCR) method. The proposed SERS-based microdroplet sensor is expected to be used as a new point-of-care diagnostic platform for quick and accurate detection of SARS-CoV-2 in the field.
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Affiliation(s)
- Sohyun Park
- Department of Chemistry, Chung-Ang University, Seoul 06974, South Korea
| | - Chang Su Jeon
- R&D Center, Speclipse Inc., Seongnam 13461, South Korea
| | - Namhyun Choi
- Department of Chemistry, Chung-Ang University, Seoul 06974, South Korea
| | - Joung-Il Moon
- Department of Chemistry, Chung-Ang University, Seoul 06974, South Korea
| | - Kang Min Lee
- Department of Chemistry, Chung-Ang University, Seoul 06974, South Korea
| | | | - Taejoon Kang
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, South Korea
| | - Jaebum Choo
- Department of Chemistry, Chung-Ang University, Seoul 06974, South Korea
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57
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Yang Z, Liu NY, Zhu Z, Xiao M, Zhong S, Xue Q, Nie L, Zhao J. Rapid and convenient detection of SARS-CoV-2 using a colorimetric triple-target reverse transcription loop-mediated isothermal amplification method. PeerJ 2022; 10:e14121. [PMID: 36248705 PMCID: PMC9558625 DOI: 10.7717/peerj.14121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 09/05/2022] [Indexed: 01/21/2023] Open
Abstract
Coronavirus Disease 2019 (COVID-19) caused by SARS-CoV-2 poses a significant threat to global public health. Early detection with reliable, fast, and simple assays is crucial to contain the spread of SARS-CoV-2. The real-time reverse transcription-polymerase chain reaction (RT-PCR) assay is currently the gold standard for SARS-CoV-2 detection; however, the reverse transcription loop-mediated isothermal amplification method (RT-LAMP) assay may allow for faster, simpler and cheaper screening of SARS-CoV-2. In this study, the triple-target RT-LAMP assay was first established to simultaneously detect three different target regions (ORF1ab, N and E genes) of SARS-CoV-2. The results revealed that the developed triplex RT-LAMP assay was able to detect down to 11 copies of SARS-CoV-2 RNA per 25 µL reaction, with greater sensitivity than singleplex or duplex RT-LAMP assays. Moreover, two different indicators, hydroxy naphthol blue (HNB) and cresol red, were studied in the colorimetric RT-LAMP assay; our results suggest that both indicators are suitable for RT-LAMP reactions with an obvious color change. In conclusion, our developed triplex colorimetric RT-LAMP assay may be useful for the screening of COVID-19 cases in limited-resource areas.
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Affiliation(s)
- Zhu Yang
- Department of Medical Microbiology and Immunology, Wannan Medical College, Wuhu, Anhui, China
| | - Nicole Y. Liu
- Department of Medical Microbiology and Immunology, Wannan Medical College, Wuhu, Anhui, China
| | - Zhiwei Zhu
- Department of Parasitology, Wannan Medical College, Wuhu, Anhui, China
| | - Minmin Xiao
- Clinical Laboratory, The Second People’s Hospital of Wuhu City, Wuhu, Anhui, China
| | - Shuzhi Zhong
- Department of Histology and Embryology, Wannan Medical College, Wuhu, Anhui, China
| | - Qiqi Xue
- Department of Parasitology, Wannan Medical College, Wuhu, Anhui, China
| | - Lina Nie
- Clinical Laboratory, The Second People’s Hospital of Wuhu City, Wuhu, Anhui, China
| | - Jinhong Zhao
- Department of Parasitology, Wannan Medical College, Wuhu, Anhui, China
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58
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Borghei YS, Samadikhah HR, Hosseinkhani S. Exploitation of N-Gene of SARS-CoV-2 to Develop a New Rapid Assay by ASOs@AuNPs. Anal Chem 2022; 94:13616-13622. [PMID: 36130119 PMCID: PMC9514053 DOI: 10.1021/acs.analchem.2c03544] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Accepted: 09/12/2022] [Indexed: 11/29/2022]
Abstract
A naked-eye (equipment-free), label-free (cost-effective), and RNA extraction-free (to speed up) method for SARS-CoV-2 (as a case study of RNA viruses) detection is developed. Here, the DNA is being used as a template for in situ formation of anisotropic gold nanoparticles (AuNPs) without any chemical modification or DNA labeling. In this study, synthesized AuNPs for the direct detection of N-gene (nucleocapsid phosphoprotein) of SARS-CoV-2 are exploited. To this aim, antisense oligonucleotides (ASOs) with an extra poly guanine tail (G12) were designed. Thus, in the presence of its viral target RNA gene and ASOs@AuNPs-RNA hybridization, there was a red shift in its localized surface plasmon resonance (LSPR), and the intensity of the LSPR peak at 690 nm of throat swab samples was compared to the threshold cycle (Ct) of a reverse-transcriptase real-time polymerase chain reaction (RT-qPCR) (as a gold standard). Results suggested that the plasmonic biosensor can detect a very low amount of SARS-CoV-2 with a detection limit close to RT-qPCR. Simplicity of the new conjugation method with hybridization and annealing without amplification and denaturation steps enabled it to perform in a microfluidic paper-based analytical device.
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Affiliation(s)
- Yasaman-Sadat Borghei
- Institute
for Convergent Science and Technology, Sharif
University of Technology, Tehran 11155-8639, Iran
| | - Hamid Reza Samadikhah
- Department
of Biology, Faculty of Sciences, Central Tehran Branch, Islamic Azad University, Tehran 19585-466, Iran
| | - Saman Hosseinkhani
- Department
of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran 14115-154, Iran
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59
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Liu KS, Mao XD, Ni W, Li TP. Laboratory detection of SARS-CoV-2: A review of the current literature and future perspectives. Heliyon 2022; 8:e10858. [PMID: 36212015 PMCID: PMC9527186 DOI: 10.1016/j.heliyon.2022.e10858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 05/16/2022] [Accepted: 09/26/2022] [Indexed: 11/06/2022] Open
Abstract
Nowadays, coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), whose infectivity is awfully strong, has been a major global threat to the public health. Since lung is the major target of SARS-CoV-2, the infection can lead to respiratory distress syndrome (RDS), multiple organ failure (MOF), and even death. The studies on viral structure and infection mechanism have found that angiotensin-converting enzyme 2 (ACE2), a pivotal enzyme affecting the organ-targeting in the RAS system, is the receptor of the SARS-CoV-2 virus. Currently, the detection of SARSCoV-2 is mainly achieved using open plate real-time reverse-transcription polymerase chain reaction (RT-PCR). While open plate method has some limitations, such as a high false-negative rate, cumbersome manual operation, aerosol pollution and leakage risks. Therefore, a convenient method to rapidly detect SARS-CoV-2 virus is urgently and extremely required for timely epidemic control with the limited resources. In this review, the current real-time methods and principles for novel coronavirus detection are summarized, with the aim to provide a reference for real-time screening of coronavirus in areas with insufficient detection capacity and inadequate medical resources. The development and establishment of a rapid, simple, sensitive and specific system to detect SARS-CoV-2 is of vital importance for distinct diagnosis and effective treatment of the virus, especially in the flu season.
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Affiliation(s)
- Kang-Sheng Liu
- Department of Clinical Laboratory, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing 210029, China
| | - Xiao-Dong Mao
- Department of Endocrinology, Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210028, China,Key Laboratory of TCM Syndrome & Treatment of Yingbing of State Administration of Traditional Chinese Medicine, Jiangsu Province Academy of Traditional Chinese Medicine, Nanjing 210028, China
| | - Wenjing Ni
- Department of Endocrinology, Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210028, China,Key Laboratory of TCM Syndrome & Treatment of Yingbing of State Administration of Traditional Chinese Medicine, Jiangsu Province Academy of Traditional Chinese Medicine, Nanjing 210028, China
| | - Tai-Ping Li
- Department of Neuro-Psychiatric Institute, The Affiliated Nanjing Brain Hospital of Nanjing Medical University, Nanjing 210029, China,Corresponding author.
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60
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Improved visual detection of DNA amplification using pyridylazophenol metal sensing dyes. Commun Biol 2022; 5:999. [PMID: 36130997 PMCID: PMC9491268 DOI: 10.1038/s42003-022-03973-x] [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: 05/25/2022] [Accepted: 09/09/2022] [Indexed: 11/09/2022] Open
Abstract
Detection of nucleic acid amplification has typically required sophisticated laboratory instrumentation, but as the amplification techniques have moved away from the lab, complementary detection techniques have been implemented to facilitate point-of-care, field, and even at-home applications. Simple visual detection approaches have been widely used for isothermal amplification methods, but have generally displayed weak color changes or been highly sensitive to sample and atmospheric effects. Here we describe the use of pyridylazophenol dyes and binding to manganese ion to produce a strong visible color that changes in response to nucleic acid amplification. This detection approach is easily quantitated with absorbance, rapidly and clearly visible by eye, robust to sample effects, and notably compatible with both isothermal and PCR amplification. Nucleic acid amplification and molecular diagnostic methods are being used in an increasing number of novel applications and settings, and the ability to reliably and sensitively detect them without the need for additional instrumentation will enable even more access to these powerful techniques.
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61
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Cao H, Mao K, Ran F, Xu P, Zhao Y, Zhang X, Zhou H, Yang Z, Zhang H, Jiang G. Paper Device Combining CRISPR/Cas12a and Reverse-Transcription Loop-Mediated Isothermal Amplification for SARS-CoV-2 Detection in Wastewater. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:13245-13253. [PMID: 36040863 PMCID: PMC9454323 DOI: 10.1021/acs.est.2c04727] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 08/16/2022] [Accepted: 08/17/2022] [Indexed: 05/04/2023]
Abstract
Wastewater-based surveillance of the COVID-19 pandemic holds great promise; however, a point-of-use detection method for SARS-CoV-2 in wastewater is lacking. Here, a portable paper device based on CRISPR/Cas12a and reverse-transcription loop-mediated isothermal amplification (RT-LAMP) with excellent sensitivity and specificity was developed for SARS-CoV-2 detection in wastewater. Three primer sets of RT-LAMP and guide RNAs (gRNAs) that could lead Cas12a to recognize target genes via base pairing were used to perform the high-fidelity RT-LAMP to detect the N, E, and S genes of SARS-CoV-2. Due to the trans-cleavage activity of CRISPR/Cas12a after high-fidelity amplicon recognition, carboxyfluorescein-ssDNA-Black Hole Quencher-1 and carboxyfluorescein-ssDNA-biotin probes were adopted to realize different visualization pathways via a fluorescence or lateral flow analysis, respectively. The reactions were integrated into a paper device for simultaneously detecting the N, E, and S genes with limits of detection (LODs) of 25, 310, and 10 copies/mL, respectively. The device achieved a semiquantitative analysis from 0 to 310 copies/mL due to the different LODs of the three genes. Blind experiments demonstrated that the device was suitable for wastewater analysis with 97.7% sensitivity and 82% semiquantitative accuracy. This is the first semiquantitative endpoint detection of SARS-CoV-2 in wastewater via different LODs, demonstrating a promising point-of-use method for wastewater-based surveillance.
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Affiliation(s)
- Haorui Cao
- State Key Laboratory of Environmental Geochemistry,
Institute of Geochemistry, Chinese Academy of Sciences,
Guiyang550081, China
- University of Chinese Academy of
Sciences, Beijing100049, China
| | - Kang Mao
- State Key Laboratory of Environmental Geochemistry,
Institute of Geochemistry, Chinese Academy of Sciences,
Guiyang550081, China
| | - Fang Ran
- State Key Laboratory of Environmental Geochemistry,
Institute of Geochemistry, Chinese Academy of Sciences,
Guiyang550081, China
| | - Pengqi Xu
- Precision Medicine Center, The Seventh
Affiliated Hospital, Sun Yat-sen University, Shenzhen518107,
China
| | - Yirong Zhao
- State Key Laboratory of Environmental Geochemistry,
Institute of Geochemistry, Chinese Academy of Sciences,
Guiyang550081, China
- University of Chinese Academy of
Sciences, Beijing100049, China
| | - Xiangyan Zhang
- Guizhou Provincial People’s
Hospital, Guiyang550002, China
| | - Hourong Zhou
- Guizhou Provincial People’s
Hospital, Guiyang550002, China
- Jiangjunshan Hospital of Guizhou
Province, Guiyang550001, China
| | - Zhugen Yang
- School of Water, Energy, and Environment,
Cranfield University, CranfieldMK43 0AL,
UK
| | - Hua Zhang
- State Key Laboratory of Environmental Geochemistry,
Institute of Geochemistry, Chinese Academy of Sciences,
Guiyang550081, China
| | - Guibin Jiang
- State Key Laboratory of Environmental Chemistry and
Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese
Academy of Sciences, Beijing100085, China
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Zai Y, Min C, Wang Z, Ding Y, Zhao H, Su E, He N. A sample-to-answer, quantitative real-time PCR system with low-cost, gravity-driven microfluidic cartridge for rapid detection of SARS-CoV-2, influenza A/B, and human papillomavirus 16/18. LAB ON A CHIP 2022; 22:3436-3452. [PMID: 35972195 DOI: 10.1039/d2lc00434h] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The pandemic of coronavirus disease 2019 (COVID-19), due to the novel coronavirus (SARS-CoV-2), has created an unprecedented threat to the global health system, especially in resource-limited areas. This challenge shines a spotlight on the urgent need for a point-of-care (POC) quantitative real-time PCR (qPCR) test for sensitive and rapid diagnosis of viral infections. In a POC system, a closed, single-use, microfluidic cartridge is commonly utilized for integration of nucleic acid preparation, PCR amplification and florescence detection. But, most current cartridge systems often involve complicated nucleic acid extraction via active pumping that relies on cumbersome external hardware, causing increases in system complexity and cost. In this work, we demonstrate a gravity-driven cartridge design for an integrated viral RNA/DNA diagnostic test that does not require auxiliary hardware for fluid pumping due to adopted extraction-free amplification. This microfluidic cartridge only contains two reaction chambers for nucleic acid lysis and amplification respectively, enabling a fast qPCR test in less than 30 min. This gravity-driven pumping strategy can help simplify and minimize the microfluidic cartridge, thus enabling high-throughput (up to 12 test cartridges per test) molecular detection via a small cartridge readout system. Thus, this work addresses the scalability limitation of POC molecular testing and can be run in any settings. We verified the analytical sensitivity and specificity of the cartridge testing for respiratory pathogens and sexually transmitted diseases using SARS-CoV-2, influenza A/B RNA samples, and human papillomavirus 16/18 DNA samples. Our cartridge system exhibited a comparable detection performance to the current gold standard qPCR instrument ABI 7500. Moreover, our system showed very high diagnostic accuracy for viral RNA/DNA detection that was well validated by ROC curve analysis. The sample-to-answer molecular testing system reported in this work has the advantages of simplicity, rapidity, and low cost, making it highly promising for prevention and control of infectious diseases in poor-resource areas.
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Affiliation(s)
- Yunfeng Zai
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Si Pai Lou 2, Nanjing 210096, China.
- Getein Biotechnology Co., Ltd., Nanjing 210000, China.
| | - Chao Min
- Getein Biotechnology Co., Ltd., Nanjing 210000, China.
| | - Zunliang Wang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Si Pai Lou 2, Nanjing 210096, China.
| | - Yongjun Ding
- Getein Biotechnology Co., Ltd., Nanjing 210000, China.
| | - Huan Zhao
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Si Pai Lou 2, Nanjing 210096, China.
- Getein Biotechnology Co., Ltd., Nanjing 210000, China.
| | - Enben Su
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Si Pai Lou 2, Nanjing 210096, China.
- Getein Biotechnology Co., Ltd., Nanjing 210000, China.
| | - Nongyue He
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Si Pai Lou 2, Nanjing 210096, China.
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Allsopp RC, Cowley CM, Barber RC, Jones C, Holmes CW, Bird PW, Gohil SG, Blackmore C, Tobin MD, Brunskill N, Baker PN, Shaw JA. A rapid RT-LAMP SARS-CoV-2 screening assay for collapsing asymptomatic COVID-19 transmission. PLoS One 2022; 17:e0273912. [PMID: 36048856 PMCID: PMC9436079 DOI: 10.1371/journal.pone.0273912] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Accepted: 08/17/2022] [Indexed: 11/18/2022] Open
Abstract
PURPOSE To demonstrate the diagnostic performance of rapid SARS-CoV-2 RT-LAMP assays, comparing the performance of genomic versus sub-genomic sequence target with subsequent application in an asymptomatic screening population. METHODS RT-LAMP diagnostic specificity (DSe) and sensitivity (DSe) was determined using 114 RT-PCR clinically positive and 88 RT-PCR clinically negative swab samples processed through the diagnostic RT-PCR service within the University Hospitals of Leicester NHS Trust. A swab-based RT-LAMP SARS-CoV-2 screening programme was subsequently made available to all staff and students at the University of Leicester (Autumn 2020), implemented to ISO 15189:2012 standards using NHS IT infrastructure and supported by University Hospital Leicester via confirmatory NHS diagnostic laboratory testing of RT-LAMP 'positive' samples. RESULTS Validation samples reporting a Ct < 20 were detected at 100% DSe and DSp, reducing to 95% DSe (100% DSp) for all samples reporting a Ct < 30 (both genomic dual sub-genomic assays). Advisory screening identified nine positive cases in 1680 symptom free individuals (equivalent to 540 cases per 100,000) with results reported back to participants and feed into national statistics within 48 hours. CONCLUSION This work demonstrates the utility of a rapid RT-LAMP assay for collapsing transmission of SARS-CoV-2 in an asymptomatic screening population.
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Affiliation(s)
- Rebecca C. Allsopp
- Leicester Cancer Research Centre, Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Caroline M. Cowley
- Leicester Molecular Diagnostics, Leicester Cancer Research Centre, University of Leicester, Leicester, United Kingdom
| | - Ruth C. Barber
- Leicester Precision Medicine Institute, University of Leicester, Leicester, United Kingdom
| | - Carolyn Jones
- Leicester Precision Medicine Institute, University of Leicester, Leicester, United Kingdom
| | - Christopher W. Holmes
- Clinical Microbiology, University Hospitals of Leicester NHS Trust, Leicester Royal Infirmary, Leicester, United Kingdom
- Department of Respiratory Sciences, University of Leicester, Leicester, United Kingdom
| | - Paul W. Bird
- Clinical Microbiology, University Hospitals of Leicester NHS Trust, Leicester Royal Infirmary, Leicester, United Kingdom
- Department of Respiratory Sciences, University of Leicester, Leicester, United Kingdom
| | - Shailesh G. Gohil
- Leicester Cancer Research Centre, Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Claire Blackmore
- Centre for Environmental Health and Sustainability, University of Leicester, Leicester, United Kingdom
| | - Martin D. Tobin
- Department of Health Sciences, University of Leicester, Leicester, United Kingdom
- Leicester NIHR Biomedical Research Centre, Leicester, United Kingdom
| | - Nigel Brunskill
- Leicester NIHR Biomedical Research Centre, Leicester, United Kingdom
- Department of Cardiovascular Sciences, University of Leicester, Leicester, United Kingdom
| | - Philip N. Baker
- Leicester NIHR Biomedical Research Centre, Leicester, United Kingdom
- College of Life Sciences, University of Leicester, Leicester, United Kingdom
| | - Jacqui A. Shaw
- Leicester Cancer Research Centre, Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
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64
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Recent advances in clustered regularly interspaced short palindromic repeats-based detection of severe acute respiratory syndrome coronavirus 2. Se Pu 2022; 40:773-781. [PMID: 36156623 PMCID: PMC9520371 DOI: 10.3724/sp.j.1123.2022.08001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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65
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Torezin Mendonça G, Cassaboni Stracke M, de Oliveira Coelho B, Bruna Soligo Sanchuki H, Klassen de Oliveira V, Klerynton Marchini F, Lucíola Zanette D, Nóbrega Aoki M, Ribeiro Viana E, Blanes L. A new RT-LAMP-on-a-Chip Instrument for SARS-CoV-2 diagnostics. Microchem J 2022; 180:107600. [PMID: 35620142 PMCID: PMC9121651 DOI: 10.1016/j.microc.2022.107600] [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: 01/10/2022] [Revised: 05/13/2022] [Accepted: 05/14/2022] [Indexed: 02/08/2023]
Abstract
This work describes the development of a Point-of-Care (POC) Lab-on-a-Chip (LOC) instrument for diagnosis of SARS-CoV-2 by Reverse-Transcription Loop-mediated isothermal amplification (RT-LAMP). The hardware is based on a Raspberry Pi computer ($35), a video camera, an Arduino Nano microcontroller, a printed circuit board as a heater and a 3D printed housing. The chips were manufactured in polymethyl methacrylate (PMMA) using a CO2 laser cutting machine and sealed with a PCR optic plastic film. The chip temperature is precisely controlled by a proportional-integral-derivative (PID) algorithm. During the RT-LAMP amplifications the chip was maintained at ∼ (65.0 ± 0.1) °C for 25 minutes and 5 minutes cooling down, totaling a 30 minutes of reaction .The software interpretation occurs in less than a second. The chip design has four 25 µL chambers, two for clinical samples and two for positive and negative control-samples. The RT-LAMP master mix solution added in the chip chambers contains the pH indicator Phenol Red, that is pink (for pH ∼ 8.0) before amplification and becomes yellow (pH ∼ 6.0) if the genetic material is amplified. The RT-LAMP SARS-CoV-2 diagnostic was made by color image recognition using the OpenCV machine vision software library. The software was programmed to automatically distinguish the HSV color parameter distribution in each one of the four chip chambers. The instrument was successfully tested for SARS-CoV-2 diagnosis, in 22 clinic samples, 11 positives and 11 negatives, achieving an assertiveness of 86% when compared to the results obtained by RT-LAMP standard reactions performed in conventional PCR equipment.
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Affiliation(s)
- Geovani Torezin Mendonça
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Oswaldo Cruz Foundation (Fiocruz), Professor Algacyr Munhoz Mader 3775 St., Curitiba, Paraná, Brazil
| | - Mateus Cassaboni Stracke
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Oswaldo Cruz Foundation (Fiocruz), Professor Algacyr Munhoz Mader 3775 St., Curitiba, Paraná, Brazil,Paraná Institute of Molecular Biology, Professor Algacyr Munhoz Mader 3775 St., Curitiba, Paraná, Brazil
| | - Bruna de Oliveira Coelho
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Oswaldo Cruz Foundation (Fiocruz), Professor Algacyr Munhoz Mader 3775 St., Curitiba, Paraná, Brazil
| | - Heloisa Bruna Soligo Sanchuki
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Oswaldo Cruz Foundation (Fiocruz), Professor Algacyr Munhoz Mader 3775 St., Curitiba, Paraná, Brazil
| | | | - Fabricio Klerynton Marchini
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Oswaldo Cruz Foundation (Fiocruz), Professor Algacyr Munhoz Mader 3775 St., Curitiba, Paraná, Brazil,Paraná Institute of Molecular Biology, Professor Algacyr Munhoz Mader 3775 St., Curitiba, Paraná, Brazil
| | - Dalila Lucíola Zanette
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Oswaldo Cruz Foundation (Fiocruz), Professor Algacyr Munhoz Mader 3775 St., Curitiba, Paraná, Brazil
| | - Mateus Nóbrega Aoki
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Oswaldo Cruz Foundation (Fiocruz), Professor Algacyr Munhoz Mader 3775 St., Curitiba, Paraná, Brazil
| | - Emilson Ribeiro Viana
- Research and Characterization of Nanomaterials and Nanodevices Laboratory (LPCA-NN), Physics Department, Federal University of Technology - Paraná, 7 de setembro 3165 Avenue, Curitiba, Paraná, Brazil
| | - Lucas Blanes
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Oswaldo Cruz Foundation (Fiocruz), Professor Algacyr Munhoz Mader 3775 St., Curitiba, Paraná, Brazil,Paraná Institute of Molecular Biology, Professor Algacyr Munhoz Mader 3775 St., Curitiba, Paraná, Brazil,Corresponding author
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66
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A lab-on-a-chip for the concurrent electrochemical detection of SARS-CoV-2 RNA and anti-SARS-CoV-2 antibodies in saliva and plasma. Nat Biomed Eng 2022; 6:968-978. [PMID: 35941191 PMCID: PMC9361916 DOI: 10.1038/s41551-022-00919-w] [Citation(s) in RCA: 93] [Impact Index Per Article: 46.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 07/01/2022] [Indexed: 12/19/2022]
Abstract
Rapid, accurate and frequent detection of the RNA of SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) and of serological host antibodies to the virus would facilitate the determination of the immune status of individuals who have Coronavirus disease 2019 (COVID-19), were previously infected by the virus, or were vaccinated against the disease. Here we describe the development and application of a 3D-printed lab-on-a-chip that concurrently detects, via multiplexed electrochemical outputs and within 2 h, SARS-CoV-2 RNA in saliva as well as anti-SARS-CoV-2 immunoglobulins in saliva spiked with blood plasma. The device automatedly extracts, concentrates and amplifies SARS-CoV-2 RNA from unprocessed saliva, and integrates the Cas12a-based enzymatic detection of SARS-CoV-2 RNA via isothermal nucleic acid amplification with a sandwich-based enzyme-linked immunosorbent assay on electrodes functionalized with the Spike S1, nucleocapsid and receptor-binding-domain antigens of SARS-CoV-2. Inexpensive microfluidic electrochemical sensors for performing multiplexed diagnostics at the point of care may facilitate the widespread monitoring of COVID-19 infection and immunity. A 3D-printed lab-on-a-chip allows for the concurrent rapid electrochemical detection of SARS-CoV-2 RNA in saliva and of anti-SARS-CoV-2 antibodies in saliva spiked with blood plasma.
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67
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Van Ngoc H, Quyen TL, Vinayaka AC, Bang DD, Wolff A. Point-of-care system for rapid real-time detection of SARS-CoV-2 virus based on commercially available Arduino platforms. Front Bioeng Biotechnol 2022; 10:917573. [PMID: 35992344 PMCID: PMC9385952 DOI: 10.3389/fbioe.2022.917573] [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: 04/11/2022] [Accepted: 06/27/2022] [Indexed: 11/13/2022] Open
Abstract
The COVID-19 pandemic emphasized the importance of rapid, portable, and on-site testing technologies necessary for resource-limited settings for effective testing and screening to reduce spreading of the infection. Realizing this, we developed a fluorescence-based point-of-care (fPOC) detection system with real-time reverse transcriptase loop-mediated isothermal amplification for rapid and quantitative detection of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus. The system is built based on the Arduino platform compatible with commercially available open-source hardware-software and off-the-shelf electronic components. The fPOC system comprises of three main components: 1) an instrument with integrated heaters, 2) optical detection components, and 3) an injection-molded polymeric cartridge. The system was tested and experimentally proved to be able to use for fast detection of the SARS-CoV-2 virus in real-time in less than 30 min. Preliminary results of testing the performance of the fPOC revealed that the fPOC could detect the SARS-CoV-2 virus at a limit of detection (LOD50%) at two to three copies/microliter (15.36 copies/reaction), which was comparable to reactions run on a standard commercial thermocycler. The performance of the fPOC was evaluated with 12 SARS-CoV-2 clinical throat swab samples that included seven positive and five negative samples, as confirmed by reverse transcription-polymerase chain reaction. The fPOC showed 100% agreement with the commercial thermocycler. This simple design of the fPOC system demonstrates the potential to greatly enhance the practical applicability to develop a totally integrated point-of-care system for rapid on-site screening of the SARS-CoV-2 virus in the management of the pandemic.
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Affiliation(s)
- Huynh Van Ngoc
- BioLabChip Group, Department of Biotechnology and Biomedicine, Technical University of Denmark (DTU-Bioengineering), Lyngby, Denmark
| | - Than Linh Quyen
- BioLabChip Group, Department of Biotechnology and Biomedicine, Technical University of Denmark (DTU-Bioengineering), Lyngby, Denmark
| | - Aaydha Chidambara Vinayaka
- Laboratory of Applied Micro and Nanotechnology (LAMINATE), Department of Biotechnology and Biomedicine, Technical University of Denmark (DTU-Bioengineering), Lyngby, Denmark
| | - Dang Duong Bang
- Laboratory of Applied Micro and Nanotechnology (LAMINATE), Department of Biotechnology and Biomedicine, Technical University of Denmark (DTU-Bioengineering), Lyngby, Denmark
| | - Anders Wolff
- BioLabChip Group, Department of Biotechnology and Biomedicine, Technical University of Denmark (DTU-Bioengineering), Lyngby, Denmark
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68
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Chandrasekaran SS, Agrawal S, Fanton A, Jangid AR, Charrez B, Escajeda AM, Son S, Mcintosh R, Tran H, Bhuiya A, de León Derby MD, Switz NA, Armstrong M, Harris AR, Prywes N, Lukarska M, Biering SB, Smock DCJ, Mok A, Knott GJ, Dang Q, Van Dis E, Dugan E, Kim S, Liu TY, Moehle EA, Kogut K, Eskenazi B, Harris E, Stanley SA, Lareau LF, Tan MX, Fletcher DA, Doudna JA, Savage DF, Hsu PD. Rapid detection of SARS-CoV-2 RNA in saliva via Cas13. Nat Biomed Eng 2022; 6:944-956. [PMID: 35953650 PMCID: PMC10367768 DOI: 10.1038/s41551-022-00917-y] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 06/30/2022] [Indexed: 11/10/2022]
Abstract
Rapid nucleic acid testing is central to infectious disease surveillance. Here, we report an assay for rapid COVID-19 testing and its implementation in a prototype microfluidic device. The assay, which we named DISCoVER (for diagnostics with coronavirus enzymatic reporting), involves extraction-free sample lysis via shelf-stable and low-cost reagents, multiplexed isothermal RNA amplification followed by T7 transcription, and Cas13-mediated cleavage of a quenched fluorophore. The device consists of a single-use gravity-driven microfluidic cartridge inserted into a compact instrument for automated running of the assay and readout of fluorescence within 60 min. DISCoVER can detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in saliva with a sensitivity of 40 copies μl-1, and was 94% sensitive and 100% specific when validated (against quantitative PCR) using total RNA extracted from 63 nasal-swab samples (33 SARS-CoV-2-positive, with cycle-threshold values of 13-35). The device correctly identified all tested clinical saliva samples (10 SARS-CoV-2-positive out of 13, with cycle-threshold values of 23-31). Rapid point-of-care nucleic acid testing may broaden the use of molecular diagnostics.
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Affiliation(s)
- Sita S Chandrasekaran
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- University of California, Berkeley-University of California, San Francisco Graduate Program in Bioengineering, Berkeley, CA, USA
| | - Shreeya Agrawal
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Alison Fanton
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- University of California, Berkeley-University of California, San Francisco Graduate Program in Bioengineering, Berkeley, CA, USA
| | - Aditya R Jangid
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Bérénice Charrez
- University of California, Berkeley-University of California, San Francisco Graduate Program in Bioengineering, Berkeley, CA, USA
| | | | - Sungmin Son
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | | | | | - Abdul Bhuiya
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
- University of California, Berkeley-University of California, San Francisco Graduate Program in Bioengineering, Berkeley, CA, USA
| | - María Díaz de León Derby
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
- University of California, Berkeley-University of California, San Francisco Graduate Program in Bioengineering, Berkeley, CA, USA
| | - Neil A Switz
- Department of Physics and Astronomy, San José State University, San José, CA, USA
| | - Maxim Armstrong
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Andrew R Harris
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | - Noam Prywes
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Maria Lukarska
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Scott B Biering
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Dylan C J Smock
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Amanda Mok
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Gavin J Knott
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Qi Dang
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Erik Van Dis
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Eli Dugan
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Shin Kim
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Tina Y Liu
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Erica A Moehle
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Katherine Kogut
- Center for Environmental Research and Community Health (CERCH), School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Brenda Eskenazi
- Center for Environmental Research and Community Health (CERCH), School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Eva Harris
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Sarah A Stanley
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Liana F Lareau
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | | | - Daniel A Fletcher
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | - Jennifer A Doudna
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA.
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA.
- Gladstone Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA, USA.
| | - David F Savage
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.
| | - Patrick D Hsu
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA.
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.
- Arc Institute, Palo Alto, CA, USA.
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69
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Arizti-Sanz J, Bradley A, Zhang YB, Boehm CK, Freije CA, Grunberg ME, Kosoko-Thoroddsen TSF, Welch NL, Pillai PP, Mantena S, Kim G, Uwanibe JN, John OG, Eromon PE, Kocher G, Gross R, Lee JS, Hensley LE, MacInnis BL, Johnson J, Springer M, Happi CT, Sabeti PC, Myhrvold C. Simplified Cas13-based assays for the fast identification of SARS-CoV-2 and its variants. Nat Biomed Eng 2022; 6:932-943. [PMID: 35637389 PMCID: PMC9398993 DOI: 10.1038/s41551-022-00889-z] [Citation(s) in RCA: 67] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 04/01/2022] [Indexed: 02/03/2023]
Abstract
The widespread transmission and evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) call for rapid nucleic acid diagnostics that are easy to use outside of centralized clinical laboratories. Here we report the development and performance benchmarking of Cas13-based nucleic acid assays leveraging lyophilised reagents and fast sample inactivation at ambient temperature. The assays, which we named SHINEv.2 (for 'streamlined highlighting of infections to navigate epidemics, version 2'), simplify the previously reported RNA-extraction-free SHINEv.1 technology by eliminating heating steps and the need for cold storage of the reagents. SHINEv.2 detected SARS-CoV-2 in nasopharyngeal samples with 90.5% sensitivity and 100% specificity (benchmarked against the reverse transcription quantitative polymerase chain reaction) in less than 90 min, using lateral-flow technology and incubation in a heat block at 37 °C. SHINEv.2 also allows for the visual discrimination of the Alpha, Beta, Gamma, Delta and Omicron SARS-CoV-2 variants, and can be run without performance losses by using body heat. Accurate, easy-to-use and equipment-free nucleic acid assays could facilitate wider testing for SARS-CoV-2 and other pathogens in point-of-care and at-home settings.
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Affiliation(s)
- Jon Arizti-Sanz
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Harvard-MIT Program in Health Sciences and Technology, Cambridge, MA, USA
| | - A'Doriann Bradley
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Yibin B Zhang
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Chloe K Boehm
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Catherine A Freije
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Michelle E Grunberg
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | | | - Nicole L Welch
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Program in Virology, Harvard Medical School, Boston, MA, USA
| | - Priya P Pillai
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Sreekar Mantena
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Gaeun Kim
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Jessica N Uwanibe
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
- Department of Biological Sciences, College of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
| | - Oluwagboadurami G John
- Department of Biological Sciences, College of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
| | - Philomena E Eromon
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
| | - Gregory Kocher
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institute of Health, Frederick, MD, USA
| | - Robin Gross
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institute of Health, Frederick, MD, USA
| | - Justin S Lee
- Biotechnology Cores Facility Branch, Division of Scientific Resources, National Center for Emerging and Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Lisa E Hensley
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institute of Health, Frederick, MD, USA
| | - Bronwyn L MacInnis
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Jeremy Johnson
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Michael Springer
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Christian T Happi
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Osun State, Nigeria
- Department of Biological Sciences, College of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Pardis C Sabeti
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Cameron Myhrvold
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
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Szunerits S, Saada H, Pagneux Q, Boukherroub R. Plasmonic Approaches for the Detection of SARS-CoV-2 Viral Particles. BIOSENSORS 2022; 12:548. [PMID: 35884352 PMCID: PMC9313406 DOI: 10.3390/bios12070548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 07/18/2022] [Accepted: 07/19/2022] [Indexed: 11/16/2022]
Abstract
The ongoing highly contagious Coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), underlines the fundamental position of diagnostic testing in outbreak control by allowing a distinction of the infected from the non-infected people. Diagnosis of COVID-19 remains largely based on reverse transcription PCR (RT-PCR), identifying the genetic material of the virus. Molecular testing approaches have been largely proposed in addition to infectivity testing of patients via sensing the presence of viral particles of SARS-CoV-2 specific structural proteins, such as the spike glycoproteins (S1, S2) and the nucleocapsid (N) protein. While the S1 protein remains the main target for neutralizing antibody treatment upon infection and the focus of vaccine and therapeutic design, it has also become a major target for the development of point-of care testing (POCT) devices. This review will focus on the possibility of surface plasmon resonance (SPR)-based sensing platforms to convert the receptor-binding event of SARS-CoV-2 viral particles into measurable signals. The state-of-the-art SPR-based SARS-CoV-2 sensing devices will be provided, and highlights about the applicability of plasmonic sensors as POCT for virus particle as well as viral protein sensing will be discussed.
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Affiliation(s)
- Sabine Szunerits
- University of Lille, CNRS, Centrale Lille, University Polytechnique Hauts-de-France, UMR 8520-IEMN, F-59000 Lille, France; (H.S.); (Q.P.); (R.B.)
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71
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Kim D, Kim SJ, Kim YK, Kwon KT, Kim S. Clinical evaluation of an innovative isothermal amplification detection system for COVID-19 diagnosis. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2022; 14:2578-2585. [PMID: 35748579 DOI: 10.1039/d2ay00815g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
A pre-integrated system design intended for a point-of-care (POC) and sample-to-result diagnostic platform with nucleic acid amplification has been developed, which is equipment/electricity-free without any permanent instruments or manual sample processing. This semi-integrated system focuses on pandemic situations that are suitable for the Affordable, Sensitive, Specific, User-friendly, Robust and rapid, Equipment-free, and Deliverable to the end-user "ASSURED" concept recommended by the World Health Organization (WHO). Nucleic acid amplification is an essential rate-limiting factor in the performance of integrated systems that involve sample preparation and detection. The ORF1ab (RdRp) gene of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been targeted by RT-LAMP optimization and evaluation using a commercial hot-pack as a heat source that successfully achieves a femto-scale (<6.8 × 102 copies per rxn) limit of detection (LOD) within 40 min (except for the RNA extraction step). Therefore, the prototype system was assessed using COVID-19-suspected clinical samples (eighty eight) and compared with the results of a commercial real-time reverse transcription polymerase chain reaction (RT-qPCR) assay (Allplex SARS-CoV-2 Assay kit (Seegene, Seoul, Republic of Korea)). These innovative approaches achieved over 95% sensitivity and specificity. In conclusion, the developed system using a hot-pack as a heat source is a promising tool that enables the rapid identification of infectious diseases in the real world.
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Affiliation(s)
- Dami Kim
- Philmedi R&D Center, Philmedi Incorporation, Seongnam, 13211, Republic of Korea
| | - Se Jin Kim
- Philmedi R&D Center, Philmedi Incorporation, Seongnam, 13211, Republic of Korea
| | - Yu Kyung Kim
- Department of Clinical Pathology, School of Medicine, Kyungpook National University, Division of Infectious Diseases, Daegu 41944, Republic of Korea
| | - Ki Tae Kwon
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Daegu, 41404, Republic of Korea.
| | - Sanghyo Kim
- Philmedi R&D Center, Philmedi Incorporation, Seongnam, 13211, Republic of Korea
- Department of Bionanotechnology, Gachon University, Seongnam, 13120, Republic of Korea.
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72
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Liu J, Wang H, Zhang L, Lu Y, Wang X, Shen M, Li N, Feng L, Jing J, Cao B, Zou X, Cheng J, Xu Y. Sensitive and Rapid Diagnosis of Respiratory Virus Coinfection Using a Microfluidic Chip-Powered CRISPR/Cas12a System. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2200854. [PMID: 35599436 DOI: 10.1002/smll.202200854] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/19/2022] [Indexed: 06/15/2023]
Abstract
The ongoing pandemic caused by severe acute respiratory syndrome coronavirus 2 is profoundly influencing the global healthcare system and people's daily lives. The high resource consumption of coronavirus disease 2019 (COVID-19) is resulting in insufficient surveillance of coinfection or resurgence of other critical respiratory epidemics, which is of public concern. To facilitate evaluation of the current coinfection situation, a microfluidic system (MAPnavi) is developed for the rapid (<40 min) and sensitive diagnosis of multiple respiratory viruses from swab samples in a fully sealed and automated manner, in which a nested-recombinase polymerase amplification and the CRISPR-based amplification system is first proposed to ensure the sensitivity and specificity. This novel system has a remarkably low limit of detection (50-200 copies mL-1 ) and is successfully applied to detect 171 clinical samples (98.5% positive predictive agreement; 100% negative predictive agreement), and the results identify 45.6% coinfection among clinical samples from patients with COVID-19. This approach has the potential to shift diagnostic and surveillance efforts from targeted testing for a high-priority virus to comprehensive testing of multiple virus sets and to greatly benefit the implementation of decentralized testing.
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Affiliation(s)
- Jiajia Liu
- State Key Laboratory of Membrane Biology, Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Huili Wang
- State Key Laboratory of Membrane Biology, Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Li Zhang
- State Key Laboratory of Membrane Biology, Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Ying Lu
- State Key Laboratory of Membrane Biology, Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Xu Wang
- State Key Laboratory of Membrane Biology, Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Minjie Shen
- State Key Laboratory of Membrane Biology, Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Nan Li
- State Key Laboratory of Membrane Biology, Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Li Feng
- CapitalBiotech Technology, Beijing, 101111, China
| | - Juhui Jing
- CapitalBiotech Technology, Beijing, 101111, China
| | - Bin Cao
- Department of Pulmonary and Critical Care Medicine, Laboratory of Clinical Microbiology and Infectious Diseases, Center for Respiratory Diseases, National Clinical Research Center of Respiratory Diseases, China-Japan Friendship Hospital, Beijing, 100029, China
| | - Xiaohui Zou
- Department of Pulmonary and Critical Care Medicine, Laboratory of Clinical Microbiology and Infectious Diseases, Center for Respiratory Diseases, National Clinical Research Center of Respiratory Diseases, China-Japan Friendship Hospital, Beijing, 100029, China
| | - Jing Cheng
- State Key Laboratory of Membrane Biology, Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing, 100084, China
- National Engineering Research Center for Beijing Biochip Technology, Beijing, 102200, China
| | - Youchun Xu
- State Key Laboratory of Membrane Biology, 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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73
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Delgado-Diaz DJ, Sakthivel D, Nguyen HHT, Farrokzhad K, Hopper W, Narh CA, Richards JS. Strategies That Facilitate Extraction-Free SARS-CoV-2 Nucleic Acid Amplification Tests. Viruses 2022; 14:v14061311. [PMID: 35746782 PMCID: PMC9230587 DOI: 10.3390/v14061311] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 06/12/2022] [Accepted: 06/13/2022] [Indexed: 02/01/2023] Open
Abstract
The COVID-19 pandemic has resulted in an unprecedented global demand for in vitro diagnostic reagents. Supply shortages and hoarding have impacted testing capacity which has led to inefficient COVID-19 case identification and transmission control, predominantly in developing countries. Traditionally, RNA extraction is a prerequisite for conducting SARS-CoV-2 nucleic acid amplification tests (NAAT); however, simplified methods of sample processing have been successful at bypassing typical nucleic acid extraction steps, enabling extraction-free SARS-CoV-2 NAAT workflows. These methods involve chemical and physical approaches that are inexpensive and easily accessible alternatives to overcome extraction kit supply shortages, while offering acceptable test performance. Here we provide an overview of three main sample preparation strategies that have been shown to facilitate extraction-free SARS-CoV-2 NAATs.
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Affiliation(s)
- David J. Delgado-Diaz
- ZIP Diagnostics Pty Ltd., Collingwood, VIC 3066, Australia; (D.S.); (H.H.T.N.); (K.F.); (W.H.); (C.A.N.); (J.S.R.)
- Correspondence:
| | - Dhanasekaran Sakthivel
- ZIP Diagnostics Pty Ltd., Collingwood, VIC 3066, Australia; (D.S.); (H.H.T.N.); (K.F.); (W.H.); (C.A.N.); (J.S.R.)
| | - Hanh H. T. Nguyen
- ZIP Diagnostics Pty Ltd., Collingwood, VIC 3066, Australia; (D.S.); (H.H.T.N.); (K.F.); (W.H.); (C.A.N.); (J.S.R.)
| | - Khashayar Farrokzhad
- ZIP Diagnostics Pty Ltd., Collingwood, VIC 3066, Australia; (D.S.); (H.H.T.N.); (K.F.); (W.H.); (C.A.N.); (J.S.R.)
| | - William Hopper
- ZIP Diagnostics Pty Ltd., Collingwood, VIC 3066, Australia; (D.S.); (H.H.T.N.); (K.F.); (W.H.); (C.A.N.); (J.S.R.)
| | - Charles A. Narh
- ZIP Diagnostics Pty Ltd., Collingwood, VIC 3066, Australia; (D.S.); (H.H.T.N.); (K.F.); (W.H.); (C.A.N.); (J.S.R.)
- Department of Medicine, University of Melbourne, Melbourne, VIC 3010, Australia
- Department of Infectious Diseases, Monash University, Melbourne, VIC 3004, Australia
| | - Jack S. Richards
- ZIP Diagnostics Pty Ltd., Collingwood, VIC 3066, Australia; (D.S.); (H.H.T.N.); (K.F.); (W.H.); (C.A.N.); (J.S.R.)
- Department of Medicine, University of Melbourne, Melbourne, VIC 3010, Australia
- Department of Infectious Diseases, Monash University, Melbourne, VIC 3004, Australia
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74
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Li Z, Bruce JL, Cohen B, Cunningham CV, Jack WE, Kunin K, Langhorst BW, Miller J, Moncion RA, Poole CB, Premsrirut PK, Ren G, Roberts RJ, Tanner NA, Zhang Y, Carlow CKS. Development and implementation of a simple and rapid extraction-free saliva SARS-CoV-2 RT-LAMP workflow for workplace surveillance. PLoS One 2022; 17:e0268692. [PMID: 35617204 PMCID: PMC9135294 DOI: 10.1371/journal.pone.0268692] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 05/04/2022] [Indexed: 01/12/2023] Open
Abstract
Effective management of the COVID-19 pandemic requires widespread and frequent testing of the population for SARS-CoV-2 infection. Saliva has emerged as an attractive alternative to nasopharyngeal samples for surveillance testing as it does not require specialized personnel or materials for its collection and can be easily provided by the patient. We have developed a simple, fast, and sensitive saliva-based testing workflow that requires minimal sample treatment and equipment. After sample inactivation, RNA is quickly released and stabilized in an optimized buffer, followed by reverse transcription loop-mediated isothermal amplification (RT-LAMP) and detection of positive samples using a colorimetric and/or fluorescent readout. The workflow was optimized using 1,670 negative samples collected from 172 different individuals over the course of 6 months. Each sample was spiked with 50 copies/μL of inactivated SARS-CoV-2 virus to monitor the efficiency of viral detection. Using pre-defined clinical samples, the test was determined to be 100% specific and 97% sensitive, with a limit of detection of 39 copies/mL. The method was successfully implemented in a CLIA laboratory setting for workplace surveillance and reporting. From April 2021-February 2022, more than 30,000 self-collected samples from 755 individuals were tested and 85 employees tested positive mainly during December and January, consistent with high infection rates in Massachusetts and nationwide.
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Affiliation(s)
- Zhiru Li
- New England Biolabs, Ipswich, Massachusetts, United States of America
| | | | - Barry Cohen
- New England Biolabs, Ipswich, Massachusetts, United States of America
| | | | - William E. Jack
- New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Katell Kunin
- New England Biolabs, Ipswich, Massachusetts, United States of America
| | | | - Jacob Miller
- New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Reynes A. Moncion
- New England Biolabs, Ipswich, Massachusetts, United States of America
| | | | | | - Guoping Ren
- New England Biolabs, Ipswich, Massachusetts, United States of America
| | | | - Nathan A. Tanner
- New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Yinhua Zhang
- New England Biolabs, Ipswich, Massachusetts, United States of America
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75
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Islam MM, Koirala D. Toward a next-generation diagnostic tool: A review on emerging isothermal nucleic acid amplification techniques for the detection of SARS-CoV-2 and other infectious viruses. Anal Chim Acta 2022; 1209:339338. [PMID: 35569864 PMCID: PMC8633689 DOI: 10.1016/j.aca.2021.339338] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 11/22/2021] [Accepted: 11/27/2021] [Indexed: 01/09/2023]
Abstract
As the COVID-19 pandemic continues to affect human health across the globe rapid, simple, point-of-care (POC) diagnosis of infectious viruses such as SARS-CoV-2 remains challenging. Polymerase chain reaction (PCR)-based diagnosis has risen to meet these demands and despite its high-throughput and accuracy, it has failed to gain traction in the rapid, low-cost, point-of-test settings. In contrast, different emerging isothermal amplification-based detection methods show promise in the rapid point-of-test market. In this comprehensive study of the literature, several promising isothermal amplification methods for the detection of SARS-CoV-2 are critically reviewed that can also be applied to other infectious viruses detection. Starting with a brief discussion on the SARS-CoV-2 structure, its genomic features, and the epidemiology of the current pandemic, this review focuses on different emerging isothermal methods and their advancement. The potential of isothermal amplification combined with the revolutionary CRISPR/Cas system for a more powerful detection tool is also critically reviewed. Additionally, the commercial success of several isothermal methods in the pandemic are highlighted. Different variants of SARS-CoV-2 and their implication on isothermal amplifications are also discussed. Furthermore, three most crucial aspects in achieving a simple, fast, and multiplexable platform are addressed.
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76
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Kong J, Li W, Hu J, Zhao S, Yue T, Li Z, Xia Y. The Safety of Cold-Chain Food in Post-COVID-19 Pandemic: Precaution and Quarantine. Foods 2022; 11:1540. [PMID: 35681292 PMCID: PMC9180738 DOI: 10.3390/foods11111540] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 05/03/2022] [Accepted: 05/20/2022] [Indexed: 02/04/2023] Open
Abstract
Since the outbreak of coronavirus disease-19 (COVID-19), cold-chain food contamination caused by the pathogenic severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has attracted huge concern. Cold-chain foods provide a congenial environment for SARS-CoV-2 survival, which presents a potential risk for public health. Strengthening the SARS-CoV-2 supervision of cold-chain foods has become the top priority in many countries. Methodologically, the potential safety risks and precaution measures of SARS-CoV-2 contamination on cold-chain food are analyzed. To ensure the safety of cold-chain foods, the advances in SARS-CoV-2 detection strategies are summarized based on technical principles and target biomarkers. In particular, the techniques suitable for SARS-CoV-2 detection in a cold-chain environment are discussed. Although many quarantine techniques are available, the field-based quarantine technique on cold-chain food with characteristics of real-time, sensitive, specific, portable, and large-scale application is urgently needed.
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Affiliation(s)
- Jia Kong
- College of Food Science and Engineering, Northwest A&F University, Xianyang 712100, China; (J.K.); (W.L.); (J.H.); (S.Z.); (T.Y.); (Z.L.)
| | - Wenxin Li
- College of Food Science and Engineering, Northwest A&F University, Xianyang 712100, China; (J.K.); (W.L.); (J.H.); (S.Z.); (T.Y.); (Z.L.)
| | - Jinyao Hu
- College of Food Science and Engineering, Northwest A&F University, Xianyang 712100, China; (J.K.); (W.L.); (J.H.); (S.Z.); (T.Y.); (Z.L.)
| | - Shixuan Zhao
- College of Food Science and Engineering, Northwest A&F University, Xianyang 712100, China; (J.K.); (W.L.); (J.H.); (S.Z.); (T.Y.); (Z.L.)
| | - Tianli Yue
- College of Food Science and Engineering, Northwest A&F University, Xianyang 712100, China; (J.K.); (W.L.); (J.H.); (S.Z.); (T.Y.); (Z.L.)
- Laboratory of Quality & Safety Risk Assessment for Agro-Products, Ministry of Agriculture, Xianyang 712100, China
| | - Zhonghong Li
- College of Food Science and Engineering, Northwest A&F University, Xianyang 712100, China; (J.K.); (W.L.); (J.H.); (S.Z.); (T.Y.); (Z.L.)
- Laboratory of Quality & Safety Risk Assessment for Agro-Products, Ministry of Agriculture, Xianyang 712100, China
| | - Yinqiang Xia
- College of Food Science and Engineering, Northwest A&F University, Xianyang 712100, China; (J.K.); (W.L.); (J.H.); (S.Z.); (T.Y.); (Z.L.)
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77
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Savonnet M, Aubret M, Laurent P, Roupioz Y, Cubizolles M, Buhot A. Kinetics of Isothermal Dumbbell Exponential Amplification: Effects of Mix Composition on LAMP and Its Derivatives. BIOSENSORS 2022; 12:bios12050346. [PMID: 35624647 PMCID: PMC9138685 DOI: 10.3390/bios12050346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 05/11/2022] [Accepted: 05/13/2022] [Indexed: 11/16/2022]
Abstract
Loop-mediated isothermal amplification (LAMP) is an exponential amplification method of DNA strands that is more and more used for its high performances. Thanks to its high sensitivity and selectivity, LAMP found numerous applications from the detection of pathogens or viruses through their genome amplification to its incorporation as an amplification strategy in protein or miRNA biomarker quantification. The LAMP method is composed of two stages: the first one consists in the transformation of the DNA strands into dumbbell structures formed of two stems and loops thanks to four primers; then, in the second stage, only two primers are required to amplify the dumbbells exponentially in numerous hairpins of increasing lengths. In this paper, we propose a theoretical framework to analyze the kinetics of the second stage of LAMP, the isothermal dumbbell exponential amplification (IDEA) as function of the physico-chemical parameters of the amplification reaction. Dedicated experiments validate the models. We believe these results may help the optimization of LAMP performances by reducing the number of experiments necessary to find the best parameters.
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Affiliation(s)
- Maud Savonnet
- Univ. Grenoble Alpes, CEA, CNRS, IRIG-SyMMES, 38000 Grenoble, France; (M.S.); (M.A.); (Y.R.)
- Microfluidic Systems and Bioengineering Lab, Technologies for Healthcare and Biology Department, Univ. Grenoble Alpes, CEA, LETI, 38000 Grenoble, France;
| | - Mathilde Aubret
- Univ. Grenoble Alpes, CEA, CNRS, IRIG-SyMMES, 38000 Grenoble, France; (M.S.); (M.A.); (Y.R.)
- Microfluidic Systems and Bioengineering Lab, Technologies for Healthcare and Biology Department, Univ. Grenoble Alpes, CEA, LETI, 38000 Grenoble, France;
| | - Patricia Laurent
- Microfluidic Systems and Bioengineering Lab, Technologies for Healthcare and Biology Department, Univ. Grenoble Alpes, CEA, LETI, 38000 Grenoble, France;
| | - Yoann Roupioz
- Univ. Grenoble Alpes, CEA, CNRS, IRIG-SyMMES, 38000 Grenoble, France; (M.S.); (M.A.); (Y.R.)
| | - Myriam Cubizolles
- Microfluidic Systems and Bioengineering Lab, Technologies for Healthcare and Biology Department, Univ. Grenoble Alpes, CEA, LETI, 38000 Grenoble, France;
- Correspondence: (M.C.); (A.B.)
| | - Arnaud Buhot
- Univ. Grenoble Alpes, CEA, CNRS, IRIG-SyMMES, 38000 Grenoble, France; (M.S.); (M.A.); (Y.R.)
- Correspondence: (M.C.); (A.B.)
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78
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Isothermal amplification using sequence-specific fluorescence detection of SARS coronavirus 2 and variants in nasal swabs. Biotechniques 2022; 72:263-272. [PMID: 35545967 PMCID: PMC9248022 DOI: 10.2144/btn-2022-0037] [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] [Indexed: 11/23/2022] Open
Abstract
Coronavirus disease 2019 is a public health challenge requiring rapid testing for the detection of infections and transmission. Nucleic acid amplification tests targeting SARS coronavirus 2 (CoV2) are used to detect CoV2 in clinical samples. Real-time reverse transcription quantitative PCR is the standard nucleic acid amplification test for CoV2, although reverse transcription loop-mediated isothermal amplification is used in diagnostics. The authors demonstrate a sequence-specific reverse transcription loop-mediated isothermal amplification-based nucleic acid amplification assay that is finished within 30 min using minimally processed clinical nasal swab samples and describe a fluorescence-quenched reverse transcription loop-mediated isothermal amplification assay using labeled primers and a quencher oligonucleotide. This assay can achieve rapid (30 min) and sensitive (1000 plaque-forming units/ml) fluorescence detection of CoV2 (WA1/2020), B.1.1.7 (Alpha) and variants of concern Delta (B.1.617.2) and Omicron (B.1.1.529) in nasal samples. The authors describe a sequence-specific nucleic acid amplification assay (fluorescence-quenched reverse transcription loop-mediated isothermal amplification) based on a modified reverse transcription loop-mediated isothermal amplification assay that utilizes a fluorescence-labeled reporter primer and a short complementary oligonucleotide quencher to detect SARS coronavirus 2 in minimally processed clinical nasal swab samples. The fluorescence-quenched reverse transcription loop-mediated isothermal amplification assay is completed in 30 min without purifying RNA and achieves reproducible, sensitive and specific (1000 plaque-forming units/ml) detection of SARS coronavirus 2 WA1/2020 and three SARS coronavirus 2 variant viruses while not signaling on three closely related human coronaviruses or two other heterologous human respiratory viruses.
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79
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Lu S, Duplat D, Benitez-Bolivar P, León C, Villota SD, Veloz-Villavicencio E, Arévalo V, Jaenes K, Guo Y, Cicek S, Robinson L, Peidis P, Pearson JD, Woodgett J, Mazzulli T, Ponce P, Restrepo S, González JM, Bernal A, Guevara-Suarez M, Pardee K, Cevallos VE, González C, Bremner R. Multicenter international assessment of a SARS-CoV-2 RT-LAMP test for point of care clinical application. PLoS One 2022; 17:e0268340. [PMID: 35544541 PMCID: PMC9094544 DOI: 10.1371/journal.pone.0268340] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 04/27/2022] [Indexed: 12/19/2022] Open
Abstract
Continued waves, new variants, and limited vaccine deployment mean that SARS-CoV-2 tests remain vital to constrain the coronavirus disease 2019 (COVID-19) pandemic. Affordable, point-of-care (PoC) tests allow rapid screening in non-medical settings. Reverse-transcription loop-mediated isothermal amplification (RT-LAMP) is an appealing approach. A crucial step is to optimize testing in low/medium resource settings. Here, we optimized RT-LAMP for SARS-CoV-2 and human β-actin, and tested clinical samples in multiple countries. "TTTT" linker primers did not improve performance, and while guanidine hydrochloride, betaine and/or Igepal-CA-630 enhanced detection of synthetic RNA, only the latter two improved direct assays on nasopharygeal samples. With extracted clinical RNA, a 20 min RT-LAMP assay was essentially as sensitive as RT-PCR. With raw Canadian nasopharygeal samples, sensitivity was 100% (95% CI: 67.6% - 100%) for those with RT-qPCR Ct values ≤ 25, and 80% (95% CI: 58.4% - 91.9%) for those with 25 < Ct ≤ 27.2. Highly infectious, high titer cases were also detected in Colombian and Ecuadorian labs. We further demonstrate the utility of replacing thermocyclers with a portable PoC device (FluoroPLUM). These combined PoC molecular and hardware tools may help to limit community transmission of SARS-CoV-2.
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Affiliation(s)
- Suying Lu
- Lunenfeld Tanenbaum Research Institute, Mt Sinai Hospital, Sinai Health System, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
- Department of Ophthalmology and Vision Science, University of Toronto, Toronto, ON, Canada
| | - David Duplat
- Centro de Investigaciones en Microbiología y Parasitología Tropical (CIMPAT), Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - Paula Benitez-Bolivar
- Centro de Investigaciones en Microbiología y Parasitología Tropical (CIMPAT), Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - Cielo León
- Centro de Investigaciones en Microbiología y Parasitología Tropical (CIMPAT), Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - Stephany D. Villota
- Centro de Investigación en Enfermedades Infecciosas y Vectoriales (CIREV), Instituto Nacional de Investigación en Salud Pública, Quito, Ecuador
| | - Eliana Veloz-Villavicencio
- Centro de Investigación en Enfermedades Infecciosas y Vectoriales (CIREV), Instituto Nacional de Investigación en Salud Pública, Quito, Ecuador
| | - Valentina Arévalo
- Centro de Investigación en Enfermedades Infecciosas y Vectoriales (CIREV), Instituto Nacional de Investigación en Salud Pública, Quito, Ecuador
| | - Katariina Jaenes
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, Canada
| | - Yuxiu Guo
- LSK Technologies Inc., Kitchener, Canada
| | | | | | - Philippos Peidis
- Lunenfeld Tanenbaum Research Institute, Mt Sinai Hospital, Sinai Health System, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
- Department of Ophthalmology and Vision Science, University of Toronto, Toronto, ON, Canada
| | - Joel D. Pearson
- Lunenfeld Tanenbaum Research Institute, Mt Sinai Hospital, Sinai Health System, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
- Department of Ophthalmology and Vision Science, University of Toronto, Toronto, ON, Canada
| | - Jim Woodgett
- Lunenfeld Tanenbaum Research Institute, Mt Sinai Hospital, Sinai Health System, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
| | - Tony Mazzulli
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
- Department of Microbiology, Sinai Health System/University Health Network, Toronto, Canada
| | - Patricio Ponce
- Centro de Investigación en Enfermedades Infecciosas y Vectoriales (CIREV), Instituto Nacional de Investigación en Salud Pública, Quito, Ecuador
| | - Silvia Restrepo
- Department of Food and Chemical Engineering, Universidad de los Andes, Bogotá, Colombia
| | - John M. González
- Grupo de Ciencias Básicas Médicas, School of Medicine, Universidad de los Andes, Bogotá, Colombia
| | - Adriana Bernal
- Laboratory of Molecular Interactions of Agricultural Microbes (LIMMA), Department of Biological Sciences, Universidad de Los Andes, Bogotá, Colombia
| | - Marcela Guevara-Suarez
- Applied genomics research group, Vicerrectoría de Investigación y Creación, Universidad de los Andes, Bogotá, Colombia
| | - Keith Pardee
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, Canada
- LSK Technologies Inc., Kitchener, Canada
- Department of Mechanical and Industrial Engineering, University of Toronto, Toronto, ON, Canada
| | - Varsovia E. Cevallos
- Centro de Investigación en Enfermedades Infecciosas y Vectoriales (CIREV), Instituto Nacional de Investigación en Salud Pública, Quito, Ecuador
| | - Camila González
- Centro de Investigaciones en Microbiología y Parasitología Tropical (CIMPAT), Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - Rod Bremner
- Lunenfeld Tanenbaum Research Institute, Mt Sinai Hospital, Sinai Health System, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
- Department of Ophthalmology and Vision Science, University of Toronto, Toronto, ON, Canada
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80
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Warneford-Thomson R, Shah PP, Lundgren P, Lerner J, Morgan J, Davila A, Abella BS, Zaret K, Schug J, Jain R, Thaiss CA, Bonasio R. A LAMP sequencing approach for high-throughput co-detection of SARS-CoV-2 and influenza virus in human saliva. eLife 2022; 11:69949. [PMID: 35532013 PMCID: PMC9084890 DOI: 10.7554/elife.69949] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 04/24/2022] [Indexed: 12/02/2022] Open
Abstract
The COVID-19 pandemic has created an urgent need for rapid, effective, and low-cost SARS-CoV-2 diagnostic testing. Here, we describe COV-ID, an approach that combines RT-LAMP with deep sequencing to detect SARS-CoV-2 in unprocessed human saliva with a low limit of detection (5–10 virions). Based on a multi-dimensional barcoding strategy, COV-ID can be used to test thousands of samples overnight in a single sequencing run with limited labor and laboratory equipment. The sequencing-based readout allows COV-ID to detect multiple amplicons simultaneously, including key controls such as host transcripts and artificial spike-ins, as well as multiple pathogens. Here, we demonstrate this flexibility by simultaneous detection of 4 amplicons in contrived saliva samples: SARS-CoV-2, influenza A, human STATHERIN, and an artificial SARS calibration standard. The approach was validated on clinical saliva samples, where it showed excellent agreement with RT-qPCR. COV-ID can also be performed directly on saliva absorbed on filter paper, simplifying collection logistics and sample handling.
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Affiliation(s)
- Robert Warneford-Thomson
- Graduate Group in Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, United States.,Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, United States.,Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, United States
| | - Parisha P Shah
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, United States.,Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, United States.,Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, United States
| | - Patrick Lundgren
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, United States
| | - Jonathan Lerner
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, United States
| | - Jason Morgan
- Department of Emergency Medicine and Penn Acute Research Collaboration, University of Pennsylvania Perelman School of Medicine, Philadelphia, United States
| | - Antonio Davila
- Department of Emergency Medicine and Penn Acute Research Collaboration, University of Pennsylvania Perelman School of Medicine, Philadelphia, United States.,University of Pennsylvania School of Nursing, Philadelphia, United States
| | - Benjamin S Abella
- Department of Emergency Medicine and Penn Acute Research Collaboration, University of Pennsylvania Perelman School of Medicine, Philadelphia, United States
| | - Kenneth Zaret
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, United States.,Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, United States
| | - Jonathan Schug
- Next-Generation Sequencing Core, Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, United States
| | - Rajan Jain
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, United States.,Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, United States.,Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, United States
| | - Christoph A Thaiss
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, United States
| | - Roberto Bonasio
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, United States.,Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, United States
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81
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Song X, Coulter FJ, Yang M, Smith JL, Tafesse FG, Messer WB, Reif JH. A lyophilized colorimetric RT-LAMP test kit for rapid, low-cost, at-home molecular testing of SARS-CoV-2 and other pathogens. Sci Rep 2022; 12:7043. [PMID: 35487969 PMCID: PMC9052177 DOI: 10.1038/s41598-022-11144-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 04/19/2022] [Indexed: 12/12/2022] Open
Abstract
Access to fast and reliable nucleic acid testing continues to play a key role in controlling the COVID-19 pandemic, especially in the context of increased vaccine break-through risks due to new variants. We report a rapid, low-cost (~ 2 USD), simple-to-use nucleic acid test kit for self-administered at-home testing without lab instrumentation. The entire sample-to-answer workflow takes < 60 min, including noninvasive sample collection, one-step RNA preparation, reverse-transcription loop-mediated isothermal amplification (RT-LAMP) in a thermos, and direct visual inspection of a colorimetric test result. To facilitate long-term storage without cold-chain, a fast one-pot lyophilization protocol was developed to preserve all required biochemical reagents of the colorimetric RT-LAMP test in a single microtube. Notably, the lyophilized RT-LAMP assay demonstrated reduced false positives as well as enhanced tolerance to a wider range of incubation temperatures compared to solution-based RT-LAMP reactions. We validated our RT-LAMP assay using simulated infected samples, and detected a panel of SARS-CoV-2 variants with successful detection of all variants that were available to us at the time. With a simple change of the primer set, our lyophilized RT-LAMP home test can be easily adapted as a low-cost surveillance platform for other pathogens and infectious diseases of global public health importance.
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Affiliation(s)
- Xin Song
- Department of Electrical and Computer Engineering, Duke University, Durham, NC, 27708, USA. .,Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA. .,Department of Computer Science, Duke University, Durham, NC, 27708, USA.
| | - Felicity J Coulter
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University, Portland, OR, 97239, USA
| | - Ming Yang
- Department of Computer Science, Duke University, Durham, NC, 27708, USA
| | - Jessica L Smith
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR, 97006, USA
| | - Fikadu G Tafesse
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University, Portland, OR, 97239, USA
| | - William B Messer
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University, Portland, OR, 97239, USA. .,Department of Medicine, Division of Infectious Diseases, Oregon Health and Science University, Portland, OR, 97239, USA. .,Program in Epidemiology, OHSU-PSU School of Public Health, Oregon Health and Science University, Portland, OR, 97239, USA.
| | - John H Reif
- Department of Electrical and Computer Engineering, Duke University, Durham, NC, 27708, USA. .,Department of Computer Science, Duke University, Durham, NC, 27708, USA.
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82
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Quyen TL, Vinayaka AC, Golabi M, Ngoc HV, Bang DD, Wolff A. Elimination of Carryover Contamination in Real-Time Reverse Transcriptase Loop-Mediated Isothermal Amplification for Rapid Detection of the SARS-CoV-2 Virus in Point-of-Care Testing. Front Cell Infect Microbiol 2022; 12:856553. [PMID: 35521217 PMCID: PMC9065284 DOI: 10.3389/fcimb.2022.856553] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 03/23/2022] [Indexed: 11/13/2022] Open
Abstract
Loop-mediated isothermal amplification (LAMP) is being used as a robust rapid diagnostic tool to prevent the transmission of infectious diseases. However, carryover contamination of LAMP-amplified products originating from previous tests has been a problem in LAMP-based bio-analytical assays. In this study, we developed a Cod-uracil-DNA-glycosylase real-time reverse transcriptase LAMP assay (Cod-UNG-rRT-LAMP) for the elimination of carryover contamination and the rapid detection of SARS-CoV-2 in point-of-care (POC) testing. Using the Cod-UNG-rRT-LAMP assay, the SARS-CoV-2 virus could be detected as low as 2 copies/µl (8 copies/reaction) within 45 min of amplification and 2.63 ± 0.17 pg (equivalent to 2.296 × 109 copies) of contaminants per reaction could be eliminated. Analysis of clinical SARS-CoV-2 samples using the Cod-UNG-rRT-LAMP assay showed an excellent agreement with a relative accuracy of 98.2%, sensitivity of 97.1%, and specificity of 95.2% in comparison to rRT-PCR. The results obtained in this study clearly demonstrate the feasibility of the use of the Cod-UNG-rRT-LAMP assay for applications toward the POC diagnosis of SARS-CoV-2 and on-site testing of other pathogens.
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Affiliation(s)
- Than Linh Quyen
- Biolabchip Group, Department of Bioengineering, Technical University of Denmark, Lyngby, Denmark
| | - Aaydha Chidambara Vinayaka
- Laboratory of Applied Micro and Nanotechnology (LAMINATE), Department of Bioengineering, Technical University of Denmark, Lyngby, Denmark
| | - Mohsen Golabi
- Laboratory of Applied Micro and Nanotechnology (LAMINATE), Department of Bioengineering, Technical University of Denmark, Lyngby, Denmark
| | - Huynh Van Ngoc
- Biolabchip Group, Department of Bioengineering, Technical University of Denmark, Lyngby, Denmark
| | - Dang Duong Bang
- Laboratory of Applied Micro and Nanotechnology (LAMINATE), Department of Bioengineering, Technical University of Denmark, Lyngby, Denmark
| | - Anders Wolff
- Biolabchip Group, Department of Bioengineering, Technical University of Denmark, Lyngby, Denmark
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83
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Li D, Duan C, Cheng W, Gong Y, Yao Y, Wang X, Wang Z, Xiang Y. A simple and rapid method to assay SARS-CoV-2 RNA based on a primer exchange reaction. Chem Commun (Camb) 2022; 58:4484-4487. [PMID: 35302142 DOI: 10.1039/d2cc00488g] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A simple method is proposed in this work for the detection of SARS-CoV-2 RNA based on a primer exchange reaction (PER). By ingeniously integrating the PER cascade and CRISPR/cas12a system, this method can achieve convenient detection of the target RNA in 40 min and distinguish a single-base mutation from the target sequence, demonstrating its superior analytical performance.
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Affiliation(s)
- Dayong Li
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, P. R. China.
| | - Chengjie Duan
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, P. R. China.
| | - Wenting Cheng
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, P. R. China.
| | - Youjing Gong
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, P. R. China.
| | - Yanheng Yao
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, P. R. China.
| | - Xiaoping Wang
- Department of Neurology, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200336, P. R. China.
| | - Zhongyun Wang
- Department of Anesthesiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, P. R. China.
| | - Yang Xiang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, P. R. China. .,State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100191, P. R. China
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84
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Odiwuor N, Xiong J, Ogolla F, Hong W, Li X, Khan FM, Wang N, Yu J, Wei H. A point-of-care SARS-CoV-2 test based on reverse transcription loop-mediated isothermal amplification without RNA extraction with diagnostic performance same as RT-PCR. Anal Chim Acta 2022; 1200:339590. [PMID: 35256137 PMCID: PMC8844505 DOI: 10.1016/j.aca.2022.339590] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 02/03/2022] [Accepted: 02/07/2022] [Indexed: 12/04/2022]
Abstract
The global public health crisis and economic losses resulting from the current novel coronavirus disease (COVID-19) pandemic have been dire. The most used real-time reverse transcription polymerase chain reaction (RT-PCR) method needs expensive equipment, technical expertise, and a long turnaround time. Therefore, there is a need for a rapid, accurate, and alternative technique of diagnosis that is deployable at resource-poor settings like point-of-care. This study combines heat deactivation and a novel mechanical lysis method by bead beating for quick and simple sample preparation. Then, using an optimized reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay to target genes encoding the open reading frame 8 (ORF8), spike and nucleocapsid proteins of the novel coronavirus, SARS-CoV-2. The test results can be read simultaneously in fluorometric and colorimetric readouts within 40 min from sample collection. We also calibrated a template transfer tool to simplify sample addition into LAMP reactions when pipetting skills are needed. Most importantly, validation of the direct RT-LAMP system based on multiplexing primers S1:ORF8 in a ratio (1:0.8) using 143 patients' nasopharyngeal swab samples showed a diagnostic performance of 99.30% accuracy, with 98.81% sensitivity and 100% selectivity, compared to commercial RT-PCR kits. Since our workflow does not rely on RNA extraction and purification, the time-to-result is two times faster than other workflows with FDA emergency use authorization. Considering all its strengths: speed, simplicity, accuracy and extraction-free, the system can be useful for optimal point-of-care testing of COVID-19.
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Affiliation(s)
- Nelson Odiwuor
- CAS Key Laboratory of Special Pathogens and Biosafety, Centre for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Sino-Africa Joint Research Centre, Nairobi, 62000 - 00200, Kenya
| | - Jin Xiong
- CAS Key Laboratory of Special Pathogens and Biosafety, Centre for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Faith Ogolla
- CAS Key Laboratory of Special Pathogens and Biosafety, Centre for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Sino-Africa Joint Research Centre, Nairobi, 62000 - 00200, Kenya
| | - Wei Hong
- CAS Key Laboratory of Special Pathogens and Biosafety, Centre for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaohong Li
- CAS Key Laboratory of Special Pathogens and Biosafety, Centre for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Fazal Mehmood Khan
- CAS Key Laboratory of Special Pathogens and Biosafety, Centre for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Nuo Wang
- CAS Key Laboratory of Special Pathogens and Biosafety, Centre for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Junping Yu
- CAS Key Laboratory of Special Pathogens and Biosafety, Centre for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Hongping Wei
- CAS Key Laboratory of Special Pathogens and Biosafety, Centre for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Sino-Africa Joint Research Centre, Nairobi, 62000 - 00200, Kenya.
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85
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Zhang Y, Tanner NA. Improving RT-LAMP detection of SARS-CoV-2 RNA through primer set selection and combination. PLoS One 2022; 17:e0254324. [PMID: 35363770 PMCID: PMC8974972 DOI: 10.1371/journal.pone.0254324] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 03/21/2022] [Indexed: 11/18/2022] Open
Abstract
Reverse transcription loop-mediated isothermal amplification (RT-LAMP) has emerged as a viable molecular diagnostic method to expand the breadth and reach of nucleic acid testing, particularly for SARS-CoV-2 detection and surveillance. While rapidly growing in prominence, RT-LAMP remains a relatively new method compared to the standard RT-qPCR, and contribution to our body of knowledge on designing LAMP primer sets and assays can have significant impact on its utility and adoption. Here we select and evaluate 18 LAMP primer sets for SARS-CoV-2 previously identified as sensitive ones under various conditions, comparing their speed and sensitivity with two LAMP formulations each with 2 reaction temperatures. We find that both LAMP formulations have some effects on the speed and detection sensitivity and identify several primer sets with similar high sensitivity for different SARS-CoV-2 gene targets. Significantly we observe a consistent sensitivity enhancement by combining primer sets for different targets, confirming and building on earlier work to create a simple, general approach to building better and more sensitive RT-LAMP assays.
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Affiliation(s)
- Yinhua Zhang
- Research Department, New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Nathan A. Tanner
- Research Department, New England Biolabs, Ipswich, Massachusetts, United States of America
- * E-mail:
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86
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Kellner MJ, Ross JJ, Schnabl J, Dekens MPS, Matl M, Heinen R, Grishkovskaya I, Bauer B, Stadlmann J, Menéndez-Arias L, Straw AD, Fritsche-Polanz R, Traugott M, Seitz T, Zoufaly A, Födinger M, Wenisch C, Zuber J, Pauli A, Brennecke J. A Rapid, Highly Sensitive and Open-Access SARS-CoV-2 Detection Assay for Laboratory and Home Testing. Front Mol Biosci 2022; 9:801309. [PMID: 35433827 PMCID: PMC9011764 DOI: 10.3389/fmolb.2022.801309] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 03/01/2022] [Indexed: 11/20/2022] Open
Abstract
RT-qPCR-based diagnostic tests play important roles in combating virus-caused pandemics such as Covid-19. However, their dependence on sophisticated equipment and the associated costs often limits their widespread use. Loop-mediated isothermal amplification after reverse transcription (RT-LAMP) is an alternative nucleic acid detection method that overcomes these limitations. Here, we present a rapid, robust, and sensitive RT-LAMP-based SARS-CoV-2 detection assay. Our 40-min procedure bypasses the RNA isolation step, is insensitive to carryover contamination, and uses a colorimetric readout that enables robust SARS-CoV-2 detection from various sample types. Based on this assay, we have increased sensitivity and scalability by adding a nucleic acid enrichment step (Bead-LAMP), developed a version for home testing (HomeDip-LAMP), and identified open-source RT-LAMP enzymes that can be produced in any molecular biology laboratory. On a dedicated website, rtlamp.org (DOI: 10.5281/zenodo.6033689), we provide detailed protocols and videos. Our optimized, general-purpose RT-LAMP assay is an important step toward population-scale SARS-CoV-2 testing.
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Affiliation(s)
- Max J. Kellner
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
- *Correspondence: Max J. Kellner, ; Andrea Pauli, ; Julius Brennecke,
| | - James J. Ross
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Jakob Schnabl
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Marcus P. S. Dekens
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Martin Matl
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Robert Heinen
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Irina Grishkovskaya
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Benedikt Bauer
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Johannes Stadlmann
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
- Department of Chemistry, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Luis Menéndez-Arias
- Centro de Biología Molecular “Severo Ochoa” (Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid), Madrid, Spain
| | - Andrew D. Straw
- Institute of Biology I and Bernstein Center Freiburg, Faculty of Biology, Albert-Ludwigs-University Freiburg, Freiburg, Germany
| | | | - Marianna Traugott
- 4th Medical Department with Infectious Diseases and Tropical Medicine, Vienna, Austria
| | - Tamara Seitz
- 4th Medical Department with Infectious Diseases and Tropical Medicine, Vienna, Austria
| | - Alexander Zoufaly
- 4th Medical Department with Infectious Diseases and Tropical Medicine, Vienna, Austria
| | - Manuela Födinger
- Institute of Laboratory Diagnostics, Vienna, Austria
- Sigmund Freud Private University, Vienna, Austria
| | - Christoph Wenisch
- 4th Medical Department with Infectious Diseases and Tropical Medicine, Vienna, Austria
| | - Johannes Zuber
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
- Medical University of Vienna, Vienna BioCenter (VBC), Vienna, Austria
| | - Andrea Pauli
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
- *Correspondence: Max J. Kellner, ; Andrea Pauli, ; Julius Brennecke,
| | - Julius Brennecke
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
- *Correspondence: Max J. Kellner, ; Andrea Pauli, ; Julius Brennecke,
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87
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Londono-Avendano MA, Libreros G, Osorio L, Parra B. A Rapid RT-LAMP Assay for SARS-CoV-2 with Colorimetric Detection Assisted by a Mobile Application. Diagnostics (Basel) 2022; 12:diagnostics12040848. [PMID: 35453896 PMCID: PMC9032071 DOI: 10.3390/diagnostics12040848] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/12/2022] [Accepted: 01/21/2022] [Indexed: 02/04/2023] Open
Abstract
Loop-mediated amplification has been promoted for SARS-CoV-2 screening, however, antigen tests are preferred in low-income countries and remote zones. Poor training in molecular biology, plus the need for RNA purification or reading instruments to overcome issues of sensitivity in colorimetric detection, are some of the reasons limiting the use of this technique. In this study, nasopharyngeal swabs, aspirates and saliva were amplified in an in-house LAMP assay and subject to colorimetric detection, achieved by the naked eye and by image analysis with a mobile application. Accuracy of detection by the naked eye ranged from 61–74% but improved to 75–86% when using the application. Sensitivity of the digital approach was 81% and specificity 83%, with poor positive predictive value, and acceptable negative predictive value. Additionally to the reported effect of some transport media’s pH, the presence of mucus and warming up of reagents while setting up the reaction critically affected performance. Accuracy per type of sample was 55, 70 and 80%, for swabs, aspirates and saliva, respectively, suggesting potential to improve the test in saliva. This assay, carried out in a closed tube, reduces contamination, has few pipetting steps and requires minimal equipment. Strategies to improve performance and implications of the use this sort of colorimetric LAMP for massive testing are discussed.
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Affiliation(s)
- María Aurora Londono-Avendano
- Departamento de Microbiología, Escuela de Ciencias Básicas, Facultad de Salud, Universidad del Valle, Calle 4B # 36-00, edificio 120, oficina 223/229, Cali 760043, Colombia; (G.L.); (B.P.)
- Correspondence: ; Tel.: +573-3212100 (ext. 5205)
| | - Gerardo Libreros
- Departamento de Microbiología, Escuela de Ciencias Básicas, Facultad de Salud, Universidad del Valle, Calle 4B # 36-00, edificio 120, oficina 223/229, Cali 760043, Colombia; (G.L.); (B.P.)
| | - Lyda Osorio
- Escuela de Salud Pública, Facultad de Salud, Universidad del Valle, Calle 4B # 36-00, edificio 120, oficina 223/229, Cali 760043, Colombia;
| | - Beatriz Parra
- Departamento de Microbiología, Escuela de Ciencias Básicas, Facultad de Salud, Universidad del Valle, Calle 4B # 36-00, edificio 120, oficina 223/229, Cali 760043, Colombia; (G.L.); (B.P.)
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88
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Zhu M, Huangfu C, Wan W, Wang M, Lv H, Zhang X, Wang F, Zhi H, Huang Y, Chen M, Zhao J, Li C, Dong X, Gao Z, Liu Y, Feng L. A Novel Virus Detection Strategy Enabled by TR512-Peptide-Based Bioorthogonal Capture and Enrichment of Preamplified Nucleic Acid. Anal Chem 2022; 94:5591-5598. [PMID: 35348340 DOI: 10.1021/acs.analchem.1c05315] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
High-cost viral nucleic acid detection devices (e.g., qPCR system) are limited resources for developing counties and rural areas, leading to underdiagnosis or even pandemics of viral infectious diseases. Herein, a novel virus detection strategy is reported. Such detection method is enabled by TR512-peptide-based biorthogonal capture and enrichment of commercially available Texas red fluorophore labeled nucleic acid on the functionalized paper. The GST-TR512 fusion protein electrostatically immobilized on the paper is constructed to retain the binding affinity of TR512-peptide toward Texas red fluorophore labeled nucleic acid released in the preamplification process, then the enrichment of analytes enhances fluorescence signal for rapid detection as volume of sample filters through the paper. The method is generally applicable to different nucleic acid preamplification strategies (PCR, RAA, CRISPR) and different virus types (Hepatitis B virus (HBV), African swine fever virus (ASFV), human papillomavirus (HPV), and severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2 or 2019 nCoV)). Finally, a full-set virus detection device is developed in house to detect the presence of Hepatitis B virus (HBV) viral gene in patients' blood samples. Taken together, we first apply TR512-peptide in the signal enrichment and the novel detection strategy may offer an inexpensive, rapid, and portable solution for areas with limited access to a standard diagnosis laboratory.
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Affiliation(s)
- Mingzhen Zhu
- Department of Instrumentation and Analytical Chemistry, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China.,University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Changxin Huangfu
- Department of Instrumentation and Analytical Chemistry, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China.,University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Wang Wan
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China
| | - Mengdie Wang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China.,University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Haochen Lv
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China
| | - Xiaobo Zhang
- Department of Instrumentation and Analytical Chemistry, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China.,University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Fengya Wang
- Department of Instrumentation and Analytical Chemistry, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China.,University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Hui Zhi
- Department of Instrumentation and Analytical Chemistry, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China.,University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Yanan Huang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China
| | - Meng Chen
- Department of Instrumentation and Analytical Chemistry, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China
| | - Jizhe Zhao
- Department of Instrumentation and Analytical Chemistry, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China
| | - Chunsheng Li
- Department of Instrumentation and Analytical Chemistry, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China
| | - Xuepeng Dong
- The Second Hospital of Dalian Medical University, 467 Zhongshan Road, Dalian 116044, P. R. China
| | - Zhenming Gao
- The Second Hospital of Dalian Medical University, 467 Zhongshan Road, Dalian 116044, P. R. China
| | - Yu Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China
| | - Liang Feng
- Department of Instrumentation and Analytical Chemistry, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, P. R. China
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89
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Page R, Scourfield E, Ficarelli M, McKellar SW, Lee KL, Maguire TJ, Bouton C, Lista MJ, Neil SJ, Malim MH, Zuckerman M, Mischo HE, Martinez-Nunez RT. Homebrew: An economical and sensitive glassmilk-based nucleic-acid extraction method for SARS-CoV-2 diagnostics. CELL REPORTS METHODS 2022; 2:100186. [PMID: 35262039 PMCID: PMC8890991 DOI: 10.1016/j.crmeth.2022.100186] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 12/26/2021] [Accepted: 02/25/2022] [Indexed: 12/22/2022]
Abstract
Management of COVID-19 and other epidemics requires large-scale diagnostic testing. The gold standard for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection remains reverse transcription quantitative PCR (qRT-PCR) analysis, which detects viral RNA more sensitively than any other method. However, the resource use and supply-chain requirements of RT-PCR have continued to challenge diagnostic laboratories worldwide. Here, we establish and characterize a low-cost method to detect SARS-CoV-2 in clinical combined nose and throat swabs, allowing for automation in high-throughput settings. This method inactivates virus material with sodium dodecylsulfate (SDS) and uses silicon dioxide as the RNA-binding matrix in combination with sodium chloride (NaCl) and isopropanol. With similar sensitivity for SARS-CoV-2 viral targets but a fraction of time and reagent expenditure compared with commercial kits, our method also enables sample pooling without loss of sensitivity. We suggest that this method will facilitate more economical widespread testing, particularly in resource-limited settings.
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Affiliation(s)
- Robert Page
- ImmunoEngineering Lab, School of Cancer and Pharmaceutical Sciences, King's College London, Guy's Cancer Centre, Great Maze Pond, London SE1 9RT, UK
| | - Edward Scourfield
- Department Infectious Diseases, School of Immunology and Microbial Sciences, Guy’s Campus, King’s College London, London SE1 9RT, UK
| | - Mattia Ficarelli
- Department Infectious Diseases, School of Immunology and Microbial Sciences, Guy’s Campus, King’s College London, London SE1 9RT, UK
| | - Stuart W. McKellar
- Department Infectious Diseases, School of Immunology and Microbial Sciences, Guy’s Campus, King’s College London, London SE1 9RT, UK
| | - Kwok Leung Lee
- Department Infectious Diseases, School of Immunology and Microbial Sciences, Guy’s Campus, King’s College London, London SE1 9RT, UK
| | - Thomas J.A. Maguire
- Department Infectious Diseases, School of Immunology and Microbial Sciences, Guy’s Campus, King’s College London, London SE1 9RT, UK
| | - Clement Bouton
- Department Infectious Diseases, School of Immunology and Microbial Sciences, Guy’s Campus, King’s College London, London SE1 9RT, UK
| | - Maria Jose Lista
- Department Infectious Diseases, School of Immunology and Microbial Sciences, Guy’s Campus, King’s College London, London SE1 9RT, UK
| | - Stuart J.D. Neil
- Department Infectious Diseases, School of Immunology and Microbial Sciences, Guy’s Campus, King’s College London, London SE1 9RT, UK
| | - Michael H. Malim
- Department Infectious Diseases, School of Immunology and Microbial Sciences, Guy’s Campus, King’s College London, London SE1 9RT, UK
| | - Mark Zuckerman
- South London Specialist Virology Centre, King’s College Hospital London, London, UK
| | - Hannah E. Mischo
- Department Infectious Diseases, School of Immunology and Microbial Sciences, Guy’s Campus, King’s College London, London SE1 9RT, UK
| | - Rocio T. Martinez-Nunez
- Department Infectious Diseases, School of Immunology and Microbial Sciences, Guy’s Campus, King’s College London, London SE1 9RT, UK
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90
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Waller L, Guo Z, Tang R, Zhang Z, Wang E, Yasuhara-Bell J, Laurent L, Lo YH. High Sensitivity, Rapid Detection of Virus in High Traffic Environments. Front Bioeng Biotechnol 2022; 10:877603. [PMID: 35402391 PMCID: PMC8989402 DOI: 10.3389/fbioe.2022.877603] [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: 02/16/2022] [Accepted: 03/11/2022] [Indexed: 12/28/2022] Open
Abstract
The global pandemic caused by the SARS-CoV-2 virus has underscored the need for rapid, simple, scalable, and high-throughput multiplex diagnostics in non-laboratory settings. Here we demonstrate a multiplex reverse-transcription loop-mediated isothermal amplification (RT-LAMP) coupled with a gold nanoparticle-based lateral flow immunoassay (LFIA) capable of detecting up to three unique viral gene targets in 15 min. RT-LAMP primers associated with three separate gene targets from the SARS-CoV-2 virus (Orf1ab, Envelope, and Nucleocapsid) were added to a one-pot mix. A colorimetric change from red to yellow occurs in the presence of a positive sample. Positive samples are run through a LFIA to achieve specificity on a multiplex three-test line paper assay. Positive results are indicated by a characteristic crimson line. The device is almost fully automated and is deployable in any community setting with a power source.
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Affiliation(s)
- Lauren Waller
- Department of Bioengineering, University of California, San Diego, San Diego, CA, United States
| | - Zhilin Guo
- Department of Mechanical and Aerospace Engineering, University of California, San Diego, San Diego, CA, United States
| | - Rui Tang
- Department of Electrical and Computer Engineering, University of California, San Diego, San Diego, CA, United States
| | - Zunming Zhang
- Department of Electrical and Computer Engineering, University of California, San Diego, San Diego, CA, United States
| | - Edward Wang
- Department of Mechanical and Aerospace Engineering, University of California, San Diego, San Diego, CA, United States
| | | | - Louise Laurent
- Department of Obstetrics and Gynecology and Reproductive Sciences, University of California, San Diego, San Diego, CA, United States
| | - Yu-Hwa Lo
- Department of Electrical and Computer Engineering, University of California, San Diego, San Diego, CA, United States
- *Correspondence: Yu-Hwa Lo,
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91
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Profiling RT-LAMP tolerance of sequence variation for SARS-CoV-2 RNA detection. PLoS One 2022; 17:e0259610. [PMID: 35324900 PMCID: PMC8947081 DOI: 10.1371/journal.pone.0259610] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 03/01/2022] [Indexed: 11/19/2022] Open
Abstract
The ongoing SARS-CoV-2 pandemic has necessitated a dramatic increase in our ability to conduct molecular diagnostic tests, as accurate detection of the virus is critical in preventing its spread. However, SARS-CoV-2 variants continue to emerge, with each new variant potentially affecting widely-used nucleic acid amplification diagnostic tests. RT-LAMP has been adopted as a quick, inexpensive diagnostic alternative to RT-qPCR, but as a newer method, has not been studied as thoroughly. Here we interrogate the effect of SARS-CoV-2 sequence mutations on RT-LAMP amplification, creating 523 single point mutation “variants” covering every position of the LAMP primers in 3 SARS-CoV-2 assays and analyzing their effects with over 4,500 RT-LAMP reactions. Remarkably, we observed only minimal effects on amplification speed and no effect on detection sensitivity at positions equivalent to those that significantly impact RT-qPCR assays. We also created primer sets targeting a specific short deletion and observed that LAMP is able to amplify even with a primer containing multiple consecutive mismatched bases, albeit with reduced speed and sensitivity. This highlights RT-LAMP as a robust technique for viral RNA detection that can tolerate most mutations in the primer regions. Additionally, where variant discrimination is desired, we describe the use of molecular beacons to sensitively distinguish and identify variant RNA sequences carrying short deletions. Together these data add to the growing body of knowledge on the utility of RT-LAMP and increase its potential to further our ability to conduct molecular diagnostic tests outside of the traditional clinical laboratory environment.
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92
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Vindeirinho JM, Pinho E, Azevedo NF, Almeida C. SARS-CoV-2 Diagnostics Based on Nucleic Acids Amplification: From Fundamental Concepts to Applications and Beyond. Front Cell Infect Microbiol 2022; 12:799678. [PMID: 35402302 PMCID: PMC8984495 DOI: 10.3389/fcimb.2022.799678] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 02/18/2022] [Indexed: 02/06/2023] Open
Abstract
COVID-19 pandemic ignited the development of countless molecular methods for the diagnosis of SARS-CoV-2 based either on nucleic acid, or protein analysis, with the first establishing as the most used for routine diagnosis. The methods trusted for day to day analysis of nucleic acids rely on amplification, in order to enable specific SARS-CoV-2 RNA detection. This review aims to compile the state-of-the-art in the field of nucleic acid amplification tests (NAATs) used for SARS-CoV-2 detection, either at the clinic level, or at the Point-Of-Care (POC), thus focusing on isothermal and non-isothermal amplification-based diagnostics, while looking carefully at the concerning virology aspects, steps and instruments a test can involve. Following a theme contextualization in introduction, topics about fundamental knowledge on underlying virology aspects, collection and processing of clinical samples pave the way for a detailed assessment of the amplification and detection technologies. In order to address such themes, nucleic acid amplification methods, the different types of molecular reactions used for DNA detection, as well as the instruments requested for executing such routes of analysis are discussed in the subsequent sections. The benchmark of paradigmatic commercial tests further contributes toward discussion, building on technical aspects addressed in the previous sections and other additional information supplied in that part. The last lines are reserved for looking ahead to the future of NAATs and its importance in tackling this pandemic and other identical upcoming challenges.
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Affiliation(s)
- João M. Vindeirinho
- National Institute for Agrarian and Veterinarian Research (INIAV, I.P), Vairão, Portugal
- Laboratory for Process Engineering, Environment, Biotechnology and Energy (LEPABE), Faculty of Engineering, University of Porto, Porto, Portugal
- Associate Laboratory in Chemical Engineering (ALiCE), Faculty of Engineering, University of Porto, Porto, Portugal
| | - Eva Pinho
- National Institute for Agrarian and Veterinarian Research (INIAV, I.P), Vairão, Portugal
- Laboratory for Process Engineering, Environment, Biotechnology and Energy (LEPABE), Faculty of Engineering, University of Porto, Porto, Portugal
- Associate Laboratory in Chemical Engineering (ALiCE), Faculty of Engineering, University of Porto, Porto, Portugal
| | - Nuno F. Azevedo
- Laboratory for Process Engineering, Environment, Biotechnology and Energy (LEPABE), Faculty of Engineering, University of Porto, Porto, Portugal
- Associate Laboratory in Chemical Engineering (ALiCE), Faculty of Engineering, University of Porto, Porto, Portugal
| | - Carina Almeida
- National Institute for Agrarian and Veterinarian Research (INIAV, I.P), Vairão, Portugal
- Laboratory for Process Engineering, Environment, Biotechnology and Energy (LEPABE), Faculty of Engineering, University of Porto, Porto, Portugal
- Associate Laboratory in Chemical Engineering (ALiCE), Faculty of Engineering, University of Porto, Porto, Portugal
- Centre of Biological Engineering (CEB), University of Minho, Braga, Portugal
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93
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Single-tube collection and nucleic acid analysis of clinical samples for SARS-CoV-2 saliva testing. Sci Rep 2022; 12:3951. [PMID: 35273232 PMCID: PMC8913774 DOI: 10.1038/s41598-022-07871-4] [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: 08/02/2021] [Accepted: 02/25/2022] [Indexed: 11/09/2022] Open
Abstract
The SARS-CoV-2 pandemic has brought to light the need for expedient diagnostic testing. Cost and availability of large-scale testing capacity has led to a lag in turnaround time and hindered contact tracing efforts, resulting in a further spread of SARS-CoV-2. To increase the speed and frequency of testing, we developed a cost-effective single-tube approach for collection, denaturation, and analysis of clinical samples. The approach utilizes 1 µL microbiological inoculation loops to collect saliva, sodium dodecyl sulfate (SDS) to inactivate and release viral genomic RNA, and a diagnostic reaction mix containing polysorbate 80 (Tween 80). In the same tube, the SDS-denatured clinical samples are introduced to the mixtures containing all components for nucleic acids detection and Tween 80 micelles to absorb the SDS and allow enzymatic reactions to proceed, obviating the need for further handling of the samples. The samples can be collected by the tested individuals, further decreasing the need for trained personnel to administer the test. We validated this single-tube sample-to-assay method with reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) and reverse transcription loop-mediated isothermal amplification (RT-LAMP) and discovered little-to-no difference between Tween- and SDS-containing reaction mixtures, compared to control reactions. This approach reduces the logistical burden of traditional large-scale testing and provides a method of deployable point-of-care diagnostics to increase testing frequency.
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94
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Waheed W, Saylan S, Hassan T, Kannout H, Alsafar H, Alazzam A. A deep learning-driven low-power, accurate, and portable platform for rapid detection of COVID-19 using reverse-transcription loop-mediated isothermal amplification. Sci Rep 2022; 12:4132. [PMID: 35260715 PMCID: PMC8903312 DOI: 10.1038/s41598-022-07954-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 02/28/2022] [Indexed: 12/24/2022] Open
Abstract
This paper presents a deep learning-driven portable, accurate, low-cost, and easy-to-use device to perform Reverse-Transcription Loop-Mediated Isothermal Amplification (RT-LAMP) to facilitate rapid detection of COVID-19. The 3D-printed device-powered using only a 5 Volt AC-DC adapter-can perform 16 simultaneous RT-LAMP reactions and can be used multiple times. Moreover, the experimental protocol is devised to obviate the need for separate, expensive equipment for RNA extraction in addition to eliminating sample evaporation. The entire process from sample preparation to the qualitative assessment of the LAMP amplification takes only 45 min (10 min for pre-heating and 35 min for RT-LAMP reactions). The completion of the amplification reaction yields a fuchsia color for the negative samples and either a yellow or orange color for the positive samples, based on a pH indicator dye. The device is coupled with a novel deep learning system that automatically analyzes the amplification results and pays attention to the pH indicator dye to screen the COVID-19 subjects. The proposed device has been rigorously tested on 250 RT-LAMP clinical samples, where it achieved an overall specificity and sensitivity of 0.9666 and 0.9722, respectively with a recall of 0.9892 for Ct < 30. Also, the proposed system can be widely used as an accurate, sensitive, rapid, and portable tool to detect COVID-19 in settings where access to a lab is difficult, or the results are urgently required.
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Affiliation(s)
- Waqas Waheed
- Department of Mechanical Engineering, Khalifa University, Abu Dhabi, UAE
| | - Sueda Saylan
- System on Chip Center (SOCC), Khalifa University, Abu Dhabi, UAE
- Department of Electrical Engineering and Computer Science, Khalifa University, Abu Dhabi, UAE
| | - Taimur Hassan
- Department of Electrical Engineering and Computer Science, Khalifa University, Abu Dhabi, UAE
- Center for Cyber-Physical Systems (C2PS), EECS Department, Khalifa University, Abu Dhabi, UAE
| | - Hussain Kannout
- Center for Biotechnology (BTC), Khalifa University, Abu Dhabi, UAE
| | - Habiba Alsafar
- Center for Biotechnology (BTC), Khalifa University, Abu Dhabi, UAE
- College of Medicine and Health Sciences, Khalifa University, Abu Dhabi, UAE
| | - Anas Alazzam
- Department of Mechanical Engineering, Khalifa University, Abu Dhabi, UAE.
- System on Chip Center (SOCC), Khalifa University, Abu Dhabi, UAE.
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95
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Papadakis G, Pantazis AK, Fikas N, Chatziioannidou S, Tsiakalou V, Michaelidou K, Pogka V, Megariti M, Vardaki M, Giarentis K, Heaney J, Nastouli E, Karamitros T, Mentis A, Zafiropoulos A, Sourvinos G, Agelaki S, Gizeli E. Portable real-time colorimetric LAMP-device for rapid quantitative detection of nucleic acids in crude samples. Sci Rep 2022; 12:3775. [PMID: 35260588 PMCID: PMC8904468 DOI: 10.1038/s41598-022-06632-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 01/27/2022] [Indexed: 02/08/2023] Open
Abstract
Loop-mediated isothermal amplification is known for its high sensitivity, specificity and tolerance to inhibiting-substances. In this work, we developed a device for performing real-time colorimetric LAMP combining the accuracy of lab-based quantitative analysis with the simplicity of point-of-care testing. The device innovation lies on the use of a plastic tube anchored vertically on a hot surface while the side walls are exposed to a mini camera able to take snapshots of the colour change in real time during LAMP amplification. Competitive features are the rapid analysis (< 30 min), quantification over 9 log-units, crude sample-compatibility (saliva, tissue, swabs), low detection limit (< 5 copies/reaction), smartphone-operation, fast prototyping (3D-printing) and ability to select the dye of interest (Phenol red, HNB). The device’s clinical utility is demonstrated in cancer mutations-analysis during the detection of 0.01% of BRAF-V600E-to-wild-type molecules from tissue samples and COVID-19 testing with 97% (Ct < 36.8) and 98% (Ct < 30) sensitivity when using extracted RNA and nasopharyngeal-swabs, respectively. The device high technology-readiness-level makes it a suitable platform for performing any colorimetric LAMP assay; moreover, its simple and inexpensive fabrication holds promise for fast deployment and application in global diagnostics.
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Affiliation(s)
- G Papadakis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, 100 N. Plastira Str., 70013, Heraklion, Greece. .,BIOPIX DNA TECHNOLOGY PC, Science and Technology Park of Crete, 100 N. Plastira Str., 70013, Heraklion, Greece.
| | - A K Pantazis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, 100 N. Plastira Str., 70013, Heraklion, Greece.,BIOPIX DNA TECHNOLOGY PC, Science and Technology Park of Crete, 100 N. Plastira Str., 70013, Heraklion, Greece
| | - N Fikas
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, 100 N. Plastira Str., 70013, Heraklion, Greece.,BIOPIX DNA TECHNOLOGY PC, Science and Technology Park of Crete, 100 N. Plastira Str., 70013, Heraklion, Greece
| | - S Chatziioannidou
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, 100 N. Plastira Str., 70013, Heraklion, Greece.,BIOPIX DNA TECHNOLOGY PC, Science and Technology Park of Crete, 100 N. Plastira Str., 70013, Heraklion, Greece.,Department of Biology, University of Crete, 70013, Voutes, Heraklion, Greece
| | - V Tsiakalou
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, 100 N. Plastira Str., 70013, Heraklion, Greece
| | - K Michaelidou
- Laboratory of Translational Oncology, School of Medicine, University of Crete, 71500, Heraklion, Greece
| | - V Pogka
- National SARS-CoV-2 Reference Laboratory, Hellenic Pasteur Institute, 127 Vas. Sofias Ave., 11521, Athens, Greece
| | - M Megariti
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, 100 N. Plastira Str., 70013, Heraklion, Greece
| | - M Vardaki
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, 100 N. Plastira Str., 70013, Heraklion, Greece.,Department of Biology, University of Crete, 70013, Voutes, Heraklion, Greece
| | - K Giarentis
- Department of Biology, University of Crete, 70013, Voutes, Heraklion, Greece
| | - J Heaney
- Advanced Pathogens Diagnostics Unit, University College London Hospitals NHS Trust, London, WC1H 9AX, UK.,UCL Great Ormond Street Institute of Child Health, London, UK
| | - E Nastouli
- Advanced Pathogens Diagnostics Unit, University College London Hospitals NHS Trust, London, WC1H 9AX, UK.,UCL Great Ormond Street Institute of Child Health, London, UK
| | - T Karamitros
- National SARS-CoV-2 Reference Laboratory, Hellenic Pasteur Institute, 127 Vas. Sofias Ave., 11521, Athens, Greece
| | - A Mentis
- National SARS-CoV-2 Reference Laboratory, Hellenic Pasteur Institute, 127 Vas. Sofias Ave., 11521, Athens, Greece
| | - A Zafiropoulos
- Laboratory of Clinical Virology, School of Medicine, University of Crete, 71500, Heraklion, Greece
| | - G Sourvinos
- Laboratory of Clinical Virology, School of Medicine, University of Crete, 71500, Heraklion, Greece
| | - S Agelaki
- Department of Biology, University of Crete, 70013, Voutes, Heraklion, Greece.,Department of Medical Oncology, University General Hospital, 71110, Heraklion, Greece
| | - E Gizeli
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, 100 N. Plastira Str., 70013, Heraklion, Greece. .,Department of Biology, University of Crete, 70013, Voutes, Heraklion, Greece.
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96
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Zhou M, Fan C, Wang L, Xu T, Zhang X. Enhanced Isothermal Amplification for Ultrafast Sensing of SARS-CoV-2 in Microdroplets. Anal Chem 2022; 94:4135-4140. [PMID: 35234445 DOI: 10.1021/acs.analchem.2c00008] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Rapid and high-throughput screening is critical to control the COVID-19 pandemic. Recombinase polymerase amplification (RPA) with highly accessible and sensitive nucleic acid amplification has been widely used for point-of-care infection diagnosis. Here, we report an integrated microdroplet array platform composed of an ultrasonic unit and minipillar array to enhance the RPA for ultrafast, high-sensitivity, and high-throughput detection of SARS-CoV-2. On such a platform, the independent microvolume reactions on individual minipillars greatly decrease the consumption of reagents. The microstreaming driven by ultrasound creates on-demand contactless microagitation in the microdroplets and promotes the interaction between RPA components, thus greatly accelerating the amplification. In the presence of microstreaming, the detection time is 6-12 min, which is 38.8-59.3% shorter than that of controls without microstreaming, and the end-point fluorescence intensity also increased 1.3-1.7 times. Furthermore, the microagitation-enhanced RPA also exhibits a lower detection limit (0.42 copy/μL) for SARS-CoV-2 in comparison to the controls. This integrated microdroplet array detection platform is expected to meet the needs for high-throughput nucleic acid testing (NAT) to improve the containment of viral transmission during the epidemic, as well as provide a potential platform for the timely detection of other pathogens or viruses.
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Affiliation(s)
- Mengyun Zhou
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen, Guangdong 518060, People's Republic of China
| | - Chuan Fan
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen, Guangdong 518060, People's Republic of China
| | - Lirong Wang
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen, Guangdong 518060, People's Republic of China
| | - Tailin Xu
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen, Guangdong 518060, People's Republic of China
| | - Xueji Zhang
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen, Guangdong 518060, People's Republic of China
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97
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Dhar BC. Diagnostic assay and technology advancement for detecting SARS-CoV-2 infections causing the COVID-19 pandemic. Anal Bioanal Chem 2022; 414:2903-2934. [PMID: 35211785 PMCID: PMC8872642 DOI: 10.1007/s00216-022-03918-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 01/01/2022] [Accepted: 01/20/2022] [Indexed: 12/23/2022]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-caused COVID-19 pandemic has transmitted to humans in practically all parts of the world, producing socio-economic turmoil. There is an urgent need for precise, fast, and affordable diagnostic testing to be widely available for detecting SARS-CoV-2 and its mutations in various phases of the disease. Early diagnosis with great precision has been achieved using real-time polymerase chain reaction (RT-PCR) and similar other molecular methods, but theseapproaches are costly and involve rigorous processes that are not easily obtainable. Conversely, immunoassays that detect a small number of antibodies have been employed for quick, low-cost tests, but their efficiency in diagnosing infected people has been restricted. The use of biosensors in the detection of SARS-CoV-2 is vital for the COVID-19 pandemic’s control. This review gives an overview of COVID-19 diagnostic approaches that are currently being developed as well as nanomaterial-based biosensor technologies, to aid future technological advancement and innovation. These approaches can be integrated into point-of-care (POC) devices to quickly identify a large number of infected patients and asymptomatic carriers. The ongoing research endeavors and developments in complementary technologies will play a significant role in curbing the spread of the COVID-19 pandemic and fill the knowledge gaps in current diagnostic accuracy and capacity.
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Affiliation(s)
- Bidhan C Dhar
- Lineberger Comprehensive Cancer Center, University of North Carolina (UNC), 205 S Columbia St, Chapel Hill, NC, 27514, USA.
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98
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Kundrod KA, Natoli ME, Chang MM, Smith CA, Paul S, Ogoe D, Goh C, Santhanaraj A, Price A, Eldin KW, Patel KP, Baker E, Schmeler KM, Richards-Kortum R. Sample-to-answer, extraction-free, real-time RT-LAMP test for SARS-CoV-2 in nasopharyngeal, nasal, and saliva samples: Implications and use for surveillance testing. PLoS One 2022; 17:e0264130. [PMID: 35213596 PMCID: PMC8880874 DOI: 10.1371/journal.pone.0264130] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 02/03/2022] [Indexed: 12/19/2022] Open
Abstract
The global COVID-19 pandemic has highlighted the need for rapid, accurate and accessible nucleic acid tests to enable timely identification of infected individuals. We optimized a sample-to-answer nucleic acid test for SARS-CoV-2 that provides results in <1 hour using inexpensive and readily available reagents. The test workflow includes a simple lysis and viral inactivation protocol followed by direct isothermal amplification of viral RNA using RT-LAMP. The assay was validated using two different instruments, a portable isothermal fluorimeter and a standard thermocycler. Results of the RT-LAMP assay were compared to traditional RT-qPCR for nasopharyngeal swabs, nasal swabs, and saliva collected from a cohort of patients hospitalized due to COVID-19. For all three sample types, positive agreement with RT-LAMP performed using the isothermal fluorimeter was 100% for samples with Ct <30 and 69-91% for samples with Ct <40. Following validation, the test was successfully scaled to test the saliva of up to 400 asymptomatic individuals per day as part of the campus surveillance program at Rice University. Successful development, validation, and scaling of this sample-to-answer, extraction-free real-time RT-LAMP test for SARS-CoV-2 adds a highly adaptable tool to efforts to control the COVID-19 pandemic, and can inform test development strategies for future infectious disease threats.
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Affiliation(s)
- Kathryn A. Kundrod
- Department of Bioengineering, Rice University, Houston, Texas, United States of America
| | - Mary E. Natoli
- Department of Bioengineering, Rice University, Houston, Texas, United States of America
| | - Megan M. Chang
- Department of Bioengineering, Rice University, Houston, Texas, United States of America
| | - Chelsey A. Smith
- Department of Bioengineering, Rice University, Houston, Texas, United States of America
| | - Sai Paul
- Department of Bioengineering, Rice University, Houston, Texas, United States of America
| | - Dereq Ogoe
- Rice 360° Institute of Global Health, Rice University, Houston, Texas, United States of America
| | - Christopher Goh
- Rice 360° Institute of Global Health, Rice University, Houston, Texas, United States of America
| | - Akshaya Santhanaraj
- Rice 360° Institute of Global Health, Rice University, Houston, Texas, United States of America
| | - Anthony Price
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Karen W. Eldin
- McGovern Medical School, The University of Texas Health Science Center, Houston, Texas, United States of America
| | - Keyur P. Patel
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Ellen Baker
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Kathleen M. Schmeler
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
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99
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Comparative Evaluation of Rapid Isothermal Amplification and Antigen Assays for Screening Testing of SARS-CoV-2. Viruses 2022; 14:v14030468. [PMID: 35336875 PMCID: PMC8951466 DOI: 10.3390/v14030468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 02/18/2022] [Accepted: 02/22/2022] [Indexed: 11/17/2022] Open
Abstract
Human transmission of SARS-CoV-2 and emergent variants of concern continue to occur globally, despite mass vaccination campaigns. Public health strategies to reduce virus spread should therefore rely, in part, on frequent screening with rapid, inexpensive, and sensitive tests. We evaluated two digitally integrated rapid tests and assessed their performance using stored nasal swab specimens collected from individuals with or without COVID-19. An isothermal amplification assay combined with a lateral flow test had a limit of detection of 10 RNA copies per reaction, and a positive percent agreement (PPA)/negative percent agreement (NPA) during the asymptomatic and symptomatic phases of 100%/100% and 95.83/100%, respectively. Comparatively, an antigen-based lateral flow test had a limit of detection of 30,000 copies and a PPA/NPA during the asymptomatic and symptomatic phases of 82.86%/98.68% and 91.67/100%, respectively. Both the isothermal amplification and antigen-based lateral flow tests had optimized detection of SARS-CoV-2 during the peak period of transmission; however, the antigen-based test had reduced sensitivity in clinical samples with qPCR Ct values greater than 29.8. Low-cost, high-throughput screening enabled by isothermal amplification or antigen-based techniques have value for outbreak control.
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100
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Suarez GD, Suarez DA, Kiu Tang YY, Zhang JX, Li J, Nagl S, Cheung PPH. Uncovering mechanisms of RT-LAMP colorimetric SARS-CoV-2 detection to improve assay reliability. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2022; 14:378-382. [PMID: 35006230 DOI: 10.1039/d1ay01395e] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Improved diagnostics are needed to manage the ongoing COVID-19 pandemic. In this study, we enhanced the color changes and sensitivity of colorimetric SARS-CoV-2 RT-LAMP assays based on triarylmethane dyes. We determined a mechanism for the color changes and obtained sensitivities of 10 RNA copies per microliter.
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Affiliation(s)
- Gianmarco D Suarez
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
- Quommni Technologies Limited, Hong Kong
| | | | | | - Jing-Xuan Zhang
- Department of Chemistry, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Jun Li
- Department of Chemistry, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
- Department of Chemistry and Key Laboratory of Organic Optoelectronics & Molecular Engineering of Ministry of Education, Tsinghua University, Beijing 100084, China
| | - Stefan Nagl
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Peter Pak-Hang Cheung
- Department of Chemical Pathology, Faculty of Medicine, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong.
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, Li Ka Shing Medical Sciences Building, Shatin, New Territories, Hong Kong
- Quommni Technologies Limited, Hong Kong
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