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Li G, Zhou J, Gao N, Liu R, Shen J. Establishment of a rapid detection method for Mycoplasma pneumoniae based on RPA-CRISPR-Cas12a technology. Clin Chim Acta 2024:119906. [PMID: 39127296 DOI: 10.1016/j.cca.2024.119906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2024] [Revised: 07/29/2024] [Accepted: 08/07/2024] [Indexed: 08/12/2024]
Abstract
Mycoplasma pneumoniae can cause respiratory infections and pneumonia, posing a serious threat to the health of children and adolescents. Early diagnosis of Mycoplasma pneumoniae infection is crucial for clinical treatment. Currently, diagnostic methods for Mycoplasma pneumoniae infection include pathogen detection, molecular biology techniques, and bacterial culture, all of which have certain limitations. Here, we developed a rapid, simple, and accurate detection method for Mycoplasma pneumoniae that does not rely on large equipment or complex operations. This technology combines the CRISPR-Cas12a system with recombinase polymerase amplification (RPA), allowing the detection results to be observed through fluorescence curves and immunochromatographic lateral flow strips.It has been validated that RPA-CRISPR/Cas12a fluorescence analysis and RPA-CRISPR/Cas12-immunochromatographic exhibit no cross-reactivity with other common pathogens, and The established detection limit was ascertained to be as low as 102 copies/µL.Additionally, 49 clinical samples were tested and compared with fluorescence quantitative polymerase chain reaction, demonstrating a sensitivity and specificity of 100%. This platform exhibits promising clinical performance and holds significant potential for clinical application, particularly in settings with limited resources, such as clinical care points or resource-constrained areas.
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Affiliation(s)
- Ge Li
- The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China, 230022; Anhui Public Health Clinical Center, Hefei, Anhui, China, 230012
| | - Jing Zhou
- The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China, 230022; Anhui Public Health Clinical Center, Hefei, Anhui, China, 230012
| | - Nana Gao
- The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China, 230022; Anhui Public Health Clinical Center, Hefei, Anhui, China, 230012
| | - Runde Liu
- The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China, 230022; Anhui Public Health Clinical Center, Hefei, Anhui, China, 230012
| | - Jilu Shen
- The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China, 230022; Anhui Public Health Clinical Center, Hefei, Anhui, China, 230012.
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Ou X, Li K, Liu M, Song J, Zuo Z, Guo Y. EXPAR for biosensing: recent developments and applications. Analyst 2024; 149:4135-4157. [PMID: 39034763 DOI: 10.1039/d4an00609g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/23/2024]
Abstract
Emerging as a promising novel amplification technique, the exponential amplification reaction (EXPAR) offers significant advantages due to its potent exponential amplification capability, straightforward reaction design, rapid reaction kinetics, and isothermal operation. The past few years have witnessed swift advancements and refinements in EXPAR-based technologies, with numerous high-performance biosensing systems documented. A deeper understanding of the EXPAR mechanism has facilitated the proposal of novel strategies to overcome limitations inherent to traditional EXPAR. Furthermore, the synergistic integration of EXPAR with diverse amplification methodologies, including the use of a CRISPR/Cas system, metal nanoparticles, aptamers, alternative isothermal amplification techniques, and enzymes, has significantly bolstered analytical efficacy, aiming to enhance specificity, sensitivity, and amplification efficiency. This comprehensive review presents a detailed exposition of the EXPAR mechanism and analyzes its primary challenges. Additionally, we summarize the latest research advancements in the biomedical field concerning the integration of EXPAR with diverse amplification technologies for sensing strategies. Finally, we discuss the challenges and future prospects of EXPAR technology in the realms of biosensing and clinical applications.
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Affiliation(s)
- Xinyi Ou
- Nanobiosensing and Microfluidic Point-of-Care Testing, Key Laboratory of Luzhou, Department of Clinical Laboratory, The Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Luzhou, 646000, PR China.
- Department of Laboratory Medicine, The Affiliated Hospital, Southwest Medical University, PR China
| | - Kunxiang Li
- Nanobiosensing and Microfluidic Point-of-Care Testing, Key Laboratory of Luzhou, Department of Clinical Laboratory, The Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Luzhou, 646000, PR China.
- Department of Laboratory Medicine, The Affiliated Hospital, Southwest Medical University, PR China
| | - Miao Liu
- Nanobiosensing and Microfluidic Point-of-Care Testing, Key Laboratory of Luzhou, Department of Clinical Laboratory, The Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Luzhou, 646000, PR China.
| | - Jiajun Song
- Nanobiosensing and Microfluidic Point-of-Care Testing, Key Laboratory of Luzhou, Department of Clinical Laboratory, The Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Luzhou, 646000, PR China.
- Department of Laboratory Medicine, The Affiliated Hospital, Southwest Medical University, PR China
| | - Zhihua Zuo
- Department of Clinical Laboratory, Nanchong Central Hospital, The Second Clinical Medical College of North Sichuan Medical College, Nanchong, Sichuan, 637003, PR China.
| | - Yongcan Guo
- Nanobiosensing and Microfluidic Point-of-Care Testing, Key Laboratory of Luzhou, Department of Clinical Laboratory, The Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Luzhou, 646000, PR China.
- Department of Laboratory Medicine, The Affiliated Hospital, Southwest Medical University, PR China
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Li X, Wang H, Qi X, Ji Y, Li F, Chen X, Li K, Li L. PCR Independent Strategy-Based Biosensors for RNA Detection. BIOSENSORS 2024; 14:200. [PMID: 38667193 PMCID: PMC11048163 DOI: 10.3390/bios14040200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 04/11/2024] [Accepted: 04/15/2024] [Indexed: 04/28/2024]
Abstract
RNA is an important information and functional molecule. It can respond to the regulation of life processes and is also a key molecule in gene expression and regulation. Therefore, RNA detection technology has been widely used in many fields, especially in disease diagnosis, medical research, genetic engineering and other fields. However, the current RT-qPCR for RNA detection is complex, costly and requires the support of professional technicians, resulting in it not having great potential for rapid application in the field. PCR-free techniques are the most attractive alternative. They are a low-cost, simple operation method and do not require the support of large instruments, providing a new concept for the development of new RNA detection methods. This article reviews current PCR-free methods, overviews reported RNA biosensors based on electrochemistry, SPR, microfluidics, nanomaterials and CRISPR, and discusses their challenges and future research prospects in RNA detection.
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Affiliation(s)
- Xinran Li
- Institute of Quality Standard and Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.L.); (X.Q.); (F.L.)
| | - Haoqian Wang
- Development Center of Science and Technology, Ministry of Agriculture and Rural Affairs, Beijing 100176, China;
| | - Xin Qi
- Institute of Quality Standard and Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.L.); (X.Q.); (F.L.)
| | - Yi Ji
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China;
| | - Fukai Li
- Institute of Quality Standard and Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.L.); (X.Q.); (F.L.)
| | - Xiaoyun Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China;
| | - Kai Li
- Institute of Quality Standard and Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.L.); (X.Q.); (F.L.)
| | - Liang Li
- Institute of Quality Standard and Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.L.); (X.Q.); (F.L.)
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Wang R, Du Y, Fu Y, Guo Y, Gao X, Guo X, Wei J, Yang Y. Ceria-Based Nanozymes in Point-of-Care Diagnosis: An Emerging Futuristic Approach for Biosensing. ACS Sens 2023; 8:4442-4467. [PMID: 38091479 DOI: 10.1021/acssensors.3c01692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
In recent years, there has been a notable increase in interest surrounding nanozymes due to their ability to imitate the functions and address the limitations of natural enzymes. The scientific community has been greatly intrigued by the study of nanoceria, primarily because of their distinctive physicochemical characteristics, which include a variety of enzyme-like activities, affordability, exceptional stability, and the ability to easily modify their surfaces. Consequently, nanoceria have found extensive use in various biosensing applications. However, the impact of its redox activity on the enzymatic catalytic mechanism remains a subject of debate, as conflicting findings in the literature have presented both pro-oxidant and antioxidant effects. Herein, we creatively propose a seesaw model to clarify the regulatory mechanism on redox balance and survey possible mechanisms of multienzyme mimetic properties of nanoceria. In addition, this review aims to showcase the latest advancements in this field by systematically discussing over 180 research articles elucidating the significance of ceria-based nanozymes in enhancing, downsizing, and enhancing the efficacy of point-of-care (POC) diagnostics. These advancements align with the ASSURED criteria established by the World Health Organization (WHO). Furthermore, this review also examines potential constraints in order to offer readers a concise overview of the emerging role of nanoceria in the advancement of POC diagnostic systems for future biosensing applications.
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Affiliation(s)
- Ruixue Wang
- College of Biological and Chemical Engineering, Qilu Institute of Technology, Jinan 250200, P. R. China
| | - Yuanyuan Du
- College of Biological and Chemical Engineering, Qilu Institute of Technology, Jinan 250200, P. R. China
| | - Ying Fu
- College of Biological and Chemical Engineering, Qilu Institute of Technology, Jinan 250200, P. R. China
| | - Yingxin Guo
- College of Biological and Chemical Engineering, Qilu Institute of Technology, Jinan 250200, P. R. China
| | - Xing Gao
- College of Biological and Chemical Engineering, Qilu Institute of Technology, Jinan 250200, P. R. China
| | - Xingqi Guo
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian 271018, P. R. China
| | - Jingjing Wei
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250200, P. R. China
| | - Yanzhao Yang
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250200, P. R. China
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Chen J, Chen Z, Meng C, Zhou J, Peng Y, Dai X, Li J, Zhong Y, Chen X, Yuan W, Ho HP, Gao BZ, Qu J, Zhang X, Zhang H, Shao Y. CRISPR-powered optothermal nanotweezers: Diverse bio-nanoparticle manipulation and single nucleotide identification. LIGHT, SCIENCE & APPLICATIONS 2023; 12:273. [PMID: 37973904 PMCID: PMC10654382 DOI: 10.1038/s41377-023-01326-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 10/26/2023] [Accepted: 11/03/2023] [Indexed: 11/19/2023]
Abstract
Optothermal nanotweezers have emerged as an innovative optical manipulation technique in the past decade, which revolutionized classical optical manipulation by efficiently capturing a broader range of nanoparticles. However, the optothermal temperature field was merely employed for in-situ manipulation of nanoparticles, its potential for identifying bio-nanoparticles remains largely untapped. Hence, based on the synergistic effect of optothermal manipulation and CRIPSR-based bio-detection, we developed CRISPR-powered optothermal nanotweezers (CRONT). Specifically, by harnessing diffusiophoresis and thermo-osmotic flows near the substrate upon optothermal excitation, we successfully trapped and enriched DNA functionalized gold nanoparticles, CRISPR-associated proteins, as well as DNA strands. Remarkably, we built an optothermal scheme for enhancing CRISPR-based single-nucleotide polymorphism (SNP) detection at single molecule level, while also introducing a novel CRISPR methodology for observing nucleotide cleavage. Therefore, this innovative approach has endowed optical tweezers with DNA identification ability in aqueous solution which was unattainable before. With its high specificity and feasibility for in-situ bio-nanoparticle manipulation and identification, CRONT will become a universal tool in point-of-care diagnosis, biophotonics, and bio-nanotechnology.
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Affiliation(s)
- Jiajie Chen
- State Key Laboratory of Radio Frequency Heterogeneous Integration, Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronics Engineering, Shenzhen University, Shenzhen, 518060, China.
| | - Zhi Chen
- State Key Laboratory of Radio Frequency Heterogeneous Integration, Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronics Engineering, Shenzhen University, Shenzhen, 518060, China
| | - Changle Meng
- State Key Laboratory of Radio Frequency Heterogeneous Integration, Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronics Engineering, Shenzhen University, Shenzhen, 518060, China
| | - Jianxing Zhou
- State Key Laboratory of Radio Frequency Heterogeneous Integration, Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronics Engineering, Shenzhen University, Shenzhen, 518060, China
| | - Yuhang Peng
- State Key Laboratory of Radio Frequency Heterogeneous Integration, Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronics Engineering, Shenzhen University, Shenzhen, 518060, China
| | - Xiaoqi Dai
- State Key Laboratory of Radio Frequency Heterogeneous Integration, Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronics Engineering, Shenzhen University, Shenzhen, 518060, China
| | - Jingfeng Li
- State Key Laboratory of Radio Frequency Heterogeneous Integration, Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronics Engineering, Shenzhen University, Shenzhen, 518060, China
| | - Yili Zhong
- State Key Laboratory of Radio Frequency Heterogeneous Integration, Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronics Engineering, Shenzhen University, Shenzhen, 518060, China
| | - Xiaolin Chen
- State Key Laboratory of Radio Frequency Heterogeneous Integration, Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronics Engineering, Shenzhen University, Shenzhen, 518060, China
| | - Wu Yuan
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Ho-Pui Ho
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Shatin, Hong Kong, China.
| | - Bruce Zhi Gao
- Department of Bioengineering and COMSET, Clemson University, Clemson, SC, 29634, USA
| | - Junle Qu
- State Key Laboratory of Radio Frequency Heterogeneous Integration, Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronics Engineering, Shenzhen University, Shenzhen, 518060, China
| | - Xueji Zhang
- School of Biomedical Engineering, Shenzhen University, Shenzhen, Guangdong, 518060, China
| | - Han Zhang
- State Key Laboratory of Radio Frequency Heterogeneous Integration, Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronics Engineering, Shenzhen University, Shenzhen, 518060, China.
| | - Yonghong Shao
- State Key Laboratory of Radio Frequency Heterogeneous Integration, Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronics Engineering, Shenzhen University, Shenzhen, 518060, China.
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Tapela K, Opurum PC, Nuokpem FY, Tetteh B, Siaw GK, Humbert MV, Tawiah-Eshun S, Barakisu AI, Asiedu K, Arhin SK, Manu AA, Appiedu-Addo SNA, Obbeng L, Quansah D, Languon S, Anyigba C, Dosoo D, Edu NKO, Oduro-Mensah D, Ampofo W, Tagoe E, Quaye O, Donkor IO, Akorli J, Aniweh Y, Christodoulides M, Mutungi J, Bediako Y, Rayner JC, Awandare GA, McCormick CJ, Quashie PK. Development of an Affordable ELISA Targeting the SARS-CoV-2 Nucleocapsid and Its Application to Samples from the Ongoing COVID-19 Epidemic in Ghana. Mol Diagn Ther 2023; 27:583-592. [PMID: 37462793 PMCID: PMC10435612 DOI: 10.1007/s40291-023-00655-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/07/2023] [Indexed: 08/18/2023]
Abstract
INTRODUCTION The true nature of the population spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in populations is often not fully known as most cases, particularly in Africa, are asymptomatic. Finding the true magnitude of SARS-CoV-2 spread is crucial to provide actionable data about the epidemiological progress of the disease for researchers and policymakers. This study developed and optimized an antibody enzyme-linked immunosorbent assay (ELISA) using recombinant nucleocapsid antigen expressed in-house using a simple bacterial expression system. METHODS Nucleocapsid protein from SARS-CoV-2 was expressed and purified from Escherichia coli. Plasma samples used for the assay development were obtained from Ghanaian SARS-CoV-2 seropositive individuals during the pandemic, while seronegative controls were plasma samples collected from blood donors before the coronavirus disease 2019 (COVID-19) pandemic. Another set of seronegative controls was collected during the COVID-19 pandemic. Antibody detection and levels within the samples were validated using commercial kits and Luminex. Analyses were performed using GraphPad Prism, and the sensitivity, specificity and background cut-off were calculated. RESULTS AND DISCUSSION This low-cost ELISA (£0.96/test) assay has a high prediction of 98.9%, and sensitivity and specificity of 97% and 99%, respectively. The assay was subsequently used to screen plasma from SARS-CoV-2 RT-PCR-positive Ghanaians. The assay showed no significant difference in nucleocapsid antibody levels between symptomatic and asymptomatic, with an increase of the levels over time. This is in line with our previous publication. CONCLUSION This study developed a low-cost and transferable assay that enables highly sensitive and specific detection of human anti-SARS-CoV-2 IgG antibodies. This assay can be modified to include additional antigens and used for continuous monitoring of sero-exposure to SARS-CoV-2 in West Africa.
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Affiliation(s)
- Kesego Tapela
- West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Legon, Accra, Ghana
- Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Legon, Accra, Ghana
| | - Precious C Opurum
- West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Legon, Accra, Ghana
| | - Franklin Y Nuokpem
- West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Legon, Accra, Ghana
- Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Legon, Accra, Ghana
| | - Becky Tetteh
- West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Legon, Accra, Ghana
- Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Legon, Accra, Ghana
| | - Godfred K Siaw
- West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Legon, Accra, Ghana
| | - Maria V Humbert
- School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD, UK
| | - Sylvia Tawiah-Eshun
- West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Legon, Accra, Ghana
| | - Anna Ibrahim Barakisu
- West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Legon, Accra, Ghana
| | - Kwame Asiedu
- West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Legon, Accra, Ghana
| | - Samuel Kojo Arhin
- West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Legon, Accra, Ghana
- Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Legon, Accra, Ghana
| | - Aaron A Manu
- West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Legon, Accra, Ghana
- Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Legon, Accra, Ghana
| | - Sekyibea N A Appiedu-Addo
- West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Legon, Accra, Ghana
| | - Louisa Obbeng
- West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Legon, Accra, Ghana
| | - Darius Quansah
- West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Legon, Accra, Ghana
- Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Legon, Accra, Ghana
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Accra, Ghana
| | - Sylvester Languon
- West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Legon, Accra, Ghana
| | - Claudia Anyigba
- West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Legon, Accra, Ghana
- Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Legon, Accra, Ghana
| | - Daniel Dosoo
- West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Legon, Accra, Ghana
| | - Nelson K O Edu
- West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Legon, Accra, Ghana
| | - Daniel Oduro-Mensah
- West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Legon, Accra, Ghana
- Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Legon, Accra, Ghana
| | - William Ampofo
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Accra, Ghana
| | - Emmanuel Tagoe
- Department of Medical Laboratory Sciences, School of Biomedical and Allied Health, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Osbourne Quaye
- West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Legon, Accra, Ghana
- Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Legon, Accra, Ghana
| | - Irene Owusu Donkor
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Accra, Ghana
| | - Jewelna Akorli
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Accra, Ghana
| | - Yaw Aniweh
- West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Legon, Accra, Ghana
- The Francis Crick Institute, 1 Midland Rd, London, NW1 1AT, UK
| | - Myron Christodoulides
- School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD, UK
| | - Joe Mutungi
- West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Legon, Accra, Ghana
| | - Yaw Bediako
- West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Legon, Accra, Ghana
- The Francis Crick Institute, 1 Midland Rd, London, NW1 1AT, UK
- Yemaachi Biotech Inc., 222 Swaniker St, Accra, Ghana
| | - Julian C Rayner
- Cambridge Institute for Medical Research, Cambridge Biomedical Campus, University of Cambridge, Cambridge, UK
| | - Gordon A Awandare
- West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Legon, Accra, Ghana
- Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Legon, Accra, Ghana
| | - Christopher J McCormick
- School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD, UK
| | - Peter Kojo Quashie
- West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Legon, Accra, Ghana.
- The Francis Crick Institute, 1 Midland Rd, London, NW1 1AT, UK.
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Yang X, Zhang B. A review on CRISPR/Cas: a versatile tool for cancer screening, diagnosis, and clinic treatment. Funct Integr Genomics 2023; 23:182. [PMID: 37231285 DOI: 10.1007/s10142-023-01117-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 05/17/2023] [Accepted: 05/18/2023] [Indexed: 05/27/2023]
Abstract
Cancer is one of the leading causes of death worldwide and it has the trend of increase incidence. However, in the past decades, as quickly developed new technologies and modified old techniques for cancer screening, diagnosis, and treatment, the cancer-caused mortality rates dropped quickly, and the survival times of cancer patients are enhanced. However, the current death rate is still about 50% and the survival patients always suffer from the side effect of current cancer treatments. Recently developed Nobel Prize-winning CRISPR/Cas technology provides new hope on cancer screening, early diagnosis, and clinic treatment as well as new drug development. Currently, four major CRISPR/Cas9-derived genome editors, CRISPR/Cas9 nucleotide sequence editor, CRISPR/Cas base editor (BE), CRISPR prime editor (PE), and CRISPR interference (CRISPRi) (including both CRISPRa and CRISPRr), were well developed and used to various research and applications, including cancer biology study and cancer screening, diagnosis, and treatment. Additionally, CRISPR/Cas12 and CRISPR/Cas13 genome editors were also widely used in cancer-related basic and applied research as well as treatment. Cancer-associated SNPs and genetic mutations as well as both oncogenes and tumor suppressor genes are perfect targets for CRISPR/Cas-based gene therapy for cancer treatment. CRISPR/Cas is also employed to modify and generate new Chimeric antigen receptor (CAR) T-cells for improving its safety, efficiency, and longer-time last for treating various cancers. Currently, there are many clinic trails of CRISPR-based gene therapy for cancer treatments. Although all CRISPR/Cas-derived genome and epigenome tools are promising methods for cancer biology study and treatment, the efficiency and long term-safety are still the major concerns for CRISPR-based gene therapy. Developing new CRISPR/Cas delivery methods and reducing the potential side effects, including off-target impacts, will enhance CRISPR/Cas application in cancer-related research, diagnosis, and therapeutical treatment.
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Affiliation(s)
- Xianguang Yang
- College of Life Science, Henan Normal University, Xinxiang, 453007, Henan, China.
| | - Baohong Zhang
- Department of Biology, East Carolina University, Greenville, NC, 27858, USA.
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8
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Fang L, Yang L, Han M, Xu H, Ding W, Dong X. CRISPR-cas technology: A key approach for SARS-CoV-2 detection. Front Bioeng Biotechnol 2023; 11:1158672. [PMID: 37214290 PMCID: PMC10198440 DOI: 10.3389/fbioe.2023.1158672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 03/31/2023] [Indexed: 05/24/2023] Open
Abstract
The CRISPR (Clustered Regularly Spaced Short Palindromic Repeats) system was first discovered in prokaryotes as a unique immune mechanism to clear foreign nucleic acids. It has been rapidly and extensively used in basic and applied research owing to its strong ability of gene editing, regulation and detection in eukaryotes. Hererin in this article, we reviewed the biology, mechanisms and relevance of CRISPR-Cas technology and its applications in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) diagnosis. CRISPR-Cas nucleic acid detection tools include CRISPR-Cas9, CRISPR-Cas12, CRISPR-Cas13, CRISPR-Cas14, CRISPR nucleic acid amplification detection technology, and CRISPR colorimetric readout detection system. The above CRISPR technologies have been applied to the nucleic acid detection, including SARS-CoV-2 detection. Common nucleic acid detection based on CRISPR derivation technology include SHERLOCK, DETECTR, and STOPCovid. CRISPR-Cas biosensing technology has been widely applied to point-of-care testing (POCT) by targeting recognition of both DNA molecules and RNA Molecules.
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Affiliation(s)
- Lijuan Fang
- Department of Laboratory Medicine, Hangzhou Ninth People’s Hospital, Hangzhou, Zhejiang Province, China
| | - Lusen Yang
- Department of Laboratory Medicine, Hangzhou Ninth People’s Hospital, Hangzhou, Zhejiang Province, China
| | - Mingyue Han
- Department of Laboratory Medicine, Hangzhou Ninth People’s Hospital, Hangzhou, Zhejiang Province, China
| | - Huimei Xu
- Department of Laboratory Medicine, Hangzhou Ninth People’s Hospital, Hangzhou, Zhejiang Province, China
| | - Wenshuai Ding
- Department of Laboratory Medicine, Hangzhou Ninth People’s Hospital, Hangzhou, Zhejiang Province, China
| | - Xuejun Dong
- Medical Laboratory, Zhejiang University Shaoxing Hospital, Shaoxing, China
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9
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Jia N, Zhou J, Xiao F, Zheng B, Huang X, Sun C, Fu J, Xu Z, Chen M, Wang Y. A CRISPR-Cas12a-Based platform for ultrasensitive, rapid, and highly specific detection of Mycoplasma pneumonia in clinical application. Front Bioeng Biotechnol 2023; 11:1022066. [PMID: 36733967 PMCID: PMC9887289 DOI: 10.3389/fbioe.2023.1022066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 01/09/2023] [Indexed: 01/19/2023] Open
Abstract
Mycoplasma pneumoniae (MP), which is responsible for a majority of community-acquired pneumonia (CAP) in children, has been largely underestimated. Here, we coupled multiple cross displacement amplification (MCDA) technique with CRISPR-Cas12a-based biosensing system to design a novel detection platform termed MP-MCDA-CRISPR assay for MP infection diagnosis and clinical application. The MP-MCDA-CRISPR assay amplified the CARDS gene of MP by MCDA method, followed by trans-cleavage of the reporter molecular upon the formation of CRISPR-Cas12a-gRNA-target DNA complex, which was confirmed by the release of fluorescent signals. A set of standard MCDA primers, an engineered CP1 primer, a quenched fluorescent ssDNA reporter, and a gRNA were designed targeting the CARDS gene of MP. The optimal temperature for MCDA pre-amplification is 64°C, and the time for CRISPR-Cas12a-gRNA biosensing process is 5 min. The limit of detection (LoD) of the MP-MCDA-CRISPR assay is 50 fg per reaction without any cross-reaction with other non-MP pathogens. The MP-MCDA-CRISPR assay accurately identified the 50 real time-PCR positive clinical samples and 78 negative ones. Taken together, the MP-MCDA-CRISPR assay designed here is a promising diagnostic tool for point-of care (POC) testing of MP infection.
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Affiliation(s)
- Nan Jia
- Experimental Research Center, Capital Institute of Pediatrics, Beijing, China
| | - Juan Zhou
- Experimental Research Center, Capital Institute of Pediatrics, Beijing, China
| | - Fei Xiao
- Experimental Research Center, Capital Institute of Pediatrics, Beijing, China
| | - Baoying Zheng
- Respiratory Medicine, Capital Institute of Pediatrics, Beijing, China
| | - Xiaolan Huang
- Experimental Research Center, Capital Institute of Pediatrics, Beijing, China
| | - Chunrong Sun
- Experimental Research Center, Capital Institute of Pediatrics, Beijing, China
| | - Jin Fu
- Experimental Research Center, Capital Institute of Pediatrics, Beijing, China
| | - Zheng Xu
- Experimental Research Center, Capital Institute of Pediatrics, Beijing, China
| | - Min Chen
- Experimental Research Center, Capital Institute of Pediatrics, Beijing, China
| | - Yi Wang
- Experimental Research Center, Capital Institute of Pediatrics, Beijing, China,*Correspondence: Yi Wang,
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10
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Omicron Variant of SARS-CoV-2: An Indian Perspective of Vaccination and Management. Vaccines (Basel) 2023; 11:vaccines11010160. [PMID: 36680006 PMCID: PMC9860853 DOI: 10.3390/vaccines11010160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 12/31/2022] [Accepted: 01/04/2023] [Indexed: 01/15/2023] Open
Abstract
Omicron variants have highly influenced the entire globe. It has a high rate of transmissibility, which makes its management tedious. There are various subtypes of omicron, namely BA.1, BA.2, BA.3, BA.4, and BA.5. Currently, one omicron subvariant BF.7 is also immersed in some parts of India. Further studies are required for a better understanding of the new immersing SARS-CoV-2 subvariant of the omicron. They differ in the mutation of the spike proteins, which alters their attachment to the host receptor and hence modifies their virulence and adaptability. Delta variants have a great disastrous influence on the entire world, especially in India. While overcoming it, another mutant catches the pace. The Indian population is highly affected by omicron variants. It alters the entire management and diagnosis system against COVID-19. It demanded forcemeat in the health care system, both qualitatively and quantitively, to cope with the omicron wave. The alteration in spike protein, which is the major target of vaccines, leads to varied immunization against the subvariants. The efficacy of vaccines against the new variant was questioned. Every vaccine had a different shielding effect on the new variant. The hesitancy of vaccination was a prevalent factor in India that might have contributed to its outbreak. The prevalence of omicron, monkeypox, and tomato flu shared some similarities and distinct features when compared to their influence on the Indian population. This review emphasizes the changes omicron brings with it and how the Indian health care system outrage this dangerous variant.
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11
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Fernandes Q, Inchakalody VP, Merhi M, Mestiri S, Taib N, Moustafa Abo El-Ella D, Bedhiafi T, Raza A, Al-Zaidan L, Mohsen MO, Yousuf Al-Nesf MA, Hssain AA, Yassine HM, Bachmann MF, Uddin S, Dermime S. Emerging COVID-19 variants and their impact on SARS-CoV-2 diagnosis, therapeutics and vaccines. Ann Med 2022; 54:524-540. [PMID: 35132910 PMCID: PMC8843115 DOI: 10.1080/07853890.2022.2031274] [Citation(s) in RCA: 206] [Impact Index Per Article: 103.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The emergence of novel and evolving variants of SARS-CoV-2 has fostered the need for change in the form of newer and more adaptive diagnostic methods for the detection of SARS-CoV-2 infections. On the other hand, developing rapid and sensitive diagnostic technologies is now more challenging due to emerging variants and varying symptoms exhibited among the infected individuals. In addition to this, vaccines remain the major mainstay of prevention and protection against infection. Novel vaccines and drugs are constantly being developed to unleash an immune response for the robust targeting of SARS-CoV-2 and its associated variants. In this review, we provide an updated perspective on the current challenges posed by the emergence of novel SARS-CoV-2 mutants/variants and the evolution of diagnostic techniques to enable their detection. In addition, we also discuss the development, formulation, working mechanisms, advantages, and drawbacks of some of the most used vaccines/therapeutic drugs and their subsequent immunological impact.Key messageThe emergence of novel variants of the SARS-CoV-2 in the past couple of months, highlights one of the primary challenges in the diagnostics, treatment, as well as vaccine development against the virus.Advancements in SARS-CoV-2 detection include nucleic acid based, antigen and immuno- assay-based and antibody-based detection methodologies for efficient, robust, and quick testing; while advancements in COVID-19 preventive and therapeutic strategies include novel antiviral and immunomodulatory drugs and SARS-CoV-2 targeted vaccines.The varied COVID-19 vaccine platforms and the immune responses induced by each one of them as well as their ability to battle post-vaccination infections have all been discussed in this review.
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Affiliation(s)
- Queenie Fernandes
- Translational Cancer Research Facility, National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar.,College of Medicine, Qatar University, Doha, Qatar
| | - Varghese Philipose Inchakalody
- Translational Cancer Research Facility, National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar
| | - Maysaloun Merhi
- Translational Cancer Research Facility, National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar
| | - Sarra Mestiri
- Translational Cancer Research Facility, National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar
| | - Nassiba Taib
- Translational Cancer Research Facility, National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar
| | - Dina Moustafa Abo El-Ella
- Translational Cancer Research Facility, National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar
| | - Takwa Bedhiafi
- Translational Cancer Research Facility, National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar
| | - Afsheen Raza
- Translational Cancer Research Facility, National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar
| | - Lobna Al-Zaidan
- Translational Cancer Research Facility, National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar
| | - Mona O Mohsen
- Translational Cancer Research Facility, National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar.,Department of Biomedical Research, Immunology RIA, University of Bern, Bern, Switzerland
| | | | - Ali Ait Hssain
- Medical Intensive Care Unit, Hamad General Hospital, Hamad Medical Corporation, Doha, Qatar
| | | | - Martin F Bachmann
- Department of Biomedical Research, Immunology RIA, University of Bern, Bern, Switzerland.,Nuffield Department of Medicine, Jenner Institute, University of Oxford, Oxford, United Kingdom
| | - Shahab Uddin
- Translational Research Institute and Dermatology Institute, Academic Health System, Hamad Medical Corporation, Doha, Qatar
| | - Said Dermime
- Translational Cancer Research Facility, National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar
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12
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Identification of Novel Antimicrobial Resistance Genes Using Machine Learning, Homology Modeling, and Molecular Docking. Microorganisms 2022; 10:microorganisms10112102. [PMID: 36363694 PMCID: PMC9693463 DOI: 10.3390/microorganisms10112102] [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: 08/25/2022] [Revised: 10/17/2022] [Accepted: 10/19/2022] [Indexed: 11/30/2022] Open
Abstract
Antimicrobial resistance (AMR) threatens the healthcare system worldwide with the rise of emerging drug resistant infectious agents. AMR may render the current therapeutics ineffective or diminish their efficacy, and its rapid dissemination can have unmitigated health and socioeconomic consequences. Just like with many other health problems, recent computational advances including developments in machine learning or artificial intelligence hold a prodigious promise in deciphering genetic factors underlying emergence and dissemination of AMR and in aiding development of therapeutics for more efficient AMR solutions. Current machine learning frameworks focus mainly on known AMR genes and are, therefore, prone to missing genes that have not been implicated in resistance yet, including many uncharacterized genes whose functions have not yet been elucidated. Furthermore, new resistance traits may evolve from these genes leading to the rise of superbugs, and therefore, these genes need to be characterized. To infer novel resistance genes, we used complete gene sets of several bacterial strains known to be susceptible or resistant to specific drugs and associated phenotypic information within a machine learning framework that enabled prioritizing genes potentially involved in resistance. Further, homology modeling of proteins encoded by prioritized genes and subsequent molecular docking studies indicated stable interactions between these proteins and the antimicrobials that the strains containing these proteins are known to be resistant to. Our study highlights the capability of a machine learning framework to uncover novel genes that have not yet been implicated in resistance to any antimicrobials and thus could spur further studies targeted at neutralizing AMR.
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13
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Li J, Tang L, Li T, Li K, Zhang Y, Ni W, Xiao MM, Zhao Y, Zhang ZY, Zhang GJ. Tandem Cas13a/crRNA-Mediated CRISPR-FET Biosensor: A One-for-All Check Station for Virus without Amplification. ACS Sens 2022; 7:2680-2690. [PMID: 36073895 DOI: 10.1021/acssensors.2c01200] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The path toward field-effect transistor (FET) application from laboratory to clinic has delivered a compelling push in the biomedical domain, yet ultrasensitive and timely pathogen identification without PCR remains a long-lasting challenge. Herein, we create a generic check station termed "CRISPR-FET", first incorporating the CRISPR/Cas13a system within the FET modality, for accelerated and unamplified detection of viral RNA. Unlike conventional FETs bearing target-specific receptors, this sensor holds three unique advancements: (i) an ingenious sensing mechanism is used, which converts the signal of a large-sized analyte into an on-chip cleavage response of an immobilized CRISPR reporter, enabling signal generation events to occur all within the Debye length; (ii) the multipurpose inspection of the CoV ORF1ab, CoV N gene, and HCV RNA unveils the potential for "one-for-all" scalable FET-based molecular diagnostics; and (iii) it is shown that Cas13a-crRNAs targeting different sites of the viral genome can be deployed in tandem to amplify the FET response, empowering the detection limit down to 1.56 aM, which is a world-record level of sensitivity in the FET for direct viral gene sensing. Notably, a brilliant clinical applicability was made in distinguishing HCV-infected patients from normal controls. Overall, this study sheds new insights into FET-based nucleic acid sensing technology and invokes a vision for its possible future roles in diagnosis of various viral diseases.
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Affiliation(s)
- Jiahao Li
- School of Laboratory Medicine, Hubei University of Chinese Medicine, 16 Huangjia Lake West Road, Wuhan 430065, P.R. China
| | - Lina Tang
- School of Laboratory Medicine, Hubei University of Chinese Medicine, 16 Huangjia Lake West Road, Wuhan 430065, P.R. China
| | - Tingxian Li
- School of Laboratory Medicine, Hubei University of Chinese Medicine, 16 Huangjia Lake West Road, Wuhan 430065, P.R. China
| | - Kun Li
- School of Laboratory Medicine, Hubei University of Chinese Medicine, 16 Huangjia Lake West Road, Wuhan 430065, P.R. China
| | - Yulin Zhang
- School of Laboratory Medicine, Hubei University of Chinese Medicine, 16 Huangjia Lake West Road, Wuhan 430065, P.R. China
| | - Wei Ni
- Hubei Provincial Hospital of Traditional Chinese Medicine, Wuhan 430061, China
| | - Meng-Meng Xiao
- Hunan Institute of Advanced Sensing and Information Technology, Xiangtan University, Hunan 411105, P. R. China
| | - Youyun Zhao
- Hubei Provincial Hospital of Traditional Chinese Medicine, Wuhan 430061, China
| | - Zhi-Yong Zhang
- Hunan Institute of Advanced Sensing and Information Technology, Xiangtan University, Hunan 411105, P. R. China
| | - Guo-Jun Zhang
- School of Laboratory Medicine, Hubei University of Chinese Medicine, 16 Huangjia Lake West Road, Wuhan 430065, P.R. China
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14
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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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15
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Mahari S, Gandhi S. Recent Advances in Electrochemical Biosensors for the Detection of Salmonellosis: Current Prospective and Challenges. BIOSENSORS 2022; 12:bios12060365. [PMID: 35735514 PMCID: PMC9221498 DOI: 10.3390/bios12060365] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 05/20/2022] [Accepted: 05/23/2022] [Indexed: 05/03/2023]
Abstract
Salmonellosis is a major cause of foodborne infections, caused by Salmonella, posing a major health risk. It possesses the ability to infiltrate the food supply chain at any point throughout the manufacturing, distribution, processing or quality control process. Salmonella infection has increased severely and requires effective and efficient methods for early monitoring and detection. Traditional methods, such as real-time polymerase chain reaction and culture plate, consume a lot of time and are labor-intensive. Therefore, new quick detection methods for on-field applications are urgently needed. Biosensors provide consumer-friendly approaches for quick on-field diagnoses. In the last few years, there has been a surge in research into the creation of reliable and advanced electrochemical sensors for the detection of Salmonella strains in food samples. Electrochemical sensors provide extensive accuracy and reproducible results. Herein, we present a comprehensive overview of electrochemical sensors for the detection of Salmonella by focusing on various mechanisms of electrochemical transducer. Further, we explain new-generation biosensors (microfluidics, CRISPR- and IOT-based) for point-of care applications. This review also highlights the limitations of developing biosensors in Salmonella detection and future possibilities.
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Affiliation(s)
- Subhasis Mahari
- DBT-National Institute of Animal Biotechnology (NIAB), Hyderabad 500032, India;
- DBT-Regional Centre for Biotechnology (RCB), Faridabad 121001, India
| | - Sonu Gandhi
- DBT-National Institute of Animal Biotechnology (NIAB), Hyderabad 500032, India;
- DBT-Regional Centre for Biotechnology (RCB), Faridabad 121001, India
- Correspondence: or
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16
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You H, Gordon CA, MacGregor SR, Cai P, McManus DP. Potential of the CRISPR-Cas system for improved parasite diagnosis: CRISPR-Cas mediated diagnosis in parasitic infections: CRISPR-Cas mediated diagnosis in parasitic infections. Bioessays 2022; 44:e2100286. [PMID: 35142378 DOI: 10.1002/bies.202100286] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/26/2022] [Accepted: 01/27/2022] [Indexed: 12/26/2022]
Abstract
CRISPR-Cas technology accelerates development of fast, accurate, and portable diagnostic tools, typified by recent applications in COVID-19 diagnosis. Parasitic helminths cause devastating diseases afflicting 1.5 billion people globally, representing a significant public health and economic burden, especially in developing countries. Currently available diagnostic tests for worm infection are neither sufficiently sensitive nor field-friendly for use in low-endemic or resource-poor settings, leading to underestimation of true prevalence rates. Mass drug administration programs are unsustainable long-term, and diagnostic tools - required to be rapid, specific, sensitive, cost-effective, and user-friendly without specialized equipment and expertise - are urgently needed for rapid mapping of helminthic diseases and monitoring control programs. We describe the key features of the CRISPR-Cas12/13 system and emphasise its potential for the development of effective tools for the diagnosis of parasitic and other neglected tropical diseases (NTDs), a key recommendation of the NTDs 2021-2030 roadmap released by the World Health Organization.
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Affiliation(s)
- Hong You
- Immunology Department, QIMR Berghofer Medical Research Institute, Queensland, Australia
| | - Catherine A Gordon
- Immunology Department, QIMR Berghofer Medical Research Institute, Queensland, Australia
| | - Skye R MacGregor
- Immunology Department, QIMR Berghofer Medical Research Institute, Queensland, Australia
| | - Pengfei Cai
- Immunology Department, QIMR Berghofer Medical Research Institute, Queensland, Australia
| | - Donald P McManus
- Immunology Department, QIMR Berghofer Medical Research Institute, Queensland, Australia
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17
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Dubey AK, Kumar Gupta V, Kujawska M, Orive G, Kim NY, Li CZ, Kumar Mishra Y, Kaushik A. Exploring nano-enabled CRISPR-Cas-powered strategies for efficient diagnostics and treatment of infectious diseases. JOURNAL OF NANOSTRUCTURE IN CHEMISTRY 2022; 12:833-864. [PMID: 35194511 PMCID: PMC8853211 DOI: 10.1007/s40097-022-00472-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 01/23/2022] [Indexed: 05/02/2023]
Abstract
UNLABELLED Biomedical researchers have subsequently been inspired the development of new approaches for precisely changing an organism's genomic DNA in order to investigate customized diagnostics and therapeutics utilizing genetic engineering techniques. Clustered Regulatory Interspaced Short Palindromic Repeats (CRISPR) is one such technique that has emerged as a safe, targeted, and effective pharmaceutical treatment against a wide range of disease-causing organisms, including bacteria, fungi, parasites, and viruses, as well as genetic abnormalities. The recent discovery of very flexible engineered nucleic acid binding proteins has changed the scientific area of genome editing in a revolutionary way. Since current genetic engineering technique relies on viral vectors, issues about immunogenicity, insertional oncogenesis, retention, and targeted delivery remain unanswered. The use of nanotechnology has the potential to improve the safety and efficacy of CRISPR/Cas9 component distribution by employing tailored polymeric nanoparticles. The combination of two (CRISPR/Cas9 and nanotechnology) offers the potential to open new therapeutic paths. Considering the benefits, demand, and constraints, the goal of this research is to acquire more about the biology of CRISPR technology, as well as aspects of selective and effective diagnostics and therapies for infectious illnesses and other metabolic disorders. This review advocated combining nanomedicine (nanomedicine) with a CRISPR/Cas enabled sensing system to perform early-stage diagnostics and selective therapy of specific infectious disorders. Such a Nano-CRISPR-powered nanomedicine and sensing system would allow for successful infectious illness control, even on a personal level. This comprehensive study also discusses the current obstacles and potential of the predicted technology. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s40097-022-00472-7.
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Affiliation(s)
- Ankit Kumar Dubey
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, 600036, Chennai, Tamil Nadu India
| | - Vijai Kumar Gupta
- Biorefining and Advanced Materials Research Center, Scotland’s Rural College (SRUC), Kings Buildings, West Mains Road, Edinburgh, EH9 3JG UK
| | - Małgorzata Kujawska
- Department of Toxicology, Poznan University of Medical Sciences, Dojazd 30, 60-631 Poznań, Poland
| | - Gorka Orive
- NanoBioCel Group, Laboratory of Pharmaceutics, School of Pharmacy, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain
- CIBER Bioengineering, Biomaterials and Nanomedicine (CIBERBBN), Institute of Health Carlos III, Madrid, Spain
- Bioaraba Health Research Institute, Nanobiocel Research Group, Vitoria-Gasteiz, Spain
- University Institute for Regenerative Medicine and Oral Implantology, UIRMI (UPV/EHU-Fundación Eduardo Anitua), Vitoria-Gasteiz, Spain
- Singapore Eye Research Institute, Singapore, Singapore
| | - Nam-Young Kim
- Department of Electronics Engineering, RFIC Bio Centre, NDAC Centre, RFIC Bio Centre, NDAC Centre, Kwangwoon University, 20 Kwangwoon-ro, Nowon-gu, Seoul, 01897 South Korea
| | - Chen-zhong Li
- Center for Cellular and Molecular Diagnostics, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112 USA
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112 USA
| | - Yogendra Kumar Mishra
- Mads Clausen Institute, NanoSYD, University of Southern Denmark, Alison 2, 6400 Sønderborg, Denmark
| | - Ajeet Kaushik
- NanoBioTech Laboratory, Health System Engineering, Department of Natural Sciences, Florida Polytechnic University, Lakeland, FL-33805 USA
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18
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Zhang W, Jiao Y, Ding C, Shen L, Li Y, Yu Y, Huang K, Li B, Wang F, Yang J. Rapid Detection of Tomato Spotted Wilt Virus With Cas13a in Tomato and Frankliniella occidentalis. Front Microbiol 2021; 12:745173. [PMID: 34745047 PMCID: PMC8564384 DOI: 10.3389/fmicb.2021.745173] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 09/24/2021] [Indexed: 12/12/2022] Open
Abstract
As one of the top 10 plant viruses, the severity of losses to crop productivity caused by the tomato spotted wilt virus (TSWV) has resulted in an urgent need to develop a more sensitive and rapid method of detection. In this study, we developed a CRISPR/Cas13a-based detection system to diagnose TSWV in tomato and western flower thrips (Frankliniella occidentalis). The detection system relies on recombinase polymerase amplification and Cas13a-mediated collateral cleavage activity. Positive results can be distinguished after 20 min by a significantly enhanced fluorescence signal. We tested the sensitivity of CRISPR/Cas13a-based detection system and found that the detection system that we developed has limits of detection that reaches 2.26 × 102 copies/μl and a 10-fold increase compared with the sensitivity of using RT-PCR to detect the virus. Furthermore, the CRISPR/Cas13a-based detection system has a high selectivity for the TSWV without interference from other viruses. The CRISPR/Cas13a-based detection system was utilized to detect the TSWV in samples of tomato leaves and the transmission vector F. occidentalis that were fully consistent with the results when RT-PCR was used to detect the virus.
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Affiliation(s)
- Wanhong Zhang
- Key Laboratory of Tobacco Pest Monitoring Controlling and Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Yubing Jiao
- Key Laboratory of Tobacco Pest Monitoring Controlling and Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Chengying Ding
- Key Laboratory of Tobacco Pest Monitoring Controlling and Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Lili Shen
- Key Laboratory of Tobacco Pest Monitoring Controlling and Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Ying Li
- Key Laboratory of Tobacco Pest Monitoring Controlling and Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Yanbi Yu
- Country Yunnan Province Company of China Tobacco Corporation, Kunming, China
| | - Kun Huang
- Honghe City Company of Yunnan Tobacco Company, Mile, China
| | - Bin Li
- Sichuan Province Company of China Tobacco Corporation, Chengdu, China
| | - Fenglong Wang
- Key Laboratory of Tobacco Pest Monitoring Controlling and Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Jinguang Yang
- Key Laboratory of Tobacco Pest Monitoring Controlling and Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
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19
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Xu X, Huang R, Yin WB. An Optimized and Efficient CRISPR/Cas9 System for the Endophytic Fungus Pestalotiopsis fici. J Fungi (Basel) 2021; 7:809. [PMID: 34682231 PMCID: PMC8539907 DOI: 10.3390/jof7100809] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 09/20/2021] [Accepted: 09/21/2021] [Indexed: 11/17/2022] Open
Abstract
Endophytic fungi are emerging as attractive producers of natural products with diverse bioactivities and novel structures. However, difficulties in the genetic manipulation of endophytic fungi limit the search of novel secondary metabolites. In this study, we improved the polyethylene glycol (PEG)-mediated protoplast transformation method by introducing the CRISPR/Cas9 system into endophytic fungus Pestalotiopsis fici. Using this approach, we performed genome editing such as site-specific gene insertion, dual-locus mutations, and long DNA fragment deletions in P. fici efficiently. The average efficiency for site-specific gene insertion and two-site gene editing was up to 48.0% and 44.4%, respectively. In addition, the genetic manipulation time with long DNA fragment (5-10 kb) deletion was greatly shortened to one week in comparison with traditional methods such as Agrobacterium tumefaciens-mediated transformation (ATMT). Taken together, the development of the CRISPR/Cas9 system in the endophytic fungus will accelerate the discovery of novel natural products and further biological study.
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Affiliation(s)
- Xinran Xu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (X.X.); (R.H.)
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Runye Huang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (X.X.); (R.H.)
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wen-Bing Yin
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (X.X.); (R.H.)
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China
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Selvam K, Najib MA, Khalid MF, Mohamad S, Palaz F, Ozsoz M, Aziah I. RT-LAMP CRISPR-Cas12/13-Based SARS-CoV-2 Detection Methods. Diagnostics (Basel) 2021; 11:diagnostics11091646. [PMID: 34573987 PMCID: PMC8467512 DOI: 10.3390/diagnostics11091646] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 08/30/2021] [Accepted: 09/06/2021] [Indexed: 12/26/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19), which is caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), has attracted public attention. The gold standard for diagnosing COVID-19 is reverse transcription–quantitative polymerase chain reaction (RT-qPCR). However, RT-qPCR can only be performed in centralized laboratories due to the requirement for advanced laboratory equipment and qualified workers. In the last decade, clustered regularly interspaced short palindromic repeats (CRISPR) technology has shown considerable promise in the development of rapid, highly sensitive, and specific molecular diagnostic methods that do not require complicated instrumentation. During the current COVID-19 pandemic, there has been growing interest in using CRISPR-based diagnostic techniques to develop rapid and accurate assays for detecting SARS-CoV-2. In this work, we review and summarize reverse-transcription loop-mediated isothermal amplification (RT-LAMP) CRISPR-based diagnostic techniques for detecting SARS-CoV-2.
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Affiliation(s)
- Kasturi Selvam
- Institute for Research in Molecular Medicine (INFORMM), Health Campus, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia; (K.S.); (M.A.N.); (M.F.K.)
| | - Mohamad Ahmad Najib
- Institute for Research in Molecular Medicine (INFORMM), Health Campus, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia; (K.S.); (M.A.N.); (M.F.K.)
| | - Muhammad Fazli Khalid
- Institute for Research in Molecular Medicine (INFORMM), Health Campus, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia; (K.S.); (M.A.N.); (M.F.K.)
| | - Suharni Mohamad
- School of Dental Sciences, Health Campus, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia;
| | - Fahreddin Palaz
- Faculty of Medicine, Hacettepe University, Ankara 06100, Turkey;
| | - Mehmet Ozsoz
- Institute for Research in Molecular Medicine (INFORMM), Health Campus, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia; (K.S.); (M.A.N.); (M.F.K.)
- Department of Biomedical Engineering, Near East University, Nicosia 99138, Turkey
- Correspondence: (M.O.); (I.A.)
| | - Ismail Aziah
- Institute for Research in Molecular Medicine (INFORMM), Health Campus, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia; (K.S.); (M.A.N.); (M.F.K.)
- Correspondence: (M.O.); (I.A.)
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