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Lee HJ, Kim HJ, Cho IS, Jeong RD. Identification of Viruses Infecting Phalaenopsis Orchids Using Nanopore Sequencing and Development of an RT-RPA-CRISPR/Cas12a for Rapid Visual Detection of Nerine Latent Virus. Int J Mol Sci 2024; 25:2666. [PMID: 38473916 DOI: 10.3390/ijms25052666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 02/22/2024] [Accepted: 02/23/2024] [Indexed: 03/14/2024] Open
Abstract
Phalaenopsis orchids are one of the most popular ornamental plants. More than thirty orchid viruses have been reported, and virus-infected Phalaenopsis orchids significantly lose their commercial value. Therefore, the development of improved viral disease detection methods could be useful for quality control in orchid cultivation. In this study, we first utilized the MinION, a portable sequencing device based on Oxford Nanopore Technologies (ONT) to rapidly detect plant viruses in Phalaenopsis orchids. Nanopore sequencing revealed the presence of three plant viruses in Phalaenopsis orchids: odontoglossum ringspot virus, cymbidium mosaic virus, and nerine latent virus (NeLV). Furthermore, for the first time, we detected NeLV infection in Phalaenopsis orchids using nanopore sequencing and developed the reverse transcription-recombinase polymerase amplification (RT-RPA)-CRISPR/Cas12a method for rapid, instrument-flexible, and accurate diagnosis. The developed RT-RPA-CRISPR/Cas12a technique can confirm NeLV infection in less than 20 min and exhibits no cross-reactivity with other viruses. To determine the sensitivity of RT-RPA-CRISPR/Cas12a for NeLV, we compared it with RT-PCR using serially diluted transcripts and found a detection limit of 10 zg/μL, which is approximately 1000-fold more sensitive. Taken together, the ONT platform offers an efficient strategy for monitoring plant viral pathogens, and the RT-RPA-CRISPR/Cas12a method has great potential as a useful tool for the rapid and sensitive diagnosis of NeLV.
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Affiliation(s)
- Hyo-Jeong Lee
- Department of Applied Biology, Institute of Environmentally Friendly Agriculture, Chonnam National University, Gwangju 61185, Republic of Korea
| | - Hae-Jun Kim
- Department of Applied Biology, Institute of Environmentally Friendly Agriculture, Chonnam National University, Gwangju 61185, Republic of Korea
| | - In-Sook Cho
- Horticultural and Herbal Crop Environment Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Wanju 55365, Republic of Korea
| | - Rae-Dong Jeong
- Department of Applied Biology, Institute of Environmentally Friendly Agriculture, Chonnam National University, Gwangju 61185, Republic of Korea
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2
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Tanny T, Sallam M, Soda N, Nguyen NT, Alam M, Shiddiky MJA. CRISPR/Cas-Based Diagnostics in Agricultural Applications. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:11765-11788. [PMID: 37506507 DOI: 10.1021/acs.jafc.3c00913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2023]
Abstract
Pests and disease-causing pathogens frequently impede agricultural production. An early and efficient diagnostic tool is crucial for effective disease management. Clustered regularly interspaced short palindromic repeats (CRISPR) and the CRISPR-associated protein (Cas) have recently been harnessed to develop diagnostic tools. The CRISPR/Cas system, composed of the Cas endonuclease and guide RNA, enables precise identification and cleavage of the target nucleic acids. The inherent sensitivity, high specificity, and rapid assay time of the CRISPR/Cas system make it an effective alternative for diagnosing plant pathogens and identifying genetically modified crops. Furthermore, its potential for multiplexing and suitability for point-of-care testing at the field level provide advantages over traditional diagnostic systems such as RT-PCR, LAMP, and NGS. In this review, we discuss the recent developments in CRISPR/Cas based diagnostics and their implications in various agricultural applications. We have also emphasized the major challenges with possible solutions and provided insights into future perspectives and potential applications of the CRISPR/Cas system in agriculture.
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Affiliation(s)
- Tanzena Tanny
- School of Environment and Science (ESC), Griffith University, Nathan, QLD 4111, Australia
- Queensland Micro and Nanotechnology Centre (QMNC), Griffith University, Nathan, QLD 4111, Australia
| | - Mohamed Sallam
- School of Environment and Science (ESC), Griffith University, Nathan, QLD 4111, Australia
- Queensland Micro and Nanotechnology Centre (QMNC), Griffith University, Nathan, QLD 4111, Australia
| | - Narshone Soda
- Queensland Micro and Nanotechnology Centre (QMNC), Griffith University, Nathan, QLD 4111, Australia
| | - Nam-Trung Nguyen
- Queensland Micro and Nanotechnology Centre (QMNC), Griffith University, Nathan, QLD 4111, Australia
| | - Mobashwer Alam
- Queensland Alliance for Agriculture & Food Innovation, The University of Queensland, Mayers Road, Nambour, QLD 4560, Australia
| | - Muhammad J A Shiddiky
- School of Environment and Science (ESC), Griffith University, Nathan, QLD 4111, Australia
- Queensland Micro and Nanotechnology Centre (QMNC), Griffith University, Nathan, QLD 4111, Australia
- Rural Health Research Institute, Charles Sturt University, Orange, NSW 2800, Australia
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3
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Guo Y, Xia H, Dai T, Liu T, Shamoun SF, CuiPing W. CRISPR/Cas12a-based approaches for efficient and accurate detection of Phytophthora ramorum. Front Cell Infect Microbiol 2023; 13:1218105. [PMID: 37441240 PMCID: PMC10333691 DOI: 10.3389/fcimb.2023.1218105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 06/08/2023] [Indexed: 07/15/2023] Open
Abstract
Introduction Phytophthora ramorum is a quarantine pathogen that causes leaf blight and shoot dieback of the crown, bark cankers and death on a number of both ornamental and forest trees, especially in North America and northern Europe, where it has produced severe outbreaks. Symptoms caused by P. ramorum can be confused with those by other Phytophthora and fungal species. Early and accurate detection of the causal pathogen P. ramorum is crucial for effective prevention and control of Sudden Oak Death. Methods In this study, we developed a P. ramorum detection technique based on a combination of recombinase polymerase amplification (RPA) with CRISPR/Cas12a technology (termed RPACRISPR/ Cas12a). Results This novel method can be utilized for the molecular identification of P. ramorum under UV light and readout coming from fluorophores, and can specifically detect P. ramorum at DNA concentrations as low as 100 pg within 25 min at 37°C. Discussion We have developed a simple, rapid, sensitive, unaided-eye visualization, RPA CRISPR/Cas12a-based detection system for the molecular identification of P. ramorum that does not require technical expertise or expensive ancillary equipment. And this system is sensitive for both standard laboratory samples and samples from the field.
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Affiliation(s)
- Yufang Guo
- Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Hongming Xia
- Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Tingting Dai
- Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Tingli Liu
- Jiangsu Provincial Key Construction Laboratory of Special Biomass Resource Utilization, Nanjing Xiaozhuang University, Nanjing, China
| | - Simon Francis Shamoun
- Natural Resources Canada, Canadian Forest Service, Pacific Forestry Centre, Victoria, BC, Canada
| | - Wu CuiPing
- Animal, Plant and Food Inspection Center, Nanjing Customs, Nanjing, Jiangsu, China
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4
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Chen Z, Yang X, Xia H, Wu C, Yang J, Dai T. A Frontline, Rapid, Nucleic Acid-Based Fusarium circinatum Detection System Using CRISPR/Cas12a Combined with Recombinase Polymerase Amplification. PLANT DISEASE 2023:PDIS05221234RE. [PMID: 36480733 DOI: 10.1094/pdis-05-22-1234-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Pitch canker caused by the fungus Fusarium circinatum is a damaging disease that affects pines in Europe, South Africa, and North America in both the southeast and west coast of the United States. Several countries, including China, have listed F. circinatum as a quarantine pathogen. Timely detection, an important pillar of the quarantine effort, can efficiently prevent the introduction of F. circinatum into new areas or facilitate management and eradication strategies in already infested sites. In this study, we developed an F. circinatum detection technique based on a combination of recombinase polymerase amplification (RPA) with CRISPR/Cas12a technology (termed RPA-CRISPR/Cas12a). After obtaining DNA, this novel method can be utilized for the molecular identification of F. circinatum using the naked eye and can specifically detect F. circinatum at DNA concentrations as low as 200 fg within 30 min at 37°C. The system is sensitive for both standard laboratory samples and samples from the field. In summary, we have developed a simple, rapid, sensitive, unaided-eye visualization, RPA-CRISPR/Cas12a-based detection system for the molecular identification of F. circinatum that does not require technical expertise or expensive ancillary equipment.
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Affiliation(s)
- Zhenpeng Chen
- Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Xiao Yang
- Plant and Pest Diagnostic Clinic, Department of Plant Industry, Clemson University, Pendleton, SC, U.S.A
| | - Hongming Xia
- Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Cuiping Wu
- Animal, Plant, and Food Inspection Center, Nanjing Customs, Nanjing, Jiangsu, China
| | - Jing Yang
- Animal, Plant, and Food Inspection Center, Nanjing Customs, Nanjing, Jiangsu, China
| | - Tingting Dai
- Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu, China
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5
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Guo Y, Xia H, Dai T, Liu T. RPA-CRISPR/Cas12a mediated isothermal amplification for visual detection of Phytophthora sojae. Front Cell Infect Microbiol 2023; 13:1208837. [PMID: 37305413 PMCID: PMC10250720 DOI: 10.3389/fcimb.2023.1208837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 05/03/2023] [Indexed: 06/13/2023] Open
Abstract
Introduction Phytophthora sojae is among the most devastating pathogens of soybean (Glycine max) and severely impacts soybean production in several countries. The resulting disease can be difficult to diagnose and other Phytophthora species can also infect soybean. Accurate diagnosis is important for management of the disease caused by P. sojae. Methods In this study, recombinase polymerase amplification (RPA) in combination with the CRISPR/Cas12a system were used for detection of P. sojae. The assay was highly specific to P. sojae. Results The test results were positive for 29 isolates of P. sojae, but negative for 64 isolates of 29 Phytophthora species, 7 Phytopythium and Pythium species, 32 fungal species, and 2 Bursaphelenchus species. The method was highly sensitive, detecting as little as 10 pg.µL-1 of P. sojae genomic DNA at 37°C in 20 min. The test results were visible under UV light and readout coming from fluorophores. In addition, P. sojae was detected from natural inoculated hypocotyls of soybean seedlings using this novel assay. The rapidity and accuracy of the method were verified using 30 soybean rhizosphere samples. Discussion In conclusion, the RPA-CRISPR/Cas12a detection assay developed here is sensitive, efficient, and convenient, and has potential for further development as a kit for monitoring root rot of soybean in the field.
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Affiliation(s)
- Yufang Guo
- Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Hongming Xia
- Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Tingting Dai
- Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Tingli Liu
- Jiangsu Provincial Key Construction Laboratory of Special Biomass Resource Utilization, Nanjing Xiaozhuang University, Nanjing, China
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6
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Yang H, Ledesma-Amaro R, Gao H, Ren Y, Deng R. CRISPR-based biosensors for pathogenic biosafety. Biosens Bioelectron 2023; 228:115189. [PMID: 36893718 DOI: 10.1016/j.bios.2023.115189] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 12/30/2022] [Accepted: 03/01/2023] [Indexed: 03/06/2023]
Abstract
Pathogenic biosafety is a worldwide concern. Tools for analyzing pathogenic biosafety, that are precise, rapid and field-deployable, are highly demanded. Recently developed biotechnological tools, especially those utilizing CRISPR/Cas systems which can couple with nanotechnologies, have enormous potential to achieve point-of-care (POC) testing for pathogen infection. In this review, we first introduce the working principle of class II CRISPR/Cas system for detecting nucleic acid and non-nucleic acid biomarkers, and highlight the molecular assays that leverage CRISPR technologies for POC detection. We summarize the application of CRISPR tools in detecting pathogens, including pathogenic bacteria, viruses, fungi and parasites and their variants, and highlight the profiling of pathogens' genotypes or phenotypes, such as the viability, and drug-resistance. In addition, we discuss the challenges and opportunities of CRISPR-based biosensors in pathogenic biosafety analysis.
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Affiliation(s)
- Hao Yang
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu, 610065, China
| | - Rodrigo Ledesma-Amaro
- Department of Bioengineering, Imperial College Centre for Synthetic Biology, Imperial College London, London, SW7 2AZ, UK
| | - Hong Gao
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu, 610065, China
| | - Yao Ren
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu, 610065, China.
| | - Ruijie Deng
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu, 610065, China.
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7
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Liu Y, Ma L, Liu W, Xie L, Wu Q, Wang Y, Zhou Y, Zhang Y, Jiao B, He Y. RPA-CRISPR/Cas12a Combined with Rolling Circle Amplification-Enriched DNAzyme: A Homogeneous Photothermal Sensing Strategy for Plant Pathogens. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:4736-4744. [PMID: 36893726 DOI: 10.1021/acs.jafc.2c07965] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Alternaria is an endemic fungus associated with brown spot disease, which is one of the most serious citrus diseases. In addition, the mycotoxins metabolized by Alternaria threaten human health seriously. Herein, a novel homogeneous and portable qualitative photothermal method based on recombinase polymerase amplification (RPA), CRISPR/Cas12a, and rolling circle amplification (RCA) for the detection of Alternaria is described. Using RCA primers as substrates for CRISPR/Cas12a trans-cleavage, the two systems, RPA-CRISPR/Cas12a and RCA-enriched G-quadruplex/hemin DNAzyme, are intelligently combined. Target DNA at fg/μL levels can be detected with high specificity. Additionally, the practicability of the proposed method is demonstrated by analyzing cultured Alternaria from different fruit and vegetable samples, as well as citrus fruit samples collected in the field. Furthermore, the implementation of this method does not require any sophisticated equipment and complicated washing steps. Therefore, it has great potential to screen Alternaria in poor laboratories.
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Affiliation(s)
- Yanlin Liu
- Key Laboratory of Quality and Safety Control of Citrus Fruits, Ministry of Agriculture and Rural Affairs, Southwest University, Chongqing 400712, P. R. China
- National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Chongqing 400712, P. R. China
| | - Lanrui Ma
- Key Laboratory of Quality and Safety Control of Citrus Fruits, Ministry of Agriculture and Rural Affairs, Southwest University, Chongqing 400712, P. R. China
- National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Chongqing 400712, P. R. China
| | - Wenjing Liu
- Institute of Agricultural Quality Standards and Testing Technology Research, Fujian Academy of Agricultural Sciences, Fujian Key Laboratory of Agro-products Qualitiy & Safety, Fuzhou 350003, P. R. China
| | - Longyingzi Xie
- Key Laboratory of Quality and Safety Control of Citrus Fruits, Ministry of Agriculture and Rural Affairs, Southwest University, Chongqing 400712, P. R. China
- National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Chongqing 400712, P. R. China
| | - Qi Wu
- Key Laboratory of Quality and Safety Control of Citrus Fruits, Ministry of Agriculture and Rural Affairs, Southwest University, Chongqing 400712, P. R. China
- National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Chongqing 400712, P. R. China
| | - Yiwen Wang
- Key Laboratory of Quality and Safety Control of Citrus Fruits, Ministry of Agriculture and Rural Affairs, Southwest University, Chongqing 400712, P. R. China
- National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Chongqing 400712, P. R. China
| | - Yan Zhou
- Key Laboratory of Quality and Safety Control of Citrus Fruits, Ministry of Agriculture and Rural Affairs, Southwest University, Chongqing 400712, P. R. China
- National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Chongqing 400712, P. R. China
| | - Yaohai Zhang
- Key Laboratory of Quality and Safety Control of Citrus Fruits, Ministry of Agriculture and Rural Affairs, Southwest University, Chongqing 400712, P. R. China
- National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Chongqing 400712, P. R. China
| | - Bining Jiao
- Key Laboratory of Quality and Safety Control of Citrus Fruits, Ministry of Agriculture and Rural Affairs, Southwest University, Chongqing 400712, P. R. China
- National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Chongqing 400712, P. R. China
| | - Yue He
- Key Laboratory of Quality and Safety Control of Citrus Fruits, Ministry of Agriculture and Rural Affairs, Southwest University, Chongqing 400712, P. R. China
- National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Chongqing 400712, P. R. China
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8
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Yang H, Zhang Y, Teng X, Hou H, Deng R, Li J. CRISPR-based nucleic acid diagnostics for pathogens. Trends Analyt Chem 2023; 160:116980. [PMID: 36818498 PMCID: PMC9922438 DOI: 10.1016/j.trac.2023.116980] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 12/28/2022] [Accepted: 02/09/2023] [Indexed: 02/17/2023]
Abstract
Pathogenic infection remains the primary threat to human health, such as the global COVID-19 pandemic. It is important to develop rapid, sensitive and multiplexed tools for detecting pathogens and their mutated variants, particularly the tailor-made strategies for point-of-care diagnosis allowing for use in resource-constrained settings. The rapidly evolving CRISPR/Cas systems have provided a powerful toolbox for pathogenic diagnostics via nucleic acid tests. In this review, we firstly describe the resultant promising class 2 (single, multidomain effector) and recently explored class 1 (multisubunit effector complexes) CRISPR tools. We present diverse engineering nucleic acid diagnostics based on CRISPR/Cas systems for pathogenic viruses, bacteria and fungi, and highlight the application for detecting viral variants and drug-resistant bacteria enabled by CRISPR-based mutation profiling. Finally, we discuss the challenges involved in on-site diagnostic assays and present emerging CRISPR systems and CRISPR cascade that potentially enable multiplexed and preamplification-free pathogenic diagnostics.
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Affiliation(s)
- Hao Yang
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu, Sichuan, 610065, China,Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084, China
| | - Yong Zhang
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu, Sichuan, 610065, China
| | - Xucong Teng
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084, China
| | - Hongwei Hou
- China National Tobacco Quality Supervision & Test Center, Zhengzhou, 450003, China,Beijing Institute of Life Science and Technology, Beijing, 102206, China
| | - Ruijie Deng
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu, Sichuan, 610065, China,Corresponding author
| | - Jinghong Li
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084, China,Corresponding author
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9
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Molecular Approaches for Detection of Trichoderma Green Mold Disease in Edible Mushroom Production. BIOLOGY 2023; 12:biology12020299. [PMID: 36829575 PMCID: PMC9953464 DOI: 10.3390/biology12020299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 02/03/2023] [Accepted: 02/05/2023] [Indexed: 02/16/2023]
Abstract
Due to the evident aggressive nature of green mold and the consequently huge economic damage it causes for producers of edible mushrooms, there is an urgent need for prevention and infection control measures, which should be based on the early detection of various Trichoderma spp. as green mold causative agents. The most promising current diagnostic tools are based on molecular methods, although additional optimization for real-time, in-field detection is still required. In the first part of this review, we briefly discuss cultivation-based methods and continue with the secondary metabolite-based methods. Furthermore, we present an overview of the commonly used molecular methods for Trichoderma species/strain detection. Additionally, we also comment on the potential of genomic approaches for green mold detection. In the last part, we discuss fast screening molecular methods for the early detection of Trichoderma infestation with the potential for in-field, point-of-need (PON) application, focusing on isothermal amplification methods. Finally, current challenges and future perspectives in Trichoderma diagnostics are summarized in the conclusions.
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10
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Lateral flow biosensor based on LAMP-CRISPR/Cas12a for sensitive and visualized detection of Salmonella spp. Food Control 2022. [DOI: 10.1016/j.foodcont.2022.109494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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11
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Botella JR. Point-of-Care DNA Amplification for Disease Diagnosis and Management. ANNUAL REVIEW OF PHYTOPATHOLOGY 2022; 60:1-20. [PMID: 36027938 DOI: 10.1146/annurev-phyto-021621-115027] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Early detection of pests and pathogens is of paramount importance in reducing agricultural losses. One approach to early detection is point-of-care (POC) diagnostics, which can provide early warning and therefore allow fast deployment of preventive measures to slow down the establishment of crop diseases. Among the available diagnostic technologies, nucleic acid amplification-based diagnostics provide the highest sensitivity and specificity, and those technologies that forego the requirement for thermocycling show the most potential for use at POC. In this review, I discuss the progress, advantages, and disadvantages of the established and most promising POC amplification technologies. The success and usefulness of POC amplification are ultimately dependent on the availability of POC-friendly nucleic acid extraction methods and amplification readouts, which are also briefly discussed in the review.
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Affiliation(s)
- José R Botella
- Plant Genetic Engineering Laboratory, School of Agriculture and Food Sciences, University of Queensland, Brisbane, Australia;
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12
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Marqués MC, Sánchez-Vicente J, Ruiz R, Montagud-Martínez R, Márquez-Costa R, Gómez G, Carbonell A, Daròs JA, Rodrigo G. Diagnostics of Infections Produced by the Plant Viruses TMV, TEV, and PVX with CRISPR-Cas12 and CRISPR-Cas13. ACS Synth Biol 2022; 11:2384-2393. [PMID: 35793201 PMCID: PMC9295153 DOI: 10.1021/acssynbio.2c00090] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Viral infections in plants threaten food security. Thus, simple and effective methods for virus detection are required to adopt early measures that can prevent virus spread. However, current methods based on the amplification of the viral genome by polymerase chain reaction (PCR) require laboratory conditions. Here, we exploited the CRISPR-Cas12a and CRISPR-Cas13a/d systems to detect three RNA viruses, namely, Tobacco mosaic virus, Tobacco etch virus, and Potato virus X, in Nicotiana benthamiana plants. We applied the CRISPR-Cas12a system to detect viral DNA amplicons generated by PCR or isothermal amplification, and we also performed a multiplexed detection in plants with mixed infections. In addition, we adapted the detection system to bypass the costly RNA purification step and to get a visible readout with lateral flow strips. Finally, we applied the CRISPR-Cas13a/d system to directly detect viral RNA, thereby avoiding the necessity of a preamplification step and obtaining a readout that scales with the viral load. These approaches allow for the performance of viral diagnostics within half an hour of leaf harvest and are hence potentially relevant for field-deployable applications.
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Affiliation(s)
- María-Carmen Marqués
- Institute
for Integrative Systems Biology (I2SysBio), CSIC—Universitat de València, Paterna 46980, Spain
| | - Javier Sánchez-Vicente
- Instituto
de Biología Molecular y Celular de Plantas, CSIC—Universitat Politècnica de València, València 46022, Spain
| | - Raúl Ruiz
- Institute
for Integrative Systems Biology (I2SysBio), CSIC—Universitat de València, Paterna 46980, Spain
| | - Roser Montagud-Martínez
- Institute
for Integrative Systems Biology (I2SysBio), CSIC—Universitat de València, Paterna 46980, Spain
| | - Rosa Márquez-Costa
- Institute
for Integrative Systems Biology (I2SysBio), CSIC—Universitat de València, Paterna 46980, Spain
| | - Gustavo Gómez
- Institute
for Integrative Systems Biology (I2SysBio), CSIC—Universitat de València, Paterna 46980, Spain
| | - Alberto Carbonell
- Instituto
de Biología Molecular y Celular de Plantas, CSIC—Universitat Politècnica de València, València 46022, Spain
| | - José-Antonio Daròs
- Instituto
de Biología Molecular y Celular de Plantas, CSIC—Universitat Politècnica de València, València 46022, Spain
| | - Guillermo Rodrigo
- Institute
for Integrative Systems Biology (I2SysBio), CSIC—Universitat de València, Paterna 46980, Spain
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13
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Li F, Xiao J, Yang H, Yao Y, Li J, Zheng H, Guo Q, Wang X, Chen Y, Guo Y, Wang Y, Shen C. Development of a Rapid and Efficient RPA-CRISPR/Cas12a Assay for Mycoplasma pneumoniae Detection. Front Microbiol 2022; 13:858806. [PMID: 35369478 PMCID: PMC8965353 DOI: 10.3389/fmicb.2022.858806] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 02/08/2022] [Indexed: 12/26/2022] Open
Abstract
Mycoplasma pneumoniae (MP) is a one of most common pathogen in causing respiratory infection in children and adolescents. Rapid and efficient diagnostic methods are crucial for control and treatment of MP infections. Herein, we present an operationally simple, rapid and efficient molecular method for MP identification, which eliminates expensive instruments and specialized personnel. The method combines recombinase polymerase amplification (RPA) with clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR associated proteins (Cas) 12a-based detection, with an optimal procedure less than 1 h from sample to result including DNA extraction (25 min), RPA reaction (39°C for 15-20 min), CRISPR/Cas12a detection (37°C for 10 min) and visual detection by naked eyes (2 min). This diagnostic method shows high sensitivity (two copies per reaction) and no cross-reactivity against other common pathogenic bacteria. Preliminary evaluation using 201 clinical samples shows sensitivity of 99.1% (107/108), specificity of 100% (93/93) and consistency of 99.5% (200/201), compared with real-time PCR method. The above data demonstrate that our developed method is reliable for rapid diagnosis of MP. In conclusion, the RPA-CRISPR/Cas12a has a great potential to be as a useful tool for reliable and quick diagnosis of MP infection, especially in primary hospitals with limited conditions.
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Affiliation(s)
- Feina Li
- Laboratory of Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Center for Children's Health, Beijing, China
| | - Jing Xiao
- Laboratory of Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Center for Children's Health, Beijing, China
| | - Haiming Yang
- Department of Respiratory Diseases II, Beijing Children's Hospital, National Clinical Research Center for Respiratory Diseases, National Center for Children's Health, Capital Medical University, Beijing, China
| | - Yao Yao
- Department of Respiratory Diseases I, Beijing Children's Hospital, National Clinical Research Center for Respiratory Diseases, National Center for Children's Health, Capital Medical University, Beijing, China
| | - Jieqiong Li
- Laboratory of Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Center for Children's Health, Beijing, China
| | - Huiwen Zheng
- Laboratory of Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Center for Children's Health, Beijing, China
| | - Qian Guo
- Laboratory of Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Center for Children's Health, Beijing, China
| | - Xiaotong Wang
- Laboratory of Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Center for Children's Health, Beijing, China
| | - Yuying Chen
- Laboratory of Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Center for Children's Health, Beijing, China
| | - Yajie Guo
- Laboratory of Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Center for Children's Health, Beijing, China
| | - Yonghong Wang
- Laboratory of Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Center for Children's Health, Beijing, China
| | - Chen Shen
- Laboratory of Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Center for Children's Health, Beijing, China
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