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Wu X, Chen S, Zhang Z, Zhang Y, Li P, Chen X, Liu M, Lu Q, Li Z, Wei Z, Xu P. Development of Recombinase Polymerase Amplification Combined with Lateral Flow Strips for Rapid Detection of Cowpea Mild Mottle Virus. THE PLANT PATHOLOGY JOURNAL 2023; 39:486-493. [PMID: 37817494 PMCID: PMC10580057 DOI: 10.5423/ppj.oa.02.2023.0033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 08/31/2023] [Accepted: 09/10/2023] [Indexed: 10/12/2023]
Abstract
Cowpea mild mottle virus (CPMMV) is a global plant virus that poses a threat to the production and quality of legume crops. Early and accurate diagnosis is essential for effective managing CPMMV outbreaks. With the advancement in isothermal recombinase polymerase amplification and lateral flow strips technologies, more rapid and sensitive methods have become available for detecting this pathogen. In this study, we have developed a reverse transcription recombinase polymerase amplification combined with lateral flow strips (RT-RPA-LFS) method for the detection of CPMMV, specifically targeting the CPMMV coat protein (CP) gene. The RT-RPA-LFS assay only requires 20 min at 40°C and demonstrates high specificity. Its detection limit was 10 copies/μl, which is approximately up to 100 times more sensitive than RT-PCR on agarose gel electrophoresis. The developed RT-RPA-LFS method offers a rapid, convenient, and sensitive approach for field detection of CPMMV, which contribute to controlling the spread of the virus.
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Affiliation(s)
- Xinyang Wu
- College of Life Sciences, China Jiliang University, Hangzhou 310018, China
- Key Laboratory of Specialty Agri-Product Quality and Hazard Controlling Technology of Zhejiang, Hangzhou 310018, China
| | - Shuting Chen
- College of Life Sciences, China Jiliang University, Hangzhou 310018, China
| | - Zixin Zhang
- College of Life Sciences, China Jiliang University, Hangzhou 310018, China
| | - Yihan Zhang
- College of Life Sciences, China Jiliang University, Hangzhou 310018, China
| | - Pingmei Li
- College of Life Sciences, China Jiliang University, Hangzhou 310018, China
| | - Xinyi Chen
- College of Life Sciences, China Jiliang University, Hangzhou 310018, China
| | - Miaomiao Liu
- College of Life Sciences, China Jiliang University, Hangzhou 310018, China
| | - Qian Lu
- College of Life Sciences, China Jiliang University, Hangzhou 310018, China
| | - Zhongyi Li
- College of Life Sciences, China Jiliang University, Hangzhou 310018, China
| | - Zhongyan Wei
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Pei Xu
- College of Life Sciences, China Jiliang University, Hangzhou 310018, China
- Key Laboratory of Specialty Agri-Product Quality and Hazard Controlling Technology of Zhejiang, Hangzhou 310018, China
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2
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Ni X, Lyu J, Wang Y, Li M, Qiao N, Jiang T, Sun X. Simultaneous detection of five viruses and two viroids affecting apples through a DNA macroarray chip. J Virol Methods 2023; 316:114730. [PMID: 37031744 DOI: 10.1016/j.jviromet.2023.114730] [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: 02/18/2023] [Revised: 03/29/2023] [Accepted: 04/06/2023] [Indexed: 04/11/2023]
Abstract
Multiple infections of various viruses and viroids in apple trees are common and have caused a significant loss in the world apple industry. To provide an early detection of any of those possible pathogens at the molecular level, a multiplex DNA macroarray chip was designed and developed for a simultaneous identification of five common apple viruses and two viroids including apple chlorotic leaf spot virus (ACLSV), apple stem pitting virus (ASPV), apple stem grooving virus (ASGV), apple mosaic virus (ApMV), apple necrosis mosaic virus (ApNMV), apple scar skin viroid (ASSVd), and apple dimple fruit viroid (ADFVd). The macroarray with a 23bp probe arranged with the coat protein (CP) gene or a target DNA segment of each viruses and viroids has demonstrated a high specificity and sensitivity without any competitions, inhibitions or cross-interferences when it was tested against more than a mixture of viral and viroid samples. To our best knowledge, this is the first report on the simultaneous detection of five different apple viruses and two viroids through using a DNA macroarray, therefore, we suggest that this detection protocol and procedure be used for any apple viral diagnosis before setting up a production nursery for virus-free apple seedlings.
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Affiliation(s)
- Xiumei Ni
- Shandong Facility Horticulture Bioengineering Research Center, Weifang University of Science and Technology, Shandong, 262700, China
| | - Jinfu Lyu
- Shandong Facility Horticulture Bioengineering Research Center, Weifang University of Science and Technology, Shandong, 262700, China
| | - Yanjuan Wang
- Shandong Dafengyuan Agriculture Co., Ltd., Shandong, 262305, China
| | - Meiqin Li
- Shandong Facility Horticulture Bioengineering Research Center, Weifang University of Science and Technology, Shandong, 262700, China
| | - Ning Qiao
- Shandong Facility Horticulture Bioengineering Research Center, Weifang University of Science and Technology, Shandong, 262700, China
| | - Tao Jiang
- Shandong Facility Horticulture Bioengineering Research Center, Weifang University of Science and Technology, Shandong, 262700, China
| | - Xiaoan Sun
- Shandong Facility Horticulture Bioengineering Research Center, Weifang University of Science and Technology, Shandong, 262700, China; Division of Plant Industry, Florida Department of Agriculture and Consumer Services (Retired), 1911 SW 34th Street, Gainesville, FL 32608, USA
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3
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Wang J, Davidson JL, Kaur S, Dextre AA, Ranjbaran M, Kamel MS, Athalye SM, Verma MS. Paper-Based Biosensors for the Detection of Nucleic Acids from Pathogens. BIOSENSORS 2022; 12:bios12121094. [PMID: 36551061 PMCID: PMC9776365 DOI: 10.3390/bios12121094] [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] [Received: 09/21/2022] [Revised: 11/14/2022] [Accepted: 11/18/2022] [Indexed: 05/17/2023]
Abstract
Paper-based biosensors are microfluidic analytical devices used for the detection of biochemical substances. The unique properties of paper-based biosensors, including low cost, portability, disposability, and ease of use, make them an excellent tool for point-of-care testing. Among all analyte detection methods, nucleic acid-based pathogen detection offers versatility due to the ease of nucleic acid synthesis. In a point-of-care testing context, the combination of nucleic acid detection and a paper-based platform allows for accurate detection. This review offers an overview of contemporary paper-based biosensors for detecting nucleic acids from pathogens. The methods and limitations of implementing an integrated portable paper-based platform are discussed. The review concludes with potential directions for future research in the development of paper-based biosensors.
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Affiliation(s)
- Jiangshan Wang
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN 47907, USA
- Birck Nanotechnology Center, Purdue University, West Lafayette, IN 47907, USA
| | - Josiah Levi Davidson
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN 47907, USA
- Birck Nanotechnology Center, Purdue University, West Lafayette, IN 47907, USA
| | - Simerdeep Kaur
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN 47907, USA
- Birck Nanotechnology Center, Purdue University, West Lafayette, IN 47907, USA
| | - Andres A. Dextre
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN 47907, USA
- Birck Nanotechnology Center, Purdue University, West Lafayette, IN 47907, USA
| | - Mohsen Ranjbaran
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN 47907, USA
- Birck Nanotechnology Center, Purdue University, West Lafayette, IN 47907, USA
| | - Mohamed S. Kamel
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN 47907, USA
- Birck Nanotechnology Center, Purdue University, West Lafayette, IN 47907, USA
- Department of Medicine and Infectious Diseases, Faculty of Veterinary Medicine, Cairo University, Giza 12211, Egypt
| | - Shreya Milind Athalye
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN 47907, USA
- Birck Nanotechnology Center, Purdue University, West Lafayette, IN 47907, USA
| | - Mohit S. Verma
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN 47907, USA
- Birck Nanotechnology Center, Purdue University, West Lafayette, IN 47907, USA
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN 47907, USA
- Correspondence:
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Rapid, Sensitive and Simultaneous Detection of Two Wheat RNA Viruses Using Reverse Transcription Recombinase Polymerase Amplification (RT-RPA). LIFE (BASEL, SWITZERLAND) 2022; 12:life12121952. [PMID: 36556317 PMCID: PMC9788578 DOI: 10.3390/life12121952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/09/2022] [Accepted: 11/19/2022] [Indexed: 11/23/2022]
Abstract
In China, wheat yellow mosaic disease is mostly caused by wheat yellow mosaic virus (WYMV) and Chinese wheat mosaic virus (CWMV). If wheat is co-infected with these two viruses, it can cause severe yellow mosaic symptoms and yield losses. Early detection of viruses is crucial for preventing disease in the field. In this study, we optimized a sensitive, specific reverse transcription recombinase polymerase amplification (RT-RPA) detection method for two viruses, WYMV and CWMV. Two sets of primers were designed based on the capsid protein (CP)-encoding genes of the two viruses, and the reaction conditions were determined. The RT-RPA method, which amplified the target amplicon by a handheld reaction mixture for 20 min, was more sensitive than PCR-CP in the detection of WYMV. Finally, the RT-RPA method was performed on 110 randomly selected field samples, demonstrating its applicability to samples from different regions and specificity for co-infected samples. This study not only describes an improved method for detecting WYMV and CWMV using RT-RPA but also demonstrates the potential of this method, which could be applied under field conditions.
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Bhat AI, Aman R, Mahfouz M. Onsite detection of plant viruses using isothermal amplification assays. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:1859-1873. [PMID: 35689490 PMCID: PMC9491455 DOI: 10.1111/pbi.13871] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 05/16/2022] [Accepted: 06/02/2022] [Indexed: 05/09/2023]
Abstract
Plant diseases caused by viruses limit crop production and quality, resulting in significant losses. However, options for managing viruses are limited; for example, as systemic obligate parasites, they cannot be killed by chemicals. Sensitive, robust, affordable diagnostic assays are needed to detect the presence of viruses in plant materials such as seeds, vegetative parts, insect vectors, or alternative hosts and then prevent or limit their introduction into the field by destroying infected plant materials or controlling insect hosts. Diagnostics based on biological and physical properties are not very sensitive and are time-consuming, but assays based on viral proteins and nucleic acids are more specific, sensitive, and rapid. However, most such assays require laboratories with sophisticated equipment and technical skills. By contrast, isothermal-based assays such as loop-mediated isothermal amplification (LAMP) and recombinase polymerase amplification (RPA) are simple, easy to perform, reliable, specific, and rapid and do not require specialized equipment or skills. Isothermal amplification assays can be performed using lateral flow devices, making them suitable for onsite detection or testing in the field. To overcome non-specific amplification and cross-contamination issues, isothermal amplification assays can be coupled with CRISPR/Cas technology. Indeed, the collateral activity associated with some CRISPR/Cas systems has been successfully harnessed for visual detection of plant viruses. Here, we briefly describe traditional methods for detecting viruses and then examine the various isothermal assays that are being harnessed to detect viruses.
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Affiliation(s)
- Alangar I. Bhat
- ICAR‐Indian Institute of Spices ResearchKozhikodeKeralaIndia
| | - Rashid Aman
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological SciencesKing Abdullah University of Science and TechnologyThuwalSaudi Arabia
| | - Magdy Mahfouz
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological SciencesKing Abdullah University of Science and TechnologyThuwalSaudi Arabia
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Tarazi R, Vaslin MFS. The Viral Threat in Cotton: How New and Emerging Technologies Accelerate Virus Identification and Virus Resistance Breeding. FRONTIERS IN PLANT SCIENCE 2022; 13:851939. [PMID: 35449884 PMCID: PMC9016188 DOI: 10.3389/fpls.2022.851939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 03/07/2022] [Indexed: 05/12/2023]
Abstract
Cotton (Gossypium spp. L., Malvaceae) is the world's largest source of natural fibers. Virus outbreaks are fast and economically devasting regarding cotton. Identifying new viruses is challenging as virus symptoms usually mimic nutrient deficiency, insect damage, and auxin herbicide injury. Traditional viral identification methods are costly and time-consuming. Developing new resistant cotton lines to face viral threats has been slow until the recent use of molecular virology, genomics, new breeding techniques (NBT), remote sensing, and artificial intelligence (AI). This perspective article demonstrates rapid, sensitive, and cheap technologies to identify viral diseases and propose their use for virus resistance breeding.
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Affiliation(s)
- Roberto Tarazi
- Plant Molecular Virology Laboratory, Department of Virology, Microbiology Institute, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
- Programa de Pós-graduação em Biotecnologia e Bioprocessos da UFRJ, Rio de Janeiro, Brazil
| | - Maite F. S. Vaslin
- Plant Molecular Virology Laboratory, Department of Virology, Microbiology Institute, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
- Programa de Pós-graduação em Biotecnologia e Bioprocessos da UFRJ, Rio de Janeiro, Brazil
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Kim NY, Lee HJ, Kim HS, Lee SH, Moon JS, Jeong RD. Identification of Plant Viruses Infecting Pear Using RNA Sequencing. THE PLANT PATHOLOGY JOURNAL 2021; 37:258-267. [PMID: 34111915 PMCID: PMC8200581 DOI: 10.5423/ppj.oa.01.2021.0009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 03/30/2021] [Accepted: 04/23/2021] [Indexed: 06/12/2023]
Abstract
Asian pear (Pyrus pyrifolia) is a widely cultivated and commercially important fruit crop, which is occasionally subject to severe economic losses due to latent viral infections. Thus, the aim of the present study was to examine and provide a comprehensive overview of virus populations infecting a major pear cultivar ('Singo') in Korea. From June 2017 to October 2019, leaf samples (n = 110) of pear trees from 35 orchards in five major pear-producing regions were collected and subjected to RNA sequencing. Most virus-associated contigs matched the sequences of known viruses, including apple stem grooving virus (ASGV) and apple stem pitting virus (ASPV). However, some contigs matched the sequences of apple green crinkle-associated virus and cucumber mosaic virus. In addition, three complete or nearly complete genomes were constructed based on transcriptome data and subjected to phylogenetic analyses. Based on the number of virus-associated reads, ASGV and ASPV were identified as the dominant viruses of 'Singo.' The present study describes the virome of a major pear cultivar in Korea, and looks into the diversity of viral communities in this cultivar. This study can provide valuable information on the complexity of genetic variability of viruses infecting pear trees.
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Affiliation(s)
- Nam-Yeon Kim
- Department of Applied Biology, Institute of Environmentally Friendly Agriculture, Chonnam National University, Gwangju 61185, Korea
| | - Hyo-Jeong Lee
- Department of Applied Biology, Institute of Environmentally Friendly Agriculture, Chonnam National University, Gwangju 61185, Korea
| | - Hong-Sup Kim
- Seed Testing & Research Center, Korea Seed & Variety Service, Gimcheon 39660, Korea
| | - Su-Heon Lee
- School of Applied Biosciences, Kyungpook National University, Daegu 98411, Korea
| | - Jae-Sun Moon
- Plant Genome Research Center, Korea Research Institute of Biosciences & Biotechnology, Daejeon 34141, Korea
| | - Rae-Dong Jeong
- Department of Applied Biology, Institute of Environmentally Friendly Agriculture, Chonnam National University, Gwangju 61185, Korea
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8
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Lee HJ, Cho IS, Ju HJ, Jeong RD. Rapid and visual detection of tomato spotted wilt virus using recombinase polymerase amplification combined with lateral flow strips. Mol Cell Probes 2021; 57:101727. [PMID: 33789127 DOI: 10.1016/j.mcp.2021.101727] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 03/09/2021] [Accepted: 03/24/2021] [Indexed: 01/18/2023]
Abstract
Tomato spotted wilt virus (TSWV) is economically important in Korea as it causes significant losses to a wide range of important ornamental and vegetable crops. Therefore, a rapid detection method is imperative for TSWV diagnosis. Specific primers and probes were designed based on the conserved sequences of the TSWV coat protein gene. In this study, an isothermal reverse transcription recombinase polymerase amplification (RT-RPA) assay, combined with lateral flow strips (LFS), was established for rapid detection of TSWV in pepper infected leaves. The RT-RPA reaction was performed at an optimal condition of 38 °C for 10 min and an LFS incubation time of approximately 5 min. There was no cross-reactivity with other viruses infecting pepper such as cucumber mosaic virus, pepper mottle virus, pepper mild mottle virus, and broad bean wilt virus 2, thus confirming the specificity of RT-RPA-LFS. The sensitivity of the RT-RPA assay was similar to that of RT-PCR, and RT-RPA-LFS was successfully applied to detect TSWV in the pepper samples collected from the field. Thus, RT-RPA-LFS assay might be a promising candidate for quick diagnosis of TSWV-infected pepper plants.
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Affiliation(s)
- Hyo-Jeong Lee
- Department of Applied Biology, Institute of Environmentally Friendly Agriculture, Chonnam National University, Gwangju, 61185, South Korea
| | - In-Sook Cho
- Horticultural and Herbal Crop Environment Division, National Institute of Horticultural and Herbal Science, RDA, Wanju, 55365, South Korea
| | - Ho-Jong Ju
- Department of Agricultural Biology, College of Agriculture & Life Sciences, Jeonbuk National University, Jeonju-si, 54896, South Korea
| | - Rae-Dong Jeong
- Department of Applied Biology, Institute of Environmentally Friendly Agriculture, Chonnam National University, Gwangju, 61185, South Korea.
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Wang W, Zhang Y, Huang Y, Chen G, Shi M, Qiao Y, Huang T, Wei T, Mo M, He X, Wei P. Rapid and visual detection of the emerging novel duck reovirus by using a specific and sensitive reverse transcription recombinase polymerase amplification method. J Virol Methods 2021; 291:114098. [PMID: 33621643 DOI: 10.1016/j.jviromet.2021.114098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 02/08/2021] [Accepted: 02/08/2021] [Indexed: 10/22/2022]
Abstract
Duck spleen necrosis disease (DSND) caused by Novel Duck Reovirus (NDRV), is an emerging infectious disease that causes severely threaten to duck industry. Currently, the popular conventional RT-PCR technique for detecting NDRV is time consuming. So, it is essential to develop a rapid and accurate molecular diagnosis techniques of the pathogen for the purpose to effective control of the disease. In our study, a simple, rapid and reliable detection method was developed by an isothermal reverse transcription-recombinase polymerase amplification (RT-RPA). The RT-RPA primers were designed targeting the S3 gene of NDRV, and its specificity was verified by testing a series of other waterfowl pathogens. A total of 20 field and experimental samples from infected ducklings were tested by the RT-RPA and compared with the results of the conventional RT-PCR and the quantitative RT-PCR simultaneously. The RT-RPA method could detect as little as 4.14 × 102 copies/μl of the target gene in the sensitivity analysis, which was 10×higher sensitive than the conventional RT-PCR. The major advantage of the RT-RPA method is that it could be performed as an isothermal reaction at 37 ℃ and completed within 20 min. In addition, no cross-reactivity was detected with other waterfowl-origin viruses. Also, the amplified products could be visualized faster, without the gel electrophoresis, by adding the SYBR Green I and observing them under an ultraviolet light. The newly developed RT-RPA method offers a simple, rapid and accurate for rapid detection of NDRV, which especially useful in on-site facilities and resource-limited areas.
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Affiliation(s)
- Weiwei Wang
- Institute for Poultry Science and Health, Guangxi University, Nanning, Guangxi, 530005, China
| | - Yan Zhang
- Institute for Poultry Science and Health, Guangxi University, Nanning, Guangxi, 530005, China
| | - Yu Huang
- Institute for Poultry Science and Health, Guangxi University, Nanning, Guangxi, 530005, China
| | - Guo Chen
- Institute for Poultry Science and Health, Guangxi University, Nanning, Guangxi, 530005, China
| | - Mengya Shi
- Institute for Poultry Science and Health, Guangxi University, Nanning, Guangxi, 530005, China
| | - Yuanzheng Qiao
- Institute for Poultry Science and Health, Guangxi University, Nanning, Guangxi, 530005, China
| | - Teng Huang
- Institute for Poultry Science and Health, Guangxi University, Nanning, Guangxi, 530005, China
| | - Tianchao Wei
- Institute for Poultry Science and Health, Guangxi University, Nanning, Guangxi, 530005, China
| | - Meilan Mo
- Institute for Poultry Science and Health, Guangxi University, Nanning, Guangxi, 530005, China
| | - Xiumiao He
- School of Marine Sciences and Biotechnology, Guangxi Key Laboratory Cultivation Base for Polysaccharide Materials and Modifications, Guangxi University for Nationalities, Nanning, Guangxi, 530006, China.
| | - Ping Wei
- Institute for Poultry Science and Health, Guangxi University, Nanning, Guangxi, 530005, China.
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Jiao J, Kong K, Han J, Song S, Bai T, Song C, Wang M, Yan Z, Zhang H, Zhang R, Feng J, Zheng X. Field detection of multiple RNA viruses/viroids in apple using a CRISPR/Cas12a-based visual assay. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:394-405. [PMID: 32886837 PMCID: PMC7868969 DOI: 10.1111/pbi.13474] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 08/20/2020] [Indexed: 05/18/2023]
Abstract
Co-infection of apple trees with several viruses/viroids is common and decreases fruit yield and quality. Accurate and rapid detection of these viral pathogens helps to reduce losses and prevent virus spread. Current molecular detection assays used for apple viruses require specialized and expensive equipment. Here, we optimized a CRISPR/Cas12a-based nucleic acid detection platform for the diagnosis of the most prevalent RNA viruses/viroid in apple, namely Apple necrotic mosaic virus (ApNMV), Apple stem pitting virus (ASPV), Apple stem grooving virus (ASGV), Apple chlorotic leaf spot virus (ACLSV) and Apple scar skin viroid (ASSVd). We detected each RNA virus/viroid directly from crude leaf extracts after simultaneous multiplex reverse transcription-recombinase polymerase amplification (RT-RPA) with high specificity. Positive results can be distinguished by the naked eye via oligonucleotide-conjugated gold nanoparticles. The CRISPR/Cas12a-RT-RPA platform exhibited comparable sensitivity to RT-qPCR, with limits of detection reaching 250 viral copies per reaction for ASPV and ASGV and 2500 copies for the others. However, this protocol was faster and simpler, requiring an hour or less from leaf harvest. Field tests showed 100% agreement with RT-PCR detection for 52 samples. This novel Cas12a-based method is ideal for rapid and reliable detection of apple viruses in the orchard without the need to send samples to a specialized laboratory.
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Affiliation(s)
- Jian Jiao
- College of HorticultureHenan Agricultural UniversityZhengzhouChina
| | - Kangkang Kong
- College of HorticultureHenan Agricultural UniversityZhengzhouChina
| | - Jinmeng Han
- College of HorticultureHenan Agricultural UniversityZhengzhouChina
| | - Shangwei Song
- College of HorticultureHenan Agricultural UniversityZhengzhouChina
| | - Tuanhui Bai
- College of HorticultureHenan Agricultural UniversityZhengzhouChina
| | - Chunhui Song
- College of HorticultureHenan Agricultural UniversityZhengzhouChina
| | - Miaomiao Wang
- College of HorticultureHenan Agricultural UniversityZhengzhouChina
| | - Zhenli Yan
- Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouHenanChina
| | - Hengtao Zhang
- Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouHenanChina
| | - Ruiping Zhang
- Zhengzhou Fruit Research InstituteChinese Academy of Agricultural SciencesZhengzhouHenanChina
| | - Jiancan Feng
- College of HorticultureHenan Agricultural UniversityZhengzhouChina
| | - Xianbo Zheng
- College of HorticultureHenan Agricultural UniversityZhengzhouChina
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Lu X, Xu H, Song W, Yang Z, Yu J, Tian Y, Jiang M, Shen D, Dou D. Rapid and simple detection of Phytophthora cactorum in strawberry using a coupled recombinase polymerase amplification-lateral flow strip assay. PHYTOPATHOLOGY RESEARCH 2021; 3:12. [PMID: 34127941 PMCID: PMC8189726 DOI: 10.1186/s42483-021-00089-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 05/27/2021] [Indexed: 05/22/2023]
Abstract
UNLABELLED Phytophthora cactorum is a devastating pathogen that infects a wide range of plants and causes Phytophthora rot disease, which has resulted in great economic losses in crop production. Therefore, the rapid and practicable detection of P. cactorum is important for disease monitoring and forecasting. In this study, we developed a lateral flow recombinase polymerase amplification (LF-RPA) assay for the sensitive visual detection of P. cactorum. Specific primers for P. cactorum were designed based on the ras-related protein gene Ypt1; all 10 P. cactorum isolates yielded positive detection results, whereas no cross-reaction occurred in related oomycete or fungal species. The detection limit for the LF-RPA assay was 100 fg of genomic DNA under optimized conditions. Combined with a simplified alkaline lysis method for plant DNA extraction, the LF-RPA assay successfully detected P. cactorum in naturally diseased strawberry samples without specialized equipment within 40 min. Thus, the LF-RPA assay developed in this study is a rapid, simple, and accurate method for the detection of P. cactorum, with the potential for further application in resource-limited laboratories. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1186/s42483-021-00089-8.
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Affiliation(s)
- Xinyu Lu
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095 China
| | - Heng Xu
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095 China
| | - Wen Song
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095 China
| | - Zitong Yang
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095 China
| | - Jia Yu
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095 China
| | - Yuee Tian
- Department of Plant Protection, Henan University of Science and Technology, Luoyang, 471000 China
| | - Min Jiang
- Pingyi County Forestry Development Center, Linyi, 273300 China
| | - Danyu Shen
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095 China
| | - Daolong Dou
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095 China
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Srivastava S, Upadhyay DJ, Srivastava A. Next-Generation Molecular Diagnostics Development by CRISPR/Cas Tool: Rapid Detection and Surveillance of Viral Disease Outbreaks. Front Mol Biosci 2020; 7:582499. [PMID: 33425987 PMCID: PMC7785713 DOI: 10.3389/fmolb.2020.582499] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Accepted: 11/04/2020] [Indexed: 12/26/2022] Open
Abstract
Virus disease spreads effortlessly mechanically or through minute insect vectors that are extremely challenging to avoid. Emergence and reemergence of new viruses such as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), H1N1 influenza virus, avian influenza virus, dengue virus, Citrus tristeza virus, and Tomato yellow leaf curl virus have paralyzed the economy of many countries. The cure for major viral diseases is not feasible; however, early detection and surveillance of the disease can obstruct their spread. Therefore, advances in the field of virus diagnosis and the development of new point-of-care testing kits become necessary globally. Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) is an emerging technology for gene editing and diagnostics development. Several rapid nucleic acid diagnostic kits have been developed and validated using Cas9, Cas12, and Cas13 proteins. This review summarizes the CRISPR/Cas-based next-generation molecular diagnostic techniques and portability of devices for field-based utilization.
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Affiliation(s)
- Sonal Srivastava
- Amity Institute of Virology and Immunology, Amity University Uttar Pradesh, Noida, India
| | | | - Ashish Srivastava
- Amity Institute of Virology and Immunology, Amity University Uttar Pradesh, Noida, India
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Zou Y, Mason MG, Botella JR. Evaluation and improvement of isothermal amplification methods for point-of-need plant disease diagnostics. PLoS One 2020; 15:e0235216. [PMID: 32598374 PMCID: PMC7323990 DOI: 10.1371/journal.pone.0235216] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Accepted: 06/10/2020] [Indexed: 01/01/2023] Open
Abstract
A number of isothermal DNA amplification technologies claim to be ideal for point-of-need (PON) applications as they enable reactions to be performed using a single-temperature heat source (e.g. water bath). Thus, we examined several isothermal amplification methods focusing on simplicity, cost, sensitivity and reproducibility to identify the most suitable method(s) for low resource PON applications. A number of methods were found unsuitable as they either involved multiple temperature incubations, were relatively expensive or required relatively large amounts target DNA for amplification. Among the methods examined, loop-mediated isothermal amplification (LAMP) and recombinase polymerase amplification (RPA) were found to be the most suitable for PON applications as they are both single step methods that provide highly sensitive and reproducible amplifications. The speed of LAMP reactions was greatly enhanced, up to 76%, with the addition of loop primers while the presence of swarm primers and the sequestration of free magnesium ions with nucleotides also enhanced the amplification speed. In contrast, we were unable to enhance RPA's performance from the original published literature. While both RPA and LAMP have some drawbacks, either isothermal technology can reliably be used for on-site diagnostics with minimal equipment.
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Affiliation(s)
- Yiping Zou
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Michael Glenn Mason
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Jose Ramon Botella
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD, Australia
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Cong F, Zeng F, Wu M, Wang J, Huang B, Wang Y, Wang Q, Zhang S, Ma L, Guo P, Zeng W. Development of a real-time reverse transcription recombinase polymerase amplification assay for rapid detection of spring viremia of carp virus. Mol Cell Probes 2019; 50:101494. [PMID: 31863825 DOI: 10.1016/j.mcp.2019.101494] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 12/09/2019] [Accepted: 12/10/2019] [Indexed: 11/26/2022]
Abstract
Spring viremia of carp virus (SVCV) is a significant pathogenic agent that can cause large-scale outbreaks of spring viremia of carp (SVC) in many types of fish and bring huge economic losses to the aquaculture industry. A simple and convenient detection method is imperative for SVCV diagnosis. In this study, the real-time reverse transcription recombinase polymerase amplification (RT-RPA) assay was developed and validated. Primers and probe targeting the conserved region of M gene were designed and applied to the real-time RT-RPA assay that performed at 39 °C for 20 min. The specificity analysis showed that no cross-reaction with other pathogenic viruses of fish was found, indicating appropriate specificity of the assay. In vitro transcribed RNA standards were used to estimate the sensitivity of the assay and the detection limit was 102copies/reaction. To further evaluate the assay, 65 clinical samples were tested using both real-time RT-RPA assay and real-time RT-PCR method. The same detection results were observed, suggesting the potential application of real-time RT-RPA assay in clinical sample detection. This is the first report on RPA assay for SVCV detection and this new developed assay would be useful in both laboratory and in the field for diagnosis of SVCV.
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Affiliation(s)
- Feng Cong
- Guangdong Laboratory Animals Monitoring Institute and Guangdong Provincial Key Laboratory of Laboratory Animals, Guangzhou, 510633, China.
| | - Fanwen Zeng
- Guangdong Laboratory Animals Monitoring Institute and Guangdong Provincial Key Laboratory of Laboratory Animals, Guangzhou, 510633, China; College of Animal Science, South China Agricultural University, Guangzhou, 510640, China.
| | - Miaoli Wu
- Guangdong Laboratory Animals Monitoring Institute and Guangdong Provincial Key Laboratory of Laboratory Animals, Guangzhou, 510633, China.
| | - Jingjing Wang
- Jiangsu Center for Control and Prevention of Aquatic Animal Infectious Diseases, Nanjing, 210000, China.
| | - Bihong Huang
- Guangdong Laboratory Animals Monitoring Institute and Guangdong Provincial Key Laboratory of Laboratory Animals, Guangzhou, 510633, China.
| | - Yingying Wang
- Key Laboratory of Fishery Drug Development, Ministry of Agriculture, Key Laboratory of Aquatic Animal Immune Technology, Guangdong Province, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510380, China.
| | - Qing Wang
- Key Laboratory of Fishery Drug Development, Ministry of Agriculture, Key Laboratory of Aquatic Animal Immune Technology, Guangdong Province, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510380, China.
| | - Shouquan Zhang
- College of Animal Science, South China Agricultural University, Guangzhou, 510640, China.
| | - Lei Ma
- Guangdong Laboratory Animals Monitoring Institute and Guangdong Provincial Key Laboratory of Laboratory Animals, Guangzhou, 510633, China.
| | - Pengju Guo
- Guangdong Laboratory Animals Monitoring Institute and Guangdong Provincial Key Laboratory of Laboratory Animals, Guangzhou, 510633, China.
| | - Weiwei Zeng
- Key Laboratory of Fishery Drug Development, Ministry of Agriculture, Key Laboratory of Aquatic Animal Immune Technology, Guangdong Province, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510380, China.
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