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Novi VT, Aboubakr HA, Moore MJ, Zarouri A, Juzwik J, Abbas A. A rapid LAMP assay for the diagnosis of oak wilt with the naked eye. PLANT METHODS 2024; 20:119. [PMID: 39103934 DOI: 10.1186/s13007-024-01254-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Accepted: 07/31/2024] [Indexed: 08/07/2024]
Abstract
BACKGROUND Oak wilt disease, caused by Bretziella fagacearum is a significant threat to oak (Quercus spp.) tree health in the United States and Eastern Canada. The disease may cause dramatic damage to natural and urban ecosystems without management. Early and accurate diagnosis followed by timely treatment increases the level of disease control success. RESULTS A rapid assay based on loop mediated isothermal amplification (LAMP) was first developed with fluorescence detection of B. fagacearum after 30-minute reaction time. Six different primers were designed to specifically bind and amplify the pathogen's DNA. To simplify the use of this assay in the field, gold nanoparticles (AuNPs) were designed to bind to the DNA amplicon obtained from the LAMP reaction. Upon inducing precipitation, the AuNP-amplicons settle as a red pellet visible to the naked eye, indicative of pathogen presence. Both infected and healthy red oak samples were tested using this visualization method. The assay was found to have high diagnostic sensitivity and specificity for the B. fagacearum isolate studied. Moreover, the developed assay was able to detect the pathogen in crude DNA extracts of diseased oak wood samples, which further reduced the time required to process samples. CONCLUSIONS In summary, the LAMP assay coupled with oligonucleotide-conjugated gold nanoparticle visualization is a promising method for accurate and rapid molecular-based diagnosis of B. fagacearum in field settings. The new method can be adapted to other forest and plant diseases by simply designing new primers.
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Affiliation(s)
- Vinni Thekkudan Novi
- Department of Bioproducts and Biosystems Engineering, University of Minnesota, 55108, St. Paul, MN, U.S.A
| | - Hamada A Aboubakr
- Department of Bioproducts and Biosystems Engineering, University of Minnesota, 55108, St. Paul, MN, U.S.A
| | - Melanie J Moore
- USDA Forest Service, Northern Research Station, 55108, St. Paul, MN, U.S.A
| | - Akli Zarouri
- Department of Bioproducts and Biosystems Engineering, University of Minnesota, 55108, St. Paul, MN, U.S.A
| | - Jennifer Juzwik
- USDA Forest Service, Northern Research Station, 55108, St. Paul, MN, U.S.A
| | - Abdennour Abbas
- Department of Bioproducts and Biosystems Engineering, University of Minnesota, 55108, St. Paul, MN, U.S.A..
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Huang T, Han Y, Chen Y, Diao Z, Ma Y, Feng L, Wang D, Zhang R, Li J. RLP system: A single-tube two-step approach with dual amplification cascades for rapid identification of EGFR T790M. Anal Chim Acta 2024; 1287:342126. [PMID: 38182396 DOI: 10.1016/j.aca.2023.342126] [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] [Received: 09/29/2023] [Revised: 12/03/2023] [Accepted: 12/07/2023] [Indexed: 01/07/2024]
Abstract
BACKGROUND The detection of cancer gene mutations in biofluids plays a pivotal role in revolutionizing disease diagnosis. The presence of a large background of wild-type sequences poses a challenge to liquid biopsy of tumor mutation genes. Suppressing the detection of wild-type sequences can reduce their interference, however, due to the minimal difference between mutant and wild-type sequences (such as single nucleotide variants differing by only one nucleotide), how to suppress the detection of wild-type sequences to the greatest extent without compromising the sensitivity of mutant sequence detection remains to be explored. SIGNIFICANCE The RLP system addresses the incompatibility between RPA and RT-PCR reactions through a physical separation strategy. Besides, due to the remarkable flexibility of locked nucleic acid probes, the RLP system emerges as a potent tool for detecting mutations across diverse genes. It excels in sensitivity and speed, tolerates plasma matrix, and is cost-effective. This bodes well for advancing the field of precision medicine. RESULTS The recombinase-assisted locked nucleic acid (LNA) probe-mediated dual amplification biosensing platform (namely RLP), which combines recombinase polymerase amplification (RPA) and LNA clamp PCR method in one tube, enabling highly sensitive and selective detection of EGFR T790M mutation under the help of well-designed LNA probes. This technique can quantify DNA targets with a limit of detection (LoD) at the single copy level and identify point mutation with mutant allelic fractions as low as 0.007 % in 45 min. Moreover, RLP has the potential for the direct detection of plasma samples without the need for nucleic acid extraction and the cost of a single test is less than 1USD. Furthermore, the RLP system is a cascading dual amplification reaction conducted in a single tube, which eliminates the risk of cross-contamination associated with opening multiple tubes and ensures the reliability of the results.
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Affiliation(s)
- Tao Huang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, China; National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China
| | - Yanxi Han
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, China; National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China
| | - Yuqing Chen
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, China; National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China
| | - Zhenli Diao
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, China; National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China
| | - Yu Ma
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, China; National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China
| | - Lei Feng
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, China; National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China
| | - Duo Wang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, China; National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China
| | - Rui Zhang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, China; National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China.
| | - Jinming Li
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, China; National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China.
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3
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Swett CL, Del Castillo Múnera J, Hellman E, Helpio E, Gastelum M, Lopez Raymundo E, Johnson H, Oguchi R, Hopkins A, Beaulieu J, Rodriguez F. Monitoring for a new I3 resistance gene-breaking race of F. oxysporum f. sp. lycopersici (Fusarium wilt) in California processing tomatoes following recent widespread adoption of resistant (F3) cultivars: Challenges with race 3 and 4 differentiation methods. FRONTIERS IN PLANT SCIENCE 2023; 14:1088044. [PMID: 37063207 PMCID: PMC10102640 DOI: 10.3389/fpls.2023.1088044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 02/27/2023] [Indexed: 06/19/2023]
Abstract
Fusarium wilt, caused by Fusarium oxysporum f. sp. lycopersici (Fol), causes losses in tomato production worldwide, with major impacts on Californian tomato processing. Single-gene resistance is the primary management tool, but its efficacy has been compromised following the emergence of two successive resistance-breaking races, which, in California, emerged within 12 years of resistance deployment. Fol race 3-resistant (F3) processing tomato cultivars (containing the I3 resistance gene) were deployed in the state starting in approximately 2009. The emergence of a new resistance-breaking race (which would be called race 4) is imminent, and early detection will be critical to delay the spread while new resistance is sought. The detection of Fol race 4 is challenged by the lack of validated, rapid, and accurate diagnostic tools. In evaluating in planta phenotyping methods, this study found that rapid seedling phenotyping is not reliable and generates false positives for nonpathogens. Longer (10 weeks) mature plant assays are the most reliable, but may not be sufficiently timely. As an additional challenge, based on field and greenhouse studies, Fol race 3 can cause symptoms in resistant F3 cultivars at frequencies greater (30%) than expected for off-types (<2%). We developed a three-F3 cultivar in planta assay to overcome the challenges this posed to differentiating Fol race 3 and Fol race 4. Using the assay, we determined that all putative resistance-breaking cases were Fol race 3; Fol race 4 was not detected in these early survey efforts. These results highlight the need for developing rapid Fol race 4 detection tools and a better understanding of the factors underlying inconsistent I3 gene expression in Fol race 3.
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Uno N, Li Z, Liu C. Single-tube one-step gel-based RT-RPA/PCR for highly sensitive molecular detection of HIV. Analyst 2023; 148:926-931. [PMID: 36722888 PMCID: PMC9928874 DOI: 10.1039/d2an01863b] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
We developed a single-tube one-step gel-based reverse transcription-recombinase polymerase amplification (RT-RPA)/polymerase chain reaction (PCR) (termed "SOG RT-RPA/PCR") to detect the human immunodeficiency virus (HIV). To improve the assay sensitivity, the RNA template is pre-amplified by RT-RPA prior to PCR. To simplify the detection process and shorten the assay time, we embedded PCR reagents into agarose gel, constructing it to physically separate the reagents from the RT-RPA reaction solution in a single tube. Due to the thermodynamic properties of agarose, the RT-RPA reaction first occurs independently on top of the PCR gel at a low temperature (e.g., 39 °C) during the SOG RT-RPA/PCR assay. Then, the RPA amplicons directly serve as the template for the second PCR amplification reaction, which begins when the PCR agarose dissolves due to the elevated reaction temperature, eliminating the need for multiple manual operations and amplicon transfer. With our SOG RT-RPA/PCR assay, we could detect 6.3 copies of HIV RNA per test, which is a 10-fold higher sensitivity than that of standalone real-time RT-PCR and RT-RPA. In addition, due to the high amplification efficiency of RPA, the SOG RT-RPA/PCR assay shows stronger fluorescence detection signals and a shorter detection time compared to the standalone real-time RT-PCR assay. Furthermore, we detected HIV viral RNA in clinical plasma samples and validated the superior performance of our assay. Thus, the SOG RT-RPA/PCR assay offers a powerful method for simple, rapid, and highly sensitive nucleic acid-based molecular detection of infectious diseases.
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Affiliation(s)
- Naoki Uno
- Department of Biomedical Engineering, University of Connecticut Health Center, 263 Farmington Avenue, Farmington, CT 06030, USA.
| | - Ziyue Li
- Department of Biomedical Engineering, University of Connecticut Health Center, 263 Farmington Avenue, Farmington, CT 06030, USA.
- Department of Biomedical Engineering, University of Connecticut, 260 Glenbrook Road, Storrs, CT 06029, USA
| | - Changchun Liu
- Department of Biomedical Engineering, University of Connecticut Health Center, 263 Farmington Avenue, Farmington, CT 06030, USA.
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5
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Chou MY, Luo J, Clarke BB, Murphy JA, Zhang N, Vines PL, Koch PL. Rapid Detection of the Recently Identified Turfgrass Pathogen Magnaporthiopsis meyeri-festucae Using Recombinase Polymerase Amplification. PLANT DISEASE 2022; 106:2441-2446. [PMID: 35188416 DOI: 10.1094/pdis-08-21-1732-re] [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: 06/14/2023]
Abstract
Magnaporthiopsis meyeri-festucae is a recently identified root-infecting pathogen of fine fescue (Festuca spp.) turfgrasses. Although it is phylogenetically similar to other root-infecting turfgrass pathogens such as M. poae, management of M. meyeri-festucae is distinct and highlights the need for fast and accurate identification. The objective of this study was to develop a rapid detection method for M. meyeri-festucae using recombinase polymerase amplification (RPA) to assist turfgrass managers in identifying the disease in the field and facilitate further epidemiological research on the pathogen. Three isolates of M. meyeri-festucae and eight isolates from four related Magnaporthiopsis species were used to test the specificity of the RPA assay targeting M. meyeri-festucae. Rapid visualization of the RPA assay results using a mixture of purified amplicon and SYBR-Safe fluorescence emitting asymmetrical cyanine dye showed that the assay was effective at detecting M. meyeri-festucae on turfgrass roots with no observed incidence of false positives or false negatives. The assay also differentiated between M. meyeri-festucae and other Magnaporthiopsis species, although overall sensitivity was lower compared with a PCR-based method. The RPA assay successfully detected M. meyeri-festucae following inoculation onto and grinding of turfgrass roots, indicating possible use as a rapid field diagnostic tool for turfgrass managers. The fast and accurate RPA M. meyeri-festucae detection method presented here will be used for additional field and laboratory applications that will help improve the management of this emerging pathogen.
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Affiliation(s)
- Ming-Yi Chou
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI 53706
| | - Jing Luo
- Department of Plant Biology, Rutgers University, New Brunswick, NJ 08901
| | - Bruce B Clarke
- Department of Plant Biology, Rutgers University, New Brunswick, NJ 08901
| | - James A Murphy
- Department of Plant Biology, Rutgers University, New Brunswick, NJ 08901
| | - Ning Zhang
- Department of Plant Biology, Rutgers University, New Brunswick, NJ 08901
| | - Phillip L Vines
- Department of Plant Biology, Rutgers University, New Brunswick, NJ 08901
| | - Paul L Koch
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI 53706
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Abstract
INTRODUCTION Recombinase polymerase amplification (RPA) is a promising and emerging technology for rapidly amplifying target nucleic acid from minimally processed samples and through small portable instruments. RPA is suitable for point-of-care testing (POCT) and on-site field testing, and it is compatible with microfluidic devices. Several detection assays have been developed, but limited research has dug deeper into the chemistry of RPA to understand its kinetics and fix its shortcomings. AREAS COVERED This review provides a detailed introduction of RPA molecular mechanism, kits formats, optimization, application, pros, and cons. Moreover, this critical review discusses the nonspecificity issue of RPA, highlights its consequences, and emphasizes the need for more research to resolve it. This review discusses the reaction kinetics of RPA in relation to target length, product quantity, and sensitivity. This critical review also questions the novelty of recombinase-aided amplification (RAA). In short, this review discusses many aspects of RPA technology that have not been discussed previously and provides a deeper insight and new perspectives of the technology. EXPERT OPINION RPA is an excellent choice for pathogen detection, especially in low-resource settings. It has a potential to replace PCR for all purposes, provided its shortcomings are fixed and its reagent accessibility is improved.
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Affiliation(s)
- Mustafa Ahmad Munawar
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Kuopio, Finland
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7
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Huang J, Liu Y, He Y, Yang X, Li Y. CRISPR-Cas13a Based Visual Detection Assays for Feline Calicivirus Circulating in Southwest China. Front Vet Sci 2022; 9:913780. [PMID: 35898546 PMCID: PMC9310557 DOI: 10.3389/fvets.2022.913780] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 05/24/2022] [Indexed: 11/30/2022] Open
Abstract
Feline calicivirus (FCV) is a well-known causative pathogen for upper respiratory infection in cats. Its high genetic variability challenges existing molecular diagnostic methods in clinical settings. Thus, we developed two sensitive and visual assays for FCV nucleic acid detection based on RPA reaction and CRISPR-Cas13a trans-cleavage activity. Recombinant plasmid DNA, crRNAs, and RPA primers were designed and prepared, respectively, targeting to FCV ORF1 gene. Besides, purified LwCas13a protein was produced by E.coli prokaryotic expression system. To confirm the validity of FCV-Cas13a assays, seven reaction systems (RSs) with different components were tested, and visual readouts were displayed by lateral flow dipstick (FCV-Cas13a-LFD) and fluorescence detector (FCV-Cas13a-FLUOR), respectively. The established FCV-Cas13a assays were capable of detecting FCV nucleic acid in presetting RSs without cross-reaction with other feline-associated pathogens, and the detection limit was as low as 5.5 copies/μl for both visual methods. Moreover, the positive rate of 56 clinical specimens detected by FCV-Cas13a assays (67.9%, 38/56) was notably higher than that of RT-qPCR (44.6%, 25/56) (p < 0.001), including 13 presumptive positive specimens. Taken together, FCV-Cas13a assays provided reliable and visual diagnostic alternatives for FCV field detection.
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Affiliation(s)
- Jian Huang
- Department of Veterinary Medicine, College of Animal Husbandry and Veterinary Medicine, Southwest Minzu University, Chengdu, China
- Veterinary Teaching Hospital of Southwest Minzu University, Chengdu, China
| | - Yunjia Liu
- Veterinary Teaching Hospital of Southwest Minzu University, Chengdu, China
| | - Yuwei He
- Veterinary Teaching Hospital of Southwest Minzu University, Chengdu, China
| | - Xiaonong Yang
- Department of Veterinary Medicine, College of Animal Husbandry and Veterinary Medicine, Southwest Minzu University, Chengdu, China
- Veterinary Teaching Hospital of Southwest Minzu University, Chengdu, China
| | - Yan Li
- Department of Veterinary Medicine, College of Animal Husbandry and Veterinary Medicine, Southwest Minzu University, Chengdu, China
- Veterinary Teaching Hospital of Southwest Minzu University, Chengdu, China
- *Correspondence: Yan Li
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8
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Moon YJ, Lee SY, Oh SW. A Review of Isothermal Amplification Methods and Food-Origin Inhibitors against Detecting Food-Borne Pathogens. Foods 2022; 11:foods11030322. [PMID: 35159473 PMCID: PMC8833899 DOI: 10.3390/foods11030322] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/17/2022] [Accepted: 01/18/2022] [Indexed: 02/06/2023] Open
Abstract
The isothermal amplification method, a molecular-based diagnostic technology, such as loop-mediated isothermal amplification (LAMP) and recombinase polymerase amplification (RPA), is widely used as an alternative to the time-consuming and labor-intensive culture-based detection method. However, food matrices or other compounds can inhibit molecular-based diagnostic technologies, causing reduced detection efficiencies, and false-negative results. These inhibitors originating from food are polysaccharides and polyphenolic compounds in berries, seafood, and vegetables. Additionally, magnesium ions needed for amplification reactions can also inhibit molecular-based diagnostics. The successful removal of inhibitors originating from food and molecular amplification reaction is therefore proposed to enhance the efficiency of molecular-based diagnostics and allow accurate detection of food-borne pathogens. Among molecular-based diagnostics, PCR inhibitors have been reported. Nevertheless, reports on the mechanism and removal of isothermal amplification method inhibitors are insufficient. Therefore, this review describes inhibitors originating from food and some compounds inhibiting the detection of food-borne pathogens during isothermal amplification.
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9
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Cassedy A, Della Bartola M, Parle-McDermott A, Mullins E, O'Kennedy R. A one-step reverse transcription recombinase polymerase amplification assay for lateral flow-based visual detection of PVY. Anal Biochem 2021; 642:114526. [PMID: 34922917 DOI: 10.1016/j.ab.2021.114526] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 12/07/2021] [Accepted: 12/11/2021] [Indexed: 12/12/2022]
Abstract
Potato virus Y (PVY) is an abundant and damaging virus which reduces crop yield and marketability. Accurate detection of this economically important virus both in-field and in seed potato is considered essential in the control of PVY spread. Current detection methods are focused on immunodetection and PCR-based methods, however, identification of PVY through isothermal amplification is a promising avenue for developing accessible, on-site diagnostics with quick turnaround times. In this work, a rapid recombinase polymerase amplification assay was developed which could readily amplify PVY nucleic acids with good sensitivity and specificity. Additionally, this assay was shown to be capable of amplification directly from RNA in a one-step amplification process, without the need for prior reverse transcription. The assay was coupled with lateral flow technology to provide a rapid visual confirmation of amplification. This nucleic-acid lateral flow immunoassay could feasibly be employed in-field, or at any location where testing is required, to aid in the detection and control of PVY.
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Affiliation(s)
- Arabelle Cassedy
- School of Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland.
| | | | | | - Ewen Mullins
- Crop Science Department, Teagasc, Oak Park, Carlow, Ireland
| | - Richard O'Kennedy
- School of Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland; Hamad Bin Khalifa University, Education City, Doha, Qatar; Qatar Foundation, Education City, Doha, Qatar.
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10
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Jauset-Rubio M, Ortiz M, O'Sullivan CK. Solid-Phase Primer Elongation Using Biotinylated dNTPs for the Detection of a Single Nucleotide Polymorphism from a Fingerprick Blood Sample. Anal Chem 2021; 93:14578-14585. [PMID: 34704755 PMCID: PMC8581964 DOI: 10.1021/acs.analchem.1c03419] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Isothermal recombinase polymerase amplification-based solid-phase primer extension is used for the optical detection of a hypertrophic cardiomyopathy associated single nucleotide polymorphism (SNP) in a fingerprick blood sample. The assay exploits four thiolated primers which have the same sequences with the exception of the 3'-terminal base. Target DNA containing the SNP site hybridizes to all four of the immobilized probes, with primer extension only taking place from the primer containing the terminal base that is complementary to the SNP under interrogation. Biotinylated deoxynucleotide triphosphates are used in the primer extension, allowing postextension addition of streptavidin-poly-horseradish peroxidase to bind to the incorporated biotinylated dNTPs. The signal generated following substrate addition can then be measured optically. The percentage of biotinylated dNTPs and the duration of primer extension is optimized and the system applied to the identification of a SNP in a fingerprick blood sample. A methodology of thermal lysis using a 1 in 5 dilution of the fingerprick blood sample prior to application of 95 °C for 30 s is used to extract genomic DNA, which is directly used as a template for solid-phase primer extension on microtiter plates, followed by optical detection. The SNP in the fingerprick sample was identified and its identity corroborated using ion torrent next generation sequencing. Ongoing work is focused on extension to the multiplexed detection of SNPs in fingerprick and other biological samples.
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Affiliation(s)
- Miriam Jauset-Rubio
- INTERFIBIO Research Group, Departament d'Enginyeria Química, Universitat Rovira i Virgili, Avinguda Països Catalans 26, 43007 Tarragona, Spain
| | - Mayreli Ortiz
- INTERFIBIO Research Group, Departament d'Enginyeria Química, Universitat Rovira i Virgili, Avinguda Països Catalans 26, 43007 Tarragona, Spain
| | - Ciara K O'Sullivan
- INTERFIBIO Research Group, Departament d'Enginyeria Química, Universitat Rovira i Virgili, Avinguda Països Catalans 26, 43007 Tarragona, Spain.,InstitucióCatalana de Recerca i Estudis Avancats (ICREA), Passeig Lluís Companys 23, 08010 Barcelona, Spain
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11
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Ivanov AV, Safenkova IV, Zherdev AV, Dzantiev BB. Recombinase Polymerase Amplification Assay with and without Nuclease-Dependent-Labeled Oligonucleotide Probe. Int J Mol Sci 2021; 22:11885. [PMID: 34769313 PMCID: PMC8584857 DOI: 10.3390/ijms222111885] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 10/28/2021] [Accepted: 10/29/2021] [Indexed: 01/18/2023] Open
Abstract
The combination of recombinase polymerase amplification (RPA) and lateral flow test (LFT) is a strong diagnostic tool for rapid pathogen detection in resource-limited conditions. Here, we compared two methods generating labeled RPA amplicons following their detection by LFT: (1) the basic one with primers modified with different tags at the terminals and (2) the nuclease-dependent one with the primers and labeled oligonucleotide probe for nuclease digestion that was recommended for the high specificity of the assay. Using both methods, we developed an RPA-LFT assay for the detection of worldwide distributed phytopathogen-alfalfa mosaic virus (AMV). A forward primer modified with fluorescein and a reverse primer with biotin and fluorescein-labeled oligonucleotide probe were designed and verified by RPA. Both labeling approaches and their related assays were characterized using the in vitro-transcribed mRNA of AMV and reverse transcription reaction. The results demonstrated that the RPA-LFT assay based on primers-labeling detected 103 copies of RNA in reaction during 30 min and had a half-maximal binding concentration 22 times lower than probe-dependent RPA-LFT. The developed RPA-LFT was successfully applied for the detection of AMV-infected plants. The results can be the main reason for choosing simple labeling with primers for RPA-LFT for the detection of other pathogens.
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Affiliation(s)
| | | | | | - Boris B. Dzantiev
- A.N. Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, Leninsky Prospect 33, 119071 Moscow, Russia; (A.V.I.); (I.V.S.); (A.V.Z.)
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12
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Arocha Rosete Y, To H, Evans M, White K, Saleh M, Trueman C, Tomecek J, Van Dyk D, Summerbell RC, Scott JA. Assessing the Use of DNA Detection Platforms Combined with Passive Wind-Powered Spore Traps for Early Surveillance of Potato and Tomato Late Blight in Canada. PLANT DISEASE 2021; 105:3610-3622. [PMID: 34743538 DOI: 10.1094/pdis-12-20-2695-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Quantitative PCR (qPCR), loop-mediated amplification (LAMP), and lateral flow strip-based recombinase polymerase amplification (RPA-LFS) assays were assessed for early detection of Phytophthora infestans, the global causal agent of potato and tomato late blight, on passive wind-powered spore traps known as Spornados. Spore traps were deployed in potato and tomato fields during the 2018, 2019, and 2020 growing seasons in the provinces of Alberta, British Columbia, Manitoba, Prince Edward Island, and Ontario. All assays used DNA extracts from Spornado cassette membranes targeting the P. infestans nuclear ribosomal internal transcribed spacer. A total of 1,003 Spornado samples were qPCR tested, yielding 115 positive samples for P. infestans spores. In further assessment of these samples, LAMP detected P. infestans in 108 (93.9%) of 115 qPCR positive samples, and RPA-LFS detected it in 103 (89.6%). None of the assays showed cross-reaction with other Phytophthora species or pathogenic fungi known to infect potato and tomato. The qPCR detected ≤1 fg of P. infestans DNA, and LAMP and RPA-LFS amplified 10 fg in as little as 10 min. All assays detected P. infestans before the first report of late blight symptoms in commercial potato or tomato fields within each region or province. The combination of Spornado passive samplers with qPCR, LAMP, or RPA-LFS proved a valuable spore trapping system for early surveillance of late blight in potato and tomato. Both LAMP and RPA-LFS showed potential as alternative approaches to qPCR for in-field monitoring of P. infestans.
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Affiliation(s)
| | - Henry To
- Sporometrics Inc., Toronto, Ontario M6K 3J1, Canada
| | - Martin Evans
- Sporometrics Inc., Toronto, Ontario M6K 3J1, Canada
| | | | | | - Cheryl Trueman
- Department of Plant Agriculture, University of Guelph, Ridgetown, Ontario N0P 2C0, Canada
| | - Joseph Tomecek
- Department of Plant Agriculture, University of Guelph, Ridgetown, Ontario N0P 2C0, Canada
| | - Dennis Van Dyk
- Ontario Ministry of Agriculture, Food and Rural Affairs, Guelph, Ontario, Canada
| | - Richard C Summerbell
- Sporometrics Inc., Toronto, Ontario M6K 3J1, Canada
- Occupational and Environmental Health, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario M5T 1R4, Canada
| | - James A Scott
- Occupational and Environmental Health, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario M5T 1R4, Canada
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