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Ji Y, Guo Y, Deng H, Zhang J, Wang Y, Dai E, Fan Z, Tang G, Jia M, Ding B. Rapid diagnosis of Tobacco mosaic virus in tobacco using time-resolved fluorescence immunoassay. FOOD AGR IMMUNOL 2023. [DOI: 10.1080/09540105.2023.2185568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/20/2023] Open
Affiliation(s)
- Yuan Ji
- China National Tobacco Quality Supervision and Test Center, Zhengzhou, People’s Republic of China
- Shandong Institute for Food and Drug Control, Jinan, People’s Republic of China
| | - Yushuang Guo
- Key Laboratory of Molecular Genetics, Guizhou Academy of Tobacco Science, Guiyang, People’s Republic of China
| | - Huimin Deng
- China National Tobacco Quality Supervision and Test Center, Zhengzhou, People’s Republic of China
| | - Jianfeng Zhang
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, People’s Republic of China
| | - Yuemao Wang
- China Tobacco Yunnan Import & Export Co., Ltd., Kunming, People’s Republic of China
| | - En Dai
- Yunnan Tobacco Co., Ltd. Kunming Branch, Kunming, People’s Republic of China
| | - Ziyan Fan
- China National Tobacco Quality Supervision and Test Center, Zhengzhou, People’s Republic of China
| | - Gangling Tang
- China National Tobacco Quality Supervision and Test Center, Zhengzhou, People’s Republic of China
| | - Mengao Jia
- Key Laboratory of Molecular Genetics, Guizhou Academy of Tobacco Science, Guiyang, People’s Republic of China
| | - Bo Ding
- Shandong Institute for Food and Drug Control, Jinan, People’s Republic of China
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, People’s Republic of China
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2
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Construction of electrochemiluminescence biosensor via click chemistry and ARGET-ATRP for detecting tobacco mosaic virus RNA. Anal Biochem 2022; 655:114834. [DOI: 10.1016/j.ab.2022.114834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 06/21/2022] [Accepted: 07/22/2022] [Indexed: 11/17/2022]
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3
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Salazar A, Ochoa-Corona FM, Olson JD, Babu B, Paret M. Probing Loop-Mediated Isothermal Amplification (LAMP) targeting two gene-fragments of rose rosette virus. PLoS One 2021; 16:e0256510. [PMID: 34843487 PMCID: PMC8629277 DOI: 10.1371/journal.pone.0256510] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 11/12/2021] [Indexed: 01/13/2023] Open
Abstract
This study explores the development of Loop-mediated isothermal amplification (LAMP) for detection of rose rosette virus (RRV), a technique with the potential to be translated to rose nurseries. RRV is a negative-sense, single-stranded RNA virus which is a member of the genus Emaravirus (Family Fimoviridae) and the causal agent of the rose rosette disease (RRD). Although RRV symptoms are characteristics, early visual diagnosis of RRD can be misleading and confusing since it may appear like herbicide damage. Moreover, it may take incubation time for symptoms to appear after virus infection. Two sets of RRV gene sequences RNA3 and RNA4 were analyzed and two sets of four LAMP primers were designed. The direct antigen-capture method for direct trapping of RRV in plastic was used for RNA extraction followed by cDNA synthesis. RT-LAMP reactions were for 1 hour at 64°C (RRV-P3) and 66.5°C (RRV-P4) using either a thermocycler or a portable dry bath. RT-qLAMP was also optimized using DNA polymerase GspSSD LD using the same RRV sets of primers. RRV was detected in symptomatic and non-symptomatic RRD tissue from Oklahoma. The limit of detection (LoD) was 1pg/μL and 1 fg/μL using Bst 2.0 LAMP and GspSSD LD quantitative LAMP, respectively. In visual colorimetric pre- and post-reactions, the LoD was 10 pg/μL and 0.1 pg/μL using hydroxy naphthol blue (HNB, 120 μM) and SYBR green I (1:10 dilution), respectively. No cross-reactivity was detected in the RT-LAMP reaction testing cDNAs of eight commonly co-infecting rose viruses and one virus taxonomically related to RRV. Four different dyes were tested, and visible colorimetric reactions were obtained with RT-LAMP Bst 2.0 combined with SYBR I or HNB. RT-qLAMP with GspSSD2.0 offers LoD equal to RT-PCR and it is faster since it works with RNA directly.
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Affiliation(s)
- Andrea Salazar
- Oklahoma State University, Stillwater, Oklahoma, United States of America
- Institute for Biosecurity and Microbial Forensic, Stillwater, Oklahoma, United States of America
- Department of Entomology and Plant Pathology, Stillwater, Oklahoma, United States of America
- Universidad de las Fuerzas Armadas- ESPE, Quito, Ecuador
| | - Francisco M. Ochoa-Corona
- Oklahoma State University, Stillwater, Oklahoma, United States of America
- Institute for Biosecurity and Microbial Forensic, Stillwater, Oklahoma, United States of America
- Department of Entomology and Plant Pathology, Stillwater, Oklahoma, United States of America
- * E-mail:
| | - Jennifer D. Olson
- Oklahoma State University, Stillwater, Oklahoma, United States of America
- Department of Entomology and Plant Pathology, Stillwater, Oklahoma, United States of America
| | - Binoy Babu
- North Florida Research and Education Center, University of Florida, Quincy, Florida, United States America
| | - Mathews Paret
- North Florida Research and Education Center, University of Florida, Quincy, Florida, United States America
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4
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Wang W, Li P, Zheng Z, Cheng D, Dong C, Yang H. Highly sensitive fluorescence detection of tobacco mosaic virus RNA based on disodium 4,4′-diazidostilbene-2,2′-disulfonate tetrahydrate in situ reaction. NEW J CHEM 2021. [DOI: 10.1039/d1nj02546e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A novel fluorescent turn-on method for TMV RNA via the reducing ability of an AA and DES in situ reaction was reported.
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Affiliation(s)
- Wenbin Wang
- Henan Key Laboratory of TCM Syndrome and Prescription in Signaling, Henan International Joint Laboratory of TCM Syndrome and Prescription in Signaling, Academy of Chinese Medical Sciences, Henan University of Chinese Medicine, Zhengzhou 450046, P. R. China
| | - Peipei Li
- Pharmacy College, Henan University of Chinese Medicine, Zhengzhou 450046, People's Republic of China
| | - Zhixian Zheng
- Pharmacy College, Henan University of Chinese Medicine, Zhengzhou 450046, People's Republic of China
| | - Di Cheng
- Pharmacy College, Henan University of Chinese Medicine, Zhengzhou 450046, People's Republic of China
| | - Chengming Dong
- Pharmacy College, Henan University of Chinese Medicine, Zhengzhou 450046, People's Republic of China
| | - Huaixia Yang
- Pharmacy College, Henan University of Chinese Medicine, Zhengzhou 450046, People's Republic of China
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5
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Panno S, Matić S, Tiberini A, Caruso AG, Bella P, Torta L, Stassi R, Davino S. Loop Mediated Isothermal Amplification: Principles and Applications in Plant Virology. PLANTS (BASEL, SWITZERLAND) 2020; 9:E461. [PMID: 32268586 PMCID: PMC7238132 DOI: 10.3390/plants9040461] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 04/02/2020] [Accepted: 04/02/2020] [Indexed: 01/14/2023]
Abstract
In the last decades, the evolution of molecular diagnosis methods has generated different advanced tools, like loop-mediated isothermal amplification (LAMP). Currently, it is a well-established technique, applied in different fields, such as the medicine, agriculture, and food industries, owing to its simplicity, specificity, rapidity, and low-cost efforts. LAMP is a nucleic acid amplification under isothermal conditions, which is highly compatible with point-of-care (POC) analysis and has the potential to improve the diagnosis in plant protection. The great advantages of LAMP have led to several upgrades in order to implement the technique. In this review, the authors provide an overview reporting in detail the different LAMP steps, focusing on designing and main characteristics of the primer set, different methods of result visualization, evolution and different application fields, reporting in detail LAMP application in plant virology, and the main advantages of the use of this technique.
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Affiliation(s)
- Stefano Panno
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128 Palermo, Italy; (A.G.C.); (P.B.); (L.T.); (R.S.)
| | - Slavica Matić
- Department of Agricultural, Forestry and Food Sciences, University of Turin, 10095 Turin, Italy;
| | - Antonio Tiberini
- Council for Agricultural Research and Economics, Research Center for Plant Protection and Certification, 00156 Rome, Italy;
| | - Andrea Giovanni Caruso
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128 Palermo, Italy; (A.G.C.); (P.B.); (L.T.); (R.S.)
| | - Patrizia Bella
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128 Palermo, Italy; (A.G.C.); (P.B.); (L.T.); (R.S.)
| | - Livio Torta
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128 Palermo, Italy; (A.G.C.); (P.B.); (L.T.); (R.S.)
| | - Raffaele Stassi
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128 Palermo, Italy; (A.G.C.); (P.B.); (L.T.); (R.S.)
| | - Salvatore Davino
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128 Palermo, Italy; (A.G.C.); (P.B.); (L.T.); (R.S.)
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), 10135 Turin, Italy
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6
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Fan X, Du Y, Cai Y, Zhang Y, Zhao X, Liang J, Yang D, Zhang Q, Zhang X, Zhang W, Xu Y, Zhao K. Rapid and sensitive detection of cucumber mosaic virus by reverse transcription loop-mediated isothermal amplification. Acta Biochim Biophys Sin (Shanghai) 2019; 51:223-226. [PMID: 30566580 DOI: 10.1093/abbs/gmy159] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 11/13/2018] [Indexed: 11/13/2022] Open
Affiliation(s)
- Xiaorui Fan
- College of Life and Environment Sciences, Shanghai Normal University, Shanghai, China
| | - Yanan Du
- College of Life and Environment Sciences, Shanghai Normal University, Shanghai, China
| | - Youming Cai
- Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Yongchun Zhang
- Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Xiao Zhao
- Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Jieling Liang
- School of Life Science, Taizhou University, Taizhou, China
| | - Dan Yang
- School of Life Science, Taizhou University, Taizhou, China
| | - Qi Zhang
- College of Life and Environment Sciences, Shanghai Normal University, Shanghai, China
| | - Xiaoxia Zhang
- College of Life and Environment Sciences, Shanghai Normal University, Shanghai, China
| | - Wanjing Zhang
- College of Life and Environment Sciences, Shanghai Normal University, Shanghai, China
| | - Yan Xu
- College of Life and Environment Sciences, Shanghai Normal University, Shanghai, China
| | - Kai Zhao
- Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
- Key Laboratory of Agricultural Genetics and Breeding, Shanghai Academy of Agricultural Sciences, Shanghai, China
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Liu H, Wu K, Wu W, Mi W, Hao X, Wu Y. A multiplex reverse transcription PCR assay for simultaneous detection of six main RNA viruses in tomato plants. J Virol Methods 2018; 265:53-58. [PMID: 30576723 DOI: 10.1016/j.jviromet.2018.12.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 12/17/2018] [Accepted: 12/18/2018] [Indexed: 02/02/2023]
Abstract
Tomato virus diseases occur all around the world, causing serious yield losses. To detect these viruses quickly and provide a basis for disease control, a multiplex reverse transcription polymerase chain reaction system was established for simultaneous detection of Tobacco mosaic virus (TMV), Cucumber mosaic virus (CMV), Tomato spotted wilt virus (TSWV), Tomato chlorosis virus (ToCV), Potato virus Y (PVY) and Potato virus X (PVX) in tomato plants, with 6 pairs of specific primers being designed based on the coat protein (CP) genes of these viruses. Transcriptional elongation factor-1α (EF-1α) from tomato was added to the multiplex RT-PCR reaction system to prevent false negatives. The concentration of the primers, annealing temperature, annealing time, extension time and amplification cycles were optimized. Expected fragments of 159 bp (ToCV), 262 bp (PVY), 362 bp (EF-1α), 430 bp (TMV), 500 bp (TSWV), 600 bp (CMV) and 705 bp (PVX) were amplified by this multiplex RT-PCR system, and their origin was confirmed by DNA sequencing. This method will have a wide application in virus detection of field samples.
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Affiliation(s)
- Huan Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Key Laboratory of Crop Pest Integrated Pest Management on Crop in Northwestern Loess Plateau, Ministry of Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Kuan Wu
- Yangling Vocational & Technical College, Yangling, Shaanxi, 712100, China
| | - Wei Wu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Key Laboratory of Crop Pest Integrated Pest Management on Crop in Northwestern Loess Plateau, Ministry of Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Weili Mi
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Key Laboratory of Crop Pest Integrated Pest Management on Crop in Northwestern Loess Plateau, Ministry of Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Xingan Hao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Key Laboratory of Crop Pest Integrated Pest Management on Crop in Northwestern Loess Plateau, Ministry of Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Yunfeng Wu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Key Laboratory of Crop Pest Integrated Pest Management on Crop in Northwestern Loess Plateau, Ministry of Agriculture, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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8
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Lu Y, Yao B, Wang G, Hong N. The detection of ACLSV and ASPV in pear plants by RT-LAMP assays. J Virol Methods 2017; 252:80-85. [PMID: 29180245 DOI: 10.1016/j.jviromet.2017.11.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 11/20/2017] [Accepted: 11/21/2017] [Indexed: 10/18/2022]
Abstract
A reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay was developed for the detection of Apple chlorotic leaf spot virus (ACLSV) and Apple stem pitting virus (ASPV), two important viruses frequently occurring in pear trees. A set of four RT-LAMP primers designed based on the highly conserved region of each CP gene of the two viruses showed high specificity and feasibility for ACLSV and ASPV detections. The RT-LAMP assays for ACLSV and ASPV in pear samples were 104 and 103 times more sensitive than that of conventional RT-PCR assays. The RT-LAMP under optimal reaction condition was subsequently utilized in the detection of the two viruses in-vitro cultures of pear and field pear samples. This study provides a rapid and sensitive tool to determine the infection statues of the two viruses in pear certification program.
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Affiliation(s)
- Yongcan Lu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; The Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Bingyu Yao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; The Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Guoping Wang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; The Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; National Indoor Conservation Center of Virus-free Germplasm of Fruit Crops, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Ni Hong
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; The Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; National Indoor Conservation Center of Virus-free Germplasm of Fruit Crops, Huazhong Agricultural University, Wuhan, Hubei 430070, China.
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9
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Banerjee A, Roy S, Sharma SK, Dutta SK, Chandra S, Ngachan SV. Reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for rapid diagnosis of chilli veinal mottle virus. Arch Virol 2016; 161:1957-61. [PMID: 27063408 DOI: 10.1007/s00705-016-2850-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 03/28/2016] [Indexed: 10/22/2022]
Abstract
Chilli veinal mottle virus (ChiVMV) causes significant economic loss to chilli cultivation in northeastern India, as well as in eastern Asia. In this study, we have developed a single-tube one-step reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for rapid, sensitive and specific diagnosis of ChiVMV. Amplification could be visualized after adding SYBR Green I (1000×) dye within 60 min under isothermal conditions at 63 °C, with a set of four primers designed based on the large nuclear inclusion protein (NIb) domain of ChiVMV (isolate KC-ML1). The RT-LAMP method was 100 times more sensitive than one-step reverse transcription polymerase chain reaction (RT-PCR), with a detection limit of 0.0001 ng of total RNA per reaction.
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Affiliation(s)
- Amrita Banerjee
- ICAR Research Complex for North Eastern Hill Region, Umiam, Meghalaya, 793 103, India.
| | - Somnath Roy
- ICAR-National Bureau of Plant Genetic Resources, Regional Station, Umiam, Meghalaya, 793 103, India
| | - Susheel Kumar Sharma
- ICAR Research Complex for NEH Region, Manipur Centre, Lamphelpat, Manipur, 795 004, India
| | - Sudip Kumar Dutta
- ICAR Research Complex for NEH Region, Mizoram Centre, Kolasib, Mizoram, 796 081, India
| | - Satish Chandra
- ICAR Research Complex for North Eastern Hill Region, Umiam, Meghalaya, 793 103, India
| | - S V Ngachan
- ICAR Research Complex for North Eastern Hill Region, Umiam, Meghalaya, 793 103, India
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10
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Velasquez N, Hossain MJ, Murphy JF. Differential disease symptoms and full-length genome sequence analysis for three strains of Tobacco etch virus. Virus Genes 2015; 50:442-9. [PMID: 25425495 DOI: 10.1007/s11262-014-1146-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Accepted: 11/12/2014] [Indexed: 11/25/2022]
Abstract
Tobacco etch virus (TEV) strains HAT, Mex21, and N have been the focus of numerous studies to dissect a host resistance mechanism in Capsicum spp. Little is known, however, about their general pathogenicity and genomic sequence data are not available on the TEV strains Mex21 and N. Four Nicotiana spp. were evaluated after inoculation with each TEV strain. Nicotiana tabacum 'Kentucky 14' and N. clevelandii plants expressed varied systemic symptoms dependent on the TEV strain; however, disease severity increased from HAT (mild mosaic symptoms) to Mex21 (more severe mosaic symptoms with stunting) to N (severe chlorosis and stunting). Nicotiana tabacum 'Samsun' plants developed relatively milder symptoms and N. glutinosa plants remained symptomless, although they were systemically infected. The genome of each TEV strain was sequenced and shown to consist of 9,495 nucleotides and a polyprotein of 3,054 amino acids. Comparison of their nucleotide sequences relative to the original HAT sequence (GenBank Accession No. M11458) revealed 95, 92, and 92 % identity for HAT-AU (from Auburn University), Mex21, and N, respectively. HAT-AU had 91 % sequence identity with Mex21 and N, while Mex21 and N were more closely related with 98 % nucleotide sequence identity. Similarly, the amino acid sequence identities for the full-length polyprotein ranged from 95 % for HAT-AU when compared with N to a high of 98 % identity between Mex21 and N.
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Affiliation(s)
- Nubia Velasquez
- Department of Entomology & Plant Pathology, Auburn University, 209 Rouse Life Sciences Building, Auburn, AL, 36849, USA
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Li R, Ling KS. Development of reverse transcription loop-mediated isothermal amplification assay for rapid detection of an emerging potyvirus: Tomato necrotic stunt virus. J Virol Methods 2014; 200:35-40. [DOI: 10.1016/j.jviromet.2014.01.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Revised: 01/18/2014] [Accepted: 01/24/2014] [Indexed: 11/26/2022]
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Arif M, Aguilar-Moreno GS, Wayadande A, Fletcher J, Ochoa-Corona FM. Primer modification improves rapid and sensitive in vitro and field-deployable assays for detection of high plains virus variants. Appl Environ Microbiol 2014; 80:320-7. [PMID: 24162574 PMCID: PMC3910988 DOI: 10.1128/aem.02340-13] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2013] [Accepted: 10/21/2013] [Indexed: 11/20/2022] Open
Abstract
A high consequence pathogen, High plains virus (HPV) causes considerable damage to wheat if the crop is infected during early stages of development. Methods for the early, accurate, and sensitive detection of HPV in plant tissues are needed for the management of disease outbreaks and reservoir hosts. In this study, the effectiveness of five methods-real-time SYBR green and TaqMan reverse transcription-quantitative PCR (RT-qPCR), endpoint RT-PCR, RT-helicase dependent amplification (RT-HDA) and the Razor Ex BioDetection System (Razor Ex)-for the broad-range detection of HPV variants was evaluated. Specific PCR primer sets and probes were designed to target the HPV nucleoprotein gene. Primer set HPV6F and HPV4R, which amplifies a product of 96 bp, was validated in silico against published sequences and in vitro against an inclusivity panel of infected plant samples and an exclusivity panel of near-neighbor viruses. The primers were modified by adding a customized 22 nucleotide long tail at the 5' terminus, raising the primers' melting temperature (Tm; ca. 10°C) to make them compatible with RT-HDA (required optimal Tm = 68°C), in which the use of primers lacking such tails gave no amplification. All of the methods allowed the detection of as little as 1 fg of either plasmid DNA carrying the target gene sequence or of infected plant samples. The described in vitro and in-field assays are accurate, rapid, sensitive, and useful for pathogen detection and disease diagnosis, microbial quantification, and certification and breeding programs, as well as for biosecurity and microbial forensics applications.
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Affiliation(s)
- M Arif
- National Institute for Microbial Forensics and Food & Agricultural Biosecurity, Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, Oklahoma, USA
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Almasi MA, Erfan Manesh M, Jafary H, Dehabadi SMH. Visual detection of Potato Leafroll virus by loop-mediated isothermal amplification of DNA with the GeneFinder™ dye. J Virol Methods 2013; 192:51-4. [PMID: 23680094 DOI: 10.1016/j.jviromet.2013.04.014] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Revised: 04/10/2013] [Accepted: 04/15/2013] [Indexed: 11/25/2022]
Abstract
The most common virus affecting potatoes in the field worldwide is Potato Leafroll virus (PLRV), belonging to the family Luteoviridae, genius Plerovirus. There are several molecular methods to detect PLRV including polymerase chain reaction (PCR), Multiplex AmpliDet RNA and double antibody sandwich ELISA (DAS-ELISA). But these techniques take a long time for 3h to two days, requiring sophisticated tools. The aim of this study was to reduce the time required to detect PLRV, using a newly designed loop-mediated isothermal amplification (LAMP) technique requiring only an ordinary water bath or thermoblock. PLRV RNA was extracted from overall 80 infected naturally potato leaves. A set of six novel primers for the LAMP reaction was designed according to the highly conserved sequence of the viral coat protein (CP) gene. LAMP was carried out under isothermal conditions, applying the Bst DNA polymerase enzyme; the LAMP products were detected visually using the GeneFinder™ florescence dye. A positive result using the GeneFinder™ dye was a color change from the original orange to green. Results confirmed LAMP with GeneFinder™ provides a rapid and safe assay for detection of PLRV. Since with other molecular methods, equipping laboratories with a thermocycler or expensive detector systems is unavoidable, this assay was found to be a simple, cost-effective molecular method that has the potential to replace other diagnostic methods in primary laboratories without the need for expensive equipment or specialized techniques. It can also be considered as a reliable alternative viral detection system in further investigations.
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Affiliation(s)
- Mohammad Amin Almasi
- Department of Agriculture and Plant Breeding, Faculty of Agriculture, Zanjan University, Zanjan, Iran
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