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Kirasi PM, Ateka EM, Avedi EK, Yegon HK, Wanjala BW, Pappu HR. A reverse transcription loop-mediated isothermal amplification assay for quick detection of tomato mosaic virus. PLoS One 2024; 19:e0304497. [PMID: 38870181 PMCID: PMC11175515 DOI: 10.1371/journal.pone.0304497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Accepted: 05/13/2024] [Indexed: 06/15/2024] Open
Abstract
Tomato mosaic virus (ToMV), an economically important virus that affects a wide range of crops, is highly contagious, and its transmission is mediated by mechanical means, and through contaminated seeds or planting materials, making its management challenging. To contain its wide distribution, early and accurate detection of infection is required. A survey was conducted between January and May, 2023 in major tomato growing counties in Kenya, namely, Baringo, Kajiado, Kirinyaga and Laikipia, to establish ToMV disease incidence and to collect samples for optimization of the reverse transcription loop-mediated isothermal amplification assay (RT-LAMP) assay. A RT-LAMP assay, utilizing primers targeting the coat protein, was developed and evaluated for its performance. The method was able to detect ToMV in tomato samples within 4:45 minutes, had a 1,000-fold higher sensitivity than conventional reverse transcription polymerase chain reaction (RT-PCR) method and was specific to ToMV. Furthermore, the practical applicability of the assay was assessed using tomato samples and other solanaecous plants. The assay was able to detect the virus in 14 tomato leaf samples collected from the field, compared to 11 samples detected by RT-PCR, further supporting the greater sensitivity of the assay. To make the assay more amenable for on-site ToMV detection, a quick-extraction method based on alkaline polyethylene glycol buffer was evaluated, which permitted the direct detection of the target virus from crude leaf extracts. Due to its high sensitivity, specificity and rapidity, the RT-LAMP method could be valuable for field surveys and quarantine inspections towards a robust management of ToMV infections.
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Affiliation(s)
- Phostine M. Kirasi
- Department of Molecular Biology and Biotechnology, Pan African University Institute for Basic Sciences, Technology and Innovation (PAUSTI), Nairobi, Kenya
- Department of Phytosanitary and Biosecurity, Kenya Plant Health Inspectorate Service, Nairobi, Kenya
| | - Elijah M. Ateka
- Department of Molecular Biology and Biotechnology, Pan African University Institute for Basic Sciences, Technology and Innovation (PAUSTI), Nairobi, Kenya
- Department of Horticulture and Food Security, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Edith K. Avedi
- Department of Molecular Biology and Biotechnology, Pan African University Institute for Basic Sciences, Technology and Innovation (PAUSTI), Nairobi, Kenya
- Department of Phytosanitary and Biosecurity, Kenya Plant Health Inspectorate Service, Nairobi, Kenya
| | - Hillary K. Yegon
- Department of Phytosanitary and Biosecurity, Kenya Plant Health Inspectorate Service, Nairobi, Kenya
| | - Bramwel W. Wanjala
- Biotechnology Research Institute, Kenya Agricultural and Livestock Research Organization, Nairobi, Kenya
| | - Hanu R. Pappu
- Department of Plant Pathology, Washington State University, Pullman, WA, United States of America
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Wani LA, Jawa P, Khan JA. Development of one step colorimetric RT-LAMP assays for rapid detection of Apple mosaic virus and Prunus necrotic ringspot virus. J Virol Methods 2023; 316:114729. [PMID: 37031745 DOI: 10.1016/j.jviromet.2023.114729] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 03/27/2023] [Accepted: 04/06/2023] [Indexed: 04/11/2023]
Abstract
Apple mosaic virus (ApMV) and Prunus necrotic ringspot virus (PNRSV), belonging to genus Ilarvirus, cause significant losses to rose and other plants of the family Rosaceae. They are easily transmitted through mechanical or vegetative means. In our previous study, the occurrence of ApMV and PNRSV in rose plants was reported. In this study, as a first step towards the development of a colorimetric Reverse Transcriptase - Loop Mediated Isothermal Amplification (RT-LAMP) assay, two primer sets were designed, each containing six primers (F3, B3, FIP, BIP, LF and LB) targeting the coat protein genes of ApMV and PNRSV. After incubation of RT-LAMP reaction mix at an isothermal temperature (65 °C/30min), the amplified products were visually confirmed with the nucleic acid intercalation dye SYBR Green I and the indicator dye Hydroxy-Naphthol Blue. The developed assays were virus specific and showed no cross amplification. Their sensitivity was 103 times higher than that of the corresponding RT-PCRs. The LAMP assays developed in this study are inexpensive, rapid and reliable for the early detection of ApMV and PNRSV, and could therefore be used in plant quarantine to control the risk of their spread.
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Affiliation(s)
- Latief A Wani
- Plant Virus Laboratory, Department of Biosciences, Jamia Millia Islamia, New Delhi - 110025, India
| | - Priyanka Jawa
- Plant Virus Laboratory, Department of Biosciences, Jamia Millia Islamia, New Delhi - 110025, India
| | - Jawaid A Khan
- Plant Virus Laboratory, Department of Biosciences, Jamia Millia Islamia, New Delhi - 110025, India.
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DeLude A, Wells R, Boomla S, Chuang SC, Urena F, Shipman A, Rubas N, Kuehu DL, Bickerton B, Peterson T, Dobhal S, Arizala D, Klair D, Ochoa-Corona F, Ali ME, Odani J, Bingham JP, Jenkins DM, Fletcher J, Stack JP, Alvarez AM, Arif M. Loop-mediated isothermal amplification (LAMP) assay for specific and rapid detection of Dickeya fangzhongdai targeting a unique genomic region. Sci Rep 2022; 12:19193. [PMID: 36357509 PMCID: PMC9649655 DOI: 10.1038/s41598-022-22023-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 10/07/2022] [Indexed: 11/11/2022] Open
Abstract
Dickeya fangzhongdai, a bacterial pathogen of taro (Colocasia esculenta), onion (Allium sp.), and several species in the orchid family (Orchidaceae) causes soft rot and bleeding canker diseases. No field-deployable diagnostic tool is available for specific detection of this pathogen in different plant tissues. Therefore, we developed a field-deployable loop-mediated isothermal amplification (LAMP) assay using a unique genomic region, present exclusively in D. fangzhongdai. Multiple genomes of D. fangzhongdai, and other species of Dickeya, Pectobacterium and unrelated genera were used for comparative genomic analyses to identify an exclusive and conserved target sequence from the major facilitator superfamily (MFS) transporter gene region. This gene region had broad detection capability for D. fangzhongdai and thus was used to design primers for endpoint PCR and LAMP assays. In-silico validation showed high specificity with D. fangzhongdai genome sequences available in the NCBI GenBank genome database as well as the in-house sequenced genome. The specificity of the LAMP assay was determined with 96 strains that included all Dickeya species and Pectobacterium species as well as other closely related genera and 5 hosts; no false positives or false negatives were detected. The detection limit of the assay was determined by performing four sensitivity assays with tenfold serially diluted purified genomic DNA of D. fangzhongdai with and without the presence of crude host extract (taro, orchid, and onion). The detection limit for all sensitivity assays was 100 fg (18-20 genome copies) with no negative interference by host crude extracts. The assays were performed by five independent operators (blind test) and on three instruments (Rotor-Gene, thermocycler and dry bath); the assay results were concordant. The assay consistently detected the target pathogen from artificially inoculated and naturally infected host samples. The developed assay is highly specific for D. fangzhongdai and has applications in routine diagnostics, phytosanitary and seed certification programs, and epidemiological studies.
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Affiliation(s)
- Anuhea DeLude
- grid.410445.00000 0001 2188 0957Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI USA
| | - Riley Wells
- grid.410445.00000 0001 2188 0957Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI USA
| | - Sherine Boomla
- grid.410445.00000 0001 2188 0957Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI USA
| | - Shu-Cheng Chuang
- grid.410445.00000 0001 2188 0957Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI USA
| | - Frank Urena
- grid.410445.00000 0001 2188 0957Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI USA ,grid.410445.00000 0001 2188 0957Department of Cell and Molecular Biology, University of Hawaii at Manoa, Honolulu, HI USA
| | - Aaron Shipman
- grid.410445.00000 0001 2188 0957Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI USA
| | - Noelle Rubas
- grid.410445.00000 0001 2188 0957Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI USA
| | - Donna Lee Kuehu
- grid.410445.00000 0001 2188 0957Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI USA ,grid.410445.00000 0001 2188 0957Department of Cell and Molecular Biology, University of Hawaii at Manoa, Honolulu, HI USA
| | - Buster Bickerton
- grid.410445.00000 0001 2188 0957Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI USA
| | - Taylor Peterson
- grid.410445.00000 0001 2188 0957Department of Human Nutrition, Food and Animal Sciences, University of Hawaii at Manoa, Honolulu, HI USA
| | - Shefali Dobhal
- grid.410445.00000 0001 2188 0957Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI USA
| | - Dario Arizala
- grid.410445.00000 0001 2188 0957Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI USA
| | - Diksha Klair
- grid.410445.00000 0001 2188 0957Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI USA
| | - Francisco Ochoa-Corona
- grid.65519.3e0000 0001 0721 7331Institute for Biosecurity & Microbial Forensics, Oklahoma State University, Stillwater, OK USA
| | - Md Emran Ali
- grid.213876.90000 0004 1936 738XDepartment of Plant Pathology, University of Georgia, Tifton, GA USA
| | - Jenee Odani
- grid.410445.00000 0001 2188 0957Department of Human Nutrition, Food and Animal Sciences, University of Hawaii at Manoa, Honolulu, HI USA
| | - Jon-Paul Bingham
- grid.410445.00000 0001 2188 0957Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI USA
| | - Daniel M. Jenkins
- grid.410445.00000 0001 2188 0957Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI USA
| | - Jacqueline Fletcher
- grid.65519.3e0000 0001 0721 7331Institute for Biosecurity & Microbial Forensics, Oklahoma State University, Stillwater, OK USA
| | - James P. Stack
- grid.36567.310000 0001 0737 1259Department of Plant Pathology, Kansas State University, Manhattan, KS USA
| | - Anne M. Alvarez
- grid.410445.00000 0001 2188 0957Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI USA
| | - Mohammad Arif
- grid.410445.00000 0001 2188 0957Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI USA
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