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Mark D, Tairo F, Ndunguru J, Kweka E, Saggaf M, Bachwenkizi H, Chiunga E, Lusana JL, Sikazwe G, Maghembe R. Assessing the effect of sample storage time on viral detection using a rapid and cost-effective CTAB-based extraction method. PLANT METHODS 2024; 20:64. [PMID: 38720311 PMCID: PMC11080235 DOI: 10.1186/s13007-024-01175-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 03/11/2024] [Indexed: 05/12/2024]
Abstract
BACKGROUND Cassava leaf samples degrade quickly during storage and transportation from distant areas. Proper sampling and efficient, low-cost storage methods are critical for obtaining sufficient quality DNA and RNA for plant virus epidemiology and improving disease control understanding. This is useful when samples are collected from remote areas far from a laboratory or in developing countries where money and materials for virus diagnostics are scarce. RESULTS The effect of sample storage duration on nucleic acid (N.A.) quality on virus detection was investigated in this study. A simple, rapid, and cost-effective CTAB-based approach (M3) for single N.A. extraction was optimized and tested alongside two existing CTAB-based methods (M1 and M2) for N.A. extraction from fresh and herbarium cassava leaves stored for; 1, 8, 26, and 56 months. The amount and quality of DNA and RNA were determined using Nanodrop 2000 c U.V.-vis Spectrophotometer and agarose gel electrophoreses. The sample degradation rate was estimated using a simple mathematical model in Matlab computational software. The results show no significant difference in mean DNA concentration between M1 and M2 but a significant difference between M3 and the other two methods at p < 0.005. The mean DNA concentration extracted using M3 was higher for 1 and 8 months of leave storage. M3 and M2 produced high concentrations at 26 and 56 months of leave storage. Using a developed scale for quality score, M3 and M2 produced high-quality DNA from fresh samples. All methods produced poor-quality DNA and RNA at 8 and 26 months of leave storage and no visual bands at the age of 56 months. Statistically, there was a significant difference in the mean DNA quality between M1 and M2, but there was no significant difference between M3 and the other two methods at p < 0.005. However, Cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV) were readily detected by RT-PCR from RNA isolated using M3. The quality of DNA declined per storage time at 0.0493 and 0.0521/month, while RNA was 0.0678 and 0.0744/month. Compared to the existing two methods, modified CTAB extracted enough high-quality N.A. in one-third the time of the existing two methods. CONCLUSION Our method provides cost-effective, quick, and simple processing of fresh and dry samples, which will quicken and guide the decision on when and what type of sample to process for plant disease management and surveillance actions.
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Affiliation(s)
- Deogratius Mark
- Tanzania Agricultural Research Institute, 6226, Dar-es-Salaam, Tanzania.
| | - Fred Tairo
- Tanzania Agricultural Research Institute, 6226, Dar-es-Salaam, Tanzania
| | - Joseph Ndunguru
- Tanzania Agricultural Research Institute, 6226, Dar-es-Salaam, Tanzania
- Tanzania Plant Health and Pesticides Authority, Arusha, P.O.Box 3024, Tanzania
| | - Elisiana Kweka
- Tanzania Agricultural Research Institute, 6226, Dar-es-Salaam, Tanzania
| | - Maliha Saggaf
- Tanzania Agricultural Research Institute, 6226, Dar-es-Salaam, Tanzania
| | - Hilda Bachwenkizi
- Tanzania Agricultural Research Institute, 6226, Dar-es-Salaam, Tanzania
| | | | - James Leonard Lusana
- School of Aquatic Sciences and Fisheries Technology, University of Dar es Salaam, 60091, Dar es Salaam, Tanzania
| | - Geofrey Sikazwe
- Mkwawa University College of Education, University of Dar es Salaam, 2513, Iringa, Tanzania
| | - Reuben Maghembe
- Biological and Marine Sciences Unit, Faculty of Natural and Applied Sciences, Marian University College, 47, Bagamoyo, Tanzania
- Department of Biological Sciences, Faculty of Science, University of Botswana, Private Bag 0704, Gaborone, Botswana
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Koh C, Saleh MC. Translating mosquito viromes into vector management strategies. Trends Parasitol 2024; 40:10-20. [PMID: 38065789 DOI: 10.1016/j.pt.2023.11.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 11/06/2023] [Accepted: 11/07/2023] [Indexed: 01/06/2024]
Abstract
Mosquitoes are best known for transmitting human and animal viruses. However, they also harbour mosquito-specific viruses (MSVs) as part of their microbiota. These are a group of viruses whose diversity and prevalence overshadow their medically relevant counterparts. Although metagenomics sequencing has remarkably accelerated the discovery of these viruses, what we know about them is often limited to sequence information, leaving much of their fundamental biology to be explored. Understanding the biology and ecology of MSVs can enlighten our knowledge of virus-virus interactions and lead to new innovations in the management of mosquito-borne viral diseases. We retrace the history of their discovery and discuss research milestones that would line the path from mosquito virome knowledge to vector management strategies.
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Affiliation(s)
- Cassandra Koh
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Viruses and RNA Interference Unit, 75015 Paris, France.
| | - Maria-Carla Saleh
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Viruses and RNA Interference Unit, 75015 Paris, France
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Wang H, Ma L, Jin Z, Cui Z, Yang H, Miao M. Highly sensitive fluorescence detection of tobacco mosaic virus RNA based on polysaccharide and ARGET ATRP double signal amplification. Talanta 2023; 257:124360. [PMID: 36801566 DOI: 10.1016/j.talanta.2023.124360] [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: 12/14/2022] [Revised: 02/01/2023] [Accepted: 02/12/2023] [Indexed: 02/17/2023]
Abstract
Plant diseases caused by tobacco mosaic viruses (TMV) reduce the yield and quality of crops and cause significant losses. Early detection and prevention of TMV has important value of research and reality. Herein, a fluorescent biosensor was constructed for highly sensitive detection of TMV RNA (tRNA) based on the principle of base complementary pairing, polysaccharides and atom transfer radical polymerization by electron transfer activated regeneration catalysts (ARGET ATRP) as double signal amplification strategy. The 5'-end sulfhydrylated hairpin capture probe (hDNA) was first immobilized on amino magnetic beads (MBs) by a cross-linking agent, which specifically recognizes tRNA. Then, chitosan binds to BIBB, providing numerous active sites for fluorescent monomer polymerization, which successfully significantly amplifying the fluorescent signal. Under optimal experimental conditions, the proposed fluorescent biosensor for the detection of tRNA has a wide detection range from 0.1 pM to 10 nM (R2 = 0.998) with a limit of detection (LOD) as low as 1.14 fM. In addition, the fluorescent biosensor showed satisfactory applicability for the qualitative and quantitative analysis of tRNA in real samples, thereby demonstrating the potential in the field of viral RNA detection.
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Affiliation(s)
- Hesen Wang
- Pharmacy College, Henan University of Chinese Medicine, Zhengzhou, 450046, People's Republic of China
| | - Lele Ma
- Pharmacy College, Henan University of Chinese Medicine, Zhengzhou, 450046, People's Republic of China
| | - Zhenyu Jin
- Pharmacy College, Henan University of Chinese Medicine, Zhengzhou, 450046, People's Republic of China
| | - Zhenzhen Cui
- 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.
| | - Mingsan Miao
- Pharmacy College, Henan University of Chinese Medicine, Zhengzhou, 450046, People's Republic of China.
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