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Várallyay E, Přibylová J, Galbacs ZN, Jahan A, Varga T, Špak J, Lenz O, Fránová J, Sedlák J, Koloniuk I. Detection of Apple Hammerhead Viroid, Apple Luteovirus 1 and Citrus Concave Gum-Associated Virus in Apple Propagation Materials and Orchards in the Czech Republic and Hungary. Viruses 2022; 14:v14112347. [PMID: 36366445 PMCID: PMC9695845 DOI: 10.3390/v14112347] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 10/22/2022] [Accepted: 10/24/2022] [Indexed: 02/01/2023] Open
Abstract
Grafting cultivars onto rootstocks is a widely used practice by the apple industry predominantly aimed at faster fruit bearing. Using high-throughput sequencing, we revealed the presence of recently described viral agents, namely apple hammerhead viroid (AHVd), apple luteovirus 1 (ALV-1), and citrus concave gum-associated virus (CCGaV), in germplasm collections and production orchards in the Czech Republic and Hungary. The HTS results were validated with RT-(q)PCR, and Northern blotting techniques. To obtain further insight about the presence of these agents, RT-PCR based surveys were carried out and showed their widespread presence alone or in mixed infections. The pathogens were present both in production areas and in feral samples. In addition, rootstock-to-scion transmission of ALV-1 and CCGaV was confirmed using commercial rootstock materials. Phylogenetic relationships based on partial sequences of distinct variants were also investigated. Furthermore, the rosy apple aphid was found to be ALV-1-positive, suggesting that it might be a potential vector of the virus.
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Affiliation(s)
- Eva Várallyay
- Genomics Research Group, Department of Plant Pathology, Institute of Plant Protection, Hungarian University of Agriculture and Life Sciences, Szent-Gyorgyi Albert Street 4, 2100 Gödöllő, Hungary
- Correspondence: (E.V.); (I.K.)
| | - Jaroslava Přibylová
- Czech Academy of Sciences, Biology Centre, Institute of Plant Molecular Biology, Branišovská 31, 37005 České Budějovice, Czech Republic
| | - Zsuzsanna Nagyne Galbacs
- Genomics Research Group, Department of Plant Pathology, Institute of Plant Protection, Hungarian University of Agriculture and Life Sciences, Szent-Gyorgyi Albert Street 4, 2100 Gödöllő, Hungary
| | - Almash Jahan
- Genomics Research Group, Department of Plant Pathology, Institute of Plant Protection, Hungarian University of Agriculture and Life Sciences, Szent-Gyorgyi Albert Street 4, 2100 Gödöllő, Hungary
| | - Tunde Varga
- Genomics Research Group, Department of Plant Pathology, Institute of Plant Protection, Hungarian University of Agriculture and Life Sciences, Szent-Gyorgyi Albert Street 4, 2100 Gödöllő, Hungary
| | - Josef Špak
- Czech Academy of Sciences, Biology Centre, Institute of Plant Molecular Biology, Branišovská 31, 37005 České Budějovice, Czech Republic
| | - Ondřej Lenz
- Czech Academy of Sciences, Biology Centre, Institute of Plant Molecular Biology, Branišovská 31, 37005 České Budějovice, Czech Republic
| | - Jana Fránová
- Czech Academy of Sciences, Biology Centre, Institute of Plant Molecular Biology, Branišovská 31, 37005 České Budějovice, Czech Republic
| | - Jiří Sedlák
- Research and Breeding Institute of Pomology Holovousy, Ltd., Holovousy 129, 50801 Holovousy, Czech Republic
| | - Igor Koloniuk
- Czech Academy of Sciences, Biology Centre, Institute of Plant Molecular Biology, Branišovská 31, 37005 České Budějovice, Czech Republic
- Correspondence: (E.V.); (I.K.)
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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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Dong Z, Zhao X, Liu J, Zhan B, Li S. Detection and Simultaneous Differentiation of Three Co-infected Viruses in Zanthoxylum armatum. PLANTS 2022; 11:plants11091242. [PMID: 35567243 PMCID: PMC9100190 DOI: 10.3390/plants11091242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 04/24/2022] [Accepted: 04/27/2022] [Indexed: 11/16/2022]
Abstract
Green Sichuan pepper (Zanthoxylum armatum) is an important economic fruit crop, which is widely planted in the southwest region of China. Recently, a serious disease, namely flower yellowing disease (FYD), broke out, and the virus of green Sichuan pepper nepovirus (GSPNeV) was identified to be highly correlated with the viral symptoms. Meanwhile, green Sichuan pepper idaeovirus (GSPIV) and green Sichuan pepper enamovirus (GSPEV) were also common viruses infecting green pepper. In our research, specific primers were designed according to the reported sequences of the three viruses, and a multiplex reverse transcription-polymerase chain reaction (RT-PCR) method for the simultaneous detection of GSPNeV, GSPIV, and GSPEV was established. The annealing temperature, extension time, and cycle number affecting the multiplex RT-PCR reaction were adjusted and optimized. Sensitivity analysis showed that the system could detect the three viruses simultaneously from the complementary deoxyribonucleic acid (cDNA) samples diluted by 10−3. The results of the ten samples detected by the multiplex RT-PCR system were consistent with the results of a single PCR, indicating that the method can be successfully used for rapid detection of field samples.
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Affiliation(s)
- Zhenfei Dong
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China;
- Department of Fruit Science, College of Horticulture, China Agricultural University, Beijing 100107, China; (X.Z.); (J.L.)
| | - Xiaoli Zhao
- Department of Fruit Science, College of Horticulture, China Agricultural University, Beijing 100107, China; (X.Z.); (J.L.)
| | - Junjie Liu
- Department of Fruit Science, College of Horticulture, China Agricultural University, Beijing 100107, China; (X.Z.); (J.L.)
| | - Binhui Zhan
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China;
- Correspondence: (B.Z.); (S.L.)
| | - Shifang Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China;
- Correspondence: (B.Z.); (S.L.)
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