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Plants
Special Issues
Identification of Plant Viruses and Viroids
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Identification of Plant Viruses and Viroids

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Protection and Biotic Interactions".

Deadline for manuscript submissions: closed (30 April 2023) | Viewed by 7003

Special Issue Editors

Dr. Francesco Faggioli

E-Mail Website
Guest Editor
Research Centre for Plant Protection and Certification, Council for Agricultural Research and Economics (CREA-DC), Via C.G. Bertero 22, 00156 Rome, Italy
Interests: plant virology; diagnosis; viroids; validation of detection methods; reference laboratory; reference material; phytosanitary measures; quarantine organisms.
Dr. Luca Ferretti

E-Mail Website
Guest Editor
Research Centre for Plant Protection and Certification, Council for Agricultural Research and Economics (CREA-DC), Via C.G. Bertero 22, 00156 Rome, Italy
Interests: plant virology; diagnosis; phytoplasmas; validation of detection methods; reference laboratory; reference material; phytosanitary measures; quarantine organisms.
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Plant viruses and viroids are recognized as increasing threats to sustainable food production and environmental protection globally. In order to minimize their impact on crops, the early detection and identification of such plant pathogens are fundamental for the further adoption of proper control strategies and phytosanitary measures aimed at limiting their spread or preventing their introduction into areas where they are not yet present. Techniques for the detection and identification of plant viruses and viroids are evolving quickly, and they play an increasingly important role in the control of these pathogens. In this context, the harmonization and validation of the detection methods used have become crucial in making the diagnosis more and more reliable as well as harmonized. This Special Issue of Plants will highlight new techniques in the detection and identification of plant viruses and viroids, with particular attention to NGS systems. Therefore, in this Special Issue, articles (original research papers, abstract, and reviews) that focus on the development and validation of new and reliable detection methods of plant viruses and viroids are welcome.

Dr. Francesco Faggioli
Dr. Luca Ferretti
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Plants is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • molecular detection methods
  • serological detection methods
  • identification methods
  • NGS
  • validation

Published Papers (4 papers)

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Research

12 pages, 3811 KiB  
Article
Analysis of Wheat Virome in Korea Using Illumina and Oxford Nanopore Sequencing Platforms
by Hyo-Jeong Lee, Sang-Min Kim and Rae-Dong Jeong
Plants 2023, 12(12), 2374; https://doi.org/10.3390/plants12122374 - 19 Jun 2023
Viewed by 1461
Abstract
Wheat (Triticum aestivum L.) is one of the most important staple crops in the world, along with maize and rice. More than 50 plant viruses are known to infect wheat worldwide. To date, there are no studies on the identification of viruses [...] Read more.
Wheat (Triticum aestivum L.) is one of the most important staple crops in the world, along with maize and rice. More than 50 plant viruses are known to infect wheat worldwide. To date, there are no studies on the identification of viruses infecting wheat in Korea. Therefore, we investigated virome in wheat from three different geographical regions where wheat is mainly cultivated in Korea using Oxford Nanopore Technology (ONT) sequencing and Illumina sequencing. Five viral species, including those known to infect wheat, were identified using high-throughput sequencing strategies. Of these, barley virus G (BVG) and Hordeum vulgare endornavirus (HvEV) were consistently present in all libraries. Sugarcane yellow leaf virus (SCYLV) and wheat leaf yellowing-associated virus (WLYaV) were first identified in Korean wheat samples. The viruses identified by ONT and Illumina sequencing were compared using a heatmap. Though the ONT sequencing approach is less sensitive, the analysis results were similar to those of Illumina sequencing in our study. Both platforms served as reliable and powerful tools for detecting and identifying wheat viruses, achieving a balance between practicality and performance. The findings of this study will provide deeper insights into the wheat virosphere and further help improve disease management strategies. Full article
(This article belongs to the Special Issue Identification of Plant Viruses and Viroids)
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17 pages, 1550 KiB  
Article
Development, Validation, and Application of Reverse Transcription Real-Time and Droplet Digital PCR Assays for the Detection of the Potyviruses Watermelon Mosaic Virus and Zucchini Yellow Mosaic Virus in Cucurbits
by Marta Luigi, Ariana Manglli, Carla Libia Corrado, Antonio Tiberini, Elisa Costantini, Luca Ferretti, Laura Tomassoli and Sabrina Bertin
Plants 2023, 12(12), 2364; https://doi.org/10.3390/plants12122364 - 19 Jun 2023
Cited by 1 | Viewed by 1250
Abstract
Among the cucurbit-infecting viruses, watermelon mosaic virus (WMV) and zucchini yellow mosaic virus (ZYMV) (Potyvirus: Potyviridae) are responsible for severe symptoms on cucumber, melon, watermelon, and zucchini cultivations worldwide. In this study, reverse transcription real-time PCR (real-time RT-PCR) and droplet-digital PCR (RT-ddPCR) assays [...] Read more.
Among the cucurbit-infecting viruses, watermelon mosaic virus (WMV) and zucchini yellow mosaic virus (ZYMV) (Potyvirus: Potyviridae) are responsible for severe symptoms on cucumber, melon, watermelon, and zucchini cultivations worldwide. In this study, reverse transcription real-time PCR (real-time RT-PCR) and droplet-digital PCR (RT-ddPCR) assays targeting the coat protein (CP) genes of WMV and ZYMV were developed and validated according to the international standards of plant pest diagnosis (EPPO PM 7/98 (5)). First, the diagnostic performance of WMV-CP and ZYMV-CP real-time RT-PCRs was evaluated, and the assays displayed an analytical sensitivity of 10−5 and 10−3, respectively. The tests also showed an optimal repeatability, reproducibility and analytical specificity, and were reliable for the virus detection in naturally infected samples and across a wide range of cucurbit hosts. Based on these results, the real-time RT-PCR reactions were adapted to set up RT-ddPCR assays. These were the first RT-ddPCR assays aiming at the detection and quantification of WMV and ZYMV and showed a high sensitivity, being able to detect until 9 and 8 copies/µL of WMV or ZYMV, respectively. The RT-ddPCRs allowed the direct estimation of the virus concentrations and opened to a broad range of applications in disease management, such as the evaluation of partial resistance in breeding processes, identification of antagonistic/synergistic events, and studies on the implementation of natural compounds in the integrated management strategies. Full article
(This article belongs to the Special Issue Identification of Plant Viruses and Viroids)
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16 pages, 2949 KiB  
Article
Development and Validation of a Duplex RT-qPCR for Detection of Peach Latent Mosaic Viroid and Comparison of Different Nucleic-Acid-Extraction Protocols
by Marta Luigi, Anna Taglienti, Carla Libia Corrado, Marco Cardoni, Simona Botti, Rita Bissani, Paola Casati, Alessandro Passera, Niccolò Miotti, Kris De Jonghe, Ellen Everaert, Antonio Olmos, Ana B. Ruiz-García and Francesco Faggioli
Plants 2023, 12(9), 1802; https://doi.org/10.3390/plants12091802 - 27 Apr 2023
Cited by 1 | Viewed by 1239
Abstract
Peach latent mosaic viroid (PLMVd) is an important pathogen that causes disease in peaches. Control of this viroid remains problematic because most PLMVd variants are symptomless, and although there are many detection tests in use, the reliability of PCR-based methods is compromised by [...] Read more.
Peach latent mosaic viroid (PLMVd) is an important pathogen that causes disease in peaches. Control of this viroid remains problematic because most PLMVd variants are symptomless, and although there are many detection tests in use, the reliability of PCR-based methods is compromised by the complex, branched secondary RNA structure of the viroid and its genetic diversity. In this study, a duplex RT-qPCR method was developed and validated against two previously published single RT-qPCRs, which were potentially able to detect all known PLMVd variants when used in tandem. In addition, in order to simplify the sample preparation, rapid-extraction protocols based on the use of crude sap or tissue printing were compared with commercially available RNA purification kits. The performance of the new procedure was evaluated in a test performance study involving five participant laboratories. The new method, in combination with rapid-sample-preparation approaches, was demonstrated to be feasible and reliable, with the advantage of detecting all different PLMVd isolates/variants assayed in a single reaction, reducing costs for routine diagnosis. Full article
(This article belongs to the Special Issue Identification of Plant Viruses and Viroids)
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20 pages, 3986 KiB  
Article
Targeted Whole Genome Sequencing (TWG-Seq) of Cucumber Green Mottle Mosaic Virus Using Tiled Amplicon Multiplex PCR and Nanopore Sequencing
by Joanne Mackie, Wycliff M. Kinoti, Sumit I. Chahal, David A. Lovelock, Paul R. Campbell, Lucy T. T. Tran-Nguyen, Brendan C. Rodoni and Fiona E. Constable
Plants 2022, 11(20), 2716; https://doi.org/10.3390/plants11202716 - 14 Oct 2022
Cited by 6 | Viewed by 2361
Abstract
Rapid and reliable detection tools are essential for disease surveillance and outbreak management, and genomic data is essential to determining pathogen origin and monitoring of transmission pathways. Low virus copy number and poor RNA quality can present challenges for genomic sequencing of plant [...] Read more.
Rapid and reliable detection tools are essential for disease surveillance and outbreak management, and genomic data is essential to determining pathogen origin and monitoring of transmission pathways. Low virus copy number and poor RNA quality can present challenges for genomic sequencing of plant viruses, but this can be overcome by enrichment of target nucleic acid. A targeted whole genome sequencing (TWG-Seq) approach for the detection of cucumber green mottle mosaic virus (CGMMV) has been developed where overlapping amplicons generated using two multiplex RT-PCR assays are then sequenced using the Oxford Nanopore MinION. Near complete coding region sequences were assembled with ≥100× coverage for infected leaf tissue dilution samples with RT-qPCR cycle quantification (Cq) values from 11.8 to 38 and in seed dilution samples with Cq values 13.8 to 27. Consensus sequences assembled using this approach showed greater than 99% nucleotide similarity when compared to genomes produced using metagenomic sequencing. CGMMV could be confidently detected in historical seed isolates with degraded RNA. Whilst limited access to, and costs associated with second-generation sequencing platforms can influence diagnostic outputs, the portable Nanopore technology offers an affordable high throughput sequencing alternative when combined with TWG-Seq for low copy or degraded samples. Full article
(This article belongs to the Special Issue Identification of Plant Viruses and Viroids)
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