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Plants
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Emerging Molecular Diagnostics for Plant Virology
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Emerging Molecular Diagnostics for Plant Virology

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 (31 May 2022) | Viewed by 17216

Special Issue Editors

Dr. Fiona Filardo

E-Mail Website
Guest Editor
Queensland Department of Agriculture, Fisheries, Ecosciences Precinct, GPO Box 267, Brisbane, QLD 4001, Australia
Interests: plant virology; virus taxonomy; plant pathology; plant molecular biology; molecular diagnostic; systematics; bioinformatics
Dr. Linda Zheng

E-Mail Website
Guest Editor
Agriculture Victoria Research, AgriBio, 5 Ring Road, Bundoora, VIC 3083, Australia
Interests: molecular diagnostics; molecular pathology
Dr. Frederic Aparicio

E-Mail Website
Guest Editor
Department of Molecular and Evolutionary Plant Virology, Instituto de Biología Molecular y Celular de Plantas (IBMCP) (UPV-CSIC), Ingeniero Fausto Elio s/n, 46022 Valencia, Spain
Interests: plant virus–host factor interactions; RNA viruses; post-transcriptional modifications during virus infection

Special Issue Information

Dear Colleagues,

Viral diseases are a major threat to sustainable agriculture, and successful disease management relies on efficient and reliable diagnostic tools for accurate virus identification. With the emergence of new viral diseases due to the ability of viruses to rapidly evolve, the movement of infected plant material around the world and the impact of climate change on virus–vector–host interactions, a variety of diagnostic tools will need to be available. In recent decades, rapid and specific diagnostic techniques such as enzyme-linked immunosorbent assays (ELISA), tissue blot immunoassays (TBIA) and molecular techniques such as DNA amplification have greatly improved viral diagnostics. More recently, high-throughput sequencing and bioinformatics have been used to obtain whole genomes of viruses, leading to the discovery of new and recombinant viruses, and species diversity within virus families. Loop-mediated isothermal amplification (LAMP) is also being utilized, enabling some virus identifications to be taken out of the lab and into the field. New and emerging techniques for viral diagnostics are likely to be used more commonly for field surveillance and to improve our understanding of viral epidemiology—a critical step towards improving disease management of viruses in order to achieve sustainable agriculture.

This Special Issue of Plants will cover a wide variety of emerging molecular-based tools, both laboratory- and field-based, aimed at identifying, classifying and understanding the epidemiology of plant viruses, including phytoplasmas.   

Dr. Fiona Filardo
Dr. Linda Zheng
Dr. Frederic Aparicio
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

  • virology
  • plant pathology
  • molecular diagnostics
  • emerging diagnostics
  • disease management
  • sustainable agriculture

Published Papers (6 papers)

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Research

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15 pages, 3940 KiB  
Article
Development of a Novel Tissue Blot Hybridization Chain Reaction for the Identification of Plant Viruses
by Fiona Filardo, Peter Vukovic, Murray Sharman, Cherie Gambley and Paul Campbell
Plants 2022, 11(17), 2325; https://doi.org/10.3390/plants11172325 - 05 Sep 2022
Viewed by 1775
Abstract
Assays for the high throughput screening of crops for virus monitoring need to be quick, easy, and low cost. One method involves using tissue blot immunoassays (TBIA), where plant stems are blotted onto nitrocellulose membrane and screened with available antibodies against a range [...] Read more.
Assays for the high throughput screening of crops for virus monitoring need to be quick, easy, and low cost. One method involves using tissue blot immunoassays (TBIA), where plant stems are blotted onto nitrocellulose membrane and screened with available antibodies against a range of viruses. TBIAs are inexpensive but limited by antibody availability and specificity. To circumvent the antibody limitations, we developed the tissue blot hybridization chain reaction (TB-HCR). As with TBIA, plant stems are blotted onto a nitrocellulose membrane, however, TB-HCR involves using nucleic acid probes instead of antibodies. We demonstrated for the first time that TB-HCR can be used for plant viruses by designing and testing probes against species from several virus genera including begomovirus, polerovirus, luteovirus, cucumovirus, and alfamovirus. We also explored different hairpin reporter methods such as biotin/streptavidin-AP and the Alexa Fluor-488 Fluorophore. TB-HCR has applications for low-cost diagnostics for large sample numbers, rapid diagnostic deployment for new viruses, and can be performed as a preliminary triage assay prior to downstream applications. Full article
(This article belongs to the Special Issue Emerging Molecular Diagnostics for Plant Virology)
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14 pages, 1579 KiB  
Article
Grapevine Badnavirus 1: Detection, Genetic Diversity, and Distribution in Croatia
by Martin Jagunić, Alfredo Diaz-Lara, Maher Al Rwahnih, Darko Preiner, Kristian Stevens, Goran Zdunić, Minsook Hwang and Darko Vončina
Plants 2022, 11(16), 2135; https://doi.org/10.3390/plants11162135 - 16 Aug 2022
Cited by 2 | Viewed by 1751
Abstract
Grapevine badnavirus 1 (GBV-1) was recently discovered in grapevine using high throughput sequencing. In order to carry out large-scale testing that will allow for better insights into virus distribution, conventional and real-time PCR assays were developed using sequences both from previously known, and [...] Read more.
Grapevine badnavirus 1 (GBV-1) was recently discovered in grapevine using high throughput sequencing. In order to carry out large-scale testing that will allow for better insights into virus distribution, conventional and real-time PCR assays were developed using sequences both from previously known, and four newly characterized isolates. Throughout the growing season and dormancy, GBV-1 can be detected by real-time PCR using available tissue, with the possibility of false-negative results early in vegetation growth. GBV-1 real-time PCR analysis of 4302 grapevine samples from the Croatian continental and coastal wine-growing regions revealed 576 (~13.4%) positive vines. In the continental wine-growing region, virus incidence was confirmed in only two collection plantations, whereas in the coastal region, infection was confirmed in 30 commercial vineyards and one collection plantation. Infection rates ranged from 1.9 to 96% at the different sites, with predominantly autochthonous grapevine cultivars infected. Conventional PCR products obtained from 50 newly discovered GBV-1 isolates, containing the 375 nucleotides long portion of the reverse transcriptase gene, showed nucleotide and amino acid identities ranging from 94.1 to 100% and from 92.8 to 100%, respectively. The reconstructed phylogenetic tree positioned the GBV-1 isolates taken from the same vineyard close to each other indicating a possible local infection event, although the tree nodes were generally not well supported. Full article
(This article belongs to the Special Issue Emerging Molecular Diagnostics for Plant Virology)
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13 pages, 4706 KiB  
Article
Tobacco Mosaic Virus Infection of Chrysanthemums in Thailand: Development of Colorimetric Reverse-Transcription Loop-Mediated Isothermal Amplification (RT–LAMP) Technique for Sensitive and Rapid Detection
by Salit Supakitthanakorn, Kanjana Vichittragoontavorn, Anurag Sunpapao, Kaewalin Kunasakdakul, Pilunthana Thapanapongworakul and On-Uma Ruangwong
Plants 2022, 11(14), 1788; https://doi.org/10.3390/plants11141788 - 06 Jul 2022
Cited by 7 | Viewed by 4220
Abstract
We detected tobacco mosaic virus (TMV), a member of the genus Tobamovirus and one of the most significant plant-infecting viruses, for the first time in a chrysanthemum in Thailand using reverse-transcription polymerase chain reaction (RT–PCR). The TMV-infected chrysanthemum leaves exhibited mosaic symptoms. We [...] Read more.
We detected tobacco mosaic virus (TMV), a member of the genus Tobamovirus and one of the most significant plant-infecting viruses, for the first time in a chrysanthemum in Thailand using reverse-transcription polymerase chain reaction (RT–PCR). The TMV-infected chrysanthemum leaves exhibited mosaic symptoms. We conducted a sequence analysis of the coat protein (CP) gene and found that the TMV detected in the chrysanthemum had 98% identity with other TMV isolates in GenBank. We carried out bioassays and showed that TMV induced mosaic and stunting symptoms in inoculated chrysanthemums. We observed the rigid rod structure of TMV under a transmission electron microscope (TEM). To enhance the speed and sensitivity of detection, we developed a colorimetric RT loop-mediated isothermal amplification (LAMP) technique. We achieved LAMP detection after 30 min incubation in isothermal conditions at 65 °C, and distinguished the positive results according to the color change from pink to yellow. The sensitivity of the LAMP technique was 1000-fold greater than that of RT–PCR, and we found no cross-reactivity with other viruses or viroids. This is the first reported case of a TMV-infected chrysanthemum in Thailand, and our colorimetric RT–LAMP TMV detection method is the first of its kind. Full article
(This article belongs to the Special Issue Emerging Molecular Diagnostics for Plant Virology)
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17 pages, 10644 KiB  
Article
The Potential of Molecular Indicators of Plant Virus Infection: Are Plants Able to Tell Us They Are Infected?
by Gardette R. Valmonte-Cortes, Sonia T. Lilly, Michael N. Pearson, Colleen M. Higgins and Robin M. MacDiarmid
Plants 2022, 11(2), 188; https://doi.org/10.3390/plants11020188 - 11 Jan 2022
Cited by 2 | Viewed by 2444
Abstract
To our knowledge, there are no reports that demonstrate the use of host molecular markers for the purpose of detecting generic plant virus infection. Two approaches involving molecular indicators of virus infection in the model plant Arabidopsis thaliana were examined: the accumulation of [...] Read more.
To our knowledge, there are no reports that demonstrate the use of host molecular markers for the purpose of detecting generic plant virus infection. Two approaches involving molecular indicators of virus infection in the model plant Arabidopsis thaliana were examined: the accumulation of small RNAs (sRNAs) using a microfluidics-based method (Bioanalyzer); and the transcript accumulation of virus-response related host plant genes, suppressor of gene silencing 3 (AtSGS3) and calcium-dependent protein kinase 3 (AtCPK3) by reverse transcriptase-quantitative PCR (RT-qPCR). The microfluidics approach using sRNA chips has previously demonstrated good linearity and good reproducibility, both within and between chips. Good limits of detection have been demonstrated from two-fold 10-point serial dilution regression to 0.1 ng of RNA. The ratio of small RNA (sRNA) to ribosomal RNA (rRNA), as a proportion of averaged mock-inoculation, correlated with known virus infection to a high degree of certainty. AtSGS3 transcript decreased between 14- and 28-days post inoculation (dpi) for all viruses investigated, while AtCPK3 transcript increased between 14 and 28 dpi for all viruses. A combination of these two molecular approaches may be useful for assessment of virus-infection of samples without the need for diagnosis of specific virus infection. Full article
(This article belongs to the Special Issue Emerging Molecular Diagnostics for Plant Virology)
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Review

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33 pages, 2198 KiB  
Review
The Potential Use of Isothermal Amplification Assays for In-Field Diagnostics of Plant Pathogens
by Aleksandr V. Ivanov, Irina V. Safenkova, Anatoly V. Zherdev and Boris B. Dzantiev
Plants 2021, 10(11), 2424; https://doi.org/10.3390/plants10112424 - 10 Nov 2021
Cited by 20 | Viewed by 4226
Abstract
Rapid, sensitive, and timely diagnostics are essential for protecting plants from pathogens. Commonly, PCR techniques are used in laboratories for highly sensitive detection of DNA/RNA from viral, viroid, bacterial, and fungal pathogens of plants. However, using PCR-based methods for in-field diagnostics is a [...] Read more.
Rapid, sensitive, and timely diagnostics are essential for protecting plants from pathogens. Commonly, PCR techniques are used in laboratories for highly sensitive detection of DNA/RNA from viral, viroid, bacterial, and fungal pathogens of plants. However, using PCR-based methods for in-field diagnostics is a challenge and sometimes nearly impossible. With the advent of isothermal amplification methods, which provide amplification of nucleic acids at a certain temperature and do not require thermocyclic equipment, going beyond the laboratory has become a reality for molecular diagnostics. The amplification stage ceases to be limited by time and instruments. Challenges to solve involve finding suitable approaches for rapid and user-friendly plant preparation and detection of amplicons after amplification. Here, we summarize approaches for in-field diagnostics of phytopathogens based on different types of isothermal amplification and discuss their advantages and disadvantages. In this review, we consider a combination of isothermal amplification methods with extraction and detection methods compatible with in-field phytodiagnostics. Molecular diagnostics in out-of-lab conditions are of particular importance for protecting against viral, bacterial, and fungal phytopathogens in order to quickly prevent and control the spread of disease. We believe that the development of rapid, sensitive, and equipment-free nucleic acid detection methods is the future of phytodiagnostics, and its benefits are already visible. Full article
(This article belongs to the Special Issue Emerging Molecular Diagnostics for Plant Virology)
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Other

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7 pages, 2027 KiB  
Technical Note
Detection and Simultaneous Differentiation of Three Co-infected Viruses in Zanthoxylum armatum
by Zhenfei Dong, Xiaoli Zhao, Junjie Liu, Binhui Zhan and Shifang Li
Plants 2022, 11(9), 1242; https://doi.org/10.3390/plants11091242 - 05 May 2022
Viewed by 1327
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) [...] Read more.
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. Full article
(This article belongs to the Special Issue Emerging Molecular Diagnostics for Plant Virology)
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