New Findings in Plant Virology toward Guiding Rational Control Strategies

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 24502

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Guest Editor
Molecular Plant Pathology Group, Agriculture Biotechnology Research Institute, National Agricultural Research and Innovation Center, H2100 Godollo, Hungary
Interests: plant virus diagnostics using small RNA HTS; grapevine; fruit trees
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Special Issue Information

Dear Colleagues,

Our opinions on “virus infection” and “quarantine” have certainly changed in the last month. It is perhaps not too much of an exaggeration to state that the emergence of the new coronavirus has resulted in an unprecedented effect on how people think about virology, virus evolution, and quarantine. In contrast to animal-infecting viruses, viruses hosted by plants have several alternative barriers to overcome. Their hosts cannot move over long distances and their cells are protected by an almost impermeable cell wall. Despite these barriers, we, as plant virologists, have also experienced an acceleration in the emergence and spread of new plant viruses due to globalization. Non-controlled markets for plants which are propagated in a vegetative way as well as the introduction of vector species into new places can lead to the movement of viruses both into new geographical places as well as into new hosts. Unfortunately, these unexpected ways in which viruses can spread have not yet been fully investigated and explored.

Molecular virus detection methods have been changing in the past decade. New methods, like high-throughput sequencing, allow us to reveal the presence of any living organism in the investigated sample. This is why records of new findings—new locations, new hosts, new vectors, and even the existence of new viruses and viroids—have also increased. Many of these findings originate from latent infections that have existed for a long time, where there has been a lack of symptoms and illness of the plant that coincides with the presence of the “new” virus.

Quarantine measures help us to protect our plants, home, and country from invading viruses, whose infections can have harmful effects. Regarding plant health, these measures include eradication of the infected plant together with a buffer zone where rigorous control is carried out. Since it is obligatory to ensure the safety of our crops and flora, control strategies must rely on firm knowledge about when and where a newly described virus deserves strict regulation.

For this Special Issue of Plants, I would like to collect reports on new and first descriptions of plant viruses and surveys in which possible new sites of virus entry are investigated, discussed, or reviewed. Papers describing the identification of plant viruses at new geographic locations, on new hosts, or including descriptions of new viruses which can be linked to already described diseases are also welcome.

To keep the message of this Special Issue concise, the discussion or conclusions of the paper should contain recommendations about possible control strategies of the investigated virus, crop, insect vector, or weed based on the new findings.

We hope that this collection can help decision makers to implement rational plant protection measures which can be observed as well as serve to prevent the spread of invading pathogens around the globe.

Dr. Éva Várallyay
Guest Editor

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Keywords

  • new descriptions of viruses
  • virus
  • HTS
  • regulation
  • vector
  • weed

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Published Papers (7 papers)

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Research

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10 pages, 2266 KiB  
Article
Grapevine Pinot Gris Virus Is Present in Different Non-Vitis Hosts
by Emese Demian, Nikoletta Jaksa-Czotter and Eva Varallyay
Plants 2022, 11(14), 1830; https://doi.org/10.3390/plants11141830 - 12 Jul 2022
Cited by 12 | Viewed by 2384
Abstract
Grapevine Pinot gris virus (GPGV) was described in Italy using a metagenomic approach: next-generation sequencing of the virus-derived small RNAs. Since that time, it has been reported all over the world. The presence of GPGV is associated with grapevine disease, but most of [...] Read more.
Grapevine Pinot gris virus (GPGV) was described in Italy using a metagenomic approach: next-generation sequencing of the virus-derived small RNAs. Since that time, it has been reported all over the world. The presence of GPGV is associated with grapevine disease, but most of the time, the disease is asymptomatic. Although the host range of this virus has not been investigated, it has been found in the non-Vitis hosts, Silene latifolia and Chenopodium album. We investigated the presence of GPGV in grapevine and other plant species growing as weeds in the vineyard. Using RT-PCR, we identified GPGV in seven non-Vitis hosts: Ailanthus, Asclepias, Crataegus, Fraxinus, Rosa, Rubus, and Sambucus. In the case of Rosa and Rubus, this finding was supported by Northern blot detection of the virus. GPGV strains in non-Vitis hosts belong to the asymptomatic clade, and are clustered according to their original geographic locations. The presence of GPGV in species other than grapevine shows that besides well-known vector and propagating material-based infections, other possible entry sites for the virus can exist, which have to be taken into consideration when developing reliable regulation strategies. Full article
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12 pages, 2163 KiB  
Article
First Detection and Molecular Characterization of Apple Stem Grooving Virus, Apple Chlorotic Leaf Spot Virus, and Apple Hammerhead Viroid in Loquat in Spain
by Celia Canales, Félix Morán, Antonio Olmos and Ana Belén Ruiz-García
Plants 2021, 10(11), 2293; https://doi.org/10.3390/plants10112293 - 25 Oct 2021
Cited by 10 | Viewed by 3223
Abstract
Loquat (Eriobotrya japonica) is an important crop in Spain. To date, only one viral species, apple stem pitting virus (ASPV), has been detected in Spanish loquat orchards. In this study, the presence of additional viruses infecting this crop in Spain was [...] Read more.
Loquat (Eriobotrya japonica) is an important crop in Spain. To date, only one viral species, apple stem pitting virus (ASPV), has been detected in Spanish loquat orchards. In this study, the presence of additional viruses infecting this crop in Spain was investigated. RT-PCR and high-throughput sequencing (HTS) of symptomatic loquat plants led to first-time detection and characterization of apple stem grooving virus (ASGV), also known as citrus tatter leaf virus (CTLV), and apple chlorotic leaf spot virus (ACLSV) from Spain with description of nearly complete genomic sequences. The frequency of ACLSV infection was the highest, with over 30% of the samples testing positive and were also detected as coinfections with ASGV and ASPV, although most of the samples infected were symptomless. Studies on all the full-length sequences available in the databases were performed in order to establish the phylogenetic relationships of the Spanish isolates of these two viral species. Moreover, apple hammerhead viroid (AHVd) was also detected to infect loquat, the first host different from apple reported for this viroid to date. Full article
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10 pages, 3232 KiB  
Communication
High-Throughput Sequencing Indicates a Novel Marafivirus in Grapevine Showing Vein-Clearing Symptoms
by Xudong Fan, Zunping Zhang, Chen Li, Fang Ren, Guojun Hu, Baodong Zhang and Yafeng Dong
Plants 2021, 10(7), 1487; https://doi.org/10.3390/plants10071487 - 20 Jul 2021
Cited by 5 | Viewed by 2651
Abstract
A putative new marafivirus was identified in a ‘Jumeigui’ grapevine exhibitting obvious vein-clearing symptoms by high-throughput sequencing, which tentatively named grapevine-associated marafivirus (GaMV). The nearly complete genomic sequence of GaMV was amplified by reverse transcription PCR, and the terminal sequences were determined using [...] Read more.
A putative new marafivirus was identified in a ‘Jumeigui’ grapevine exhibitting obvious vein-clearing symptoms by high-throughput sequencing, which tentatively named grapevine-associated marafivirus (GaMV). The nearly complete genomic sequence of GaMV was amplified by reverse transcription PCR, and the terminal sequences were determined using the rapid amplification of cDNA ends method. The nearly complete genome of GaMV is 6346 bp long, excluding the poly(A) tail, and shows 51.2–62.3% nucleotide identity with other members of the genera Marafivirus, Maculavirus and Tymovirus in the family Tymoviridae. Additionally, it includes five functional domains homologous to those found in members of these genera. A phylogenetic analysis showed that GaMV clustered with other species-related marafiviruses. These data support GaMV being a representative member of a novel species in the genus Marafivirus. Furthermore, GaMV was graft-transmissible and 26 of 516 (5.04%) grapevine samples from five provinces in China tested positive by reverse transcription PCR. The coat protein of GaMV isolates shared 91.7–100% and 96.7–100% identities at the nt and aa levels, respectively. The coat protein-based phylogenetic trees revealed three well-defined clusters. Full article
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14 pages, 8438 KiB  
Article
Distribution and Genetic Diversity of Grapevine Viruses in Russia
by Elena Porotikova, Uliana Terehova, Vitalii Volodin, Eugeniya Yurchenko and Svetlana Vinogradova
Plants 2021, 10(6), 1080; https://doi.org/10.3390/plants10061080 - 27 May 2021
Cited by 11 | Viewed by 3720
Abstract
Viral diseases can seriously damage the vineyard productivity and the quality of grape and wine products. Therefore, the study of the species composition and range of grapevine viruses is important for the development and implementation of strategies and tactics to limit their spread [...] Read more.
Viral diseases can seriously damage the vineyard productivity and the quality of grape and wine products. Therefore, the study of the species composition and range of grapevine viruses is important for the development and implementation of strategies and tactics to limit their spread and increase the economic benefits of viticulture. In 2014–2019, we carried out a large-scale phytosanitary monitoring of Russian commercial vineyards in the Krasnodar region, Stavropol region and Republic of Crimea. A total of 1857 samples were collected and tested for the presence of Grapevine rupestris stem pitting-associated virus (GRSPaV), Grapevine virus A (GVA), Grapevine leafroll-associated virus-1 (GLRaV-1), Grapevine leafroll-associated virus-2 (GLRaV-2), Grapevine leafroll-associated virus-3 (GLRaV-3), Grapevine fanleaf virus (GFLV), and Grapevine fleck virus (GFkV) using RT-PCR. Out of all samples tested, 54.5% were positive for at least one of the viruses (GRSPaV, GVA, GLRaV-1, GLRaV-2, GLRaV-3, GFLV, GFkV) in the Stavropol region, 49.8% in the Krasnodar region and 49.5% in the Republic of Crimea. Some plants were found to be infected with several viruses simultaneously. In the Republic of Crimea, for instance, a number of plants were infected with five viruses. In the Krasnodar region and the Republic of Crimea, 4.7% and 3.3% of the samples were predominantly infected with both GFkV and GRSPaV, whereas in the Stavropol region, 6% of the selected samples had both GLRaV-1 and GVA infections. We carried out a phylogenetic analysis of the coat protein genes of the detected viruses and identified the presence of GVA of groups I and IV, GRSPaV of groups BS and SG1, GLRaV-1 of group III, GLRaV-2 of groups PN and H4, GLRaV-3 of groups I and III. The results obtained make it possible to assess the viral load and the distribution of the main grapevine viruses on plantations in the viticultural zones of Russia, emphasizing the urgent need to develop and implement long-term strategies for the control of viral diseases of grapes. Full article
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8 pages, 2321 KiB  
Communication
Identification and Sequence Analysis of a Novel Ilarvirus Infecting Sweet Cherry
by Chrysoula G. Orfanidou, Fei Xing, Jun Zhou, Shifang Li, Nikolaos I. Katis and Varvara I. Maliogka
Plants 2021, 10(3), 514; https://doi.org/10.3390/plants10030514 - 10 Mar 2021
Cited by 8 | Viewed by 2789
Abstract
In the present study, we utilized high throughput and Sanger sequencing to determine the complete nucleotide sequence of a putative new ilarvirus species infecting sweet cherry, tentatively named prunus virus I (PrVI). The genome of PrVI is comprised of three RNA segments of [...] Read more.
In the present study, we utilized high throughput and Sanger sequencing to determine the complete nucleotide sequence of a putative new ilarvirus species infecting sweet cherry, tentatively named prunus virus I (PrVI). The genome of PrVI is comprised of three RNA segments of 3474 nt (RNA1), 2911 nt (RNA2), and 2231 nt (RNA3) and features conserved motifs representative of the genus Ilarvirus. BlastN analysis revealed 68.1–71.9% nt identity of PrVI with strawberry necrotic shock virus (SNSV). In subsequent phylogenetic analysis, PrVI was grouped together with SNSV and blackberry chlorotic ringspot virus (BCRV), both members of subgroup 1 of ilarviruses. In addition, mini-scale surveys in stone fruit orchards revealed the presence of PrVI in a limited number of sweet cherries and in one peach tree. Overall, our data suggest that PrVI is a novel species of the genus Ilarvirus and it consists the fifth member of the genus that is currently known to infect Prunus spp. Full article
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11 pages, 1837 KiB  
Article
Millet Could Be both a Weed and Serve as a Virus Reservoir in Crop Fields
by György Pasztor, Zsuzsanna Galbacs N., Tamas Kossuth, Emese Demian, Erzsebet Nadasy, Andras P. Takacs and Eva Varallyay
Plants 2020, 9(8), 954; https://doi.org/10.3390/plants9080954 - 28 Jul 2020
Cited by 4 | Viewed by 3486
Abstract
Millet is a dangerous weed in crop fields. A lack of seed dormancy helps it to spread easily and be present in maize, wheat, and other crop fields. Our previous report revealed the possibility that millet can also play a role as a [...] Read more.
Millet is a dangerous weed in crop fields. A lack of seed dormancy helps it to spread easily and be present in maize, wheat, and other crop fields. Our previous report revealed the possibility that millet can also play a role as a virus reservoir. In that study, we focused on visual symptoms and detected the presence of several viruses in millet using serological methods, which can only detect the presence of the investigated pathogen. In this current work, we used small RNA high-throughput sequencing as an unbiased virus diagnostic method to uncover presenting viruses in randomly sampled millet grown as a volunteer weed in two maize fields, showing stunting, chlorosis, and striped leaves. Our results confirmed the widespread presence of wheat streak mosaic virus at both locations. Moreover, barley yellow striate mosaic virus and barley virus G, neither of which had been previously described in Hungary, were also identified. As these viruses can cause severe diseases in wheat and other cereals, their presence in a weed implies a potential infection risk. Our study indicates that the presence of millet in fields requires special control to prevent the emergence of new viral diseases in crop fields. Full article
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Review

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17 pages, 336 KiB  
Review
An Annotated List of Legume-Infecting Viruses in the Light of Metagenomics
by Elisavet K. Chatzivassiliou
Plants 2021, 10(7), 1413; https://doi.org/10.3390/plants10071413 - 10 Jul 2021
Cited by 20 | Viewed by 4016
Abstract
Legumes, one of the most important sources of human food and animal feed, are known to be susceptible to a plethora of plant viruses. Many of these viruses cause diseases which severely impact legume production worldwide. The causal agents of some important virus-like [...] Read more.
Legumes, one of the most important sources of human food and animal feed, are known to be susceptible to a plethora of plant viruses. Many of these viruses cause diseases which severely impact legume production worldwide. The causal agents of some important virus-like diseases remain unknown. In recent years, high-throughput sequencing technologies have enabled us to identify many new viruses in various crops, including legumes. This review aims to present an updated list of legume-infecting viruses. Until 2020, a total of 168 plant viruses belonging to 39 genera and 16 families, officially recognized by the International Committee on Taxonomy of Viruses (ICTV), were reported to naturally infect common bean, cowpea, chickpea, faba-bean, groundnut, lentil, peas, alfalfa, clovers, and/or annual medics. Several novel legume viruses are still pending approval by ICTV. The epidemiology of many of the legume viruses are of specific interest due to their seed-transmission and their dynamic spread by insect-vectors. In this review, major aspects of legume virus epidemiology and integrated control approaches are also summarized. Full article
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