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Viruses
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Emerging Plant Viruses
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Emerging Plant Viruses

A special issue of Viruses (ISSN 1999-4915). This special issue belongs to the section "Viruses of Plants, Fungi and Protozoa".

Deadline for manuscript submissions: closed (30 June 2023) | Viewed by 23851

Special Issue Editors

Dr. Jean-Michel Hily

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Guest Editor
Institut Français de la Vigne et du Vin, IFV, Domaine de l'Espiguette, 30240 Le Grau-Du-Roi, France
Interests: grapevine; virology; detection; HTS; virome; plant-virus interaction; pathogens
Dr. Nils Poulicard

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Guest Editor
PHIM, Plant Health Institute, Université de Montpellier, IRD, INRAE, CIRAD, SupAgro, 911 Avenue Agropolis, 34394 Montpellier, France
Interests: virus evolution; epidemiology; virus ecology; phylogeography; rice; developping countries

Special Issue Information

Dear Colleagues,

Emerging (and re-emerging) plant viruses are a major threat to food security and the economic stability of societies. The conditions that favour viral emergence are known, starting with an increase in close interactions between wild and cultivated compartments, and modifications to the climate, farming practices and international trades, as well as to the capacity of viruses to quickly evolve and adapt to new hosts.

The ‘emerging plant viruses’ Special Issue of MDPI includes studies covering most aspects of new and re-emerging viruses that impact any staple food and cash crops. Topics of interest include but are not limited to virus discovery, mechanisms of virus entry, pathogenesis, ecology, epidemiology, and decision making at national or international levels that discuss means of detecting, controlling and preventing potential outbreak. Research and reviews are welcomed.

Dr. Jean-Michel Hily
Dr. Nils Poulicard
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. Viruses is an international peer-reviewed open access monthly 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 2600 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

  • virome
  • high-throughput sequencing
  • molecular and field epidemiology
  • evolution
  • modeling analyses
  • adaptation (host jump/spillover)
  • phylogenomics
  • detection/diagnostic
  • decision-making tools/regulation
  • vectors

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Published Papers (9 papers)

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Research

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12 pages, 1361 KiB  
Article
Absence of Seed-Mediated Transmission of Cucumber Mosaic Virus in Espelette Pepper Crops despite Widespread and Recurrent Epidemics
by Judith Hirsch, Marion Szadkowski, Catherine Wipf-Scheibel, Elise Lepage, Paul Dumeaux, Elodie Nguyen, Eric Verdin, Benoît Moury and Loup Rimbaud
Viruses 2023, 15(11), 2159; https://doi.org/10.3390/v15112159 - 27 Oct 2023
Viewed by 1460
Abstract
In the past decade, severe epidemics of cucumber mosaic virus (CMV) have caused significant damage to Espelette pepper crops. This virus threatens the production of Espelette pepper, which plays a significant role in the local economy and touristic attractiveness of the French Basque [...] Read more.
In the past decade, severe epidemics of cucumber mosaic virus (CMV) have caused significant damage to Espelette pepper crops. This virus threatens the production of Espelette pepper, which plays a significant role in the local economy and touristic attractiveness of the French Basque Country, located in southwestern France. In 2021 and 2022, CMV was detected via double-antibody sandwich enzyme-linked immunosorbent assays (DAS-ELISAs) in Gorria pepper seed lots harvested from naturally infected fields scattered throughout the entire Espelette pepper production area. These seed lots were used in greenhouse grow-out tests to determine whether CMV could be transmitted to seedlings from contaminated seeds, using visual symptom assessment, DAS-ELISAs, and reverse transcription-polymerase chain reaction (RT-PCR). Despite the widespread occurrence of CMV in seeds of field samples, the grow-out experiments on a total of over 5000 seedlings yielded no evidence of seed transmission of local CMV isolates in Gorria pepper. Therefore, rather than seeds from infected pepper plants, sources of CMV inoculum in Espelette are more likely to be alternative hosts present in and around pepper fields that can allow for the survival of CMV during the off-season. These results have important epidemiological implications and will guide the choice of effective measures to control current epidemics. Full article
(This article belongs to the Special Issue Emerging Plant Viruses)
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31 pages, 13149 KiB  
Article
Ecological Strategies for Resource Use by Three Bromoviruses in Anthropic and Wild Plant Communities
by Bisola Babalola, Aurora Fraile, Fernando García-Arenal and Michael McLeish
Viruses 2023, 15(8), 1779; https://doi.org/10.3390/v15081779 - 21 Aug 2023
Cited by 1 | Viewed by 1327
Abstract
Ecological strategies for resource utilisation are important features of pathogens, yet have been overshadowed by stronger interest in genetic mechanisms underlying disease emergence. The purpose of this study is to ask whether host range and transmission traits translate into ecological strategies for host-species [...] Read more.
Ecological strategies for resource utilisation are important features of pathogens, yet have been overshadowed by stronger interest in genetic mechanisms underlying disease emergence. The purpose of this study is to ask whether host range and transmission traits translate into ecological strategies for host-species utilisation in a heterogeneous ecosystem, and whether host utilisation corresponds to genetic differentiation among three bromoviruses. We combine high-throughput sequencing and population genomics with analyses of species co-occurrence to unravel the ecological strategies of the viruses across four habitat types. The results show that the bromoviruses that were more closely related genetically did not share similar ecological strategies, but that the more distantly related pair did. Shared strategies included a broad host range and more frequent co-occurrences, which both were habitat-dependent. Each habitat thus presents as a barrier to gene flow, and each virus has an ecological strategy to navigate limitations to colonising non-natal habitats. Variation in ecological strategies could therefore hold the key to unlocking events that lead to emergence. Full article
(This article belongs to the Special Issue Emerging Plant Viruses)
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12 pages, 4283 KiB  
Article
Seed Transmission of Wheat Streak Mosaic Virus and Triticum Mosaic Virus in Differentially Resistant Wheat Cultivars
by Saurabh Gautam, Senthilraja Chinnaiah, Benjamin Herron, Fekede Workneh, Charles M. Rush and Kiran R. Gadhave
Viruses 2023, 15(8), 1774; https://doi.org/10.3390/v15081774 - 21 Aug 2023
Cited by 3 | Viewed by 1708
Abstract
Wheat streak mosaic virus (WSMV) and Triticum mosaic virus (TriMV) are important viral pathogens of wheat in the Great Plains. These viruses individually or in mixed infections with High Plains wheat mosaic virus cause a devastating wheat streak mosaic (WSM) disease. Although seed [...] Read more.
Wheat streak mosaic virus (WSMV) and Triticum mosaic virus (TriMV) are important viral pathogens of wheat in the Great Plains. These viruses individually or in mixed infections with High Plains wheat mosaic virus cause a devastating wheat streak mosaic (WSM) disease. Although seed transmission of WSMV has been studied, no information is currently available on that of TriMV. Furthermore, no study has explored the implications of mixed infections of WSMV and TriMV on seed transmission of one or both viruses. To study both aspects, seeds from differentially resistant field-grown wheat plants (cv. TAM 304 (susceptible), Joe (WSMV resistant, Wsm2 gene), and Breakthrough (BT) (WSMV and TriMV resistant, Wsm1 gene)) showing characteristic WSM symptoms were collected and analyzed to quantify both viruses using qRT-PCR. The percentage of seeds tested positive for WSMV or TriMV individually and in mixed infection varied with cultivar and virus combinations; 13% of TAM 304 seeds tested positive for WSMV, followed by 8% of BT and 4% of Joe seeds. Similarly, TriMV was detected in 12% of BT seeds, followed by 11% of TAM 304 and 8% of Joe seeds. Lastly, mixed infection was detected in 7% of TAM 304 seeds, followed by 4% in BT, and 2% in Joe. Dissection of field-collected seeds into three parts, embryo, endosperm, and seed coat, revealed both WSMV and TriMV accumulated only in the seed coat. Consistent with seeds, percent infection of WSMV or TriMV in the plants that emerged from infected seeds in each treatment varied with cultivar and virus combinations (WSMV: BT 3%; Joe 2%; TAM 304 9%; TriMV: BT 7%; Joe 8%; and TAM 304 10%). Plants infected with mixed viruses showed more pronounced WSM symptoms compared to individual infections. However, both viruses were present only in a few plants (BT: 2%, Joe: 1%, and TAM 304: 4%). Taken together, this study showed that TriMV was transmitted vertically at a higher frequency than WSMV in resistant cultivars, and the seed transmission of TriMV with WSMV increased the virulence of both pathogens (measured via WSM symptom severity) in the emerged plants. Furthermore, Wsm1 and Wsm2 genes considerably reduced WSMV transmission via infected seeds. However, no such effects were observed on TriMV, especially in progeny plants. These results reiterated the importance of planting clean seeds and highlighted the immediate need to identify/develop new sources of TriMV resistance to effectively manage the recurring WSM epidemic. Full article
(This article belongs to the Special Issue Emerging Plant Viruses)
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21 pages, 4244 KiB  
Article
Expanding the Repertoire of the Plant-Infecting Ophioviruses through Metatranscriptomics Data
by Humberto Debat, Maria Laura Garcia and Nicolas Bejerman
Viruses 2023, 15(4), 840; https://doi.org/10.3390/v15040840 - 25 Mar 2023
Cited by 6 | Viewed by 1843
Abstract
Ophioviruses (genus Ophiovirus, family Aspiviridae) are plant-infecting viruses with non-enveloped, filamentous, naked nucleocapsid virions. Members of the genus Ophiovirus have a segmented single-stranded negative-sense RNA genome (ca. 11.3–12.5 kb), encompassing three or four linear segments. In total, these segments encode four [...] Read more.
Ophioviruses (genus Ophiovirus, family Aspiviridae) are plant-infecting viruses with non-enveloped, filamentous, naked nucleocapsid virions. Members of the genus Ophiovirus have a segmented single-stranded negative-sense RNA genome (ca. 11.3–12.5 kb), encompassing three or four linear segments. In total, these segments encode four to seven proteins in the sense and antisense orientation, both in the viral and complementary strands. The genus Ophiovirus includes seven species with viruses infecting both monocots and dicots, mostly trees, shrubs and some ornamentals. From a genomic perspective, as of today, there are complete genomes available for only four species. Here, by exploring large publicly available metatranscriptomics datasets, we report the identification and molecular characterization of 33 novel viruses with genetic and evolutionary cues of ophioviruses. Genetic distance and evolutionary insights suggest that all the detected viruses could correspond to members of novel species, which expand the current diversity of ophioviruses ca. 4.5-fold. The detected viruses increase the tentative host range of ophioviruses for the first time to mosses, liverwort and ferns. In addition, the viruses were linked to several Asteraceae, Orchidaceae and Poaceae crops/ornamental plants. Phylogenetic analyses showed a novel clade of mosses, liverworts and fern ophioviruses, characterized by long branches, suggesting that there is still plenty of unsampled hidden diversity within the genus. This study represents a significant expansion of the genomics of ophioviruses, opening the door to future works on the molecular and evolutionary peculiarity of this virus genus. Full article
(This article belongs to the Special Issue Emerging Plant Viruses)
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6 pages, 1537 KiB  
Communication
First Detection and Genome Characterization of a New RNA Virus, Hibiscus Betacarmovirus, and a New DNA Virus, Hibiscus Soymovirus, Naturally Infecting Hibiscus spp. in Hawaii
by Xupeng Wang, Adriana E. Larrea-Sarmiento, Alejandro Olmedo-Velarde, Alexandra Kong, Wayne Borth, Jon Y Suzuki, Marisa M Wall, Michael J Melzer and John Hu
Viruses 2023, 15(1), 90; https://doi.org/10.3390/v15010090 - 29 Dec 2022
Cited by 2 | Viewed by 2291
Abstract
Hibiscus (Hibiscus spp., family Malvaceae) leaves exhibiting symptoms of mosaic, ringspot, and chlorotic spots were collected in 2020 on Oahu, HI. High-throughput sequencing analysis was conducted on ribosomal RNA-depleted composite RNA samples extracted from symptomatic leaves. About 77 million paired-end reads and [...] Read more.
Hibiscus (Hibiscus spp., family Malvaceae) leaves exhibiting symptoms of mosaic, ringspot, and chlorotic spots were collected in 2020 on Oahu, HI. High-throughput sequencing analysis was conducted on ribosomal RNA-depleted composite RNA samples extracted from symptomatic leaves. About 77 million paired-end reads and 161,970 contigs were generated after quality control, trimming, and de novo assembly. Contig annotation with BLASTX/BLASTN searches revealed a sequence (contig 1) resembling the RNA virus, hibiscus chlorotic ringspot virus (genus Betacarmovirus), and one (contig 2) resembling the DNA virus, peanut chlorotic streak virus (genus Soymovirus). Further bioinformatic analyses of the complete viral genome sequences indicated that these viruses, with proposed names of hibiscus betacarmovirus and hibiscus soymovirus, putatively represent new species in the genera Betacarmovirus and Soymovirus, respectively. RT-PCR using specific primers, designed based on the retrieved contigs, coupled with Sanger sequencing, further confirmed the presence of these viruses. An additional 54 hibiscus leaf samples from other locations on Oahu were examined to determine the incidence and distribution of these viruses. Full article
(This article belongs to the Special Issue Emerging Plant Viruses)
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18 pages, 4048 KiB  
Article
Common but Nonpersistent Acquisitions of Plant Viruses by Plant-Associated Fungi
by Xinran Cao, Jie Liu, Jianguo Pang, Hideki Kondo, Shengqi Chi, Jianfeng Zhang, Liying Sun and Ida Bagus Andika
Viruses 2022, 14(10), 2279; https://doi.org/10.3390/v14102279 - 17 Oct 2022
Cited by 17 | Viewed by 3464
Abstract
Investigating a virus’s host range and cross-infection is important for better understanding the epidemiology and emergence of viruses. Previously, our research group discovered a natural infection of a plant RNA virus, cumber mosaic virus (genus Cucumovirus, family Bromoviridae), in a plant [...] Read more.
Investigating a virus’s host range and cross-infection is important for better understanding the epidemiology and emergence of viruses. Previously, our research group discovered a natural infection of a plant RNA virus, cumber mosaic virus (genus Cucumovirus, family Bromoviridae), in a plant pathogenic basidiomycetous fungus, Rhizoctonia solani, isolated from a potato plant grown in the field. Here, we further extended the study to investigate whether similar cross-infection of plant viruses occurs widely in plant-associated fungi in natural conditions. Various vegetable plants such as spinach, leaf mustard, radish, celery, and other vegetables that showed typical virus-like diseases were collected from the fields in Shandong Province, China. High-throughput sequencing revealed that at least 11 known RNA viruses belonging to different genera, including Potyvirus, Fabavirus, Polerovirus, Waikavirus, and Cucumovirus, along with novel virus candidates belonging to other virus genera, infected or associated with the collected vegetable plants, and most of the leaf samples contained multiple plant viruses. A large number of filamentous fungal strains were isolated from the vegetable leaf samples and subjected to screening for the presence of plant viruses. RT-PCR and Sanger sequencing of the PCR products revealed that among the 169 fungal strains tested, around 50% were carrying plant viruses, and many of the strains harbored multiple plant viruses. The plant viruses detected in the fungal isolates were diverse (10 virus species) and not limited to particular virus genera. However, after prolonged maintenance of the fungal culture in the laboratory, many of the fungal strains have lost the virus. Sequencing of the fungal DNA indicated that most of the fungal strains harboring plant viruses were related to plant pathogenic and/or endophytic fungi belonging to the genera Alternaria, Lecanicillium, and Sarocladium. These observations suggest that the nonpersistent acquisition of plant viruses by fungi may commonly occur in nature. Our findings highlight a possible role for fungi in the life cycle, spread, and evolution of plant viruses. Full article
(This article belongs to the Special Issue Emerging Plant Viruses)
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12 pages, 1991 KiB  
Article
Garlic Potyviruses Are Translocated to the True Seeds through the Vegetative and Reproductive Systems of the Mother Plant
by Einat Shemesh-Mayer, Dana Gelbart, Eduard Belausov, Nisan Sher, Ahuva Daus, Haim D. Rabinowitch and Rina Kamenetsky-Goldstein
Viruses 2022, 14(10), 2092; https://doi.org/10.3390/v14102092 - 21 Sep 2022
Cited by 5 | Viewed by 2825
Abstract
Garlic lost its ability to produce true seeds millennia ago, and today non-fertile commercial cultivars are propagated only vegetatively. Garlic viruses are commonly carried over from one generation of vegetative propagules to the other, while nematodes and arthropods further transmit the pathogens from [...] Read more.
Garlic lost its ability to produce true seeds millennia ago, and today non-fertile commercial cultivars are propagated only vegetatively. Garlic viruses are commonly carried over from one generation of vegetative propagules to the other, while nematodes and arthropods further transmit the pathogens from infected to healthy plants. A recent breakthrough in the production of true (botanical) garlic seeds resulted in rapid scientific progress, but the question of whether viruses are transmitted via seeds remains open and is important for the further development of commercial seed production. We combined morpho-physiological analysis, fluorescence in situ hybridization (FISH), and PCR analysis to follow potyvirus localization and translocation within garlic fertile plants and seeds. Spatial distribution was recorded in both vegetative and reproductive organs. We conclude that garlic potyviruses are translocated to the seeds from the infected mother plant during flower development and post-fertilization, while pollen remains virus-free and does not contribute to seed infection. Therefore, the main practical goal for virus-clean seed production in garlic is the careful maintenance of virus-free mother plants. Although garlic pollen is free of potyviral infection, the male parents’ plants also need to be protected from contamination, since viral infection weakens plants, reducing flowering ability and pollen production. Full article
(This article belongs to the Special Issue Emerging Plant Viruses)
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Review

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14 pages, 1408 KiB  
Review
A Guide to Cannabis Virology: From the Virome Investigation to the Development of Viral Biotechnological Tools
by Niccolò Miotti, Alessandro Passera, Claudio Ratti, Mattia Dall’Ara and Paola Casati
Viruses 2023, 15(7), 1532; https://doi.org/10.3390/v15071532 - 12 Jul 2023
Cited by 6 | Viewed by 2761
Abstract
Cannabis sativa cultivation is experiencing a period of renewed interest due to the new opportunities for its use in different sectors including food, techno-industrial, construction, pharmaceutical and medical, cosmetics, and textiles. Moreover, its properties as a carbon sequestrator and soil improver make it suitable [...] Read more.
Cannabis sativa cultivation is experiencing a period of renewed interest due to the new opportunities for its use in different sectors including food, techno-industrial, construction, pharmaceutical and medical, cosmetics, and textiles. Moreover, its properties as a carbon sequestrator and soil improver make it suitable for sustainable agriculture and climate change mitigation strategies. The increase in cannabis cultivation is generating conditions for the spread of new pathogens. While cannabis fungal and bacterial diseases are better known and characterized, viral infections have historically been less investigated. Many viral infection reports on cannabis have recently been released, highlighting the increasing threat and spread of known and unknown viruses. However, the available information on these pathogens is still incomplete and fragmentary, and it is therefore useful to organize it into a single structured document to provide guidance to growers, breeders, and academic researchers. This review aims to present the historical excursus of cannabis virology, from the pioneering descriptions of virus-like symptoms in the 1940s/50s to the most recent high-throughput sequencing reports. Each of these viruses detected in cannabis will be categorized with an increasing degree of threat according to its potential risk to the crop. Lastly, the development of viral vectors for functional genetics studies will be described, revealing how cannabis virology is evolving not only for the characterization of its virome but also for the development of biotechnological tools for the genetic improvement of this crop. Full article
(This article belongs to the Special Issue Emerging Plant Viruses)
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23 pages, 810 KiB  
Review
Viruses of Yams (Dioscorea spp.): Current Gaps in Knowledge and Future Research Directions to Improve Disease Management
by Mame Boucar Diouf, Ruth Festus, Gonçalo Silva, Sébastien Guyader, Marie Umber, Susan Seal and Pierre Yves Teycheney
Viruses 2022, 14(9), 1884; https://doi.org/10.3390/v14091884 - 26 Aug 2022
Cited by 10 | Viewed by 4609
Abstract
Viruses are a major constraint for yam production worldwide. They hamper the conservation, movement, and exchange of yam germplasm and are a threat to food security in tropical and subtropical areas of Africa and the Pacific where yam is a staple food and [...] Read more.
Viruses are a major constraint for yam production worldwide. They hamper the conservation, movement, and exchange of yam germplasm and are a threat to food security in tropical and subtropical areas of Africa and the Pacific where yam is a staple food and a source of income. However, the biology and impact of yam viruses remains largely unknown. This review summarizes current knowledge on yam viruses and emphasizes gaps that exist in the knowledge of the biology of these viruses, their diagnosis, and their impact on production. It provides essential information to inform the implementation of more effective virus control strategies. Full article
(This article belongs to the Special Issue Emerging Plant Viruses)
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