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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 2021) | Viewed by 42059

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Dr. Olivier Lemaire

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Guest Editor

Grapevine virology and virus transmission team, Institut National pour la Recherche en Agriculture, Alimentation et Environnement (INRAE), Centre Grand-Est Colmar, France
Interests: virology, grapevine, molecular diversity, HTS, detection, plant–virus interactions, resistance, biocontrol, integrated grapevine health management

Dr. Etienne Herrbach

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Guest Editor

Grapevine virology and virus transmission team, Institut National pour la Recherche en Agriculture, Alimentation et Environnement (INRAE), Centre Grand-Est Colmar, France
Interests: entomology, insect vectors of plant viruses, grapevine, scale insects, aphids

Special Issue Information

Dear Colleagues,

Family Closteroviridae gathers over 50 species of phloem-associated plant viruses exhibiting remarkable structural, molecular and biological features that puzzle scientists and induce deleterious effects on many major crops worldwide. Virions are flexuous particles that are the longest for plant viruses, up to 2000 nm in length. The helicoidal capsid consists of the main coat protein (CP), apart from a unique structure at the 5’ end of the particle, called ‘rattlesnake’. The single-stranded (+) RNA genome is composed of 13,000-19,000 nucleotides and is either monopartite in genera Closterovirus (type species Beet yellows virus, BYV), Ampelovirus (type Grapevine leafroll-associated virus-3, GLRaV-3) and Velarivirus (type Grapevine leafroll-associated virus-7, GLRaV-7), or bi/tripartite in genus Crinivirus (type Lettuce infectious yellows virus, LIYV). With the dawn of high-throughput sequencing, knowledge of molecular diversity of closterovirids has made tremendous progress, shedding light on common mixed-infections of viral species within this family or from other families. Their large genome is expressed through various mechanisms. The 5’ proximal ORF constitutes the replication-associated module, sometimes including an intriguing AlkB domain, and the 3’ half includes proteins with multifunctional features associated with virus–plant–vector interactions, virion assembly, and suppression of the host RNA silencing.

In nature, closterovirids are mostly transmitted by vectors depending on the genus following the semi-persistent non-circulative mode: aphids (Closterovirus), coccoids (Ampelovirus), whiteflies (Crinivirus), whereas the vectors, if any, of Velarivirus members are unknown. Their host range is generally narrow, rarely wide. Many closterovirids infect and damage crops worldwide, including major perennials (except criniviruses) where AlkB domain is expressed. Advances in the study of Closteroviridae in the era of ‘Omics’ provide new insights into their outstanding properties and will pave the way to innovative control strategies, with special emphasis on biocontrol and cross-protection strategies. This Special Issue will contribute by increasing our knowledge of this intriguing family of plant viruses with the latest scientific and technical advances, with special emphasis on the following topics: their remarkable genomic properties, the evolution of their genomes, their poorly known interactions with hosts and vectors, and their complex epidemiology for developing sustainable control strategies.

Dr. Olivier Lemaire
Dr. Etienne Herrbach
Guest Editors

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Keywords

closterovirus
ampelovirus
velarivirus
crinivirus
gene expression
evolution
phylogenomics
virome
molecular and field epidemiology
plant–virus–vector and virus–virus interactions
integrated management

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Published Papers (13 papers)

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19 pages, 5860 KiB

Open AccessArticle

Grapevine Leafroll-Associated Virus 3 Genotype Influences Foliar Symptom Development in New Zealand Vineyards

by Kar Mun Chooi, Vaughn A. Bell, Arnaud G. Blouin, Daniel Cohen, Dion Mundy, Warwick Henshall and Robin M. MacDiarmid

Viruses 2022, 14(7), 1348; https://doi.org/10.3390/v14071348 - 21 Jun 2022

Cited by 7 | Viewed by 2516

Abstract

Grapevine leafroll disease (GLD) constrains wine production worldwide. In New Zealand, the main causal agent of GLD is grapevine leafroll-associated virus 3 (GLRaV-3). To control GLD, an integrated management program is used and includes removing (roguing) GLRaV-3-infected vines from the vineyard. The classical foliar symptoms from virus-infected red-berry cultivars are leaves with dark red intervein, green veins, and downward rolling of margins. Growers use these phenotypic cues to undertake visual symptom identification (VSI) for GLD. However, the influence of the known large genetic variation among GLRaV-3 isolates on the foliar symptoms from different grapevine cultivars remains undescribed, especially in cool-climate growing environments, such as New Zealand. Over three vintages (2015, 2016, and 2017), VSI for GLD was undertaken at three field sites in New Zealand (Auckland, Hawke’s Bay, and Marlborough), each including four cultivars (Merlot, Pinot noir, Sauvignon blanc, and Pinot gris) infected with three GLRaV-3 genotypes (Groups I, VI, and X) or GLRaV-3-uninfected control plants. Throughout this study, no visual symptoms were observed on white-berry cultivars infected with GLRaV-3. For red-berry cultivars, the greatest variability in observed foliar symptoms among regional study sites, cultivars, and GLRaV-3 genotypes was observed early in the growing season. In particular, Group X had significantly delayed symptom expression across all three sites compared with Groups I and VI. As the newly infected, young vines matured in years 2 and 3, the GLRaV-3 genotype, cultivar, region, and environmental conditions had minimal influence on the accuracy of VSI, with consistently high (>95%) within-vintage identification by the end of each vintage. The results from this study strongly support the use of VSI for the GLD management of red-berry cultivar grapevines, Merlot and Pinot noir, as a reliable and cost-effective tool against GLD. Full article

(This article belongs to the Special Issue Closteroviridae)

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17 pages, 6084 KiB

Open AccessArticle

Nuances of Responses to Two Sources of Grapevine Leafroll Disease on Pinot Noir Grown in the Field for 17 Years

by Jean-Sébastien Reynard, Justine Brodard, Vivian Zufferey, Markus Rienth, Paul Gugerli, Olivier Schumpp and Arnaud G. Blouin

Viruses 2022, 14(6), 1333; https://doi.org/10.3390/v14061333 - 18 Jun 2022

Cited by 4 | Viewed by 2763

Abstract

Grapevine leafroll disease (GLD) is one of the most economically damaging virus diseases in grapevine, with grapevine leafroll-associated virus 1 (GLRaV-1) and grapevine leafroll-associated virus 3 (GLRaV-3) as the main contributors. This study complements a previously published transcriptomic analysis and compared the impact of two different forms of GLD to a symptomless control treatment: a mildly symptomatic form infected with GLRaV-1 and a severe form with exceptionally early leafroll symptoms (up to six weeks before veraison) infected with GLRaV-1 and GLRaV-3. Vine physiology and fruit composition in 17-year-old Pinot noir vines were measured and a gradient of vigor, yield, and berry quality (sugar content and berry weight) was observed between treatments. Virome composition, confirmed by individual RT-PCR, was compared with biological indexing. Three divergent viromes were recovered, containing between four to seven viruses and two viroids. They included the first detection of grapevine asteroid mosaic-associated virus in Switzerland. This virus did not cause obvious symptoms on the indicators used in biological indexing. Moreover, the presence of grapevine virus B (GVB) did not cause the expected corky bark symptoms on the indicators, thus underlining the important limitations of the biological indexing. Transmission of GLRaV-3 alone or in combination with GVB by Planococcus comstocki mealybug did not reproduce the strong symptoms observed on the donor plant infected with a severe form of GLD. This result raises questions about the contribution of each virus to the symptomatology of the plant. Full article

(This article belongs to the Special Issue Closteroviridae)

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9 pages, 1467 KiB

Open AccessCommunication

Transmission of Grapevine leafroll-associated virus-1 (Ampelovirus) and Grapevine virus A (Vitivirus) by the Cottony Grape Scale, Pulvinaria vitis (Hemiptera: Coccidae)

by Gérard Hommay, Antoine Alliaume, Catherine Reinbold and Etienne Herrbach

Viruses 2021, 13(10), 2081; https://doi.org/10.3390/v13102081 - 15 Oct 2021

Cited by 6 | Viewed by 2462

Abstract

The cottony grape scale Pulvinaria vitis is a scale insect colonizing grapevine; however, its capacity as a vector of grapevine viruses is poorly known in comparison to other scale species that are vectors of viral species in the genera Ampelovirus and Vitivirus. The ability of P. vitis to transmit the ampeloviruses Grapevine leafroll-associated viruses [GLRaV]−1, −3, and −4, and the vitivirus Grapevine virus A (GVA), to healthy vine cuttings was assessed. The scale insects used originated from commercial vine plots located in Alsace, Eastern France. When nymphs sampled from leafroll-infected vineyard plants were transferred onto healthy cuttings, only one event of transmission was obtained. However, when laboratory-reared, non-viruliferous nymphs were allowed to acquire viruses under controlled conditions, both first and second instar nymphs derived from two vineyards were able to transmit GLRaV−1 and GVA. This is the first report of GLRaV−1 and GVA transmission from grapevine to grapevine by this species. Full article

(This article belongs to the Special Issue Closteroviridae)

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11 pages, 1248 KiB

Open AccessArticle

Nuances of Whitefly Vector–Crinivirus Interactions Revealed in the Foregut Retention and Transmission of Lettuce Chlorosis Virus by Two Bemisia tabaci Cryptic Species

by Angel Y. S. Chen, Jaclyn S. Zhou, Jin-Xiang Liu and James C. K. Ng

Viruses 2021, 13(8), 1578; https://doi.org/10.3390/v13081578 - 10 Aug 2021

Viewed by 2319

Abstract

Lettuce infectious yellows virus is the first crinivirus for which the retention of purified virions ingested into the whitefly (Bemisia tabaci New World (NW)) vector’s foregut, has been demonstrated to be a requisite for successful virus transmission. This key finding supports the hypothesis that the determinant of foregut retention and transmission is present on the virion itself. However, whether this is also true for other criniviruses has not been established. Here, we provide evidence that lettuce chlorosis virus (LCV) acquired from plants is retained in the foreguts of both the B. tabaci NW and Middle East–Asia Minor 1 (MEAM1) vector species and transmitted upon inoculation feeding. An association between foregut retention and transmission by NW vectors is also observed following the acquisition and inoculation feeding of LCV virions purified using a standard procedure involving 2% or 4% (v/v) Triton™ X-100 (TX-100). However, while virions purified with 2% or 4% TX-100 are also retained in the foreguts of MEAM1 vectors, transmission is observed with the 4% TX-100-purified virions or when more vectors are used for acquisition and inoculation feeding. These results suggest that an intrinsic difference exists between NW and MEAM1 vectors in their interactions with, and transmission of, LCV virions. Full article

(This article belongs to the Special Issue Closteroviridae)

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11 pages, 499 KiB

Open AccessArticle

Studies on the Occurrence of Viruses in Planting Material of Grapevines in Southwestern Germany

by Noemi Messmer, Patricia Bohnert, Stefan Schumacher and René Fuchs

Viruses 2021, 13(2), 248; https://doi.org/10.3390/v13020248 - 5 Feb 2021

Cited by 9 | Viewed by 2095

Abstract

Viral diseases in viticulture lead to annual losses in the quantity and quality of grape production. Since no direct control measures are available in practice, preventive measures are taken to keep the vines healthy. These include, for example, the testing of propagation material for viruses such as Arabis mosaic virus (ArMV), Grapevine fanleaf virus (GFLV) or Grapevine leafroll-associated virus 1 (GLRaV-1) and 3 (GLRaV-3). As long-term investigations have shown, GLRaV-1 (2.1%) occurs most frequently in southwestern German wine-growing regions, whereas GLRaV-3 (<0.1%) is almost never found. However, tests conducted over 12 years indicate that there is no general decline in virus-infected planting material. Thus, it can be assumed that a spread of the viruses via corresponding vectors still takes place unhindered. Beyond the examinations regulated within the German Wine Growing Ordinance, one-time tests were carried out on Grapevine Pinot gris virus (GPGV). This analysis showed that GPGV was found in 17.2% of the samples. Full article

(This article belongs to the Special Issue Closteroviridae)

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17 pages, 1173 KiB

Open AccessArticle

Citrus Tristeza Virus Genotype Detection Using High-Throughput Sequencing

by Rachelle Bester, Glynnis Cook and Hans J. Maree

Viruses 2021, 13(2), 168; https://doi.org/10.3390/v13020168 - 23 Jan 2021

Cited by 21 | Viewed by 3699

Abstract

The application of high-throughput sequencing (HTS) has successfully been used for virus discovery to resolve disease etiology in many agricultural crops. The greatest advantage of HTS is that it can provide a complete viral status of a plant, including information on mixed infections of viral species or virus variants. This provides insight into the virus population structure, ecology, or evolution and can be used to differentiate among virus variants that may contribute differently toward disease etiology. In this study, the use of HTS for citrus tristeza virus (CTV) genotype detection was evaluated. A bioinformatic pipeline for CTV genotype detection was constructed and evaluated using simulated and real data sets to determine the parameters to discriminate between false positive read mappings and true genotype-specific genome coverage. A 50% genome coverage cut-off was identified for non-target read mappings. HTS with the associated bioinformatic pipeline was validated and proposed as a CTV genotyping assay. Full article

(This article belongs to the Special Issue Closteroviridae)

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12 pages, 928 KiB

Open AccessEditor’s ChoiceArticle

Semipersistently Transmitted, Phloem Limited Plant Viruses Are Inoculated during the First Subphase of Intracellular Stylet Penetrations in Phloem Cells

by Jaime Jiménez, Aránzazu Moreno and Alberto Fereres

Viruses 2021, 13(1), 137; https://doi.org/10.3390/v13010137 - 19 Jan 2021

Cited by 6 | Viewed by 3248

Abstract

The green peach aphid Myzus persicae Sulzer is the main vector of the semipersistently transmitted and phloem-limited Beet yellows virus (BYV, Closterovirus). Studies monitoring the M. persicae probing behavior by using the Electrical penetration graphs (EPG) technique revealed that inoculation of BYV occurs during unique brief intracellular punctures (phloem-pds) produced in companion and/or sieve element cells. Intracellular stylet punctures (or pds) are subdivided in three subphases (II-1, II-2 and II-3), which have been related to the delivery or uptake of non-phloem limited viruses transmitted in a non-persistent or semipersistent manner. As opposed to non-phloem limited viruses, the specific pd subphase(s) involved in the successful delivery of phloem limited viruses by aphids remain unknown. Therefore, we monitored the feeding process of BYV-carrying M. persicae individuals in sugar beet plants by the EPG technique and the feeding process was artificially terminated at each phloem-pd subphase. Results revealed that aphids that only performed the subphase II-1 of the phloem-pd transmitted BYV at similar efficiency than those allowed to perform subphase II-2 or the complete phloem-pd. This result suggests that BYV inoculation occurs during the first subphase of the phloem-pd. The specific transmission mechanisms involved in BYV delivery in phloem cells are discussed. Full article

(This article belongs to the Special Issue Closteroviridae)

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10 pages, 2603 KiB

Open AccessArticle

Discovery and Characterization of a Novel Ampelovirus on Firespike

by Yaqin Wang, Yu Song, Yongzhi Wang, Mengji Cao, Tao Hu and Xueping Zhou

Viruses 2020, 12(12), 1452; https://doi.org/10.3390/v12121452 - 16 Dec 2020

Cited by 6 | Viewed by 2593

Abstract

A novel RNA virus was identified in firespike (Odontonema tubaeforme) plants exhibiting leaf curling and chlorosis. The molecular features of the viral genomic RNA and proteins resemble those of ampeloviruses. Based on sequence comparisons and phylogenetic analysis, we propose a new species in the genus Ampelovirus, which we have tentatively named Firespike leafroll-associated virus (FLRaV). Bioassays showed that the virus is mechanically transmissible to Nicotiana benthamiana. In addition, a full-length cDNA clone of FLRaV could successfully infect N. benthamiana via agroinfiltration. Full article

(This article belongs to the Special Issue Closteroviridae)

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16 pages, 3526 KiB

Open AccessArticle

Spatial Distribution Patterns of Parthenolecanium corni (Hemiptera, Coccidae) and of the Ampelovirus GLRaV-1 and the Vitivirus GVA in a Commercial Vineyard

by Gérard Hommay, Louis Wiss, Catherine Reinbold, Joël Chadoeuf and Etienne Herrbach

Viruses 2020, 12(12), 1447; https://doi.org/10.3390/v12121447 - 16 Dec 2020

Cited by 6 | Viewed by 2785

Abstract

Distribution patterns of the European fruit lecanium Parthenolecanium corni (Bouché) and of grapevine leafroll-associated virus-1 (GLRaV-1) and grapevine virus A (GVA) were monitored from 2003 to 2015 in a Riesling vine plot in the northeast of France. Virus spread was compared between two periods: 2003–2008 and 2009–2014. The percentage of infected vines increased from 54 to 78% for GLRaV-1 and from 14 to 26% for GVA. The spatial distribution of viruses and of P. corni was analysed using permutation tests and revealed an aggregative pattern. Virus distribution was not associated with the density of P. corni population on grapevines. However, GLRaV-1 and GVA spread mainly from initially infected vines. New GLRaV-1 and GVA infections were more frequent on vines near primarily infected vines, first anisotropically along the row, then between neighbouring rows. Virus spread was similar to those described in literature with grapevine mealybug species. This slow vine-to-vine progression suggests that P. corni was responsible for the virus spread, in accordance with the low mobility and low transmission capacities of its local population. Full article

(This article belongs to the Special Issue Closteroviridae)

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14 pages, 1841 KiB

Open AccessArticle

Citrus tristeza virus P33 Protein Is Required for Efficient Transmission by the Aphid Aphis (Toxoptera) citricidus (Kirkaldy)

by Turksen Shilts, Choaa El-Mohtar, William O. Dawson and Nabil Killiny

Viruses 2020, 12(10), 1131; https://doi.org/10.3390/v12101131 - 6 Oct 2020

Cited by 11 | Viewed by 3661

Abstract

Plant viruses are threatening many valuable crops, and Citrus tristeza virus (CTV) is considered one of the most economically important plant viruses. CTV has destroyed millions of citrus trees in many regions of the world. Consequently, understanding of the transmission mechanism of CTV by its main vector, the brown citrus aphid, Aphis (Toxoptera) citricidus (Kirkaldy), may lead to better control strategies for CTV. The objective of this study was to understand the CTV–vector relationship by exploring the influence of viral genetic diversity on virus transmission. We built several infectious clones with different 5′-proximal ends from different CTV strains and assessed their transmission by the brown citrus aphid. Replacement of the 5′- end of the T36 isolate with that of the T30 strain (poorly transmitted) did not increase the transmission rate of T36, whereas replacement with that of the T68-1 isolate (highly transmitted) increased the transmission rate of T36 from 1.5 to 23%. Finally, substitution of p33 gene of the T36 strain with that of T68 increased the transmission rate from 1.5% to 17.8%. Although the underlying mechanisms that regulate the CTV transmission process by aphids have been explored in many ways, the roles of specific viral proteins are still not explicit. Our findings will improve our understanding of the transmission mechanisms of CTV by its aphid vector and may lead to the development of control strategies that interfere with its transmission by vector. Full article

(This article belongs to the Special Issue Closteroviridae)

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9 pages, 787 KiB

Open AccessArticle

A Lectin Disrupts Vector Transmission of a Grapevine Ampelovirus

by Cecilia A. Prator and Rodrigo P. P. Almeida

Viruses 2020, 12(8), 843; https://doi.org/10.3390/v12080843 - 1 Aug 2020

Cited by 4 | Viewed by 2843

Abstract

Grapevine leafroll disease is one of the most important virus diseases of grapevines and occurs in every major grape-growing region of the world. The vector-transmission mechanisms of the causative agent, Grapevine leafroll-associated virus 3 (GLRaV-3), remain poorly understood. We show that the vine mealybug, Planococcus ficus, feeds through a membrane feeding system on GLRaV-3 viral purifications from both V. vinifera and N. benthamiana and transmits the virus to test plants from plants from both species. Building on this strategy, we used an immunofluorescence approach to localize virions to two retention sites in P. ficus mouthparts. Assays testing molecules capable of blocking virus transmission demonstrated that GLRaV-3-transmission by P. ficus could be disrupted. Our results indicate that our membrane feeding system and transmission-blocking assays are a valid approach and can be used to screen other candidate blocking molecules. Full article

(This article belongs to the Special Issue Closteroviridae)

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Review

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23 pages, 1713 KiB

Open AccessReview

Probing into the Effects of Grapevine Leafroll-Associated Viruses on the Physiology, Fruit Quality and Gene Expression of Grapes

by Yashu Song, Robert H. Hanner and Baozhong Meng

Viruses 2021, 13(4), 593; https://doi.org/10.3390/v13040593 - 31 Mar 2021

Cited by 32 | Viewed by 5011

Abstract

Grapevine leafroll is one of the most widespread and highly destructive grapevine diseases that is responsible for great economic losses to the grape and wine industries throughout the world. Six distinct viruses have been implicated in this disease complex. They belong to three genera, all in the family Closteroviridae. For the sake of convenience, these viruses are named as grapevine leafroll-associated viruses (GLRaV-1, -2, -3, -4, -7, and -13). However, their etiological role in the disease has yet to be established. Furthermore, how infections with each GLRaV induce the characteristic disease symptoms remains unresolved. Here, we first provide a brief overview on each of these GLRaVs with a focus on genome structure, expression strategies and gene functions, where available. We then provide a review on the effects of GLRaV infection on the physiology, fruit quality, fruit chemical composition, and gene expression of grapevine based on the limited information so far reported in the literature. We outline key methodologies that have been used to study how GLRaV infections alter gene expression in the grapevine host at the transcriptomic level. Finally, we present a working model as an initial attempt to explain how infections with GLRaVs lead to the characteristic symptoms of grapevine leafroll disease: leaf discoloration and downward rolling. It is our hope that this review will serve as a starting point for grapevine virology and the related research community to tackle this vastly important and yet virtually uncharted territory in virus-host interactions involving woody and perennial fruit crops. Full article

(This article belongs to the Special Issue Closteroviridae)

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17 pages, 15672 KiB

Open AccessReview

Walking Together: Cross-Protection, Genome Conservation, and the Replication Machinery of Citrus tristeza virus

by Svetlana Y. Folimonova, Diann Achor and Moshe Bar-Joseph

Viruses 2020, 12(12), 1353; https://doi.org/10.3390/v12121353 - 26 Nov 2020

Cited by 15 | Viewed by 3774

Abstract

“Cross-protection”, a nearly 100 years-old virological term, is suggested to be changed to “close protection”. Evidence for the need of such change has accumulated over the past six decades from the laboratory experiments and field tests conducted by plant pathologists and plant virologists working with different plant viruses, and, in particular, from research on Citrus tristeza virus (CTV). A direct confirmation of such close protection came with the finding that “pre-immunization” of citrus plants with the variants of the T36 strain of CTV but not with variants of other virus strains was providing protection against a fluorescent protein-tagged T36-based recombinant virus variant. Under natural conditions close protection is functional and is closely associated both with the conservation of the CTV genome sequence and prevention of superinfection by closely similar isolates. It is suggested that the mechanism is primarily directed to prevent the danger of virus population collapse that could be expected to result through quasispecies divergence of large RNA genomes of the CTV variants continuously replicating within long-living and highly voluminous fruit trees. This review article provides an overview of the CTV cross-protection research, along with a discussion of the phenomenon in the context of the CTV biology and genetics. Full article

(This article belongs to the Special Issue Closteroviridae)

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