Occurrence of grapevine leafroll-associated virus complex in Napa Valley

Assessment of Symptoms of Grapevine Leafroll Disease and Relationship with Yield and Quality of Pinot Noir Grape Must in a 10-Year Study Period

Grapevine leafroll disease (GLD) is caused by one or more of the Grapevine leafroll-associated viruses (GLRaVs). GLD's symptoms are expected to be evident in indicator cultivars, regardless of the GLRaV(s) involved. In the present study, disease incidence (I) and severity (S), symptoms before veraison (Sy < V), a disease severity index (DSI) and an earliness index (EI) (2013-2022) were recorded in order to examine the factors affecting the evolution of GLD in Pinot noir graft inoculated with scions infected with GLRaV-3 that, in origin, showed a diversity of GLD symptoms. Strong correlations between I and S (r = 0.94) and between Sy < V and EI (r = 0.94) were observed; early symptoms proved good predictors of incidence and severity after veraison and of yield and sugar content of the must. The environmental conditions and time after infection did not modify the wide range of symptoms (I: 0-81.5%; S: 0.1-4) that corresponded with the variation in losses (<0-88% for yield and <0-24% for sugar content). With all other factors being constant, the significant differences between plants were mainly due to the GLRaVs present. Plants infected with some GLRaV-3 isolates always had mild symptoms or remained asymptomatic 10 years after grafting but remained a source of infection for GLRaV vectors.

Optimization of SAW Sensors for Nanoplastics and Grapevine Virus Detection

In this work, we report the parametric optimization of surface acoustic wave (SAW) delay lines on Lithium niobate for environmental monitoring applications. First, we show that the device performance can be improved by acting opportunely on geometrical design parameters of the interdigital transducers such as the number of finger pairs, the finger overlap length and the distance between the emitter and the receiver. Then, the best-performing configuration is employed to realize SAW sensors. As aerosol particulate matter (PM) is a major threat, we first demonstrate a capability for the detection of polystyrene particles simulating nanoparticulates/nanoplastics, and achieve a limit of detection (LOD) of 0.3 ng, beyond the present state-of-the-art. Next, the SAW sensors were used for the first time to implement diagnostic tools able to detect Grapevine leafroll-associated virus 3 (GLRaV-3), one of the most widespread viruses in wine-growing areas, outperforming electrochemical impedance sensors thanks to a five-times better LOD. These two proofs of concept demonstrate the ability of miniaturized SAW sensors for carrying out on-field monitoring campaigns and their potential to replace the presently used heavy and expensive laboratory instrumentation.

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

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.

Predominance and Diversity of GLRaV-3 in Native Vines of Mediterranean Croatia

Sixteen grapevine cultivars from Mediterranean Croatia were surveyed for the presence of 10 of the most economically important grapevine viruses. The presence of Grapevine fanleaf virus (GFLV), Arabis mosaic virus (ArMV), Grapevine leafroll associated virus-1, -2, and -3 (GLRaV-1; GLRaV-2 and GLRaV-3), Grapevine virus A (GVA) and B (GVB), Grapevine fleck virus (GFkV), Grapevine rupestris stem pitting associated virus (GRSPaV), and Grapevine Pinot gris virus (GPGV) were tested by reverse transcription polymerase chain reaction (RT-PCR) and enzyme-linked immunosorbent assay (ELISA). All 71 analyzed clones were positive for the presence of one or more viruses. The most abundant one, detected in almost 95% of samples was GLRaV-3. In most of cases it was reported in mixed infections with GVA, GRSPaV, and GPGV. Virus genomes of GLRaV-3 infected vines were further characterized molecularly in order to determine their genetic diversity. Different genomic variants of heat shock 70 protein homologue (HSP70h) were identified by single-strand conformation polymorphism (SSCP) and sequenced. Sequence analysis confirmed their clustering into phylogenetic group I and/or phylogenetic group II. This study emphasizes the wide virus heterogenicity in Mediterranean vines and the predominant presence of GLRaV-3 phylogenetic groups I and II, either individually or in combination.

Development of a Mating Disruption Program for a Mealybug, Planococcus ficus, in Vineyards

Simple Summary

The vine mealybug is a key insect pest of vineyards that currently is controlled by one or more insecticide applications per season. Here, we sought to develop a more sustainable control tool by using the mealybug’s sex pheromone to reduce mating and thereby lower pest damage. The mature female mealybug emits a sex pheromone that the winged adult male uses to find and mate with females. Synthetically produced sex pheromone, specific to the vine mealybug, was enclosed in commercial dispensers and deployed in vineyards in 2004–2007 studies to determine if mating disruption could provide a viable control option. Trials were conducted in commercial vineyards with cooperating farmers. Across all trials, mating disruption reduced pheromone trap captures of adult male mealybugs—an indication that the population numbers were lowered—and there was often a reduction mealybug numbers on vines and/or crop damage. There was not a clear reduction in the proportion of female mealybugs with ovisacs (a cottony-like mass containing mealybug eggs), but this may have resulted from the production of non-viable ovisacs that were not differentiated in the field samples. Pheromone trap captures were never lowered to zero (often called trap shut down), possibly because trials were conducted in vineyards with unusually high mealybug densities. Trap capture patterns commonly began low in April-May, increased in mid-July or August, and often decreased in September–October when post-harvest insecticides were applied. Results over all years suggest season-long coverage or late season coverage may be as or more important than dose per hectare. This research was used to help initiate the commercialization of mating disruption products for the vine mealybug, which are now being successfully used throughout the world’s grape-growing regions where this pest is found.

Abstract

The vine mealybug (VMB), Planococcus ficus (Hemiptera: Pseudococcidae), is a key insect pest of vineyards, and improvements in sustainable control of this pest are needed to meet increasing consumer demand for organically farmed products. One promising option is mating disruption. In a series of experiments conducted from 2004 to 2007, we tested the effects of mating disruption on trap captures of Pl. ficus males in pheromone-baited traps, on Pl. ficus numbers and age structure on vines, and on damage to grape clusters. From 2004 to 2005, the effects of dispenser load (mg active ingredient per dispenser) were also assessed, and dispensers were compared to a flowable formulation. Across all trials, mating disruption consistently reduced pheromone trap captures and often reduced mealybug numbers on vines and/or crop damage, regardless of the pheromone dose that was applied. Reductions in Pl. ficus densities in mating disruption plots were not accompanied by clear effects on mealybug population age structure; however, production of non-viable ovisacs by unmated females may have obscured differences in proportional representation of ovisacs. Pheromone trap captures were never lowered to zero (often called trap shut down), possibly because trials were conducted in vineyards with unusually high Pl. ficus densities. Trap-capture patterns in both treated and control plots commonly began low in April–May, increased in mid-July or August, and often decreased in September–October when post-harvest insecticides were applied. During the four-year trial, the release rate from plastic sachet dispensers was improved by industry cooperators as pheromone was released too quickly (2004) or not completely released during the season (2005–2006). The flowable formulation performed slightly better than dispensers at the same application dose. Results over all years suggest season-long coverage or late-season coverage may be as or more important than dose per hectare. Development of a dispenser with optimized season-long pheromone emission or targeted seasonal periods should be a future goal.

A Lectin Disrupts Vector Transmission of a Grapevine Ampelovirus

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.

Comparison of two different host plant genera responding to grapevine leafroll-associated virus 3 infection

Grapevine leafroll-associated virus 3 (GLRaV-3) is one of the most important viruses of grapevine but, despite this, there remain several gaps in our understanding of its biology. Because of its narrow host range - limited to Vitis species - and because the virus is restricted to the phloem, most GLRaV-3 research has concentrated on epidemiology and the development of detection assays. The recent discovery that GLRaV-3 can infect Nicotiana benthamiana, a plant model organism, makes new opportunities available for research in this field. We used RNA-seq to compare both V. vinifera and P1/HC-Pro N. benthamiana host responses to GLRaV-3 infection. Our analysis revealed that the majority of DEGs observed between the two hosts were unique although responses between the two hosts also showed several shared gene expression results. When comparing gene expression patterns that were shared between the two hosts, we observed the downregulation of genes associated with stress chaperones, and the induction of gene families involved in primary plant physiological processes. This is the first analysis of gene expression profiles beyond Vitis to mealybug-transmitted GLRaV-3 and demonstrates that N. benthamiana could serve as a useful tool for future studies of GLRaV-3-host interactions.

Detection of new vitiviruses infecting grapevine in California

Recently, five new viruses from the genus Vitivirus were identified and named grapevine virus G, H, I, J and L. These viruses were targeted in a survey to evaluate their prevalence in different grapevine populations in California. Excluding a single detection of GVJ, other vitiviruses were detected infecting several grapevine selections via RT-PCR and later confirmed by sequencing. This paper represents the first report of GVG, GVH and GVI in California. In a preliminary analysis, the sequence diversity between identified isolates of GVG, GVH, GVI and GVL was investigated using distance matrices and phylogenetics. Finally, coinfections involving diverse vitiviruses and leafroll viruses were evidenced.

Development of sensitive molecular assays for the detection of grapevine leafroll-associated virus 3 in an insect vector

Grapevine leafroll-associated virus 3 (GLRaV-3) is an economically significant virus of grapevines, with secondary spread mediated by several species of mealybug and soft scale insects. To better understand virus-vector interactions, sensitive virus detection in these insects is a key tool. In this research, two new hydrolysis-probe-based real-time assays for GLRaV-3 detection were developed and compared to three existing assays. Of the five assays compared, the one-step RT-qPCR probe-based assay was the most sensitive and reliable, with as few as 10 virus RNA copies detected. This is the first description of a real-time molecular assay for virus detection in mealybugs with such sensitivity.

A Novel Genetic Variant of Grapevine leafroll-associated virus-3 (GLRaV-3) from Idaho Grapevines

Grapevine leafroll-associated virus-3 (GLRaV-3) is a major constraint on profitable grapevine cultivation. The virus is transmitted efficiently by mealybugs and soft scale insects, or through vegetative propagation by cuttings, and is present worldwide, wherever grapevines are grown. GLRaV-3 exists as a complex of genetic variants currently classified in several phylogenetic groups that can differ from each other by as much as 30% in nucleotide sequence of the whole genome. In the course of the GLRaV-3 testing of wine grapes in southern Idaho, plants of two grapevine cultivars were found to harbor a novel genetic variant of GLRaV-3, named ID45, which exhibited ≤80% nucleotide sequence identity level to the known GLRaV-3 isolates in its most conserved HSP70h gene. The ID45 variant caused no foliar symptoms in 'Cabernet Sauvignon' in the fall, and was demonstrated to have poor reactivity to commercial virus-specific antibodies. The entire 18,478-nt genome sequence of the GLRaV-3-ID45 was determined using a combination of high-throughput and conventional Sanger sequencing, and demonstrated to have typical organization for the genus Ampelovirus (family Closteroviridae), with only 70 to 77% identity level to the GLRaV-3 genomes from other established phylogroups. We concluded that ID45 represented a new phylogenetic group IX of GLRaV-3. Database search using ID45 nucleotide sequence as a query suggested that this novel ID45 variant is present in at least one other grape-growing state in the U.S., California, and in Brazil. An RT-PCR based test was developed to distinguish ID45 from the predominant GLRaV-3 phylogroup I found in Idaho in single and mixed infections.

Characterization of grapevine leafroll-associated virus 3 genetic variants and application towards RT-qPCR assay design

Grapevine leafroll-associated virus 3 (GLRaV-3) is the most widely prevalent and economically important of the complex of RNA viruses associated with grapevine leafroll disease (GLD). Phylogenetic studies have grouped GLRaV-3 isolates into nine different monophyletic groups and four supergroups, making GLRaV-3 a genetically highly diverse virus species. In addition, new divergent variants have been discovered recently around the world. Accurate identification of the virus is an essential component in the management and control of GLRaV-3; however, the diversity of GLRaV-3, coupled with the limited sequence information, have complicated the development of a reliable detection assay. In this study, GLRaV-3 sequence data available in GenBank and those generated at Foundation Plant Services, University of California-Davis, was used to develop a new RT-qPCR assay with the capacity to detect all known GLRaV-3 variants. The new assay, referred to as FPST, was challenged against samples that included plants infected with different GLRaV-3 variants and originating from 46 countries. The FPST assay detected all known GLRaV-3 variants, including the highly divergent variants, by amplifying a small highly conserved region in the 3' untranslated terminal region (UTR) of the virus genome. The reliability of the new RT-qPCR assay was confirmed by an enzyme linked immunosorbent assay (ELISA) that can detect all known GLRaV-3 variants characterized to date. Additionally, three new GLRaV-3 divergent variants, represented by four isolates, were identified using a hierarchical testing process involving the FPST assay, GLRaV-3 variant-specific assays and high-throughput sequencing analysis. These variants were distantly related to groups I, II, III, V, VI, VII and IX, but much similar to GLRaV-3 variants with no assigned group; thus, they may represent new clades. Finally, based on the phylogenetic analysis, a new GLRaV-3 subclade is proposed and named as group X.

Incidence of Grapevine Leafroll Disease: Effects of Grape Mealybug (Pseudococcus maritimus) Abundance and Pathogen Supply

Studies of spatiotemporal dynamics are central to efforts to characterize the epidemiology of infectious disease, such as mechanism of pathogen spread and pathogen or vector sources in the landscape, and are critical to the development of effective disease management programs. To that end, we conducted a multi-year study of 20 vineyard blocks in coastal northern California to relate the dynamics of a mealybug vector, Pseudococcus maritimus (Ehrhorn) (Hemiptera: Pseudococcidae), to incidence of grapevine leafroll disease (GLD). In each vineyard block, a subset of vines were scored visually for relative mealybug abundance, disease was quantified by visual assessment, and virus presence was verified using standard laboratory molecular assays. GLD incidence was analyzed with a classification and regression tree, and with a hierarchical model that also captured variability among blocks and heterogeneity within blocks. Both analyses found strong interannual variability in incidence, with the hierarchical model also capturing substantial between- and within-block heterogeneity, but with significant contributions of vector abundance and pathogen supply (prior disease incidence) to the frequency of newly diseased vines. These results strengthen further the conclusion that mealybug vectors are causally related to pathogen spread in this system and are therefore an important target for management. Moreover, they are consistent with relatively efficient secondary spread of the pathogen, suggesting an important role for the removal of diseased vines as a tool to mitigate further damage.

Infection and Colonization of Nicotiana benthamiana by Grapevine leafroll-associated virus 3

Grapevine leafroll disease is an increasing problem in all grape-growing regions of the world. The most widespread agent of the disease, Grapevine leafroll-associated virus 3 (GLRaV-3), has never been shown to infect species outside of the genus Vitis. Virus transmission to several plant species used as model systems was tested using the vine mealybug, Planococcus ficus. We show that GLRaV-3 is able to infect Nicotiana benthamiana. Working with GLRaV-3 infected N. benthamiana revealed distinct advantages in comparison with its natural host Vitis vinifera, yielding both higher viral protein and virion concentrations in western blot and transmission electron microscopy observations, respectively. Immunogold labelling of thin sections through N. benthamiana petioles revealed filamentous particles in the phloem cells of GLRaV-3 positive plants. Comparison of assembled whole genomes from GLRaV-3 infected V. vinifera vs. N. benthamiana revealed substitutions in the 5' UTR. These results open new avenues and opportunities for GLRaV-3 research.

Viral Diversity in Autochthonous Croatian Grapevine Cultivars

A survey was conducted on nine autochthonous grapevine cultivars grown along the Croatian coastal region. In total, 48 vines (44 from germplasm collection, 4 from vineyards) originating from 23 sites were tested for 26 viruses using molecular methods. Results revealed high infection rates with Grapevine leafroll-associated virus 3 (GLRaV-3); Grapevine virus A (GVA, both 91.7%); Grapevine fleck virus (GFkV, 87.5%); and Grapevine rupestris stem pitting-associated virus (GRSPaV, 83.3%). Other detected viruses were: Grapevine fanleaf virus (GFLV); Grapevine leafroll-associated viruses 1, 2, and strains of 4 (GLRaV-1, GLRaV-2, GLRaV-4); Grapevine viruses B, D, F (GVB, GVD, GVF); Grapevine red globe virus (GRGV); Grapevine vein feathering virus (GVFV); Grapevine Syrah virus 1 (GSyV-1); and Grapevine Pinot gris virus (GPGV). No virus-free vine was found. Mixed infections were determined in all vines, the number of viruses in a single vine ranged from three to nine. GLRaV-3 variant typing confirmed presence of group I, II, and III. Four vines with leaf deformation and mottling were positive for GPGV. Seven viruses (GLRaV-4-like group, GVD, GVE, GVF, GRGV, GSyV-1, and GVFV) were detected for the first time in Croatia. This survey confirmed the deteriorated sanitary status of autochthonous Croatian grapevine cultivars.

A Synoptic Analysis of the Temporal and Spatial Aspects of Grapevine Leafroll Disease in a Historic Napa Vineyard and Experimental Vine Blocks

Five Grapevine leafroll-associated virus 3 (GLRaV-3) epidemics were analyzed utilizing a standardized approach to robustly characterize the temporal and spatial parameters. Published data included in the analysis are from Spain, New Zealand, and Napa Valley, CA together with new data from a historic vineyard in Napa Valley, CA. Linear regression analyses of logit-transformed incidence data indicated a maximum average increase of 11% per year in disease incidence, with considerable variation among locations. Spatial analyses, including distribution fitting, examination of the effective sample size, and evaluation of the parameters of the binary power law fitted to variance data for disease incidence, indicated a high degree of consistency among the data sets. In all cases, except at very low disease incidence, a high degree of spatial aggregation was noted, with evidence that the degree of aggregation varied as a function of mean disease incidence. The polyetic dynamics of disease follow a logistic-like pattern over multiple seasons, consistent with limitation by inoculum availability (infected vines) at low incidence and limitation by disease-free vines at high incidence.

Relative Prevalence of Grapevine Leafroll-Associated Virus Species in Wine Grape-Growing Regions of California

Some diseases manifest as one characteristic set of symptoms to the host, but can be caused by multiple pathogens. Control treatments based on plant symptoms can make it difficult to effectively manage such diseases, as the biology of the underlying pathogens can vary. Grapevine leafroll disease affects grapes worldwide, and is associated with several viral species in the family Closteroviridae. Whereas some of the viruses associated with this disease are transmitted by insect vectors, others are only graft-transmissible. In three regions of California, we surveyed vineyards containing diseased vines and screened symptomatic plants for all known viral species associated with grapevine leafroll disease. Relative incidence of each virus species differed among the three regions regions, particularly in relation to species with known vectors compared with those only known to be graft-transmitted. In one region, the pathogen population was dominated by species not known to have an insect vector. In contrast, populations in the other surveyed regions were dominated by virus species that are vector-transmissible. Our survey did not detect viruses associated with grapevine leafroll disease at some sites with characteristic disease symptoms. This could be explained either by undescribed genetic diversity among these viruses that prevented detection with available molecular tools at the time the survey was performed, or a misidentification of visual symptoms that may have had other underlying causes. Based on the differences in relative prevalence of each virus species among regions and among vineyards within regions, we expect that region and site-specific management strategies are needed for effective disease control.

Biological, Serological, and Molecular Characterization of a Highly Divergent Strain of Grapevine leafroll-associated virus 4 Causing Grapevine Leafroll Disease

The complete genome sequence of a highly divergent strain of Grapevine leafroll-associated virus 4 (GLRaV-4) was determined using 454 pyrosequencing technology. This virus, designated GLRaV-4 Ob, was detected in Vitis vinifera 'Otcha bala' from our grapevine virus collection at Agroscope. The GLRaV-4 Ob genome length and organization share similarities with members of subgroup II in the genus Ampelovirus (family Closteroviridae). Otcha bala was graft-inoculated onto indicator plants of cultivar Gamay to evaluate the biological properties of this new strain, and typical leafroll symptoms were induced. A monoclonal antibody for the rapid detection of GLRaV-4 Ob by enzyme-linked immunosorbent assay is available, thus facilitating large-scale diagnostics of this virus. Based on the relatively small size of the coat protein, the reduced amino acid identity and the distinct serological properties, our study clearly shows that GLRaV-4 Ob is a divergent strain of GLRaV-4. Furthermore, molecular and serological data revealed that the AA42 accession from which GLRaV-7 was originally reported is in fact co-infected with GLRaV-4 Ob and GLRaV-7. This finding challenges the idea that GLRaV-7 is a leafroll-causing agent.

Interactions Within Susceptible Hosts Drive Establishment of Genetically Distinct Variants of an Insect-Borne Pathogen

Coinfections are common, leading to pathogen interactions during transmission and establishment in a host. However, few studies have tested the relative strengths of pathogen interactions in vectors and hosts that determine the outcome of infection. We tested interactions between two genetically distinct variants of the mealybug-transmitted Grapevine leafroll-associated virus 3. The transmission efficiency of each variant in single variant inoculations by two vector species was determined. The effects of vector species, a coinfected source, and simultaneous inoculation from multiple hosts to one host on variant establishment were examined. Within-vector interactions could have a role in transmission from hosts containing mixed infections, but not when vectors were moved from separate singly infected source plants to a single recipient plant. The invasive Planococcus ficus (Signoret) was a more efficient vector than Pseudococcus viburni (Signoret). Transmission efficiency of the two variants did not differ in single variant inoculations. Overall infections were the same whether from singly or coinfected source plants. In mixed inoculations, establishment of one variant was reduced. Mixed inoculations from two singly infected source plants resulted in fewer mixed infections than expected by chance. Therefore, the observed outcome was determined subsequent to host inoculation rather than in the vector. The outcome may be due to resource competition between pathogens. Alternatively apparent competition may be responsible; the pathogens' differential ability to overcome host defenses and colonize the host may determine the final outcome of new infections. Detailed knowledge of interactions between pathogens during transmission and establishment could improve understanding and management of disease spread.

Phylogenomic analysis reveals deep divergence and recombination in an economically important grapevine virus

The evolutionary history of the exclusively grapevine (Vitis spp.) infecting, grapevine leafroll-associated virus 3 (GLRaV-3) has not been studied extensively, partly due to limited available sequence data. In this study we trace the evolutionary history of GLRaV-3, focussing on isolate GH24, a newly discovered variant. GH24 was discovered through the use of next-generation sequencing (NGS) and the whole genome sequence determined and validated with Sanger sequencing. We assembled an alignment of all 13 available whole genomes of GLRaV-3 isolates and all other publicly available GLRaV-3 sequence data. Using multiple recombination detection methods we identified a clear signal for recombination in one whole genome sequence and further evidence for recombination in two more, including GH24. We inferred phylogenetic trees and networks and estimated the ages of common ancestors of GLRaV-3 clades by means of relaxed clock models calibrated with asynchronous sampling dates. Our results generally confirm previously identified variant groups as well as two new groups (VII and VIII). Higher order groups were defined as supergroups designated A to D. Supergroup A includes variant groups I-V and supergroup B group VI and its related unclassified isolates. Supergroups C and D are less well known, including the newly identified groups VII (including isolate GH24) and VIII respectively. The inferred node ages suggest that the origins of the major groups of GLRaV-3, including isolate GH24, may have occurred prior to worldwide cultivation of grapevines, whilst the current diversity represents closely related isolates that diverged from common ancestors within the last century.

Safeguarding Fruit Crops in the Age of Agricultural Globalization

The expansion of fruit production and markets into new geographic areas provides novel opportunities and challenges for the agricultural and marketing industries. Evidence that fruit consumption helps prevent nutrient deficiencies and reduces the risk of cardiovascular disease and cancer has assisted in the expansion of all aspects of the fruit industry. In today's competitive global market environment, producers need access to the best plant material available in terms of genetics and health if they are to maintain a competitive advantage in the market. An ever-increasing amount of plant material in the form of produce, nursery plants, and breeding stock moves vast distances, and this has resulted in an increased risk of pest and disease introductions into new areas. One of the primary concerns of the global fruit industry is a group of systemic pathogens for which there are no effective remedies once plants are infected. These pathogens and diseases require expensive management and control procedures at nurseries and by producers locally and nationally. Here, we review (i) the characteristics of some of these pathogens, (ii) the history and economic consequences of some notable disease epidemics caused by these pathogens, (iii) the changes in agricultural trade that have exacerbated the risk of pathogen introduction, (iv) the path to production of healthy plants through the U.S. National Clean Plant Network and state certification programs, (v) the economic value of clean stock to nurseries and fruit growers in the United States, and (vi) current efforts to develop and harmonize effective nursery certification programs within the United States as well as with global trading partners.

Control of viruses infecting grapevine

Grapevine is a high value vegetatively propagated fruit crop that suffers from numerous viruses, including some that seriously affect the profitability of vineyards. Nowadays, 64 viruses belonging to different genera and families have been reported in grapevines and new virus species will likely be described in the future. Three viral diseases namely leafroll, rugose wood, and infectious degeneration are of major economic importance worldwide. The viruses associated with these diseases are transmitted by mealybugs, scale and soft scale insects, or dagger nematodes. Here, we review control measures of the major grapevine viral diseases. More specifically, emphasis is laid on (i) approaches for the production of clean stocks and propagative material through effective sanitation, robust diagnosis, as well as local and regional certification efforts, (ii) the management of vectors of viruses using cultural, biological, and chemical methods, and (iii) the production of resistant grapevines mainly through the application of genetic engineering. The benefits and limitations of the different control measures are discussed with regard to accomplishments and future research directions.

Relative quantitation goes viral: An RT-qPCR assay for a grapevine virus

Accurate detection and quantitation of viruses can be beneficial to plant-virus interaction studies. In this study, three SYBR green real-time RT-PCR assays were developed to quantitate grapevine leafroll-associated virus 3 (GLRaV-3) in infected vines. Three genomic regions (ORF1a, coat protein and 3'UTR) were targeted to quantitate GLRaV-3 relative to three stably expressed reference genes (actin, GAPDH and α-tubulin). These assays were able to detect all known variant groups of GLRaV-3, including the divergent group VI, with equal efficiency. No link could be established between the concentration ratios of the different genomic regions and subgenomic RNA (sgRNA) expression. However, a significant lower virus concentration ratio for plants infected with variant group VI compared to variant group II was observed for the ORF1a, coat protein and the 3'UTR. Significant higher accumulation of the virus in the growth tip was also detected for both variant groups. The quantitation of viral genomic regions under different conditions can contribute to elucidating disease aetiology and enhance knowledge about virus ecology.

Grapevine Leafroll: A Complex Viral Disease Affecting a High-Value Fruit Crop

Grapevine (Vitis spp.) is one of the most widely grown fruit crops in the world. It is a deciduous woody perennial vine for which the cultivation of domesticated species began approximately 6,000 to 8,000 years ago in the Near East. Grapevines are broadly classified into red- and white-berried cultivars based on their fruit skin color, although yellow, pink, crimson, dark blue, and black-berried cultivars also exist. Grapevines can be subject to attacks by many different pests and pathogens, including graft-transmissible agents such as viruses, viroids, and phytoplasmas. Among the virus and virus-like diseases, grapevine leafroll disease (GLD) is by far the most widespread and economically damaging viral disease of grapevines in many regions around the world. The global expansion of the grape and wine industry has seen a parallel increase in the incidence and economic impact of GLD. Despite the fact that GLD was recognized as a potential threat to grape production for several decades, our knowledge of the nature of the disease is still quite limited due to a variety of challenges related to the complexity of this virus disease, the association of several distinct GLD-associated viruses, and contrasting symptoms in red- and white-berried cultivars. In view of the growing significance of GLD to wine grape production worldwide, this feature article provides an overview of the state of knowledge on the biology and epidemiology of the disease and describes management strategies currently deployed in vineyards.

Temporal and spatial scaling of the genetic structure of a vector-borne plant pathogen

The ecology of plant pathogens of perennial crops is affected by the long-lived nature of their immobile hosts. In addition, changes to the genetic structure of pathogen populations may affect disease epidemiology and management practices; examples include local adaptation of more fit genotypes or introduction of novel genotypes from geographically distant areas via human movement of infected plant material or insect vectors. We studied the genetic structure of Xylella fastidiosa populations causing disease in sweet orange plants in Brazil at multiple scales using fast-evolving molecular markers (simple-sequence DNA repeats). Results show that populations of X. fastidiosa were regionally isolated, and that isolation was maintained for populations analyzed a decade apart from each other. However, despite such geographic isolation, local populations present in year 2000 were largely replaced by novel genotypes in 2009 but not as a result of migration. At a smaller spatial scale (individual trees), results suggest that isolates within plants originated from a shared common ancestor. In summary, new insights on the ecology of this economically important plant pathogen were obtained by sampling populations at different spatial scales and two different time points.

Past and future of a century old Citrus tristeza virus collection: a California citrus germplasm tale

Citrus tristeza virus (CTV) isolates collected from citrus germplasm, dooryard and field trees in California from 1914 have been maintained in planta under quarantine in the Citrus Clonal Protection Program (CCPP), Riverside, California. This collection, therefore, represents populations of CTV isolates obtained over time and space in California. To determine CTV genetic diversity in this context, genotypes of CTV isolates from the CCPP collection were characterized using multiple molecular markers (MMM). Genotypes T30, VT, and T36 were found at high frequencies with T30 and T30+VT genotypes being the most abundant. The MMM analysis did not identify T3 and B165/T68 genotypes; however, biological and phylogenetic analysis suggested some relationships of CCPP CTV isolates with these two genotypes. Phylogenetic analysis of the CTV coat protein (CP) gene sequences classified the tested isolates into seven distinct clades. Five clades were in association with the standard CTV genotypes T30, T36, T3, VT, and B165/T68. The remaining two identified clades were not related to any standard CTV genotypes. Spatiotemporal analysis indicated a trend of reduced genotype and phylogenetic diversity as well as virulence from southern California (SC) at early (1907-1957) in comparison to that of central California (CC) isolates collected from later (1957-2009) time periods. CTV biological characterization also indicated a reduced number and less virulent stem pitting (SP) CTV isolates compared to seedling yellows isolates introduced to California. This data provides a historical insight of the introduction, movement, and genetic diversity of CTV in California and provides genetic and biological information useful for CTV quarantine, eradication, and disease management strategies such as CTV-SP cross protection.

Occurrence of Grapevine Leafroll-Associated Viruses in China

To characterize the prevalence of viruses associated with grapevine leafroll disease in China, 249 grapevine (Vitis spp.) samples (86 popular cultivars and a rootstock) from 19 provinces and regions were collected and tested for Grapevine leafroll-associated virus 1 (GLRaV-1), GLRaV-2, GLRaV-3, GLRaV-4, and GLRaV-4 strain 5 by SYBR Green real-time reverse-transcription polymerase chain reaction (RT-PCR), and RT-PCR and sequencing. GLRaV-3 was found in 100% of the samples while GLRaV-1, GLRaV-2, and GLRaV-4 were detected in 24.9% (62/249), 15.3% (38/249), and 0.80% (2/249) of the samples, respectively. Single infections with GLRaV-3 were found in 66.3% (165/249) of the samples, and the remaining samples were mixed infections of GLRaV-3 with one or two other GLRaVs, those with GLRaV-1 being the most common (18.5%, 46/249). The genetic variability of Chinese GLRaV-3 isolates was characterized based on the coat protein (CP) gene. In total, 153 full-length CP gene sequences (94 sequences newly generated) of Chinese GLRaV-3 isolates from different grapevine-growing regions showed 89.3 to 100.0% and 92.7 to 100.0% identity at the nucleotide and amino acid levels, respectively. The average nucleotide diversity for the population of Chinese GLRaV-3 isolates was estimated at 0.037 (standard error = 0.0032). GLRaV-3 isolates from China segregated into five distinct phylogenetic groups and two novel recombination events were found in the viral population. This is the first and most extensive report of the prevalent species of GLRaV in China, which also provides an assessment of genetic variability of GLRaV-3 Chinese isolates.

Genetic variability and evolutionary dynamics of viruses of the family Closteroviridae

RNA viruses have a great potential for genetic variation, rapid evolution and adaptation. Characterization of the genetic variation of viral populations provides relevant information on the processes involved in virus evolution and epidemiology and it is crucial for designing reliable diagnostic tools and developing efficient and durable disease control strategies. Here we performed an updated analysis of sequences available in Genbank and reviewed present knowledge on the genetic variability and evolutionary processes of viruses of the family Closteroviridae. Several factors have shaped the genetic structure and diversity of closteroviruses. (I) A strong negative selection seems to be responsible for the high genetic stability in space and time for some viruses. (2) Long distance migration, probably by human transport of infected propagative plant material, have caused that genetically similar virus isolates are found in distant geographical regions. (3) Recombination between divergent sequence variants have generated new genotypes and plays an important role for the evolution of some viruses of the family Closteroviridae. (4) Interaction between virus strains or between different viruses in mixed infections may alter accumulation of certain strains. (5) Host change or virus transmission by insect vectors induced changes in the viral population structure due to positive selection of sequence variants with higher fitness for host-virus or vector-virus interaction (adaptation) or by genetic drift due to random selection of sequence variants during the population bottleneck associated to the transmission process.

Evidence of Grapevine leafroll associated virus-1-3, Grapevine fleck virus and Grapevine virus B Occurring in Himachal Pradesh, India

During a survey conducted in the grapevine orchards of Himachal Pradesh, variety of symptoms ranging from leaf yellowing, vein greening, reduced leaf size, downward rolling/cup shaped leaves to reduced fruit bearing were observed. Symptomatic leaf samples were collected and analyzed by serological (DAS-ELISA) and molecular methods (RT-PCR, PCR) for viruses and phytoplasma known worldwide on grapevine. DAS-ELISA was used for detection of Grapevine leafroll associated virus 1, 2 and 3 (GLRaV-1, 2 & 3), Grapevine virus A (GVA), Grapevine fan leaf virus (GFLV), Grapevine fleck virus (GFkV) and successfully detected GLRaV-1 & 3 and GFkV. All these samples were complemented with RT- PCR along with GVb and phytoplasma (additional to ELISA) using specific primers. Specific amplification in RT-PCR for GLRaV-1 (~232 bp), GLRaV-3 (~300 bp), GFkV (~179 bp) and GVB (~440 bp) confirmed the presence of these pathogens. Overall, ELISA and RT-PCR results confirmed the presence GLRaV-3 (66.7 %), GLRaV-1& GFkV (50 %), and Grapevine virus B (GVB) (12.5 %) in symptomatic plants. None of the samples were found positive for GFLV, GLRaV-2 and phytoplasma. Mixed infection was common and none of the plants were found virus free. To the best of our knowledge this is the first report of detection of GFkV and GVB in India.

Ecology and management of grapevine leafroll disease

Grapevine leafroll disease (GLD) is caused by a complex of vector-borne virus species in the family Closteroviridae. GLD is present in all grape-growing regions of the world, primarily affecting wine grape varieties. The disease has emerged in the last two decades as one of the major factors affecting grape fruit quality, leading to research efforts aimed at reducing its economic impact. Most research has focused on the pathogens themselves, such as improved detection protocols, with limited work directed toward disease ecology and the development of management practices. Here we discuss the ecology and management of GLD, focusing primarily on Grapevine leafroll-associated virus 3, the most important virus species within the complex. We contextualize research done on this system within an ecological framework that forms the backbone of the discussion regarding current and potential GLD management strategies. To reach this goal, we introduce various aspects of GLD biology and ecology, followed by disease management case studies from four different countries and continents (South Africa, New Zealand, California-USA, and France). We review ongoing regional efforts that serve as models for improved strategies to control this economically important and worldwide disease, highlighting scientific gaps that must be filled for the development of knowledge-based sustainable GLD management practices.

Grapevine leafroll-associated virus 3

Grapevine leafroll disease (GLD) is one of the most important grapevine viral diseases affecting grapevines worldwide. The impact on vine health, crop yield, and quality is difficult to assess due to a high number of variables, but significant economic losses are consistently reported over the lifespan of a vineyard if intervention strategies are not implemented. Several viruses from the family Closteroviridae are associated with GLD. However, Grapevine leafroll-associated virus 3 (GLRaV-3), the type species for the genus Ampelovirus, is regarded as the most important causative agent. Here we provide a general overview on various aspects of GLRaV-3, with an emphasis on the latest advances in the characterization of the genome. The full genome of several isolates have recently been sequenced and annotated, revealing the existence of several genetic variants. The classification of these variants, based on their genome sequence, will be discussed and a guideline is presented to facilitate future comparative studies. The characterization of sgRNAs produced during the infection cycle of GLRaV-3 has given some insight into the replication strategy and the putative functionality of the ORFs. The latest nucleotide sequence based molecular diagnostic techniques were shown to be more sensitive than conventional serological assays and although ELISA is not as sensitive it remains valuable for high-throughput screening and complementary to molecular diagnostics. The application of next-generation sequencing is proving to be a valuable tool to study the complexity of viral infection as well as plant pathogen interaction. Next-generation sequencing data can provide information regarding disease complexes, variants of viral species, and abundance of particular viruses. This information can be used to develop more accurate diagnostic assays. Reliable virus screening in support of robust grapevine certification programs remains the cornerstone of GLD management.

Molecular characterisation of two divergent variants of grapevine leafroll-associated virus 3 in New Zealand

Partial genomic sequences of two divergent grapevine leafroll-associated virus 3 (GLRaV-3) variants, NZ1-B and NZ2, from New Zealand were determined and analysed (11,827 nt and 7,612 nt, respectively). At the nucleotide level, both variants are more than 20 % different from the previously published GLRaV-3 sequences, from phylogenetic groups 1 to 5. Phylogenetic analysis indicated that NZ1-B is a variant of the previously identified divergent NZ-1, while NZ2 is a novel sequence with only 76 % nucleotide sequence identity to GLRaV-3 variants NZ-1, GH11, and GH30. Therefore, NZ2 is a new variant of GLRaV-3. Amino acid sequence analysis of the NZ1-B and NZ2 coat proteins indicated significant substitutions that are predicted to alter the coat protein structure, which potentially leads to the observed reduced immunological reactivity of both variants to the Bioreba anti-GLRaV-3 conjugated monoclonal antibody.

Genetic diversity analyses reveal novel recombination events in Grapevine leafroll-associated virus 3 in China

Grapevine leafroll-associated virus 3 (GLRaV-3) is the most prevalent causal agent of grapevine leafroll disease (GLD). Of the 75 grapevine samples collected from three regions in China, 46.7% and 94.7% of samples tested positive for GLRaV-3 in reverse transcription-PCR (RT-PCR) and reverse transcription nested PCR (RT-nPCR), respectively. The SSCP analysis for the clones of complete CP gene from 16 GLRaV-3 isolates showed that 15 isolates contained one predominant haplotype and one isolate had no predominant haplotype. The sequences of the CP genes showed 89.9-100% identities at the nucleotide level. Phylogenetic analysis of the CP gene sequences revealed the existence of four well defined variant groups, which corresponded to previously reported phylogenetic groups (1, 2, 3, and 5). Two new sub-groups designated as sub-group 1B and sub-group 3B in groups 1 and 3, respectively, were identified in the Chinese GLRaV-3 population. Recombination analyses illustrated that those two new sub-groups (1B and 3B) were emerged as a result of recombination events between variants in groups 1 and 2, and variants in groups 1 and 3, respectively. These results further indicated that the variants in those new sub-groups are viable and evolutionary successful. Recombinants with highly similar coat protein structure to variants of group 1 were abundantly found in the viral population. In addition, these analyses provided evidence about CP gene as one of the recombination hotspots in GLRaV-3 genome. The population genetic parameters of all available CP sequences suggested that the recombinants might have emerged due to population bottlenecks during transmission. The results provide new insights into the variability and evolution of GLRaV-3.

A divergent variant of Grapevine leafroll-associated virus 3 is present in California

BACKGROUND

Grapevine leafroll-associated viruses are a problem for grape production globally. Symptoms are caused by a number of distinct viral species. During a survey of Napa Valley vineyards (California, USA), we found evidence of a new variant of Grapevine leafroll-associated virus 3 (GLRaV-3). We isolated its genome from a symptomatic greenhouse-raised plant and fully sequenced it.

FINDINGS

In a maximum likelihood analysis of representative GLRaV-3 gene sequences, the isolate grouped most closely with a recently sequenced variant from South Africa and a partial sequence from New Zealand. These highly divergent GLRaV-3 variants have predicted proteins that are more than 10% divergent from other GLRaV-3 variants, and appear to be missing an open reading frame for the p6 protein.

CONCLUSIONS

This divergent GLRaV-3 phylogroup is already present in grape-growing regions worldwide and is capable of causing symptoms of leafroll disease without the p6 protein.

The p19.7 RNA silencing suppressor from Grapevine leafroll-associated virus 3 shows different levels of activity across phylogenetic groups

At least five phylogenetic groups have been reported for Grapevine leafroll-associated virus 3 (GLRaV-3). The p19.7 protein encoded by the GLRaV-3 was previously identified as an RNA silencing suppressor. In this study, five constructs of p19.7 belonging to different groups were compared for their suppressing activity. For each p19.7 variant, the accumulation level of green fluorescent protein mRNA and specific siRNAs were determined using co-infiltration assays in transgenic 16C Nicotiana benthamiana. Differences in the suppressing activity were found among the variants assayed. Some constructs originated viral-like mosaic symptoms that evolved to necrosis. The intensity of these symptoms appeared to be related to the strength of the suppressor activity. A comparison of the protein sequences revealed a few amino acid substitutions that may be associated with the observed differences in the suppressing activity.