Detection and Sequence Analysis of Grapevine Leafroll‐Associated Virus 2 Isolates from China

Several grapevine leafroll‐associated viruses (GLRaVs) have been found frequently in grapevines behaving GLD. Among them, GLRaV‐2 is the only one belonging to Closterovirus, and mainly induces leafroll symptoms and graft incompatibility. In this study, new degenerate primer pairs designed against the HSP70 gene were applied in polymerase chain reaction (PCR) and nested PCR (nPCR) to detect GLRaV‐2 in 132 samples collected from 14 provinces and regions of China. Of the samples, 51.5% were infected with GLRaV‐2, and most did not exhibit GLD symptoms. Some popular grape cultivars had a high incidence of GLRaV‐2 infection, such as Cabernet Sauvignon (92.3%), Chardonnay (80%), Red Globe (75%) and Italian Riesling (73.7%). ‘Beta’ rootstocks, previously identified as negative samples, were also found to be highly infected with GLRaV‐2 (50%). GLRaV‐2 isolates obtained in this study showed identities ranging from 68.9% to 100% and 76.47% to 100.0% at the nucleotide and amino acid levels, respectively. Phylogenetic analysis based on the HSP70 gene showed that all GLRaV‐2 isolates in China belong to three of five reported phylogenetic groups. Different variants belonging to the PN and RG groups were present in a single isolate. The results showed that the new degenerate primer pairs could detect more GLRaV‐2 isolates than the previously reported primers. This is the first detailed report on the prevalence and gene diversity of GLRaV‐2 in China and also provides an nPCR method to improve the sensitivity of PCR as an alternative method when no real‐time PCR device is available.     

Development,histological observations and Grapevine leafroll‐associated virus‐3 localisation in in vitro grapevine micrografts

Development, histological process and Grapevine leafroll‐associated virus‐3 localisation were studied in micrografts of three scion/rootstock combinations: healthy/healthy, healthy/infected and infected/healthy. Earlier bud break and faster growth in scions of micrografts were obtained when the healthy shoot segments were used as scions, while earlier bud break in rootstocks and greater fresh weight of roots in micrografts were produced when the healthy shoot segments were used as rootstocks. All histological processes including callus initiation and formation in micrografting conjunctions, and initiation of new cambial cells followed by vascular bundle development connecting scions and rootstocks were similar in micrografts, regardless of the sanitary status of the scions and rootstocks used for micrografting. Virus infection in micrografting conjunctions and systematic infection in micrografts were much more efficient and faster in micrografting combination of the infected scions/healthy rootstocks than in the healthy scions/infected rootstocks. To the best of our knowledge, this is the first report addressing histological process of micrograft development and virus localisation in micrografts. In vitro culture system established in this study facilitates studies on the ‘pure’ impact of the viral infection on micrografting.     

Brief Report of a New Highly Divergent Variant of Grapevine leafroll‐associated virus 3 (GLRaV‐3)

The alignment of the complete genomes of genetic variants of Grapevine leafroll‐associated virus 3 (GLRaV‐3) representing phylogenetic groups I, II, III and VI revealed numerous regions with exceptionally high divergence between group I to III and group VI variants. Oligonucleotide primers universal for all the above groups of the virus were designed in conserved short stretches of sequences flanking the divergent regions in the helicase (Hel) and RNA‐dependent RNA polymerase (RdRP) domains of the replicase gene and the divergent copy of the capsid protein (dCP) gene. Cloning and sequencing of the 549‐bp RT‐PCR amplicon of the helicase domain from grapevine cv. Shiraz lead to the detection of a variant of GLRaV‐3, which shared only 69.6–74.1% nt similarity with other variants, including the recently reported, new, highly divergent variant, isolate 139. This was confirmed by the results of the analysis of 517‐bp amplicon of the HSP70 gene of GLRaV‐3 generated in RT‐nested PCR based on degenerate primers for the simultaneous amplification of members of the Closteroviridae family designed by Dovas and Katis (J Virol Methods, 109, 2003, 217). In this genomic region, the variant shares 72.3–78.7% nt similarity with other variants of GLRaV‐3. This previously unreported, new, highly divergent variant was provisionally named GTG10. From the alignment of the HSP70 sequences primers for the specific RT‐nested PCR amplification of the variant GTG10 and members of group VI, and specific simultaneous amplification of variants of groups I, II and III, were designed. The results obtained from brief testing of various grapevines using all these primers suggest a relatively limited presence of GTG10 variant in vineyards.     

Characterization of silencing suppressor p24 of Grapevine leafroll‐associated virus 2

Grapevine leafroll‐associated virus 2 (GLRaV‐2) p24 has been reported to be an RNA silencing suppressor (RSS). However, the mechanisms underlying p24's suppression of RNA silencing are unknown. Using Agrobacterium infiltration‐mediated RNA silencing assays, we showed that GLRaV‐2 p24 is a strong RSS triggered by positive‐sense green fluorescent protein (GFP) RNA, and that silencing suppression by p24 effectively blocks the accumulation of small interfering RNAs. Deletion analyses showed that the region of amino acids 1–188, which contains all predicted α‐helices and β‐strands, is required for the RSS activity of p24. Hydrophobic residues I35/F38/V85/V89/W149 and V162/L169/L170, previously shown to be critical for p24 self‐interaction, are also crucial for silencing suppression, and western blotting results suggested that a lack of self‐interaction ability results in decreased p24 accumulation in plants. The mutants showed greatly weakened or a lack of RSS activity. Substitution with two basic residues at positions 2 or 86, putatively involved in RNA binding, totally abolished the RSS activity of p24, suggesting that p24 uses an RNA‐binding strategy to suppress RNA silencing. Our results also showed that W54 in the WG/GW‐like motif (W54/G55) is crucial for the RSS activity of p24, whereas p24 does not physically interact with AGO1 of Nicotiana benthamiana. Furthermore, p24 did not promote AGO1 degradation, but significantly up‐regulated AGO1 mRNA expression, and this effect was correlated with the RSS activity of p24, indicating that p24 may interfere with microRNA‐directed processes. The presented results contribute to our understanding of viral suppression of RNA silencing and the molecular mechanisms underlying GLRaV‐2 infection.     

Effects of Grapevine leafroll‐associated virus 3 on the physiology in asymptomatic plants of Vitis vinifera

Grapevine leafroll disease is one of the most important viral diseases of grapevine (Vitis vinifera) worldwide. Grapevine leafroll‐associated virus 3 (GLRaV‐3) is the most predominant virus species causing this disease. Therefore, it is important to identify GLRaV‐3 effects, especially in plants which do not systematically show visual symptoms. In this study, effects of GLRaV‐3 on grapevine physiology were evaluated in asymptomatic plants of Malvasía de Banyalbufar and Cabernet Sauvignon cvs. Absolute virus quantification was performed in order to determine the level of infection of the treatment. The net carbon dioxide (CO₂) assimilation (A_N) and electron transport rate (J_flux) were the main parameters affected by the virus. The A_N reduction in infected plants was attributed to restrictions in CO₂ diffusion caused by anatomical leaf changes and a reduction of Rubisco activity. Those effects were more evident in Malvasia de Banyalbufar plants. The reduction of A_N leads to a decrease in the total oxygen uptake rate by the activity of the cytochrome oxidase pathway, producing slight differences in plant growth. Therefore, even though no symptoms were expressed in the plants, the effects of the virus compromised the plant vital processes, showing the importance of early detection of the virus in order to fight against the infection.     

A combined RT‐PCR and dot‐blot hybridization method reveals the coexistence of SJNNV and RGNNV betanodavirus genotypes in wild meagre (Argyrosomus regius)

Aims: To detect the possible coexistence of striped jack nervous necrosis virus (SJNNV) and red‐spotted grouper nervous necrosis virus (RGNNV) genotypes in a single fish, a methodology based on the combination of PCR amplification and blot hybridization has been developed and applied in this study. Methods and Results: The degenerate primers designed for the PCR procedure target the T4 region within the capsid gene, resulting in the amplification of both genotypes. The subsequent hybridization of these amplification products with two different specific digoxigenin‐labelled probes resulted in the identification of both genotypes separately. The application of the RT‐PCR protocol to analyse blood samples from asymptomatic wild meagre (Argyrosomus regius) specimens has shown a 46·87% of viral nervous necrosis virus carriers. The combination of RT‐PCR and blot hybridization increases the detection rate up to 90·62%, and, in addition, it has shown the coexistence of both genotypes in 18 out of the 32 specimens analysed (56·25%). Conclusions: This study reports the coexistence of betanodaviruses belonging to two different genotypes (SJNNV and RGNNV) in wild fish specimens. Significance and Impact of the Study: This is the first report demonstrating the presence of SJNNV and RGNNV genotypes in the same specimen. This study also demonstrates a carrier state in this fish species for the first time.