Grapevine Pinot Gris Virus Isolates Research Articles

Monitoring the Spread of Grapevine Viruses in Vineyards of Contrasting Agronomic Practices: A Metagenomic Investigation.

This study investigated the transmission of grapevine viruses, specifically grapevine red blotch virus (GRBV) and grapevine Pinot gris virus (GPGV), in vineyards in Niagara Region, Ontario, Canada. Forty sentinel vines that were confirmed free of GRBV and GPGV by both high-throughput sequencing (HTS) and endpoint polymerase chain reaction (PCR) were introduced to two vineyards (one organic and one conventional) that were heavily infected with both GRBV and GPGV. Four months post-introduction, the sentinel vines were relocated to a phytotron. The HTS results from 15 months post-introduction revealed a widespread infection of GPGV among the sentinel vines but did not detect any GRBV. The GPGV infection rate of sentinel vines in the organic vineyard (13/18) was higher than in the conventional vineyard (1/19). The possibility of an alternative viral reservoir was assessed by testing the most abundant plants in between rows (Medicago sativa, Trifolium repens, Cirsium arvense and Taraxacum officinale), perennial plants in border areas (Fraxinus americana, Ulmus americana, Rhamnus cathartica) and wild grape (unknown Vitis sp.). The HTS result showed that cover crops and perennial plants did not harbor any grapevine viruses, while 4/5 wild grapes tested positive for GPGV but not GRBV. A pairwise sequence identity analysis revealed high similarities between the GPGV isolates found in the established vines on the vineyard and the newly contracted GPGV isolates in the sentinel vines, implicating a recent transmission event. This work provides novel insights into the spread of grapevine viruses in Niagara Region and is also the first direct proof of the spread of GPGV in natural vineyard conditions in North America.

The genetic variability of grapevine Pinot gris virus (GPGV) in Australia

Grapevine Pinot gris virus (GPGV; genus Trichovirus in the family Betaflexiviridae) was detected in Australia in 2016, but its impact on the production of nursery material and fruit in Australia is still currently unknown. This study investigated the prevalence and genetic diversity of GPGV in Australia. GPGV was detected by reverse transcription-polymerase chain reaction (RT-PCR) in a range of rootstock, table and wine grape varieties from New South Wales, South Australia, and Victoria, with 473/2171 (21.8%) samples found to be infected. Genomes of 32 Australian GPGV isolates were sequenced and many of the isolates shared high nucleotide homology. Phylogenetic and haplotype analyses demonstrated that there were four distinct clades amongst the 32 Australian GPGV isolates and that there were likely to have been at least five separate introductions of the virus into Australia. Recombination and haplotype analysis indicate the emergence of new GPGV strains after introduction into Australia. When compared with 168 overseas GPGV isolates, the analyses suggest that the most likely origin of Australian GPGV isolates is from Europe. There was no correlation between specific GPGV genotypes and symptoms such as leaf mottling, leaf deformation, and shoot stunting, which were observed in some vineyards, and the virus was frequently found in symptomless grapevines.

Phylogenetic and Evolutionary Studies of Grapevine Pinot Gris Virus Isolates from Canada.

This study investigated the phylogenetic relationship of grapevine Pinot gris virus (GPGV) isolates from Canada with GPGV isolates reported worldwide. Full-length genomes of 25 GPGV isolates representing the main four grape-growing regions in Canada (British Columbia, Ontario, Nova Scotia and Quebec) were sequenced and compared to genomes of 43 GPGV isolates representing eight countries and three continents. Phylogenetic analysis based on full genome sequences revealed an unambiguous separation of North American GPGV isolates with isolates from Europe and Asia. Within the North American clade, GPGV isolates from the USA segregated into a distinct subclade, whereas the relationships amongst GPGV isolates from different regions of Canada were not clearly defined. The phylogenetic analysis of the overlapping regions of MP and CP genes involving 169 isolates from 14 countries resulted in two distinctive clades, which were seemingly independent of their country of origin. Clade 1 included the majority of asymptomatic isolates (81% asymptomatic), whereas clade 2 was predominantly formed of symptomatic isolates (78% symptomatic). This research is the first study focused on the genetic variability and origin of GPGV in Canada.

Occurrence and Genetic Characterization of Grapevine Pinot Gris Virus in Russia.

Grapevine Pinot gris virus (GPGV) is a widespread grapevine pathogen associated with symptoms of leaf mottling and deformation. In order to study the distribution and genetic diversity of GPGV in Russia, we tested 1347 grapevine samples from 3 regions of Russia–the Krasnodar Krai, Stavropol Krai, and Republic of Crimea—using duplex real-time RT-PCR. GPGV was detected in 993 grapevines, both symptomatic and asymptomatic. In 119 isolates, we sequenced complete movement protein (MP) and coat protein (CP) genes of the GPGV genome. The percentage of identity of the obtained nucleotide MP/CP sequences with the closest isolates from the GenBank was 97.75–99.56%. A phylogenetic analysis showed that these Russian GPGV isolates are mainly grouped with previously described representative asymptomatic isolates. New post-translational modifications of the MP and CP at the positions of polymorphisms in the genomes of Russian isolates were predicted. The present work is the first study on the distribution and genetic diversity of GPGV in Russia.

Molecular analysis of grapevine Pinot gris virus and its association with grapevine leaf mottling and deformation on ‘Vermentino’ grapevines in Sardinia

In 2017–2018, grapevines of cultivar ‘Vermentino’ infected with grapevine Pinot gris virus (GPGV) in Sardinia, Italy, exhibited leaf symptoms of mosaic, chlorotic mottling, and curling, and stunted shoots. Disease incidence assessed in 2018 was greater (67%, 103 symptomatic plants out of 153 monitored) than in 2017 (26%, 40 of 153 plants). All symptomatic samples tested by RT-PCR were positive for GPGV in both years, while 70% (53 of 76) of the asymptomatic samples in 2017, and 42% (19 of 45) in 2018, were also positive for GPGV. Characterizing six GPGV isolates from ‘Vermentino’ by RT-PCR and sequencing of a genomic fragment covering the movement and coat protein genes showed high conservation at the nucleotide level (98.7% to 100.0%) among Sardinian isolates and isolates for which sequence information is available in GenBank. Phylogenetic analysis indicated that most Sardinian GPGV isolates grouped with other European isolates. This is the first characterization of GPGV in a Sardinian vineyard.

Emerging and population analysis of Grapevine Pinot gris virus isolates from Iran.

The online version contains supplementary material available at 10.1007/s13205-021-02914-5.

Incidence of GLMD-Like Symptoms on Grapevines Naturally Infected by Grapevine Pinot gris virus, Boron Content and Gene Expression Analysis of Boron Metabolism Genes

Grapevine Pinot gris virus (GPGV) is considered to be a causal agent of Grapevine Leaf Mottling and Deformation (GLMD) disease that has been reported worldwide through the grapevine-growing regions. Seven grapevines that were collected from a vineyard in the Czech Republic were tested for the presence of GPGV in leaf and phloem tissues. Each of the seven grapevines was infected by GPGV, from which sic symptoms were mostly shown without a typical mottling. The phylogeny based on RNA-dependent RNA polymerase and movement/coat protein sequences indicated the same origin of the GPGV isolates. The GPGV titer was the highest in the grapevines with the highest GLMD-like symptoms; however, some of the grapevines with milder GLMD-like symptoms had a lower GPGV titer than the asymptomatic grapevine. Soil analysis showed uneven boron content in the direct vicinity of the grapevines, while the boron content in the grapevines was more, even showing no boron deficiency. The quantitative analysis of selected gene expressions associated with boron efflux and transport only partially explained the boron content in the soil and grapevines and only in the grapevines growing in soils with the highest or lowest boron contents. The VvBor2 and VvNIP5 genes had a higher expression and VvNIP6 had a lower expression in the grapevine growing in the soil with the lowest boron content, while a low expression of VvBor1 and VvBor2 was observed in the grapevine that was grown in the soil with the highest boron content.

First report of grapevine Pinot gris virus and grapevine leafroll-associated virus 2 in Bulgarian vineyards

During 2016–2019, surveys of viruses were conducted in Bulgarian vineyards. Grapevine Pinot gris virus (GPGV) and grapevine leafroll-associated virus 2 (GLRaV-2) were detected by ELISA and RT-PCR in randomly collected samples. Phylogenetic analyses of the nucleotide sequence of a partial coat protein gene fragment indicated that the Bulgarian GPGV isolates grouped with isolates from Europe and the Americas while Bulgarian GLRaV-2 isolates clustered with isolates of the PN1 group. This is the first report of GPGV and GLRaV-2 in Bulgaria.

Identification of grapevine Pinot gris virus in free-living Vitis spp. located in riparian areas adjacent to commercial vineyards.

Grapevine Pinot gris virus (GPGV) is a recently identified pathogen of grapevines in California. To advance our knowledge about the epidemiology of GPGV, we investigated if free-living Vitis spp. can represent a source of virus infection. In 2019 a field survey of GPGV infection was conducted in Napa County. During the inspection 60 free-living vines in riparian habitats near commercial vineyards with GPGV infection were sampled. Samples were tested by real-time reverse transcription PCR (RT-PCR), identifying 23 free-living Vitis spp. positive for GPGV. Later, GPGV infection was confirmed in these plants via end-point RT-PCR and Sanger sequencing. Based on sequence analysis, detected GPGV isolates are more related to the asymptomatic variant of the virus. Vitis species ancestry was determined by DNA fingerprinting. GPGV-infected material included V. californica, V. californica × V. vinifera hybrids and hybrid rootstock cultivars. Here, GPGV is reported for the first time in free-living Vitis spp. The results of this study will support the development of management strategies for GPGV in California and beyond.

OCCURRENCE AND MOLECULAR GENETIC CHARACTERISTICS OF GRAPEVINE PINOT GRIS VIRUS IN RUSSIA

For the first time in Russia Grapevine Pinot gris virus (GPGV) was detected on the vineyards of the Stavropol Territory and the Republic of Crimea. It has been discovered by real-time PCR that the distribution of GPGV in the vineyards of the Krasnodar Territory is 82%, in the Stavropol Territory - 94% and in the Republic of Crimea - 68%. Nucleotide percentage similarity of the Russian GPGV isolates in comparison with the closest isolates from Genbank was 97,5-99,5%.

Survey and Diversity of Grapevine Pinot gris virus in Algeria and Comprehensive High-Throughput Small RNA Sequencing Analysis of Two Isolates from Vitis vinifera cv. Sabel Revealing High Viral Diversity.

Grapevine Pinot gris virus (GPGV) is a putative causal agent of grapevine leaf mottling and deformation disease that has been reported worldwide throughout the grapevine-growing regions. Fifty-four grapevines collected from five Algerian grapevine-growing regions were tested for the presence of GPGV in phloem tissues. Eight of the tested grapevines were infected by GPGV. Viromes of two selected Vitis vinifera cv. Sabel grapevines infected by GPGV and showing virus-like symptoms were analyzed by small RNA sequencing. Phylogenetic analyses of the partial coding sequence (cds) of the RNA-dependent RNA polymerase (RdRp) domain showed that all Algerian GPGV isolates were grouped with some already-described asymptomatic isolates. This study provides the first survey of the occurrence of GPGV in Algeria. Moreover, Grapevine fleck virus, Grapevine rupestris stem pitting-associated virus, Grapevine virus B, Grapevine rupestris vein feathering virus, Hop stunt viroid and Grapevine yellow speckle viroid 1 were detected in Algeria for the first time.

Believing is seeing: lessons from emerging viruses in grapevine

Among the grapevine viruses recently identified, grapevine vein clearing virus (GVCV), grapevine Pinot gris virus (GPGV) and grapevine red blotch virus (GRBV) have emerged in the last decade as new threats to the grape and wine industry. Initially reported in Italy (GPGV) and the USA (GVCV and GRBV), GPGV and GRBV have a wider distribution at present, likely as a result of an extensive exchange of infected, propagative material, while GVCV seems to remain restricted to the mid-western regions in the USA. Much progress has been made on the ecology of these three emerging viruses since the last reviews were published in 2017 (Cieniewicz et al. 2017a; Qiu and Schoelz 2017; Saldarelli et al. 2017). Here we compile and critically analyze the latest information on these three viruses with a special emphasis on the (i) association between the genetic make-up of GPGV isolates and chlorotic mottling and leaf deformation symptoms, (ii) epidemiological and ecological attributes of GVCV and GRBV, and (iii) impacts of GRBV, particularly on molecular underpinnings of fruit ripening physiological pathways. Common trends among these three emerging grapevine viruses but also some unique characteristics are highlighted. Finally, we conclude on how critical it is to embrace ‘believing is seeing’ in the case of emerging grapevine viruses to remain relevant and impactful in providing research-based management solutions, while leading a sustained dialogue with grape grower’s communities, extension educators, policy makers and regulatory authorities.

Bağlarda Yeni Saptanan Virüslerin Hatay ve Tekirdağ İli Bağ Alanlarında PCR Yöntemiyle Belirlenmesi ve Moleküler Karakterizasyonu

Son yıllarda yeni nesil sekans analiz tekniklerinin yaygın olarak kullanılması bağlarda ve diğer bitki türlerinde etiyolojisi bilinmeyen birçok virüs hastalığının etmeninin belirlenmesini sağlamıştır.. Bağlarda bu teknoloji ile saptanan yeni virüslerden en önemlileri Grapevine Pinot Gris Virus (GPGV), Grapevine Syrah Virus-1 (GSyV-1), Grapevine Red-blotch associated Virus (GRBaV) ve Grapevine Roditis Leaf Discoloration Virus (GRLDaV)‘dür. Bu çalışmanın amacı Tekirdağ ve Hatay ili bağ alanlarında GPGV, GSyV-1, GRBaV ve GRLDaV varlığının PCR ve DNA dizileme yöntemleriyle saptanması ve karakterizasyonlarının yapılmasıdır. Bu çalışma kapsamında virüs benzeri simptom gösteren omcaların yanı sıra simptomsuz omcalardan da örnekler alınmış ve toplam olarak Tekirdağ ilinden 191, Hatay ilinden ise 111 örnek toplanmıştır. Tekirdağ ilinden toplanan bağ örneklerinde %43,62 oranında GPGV, %1,04 oranında GSyV1 saptanmıştır. Hatay ilinden toplanan örneklerde ise sadece %0,9 oranında GSyV1 saptanmış ve testlenen örnekler GPGV, GRBaV, GRLDaV açısından temiz bulunmuştur. Tekirdağ örneklerinin GPGV için yapılan RT-PCR analizlerinde kısmi kılıf protein, hareketlilik, ve replikaz genlerini çoğaltan primerler kullanıldığında sırasıyla 411 bp, 302 bp ve 618 bp büyüklüğünde PCR ürünleri elde edilmiştir Bu ürünlerin doğrudan iki yönlü sekans analizi sonucunda ve her üç gen bölgesinin de nükleotid dizilimlerinin gen bankasında kayıtlı farklı GPGV izolatları ile yüksek oranda homoloji gösterdiği saptanmıştır.

Analysis of new grapevine Pinot gris virus (GPGV) isolates from Northeast Italy provides clues to track the evolution of a newly emerging clade.

Grapevine Pinot gris disease (GPGD) has been associated with a trichovirus, namely grapevine Pinot gris virus (GPGV), although the virus has been reported in both symptomatic and asymptomatic plants. Despite the puzzling aetiology of the disease and potentially important role of GPGV, the number of fully sequenced isolates is still rather limited. With the aim of increasing the knowledge on intraspecific diversity and evolution, nine GPGV isolates were collected from different vineyards in the Friuli Venezia Giulia region (Northeast Italy), cloned, sequenced, and subjected to robust phylogenetic and other analyses. The results provided hints on the evolutionary history of the virus, the occurrence of recombination, and the presence of clade-specific SNPs in sites of putative protein modifications with potential impact on the interaction with the host.

Incidence, distribution and limited genetic variability among Turkish isolates of Grapevine Pinot gris virus from different grapevine cultivars

Grapevine Pinot gris virus (GPGV) was firstly identified in northern Italy by deep sequencing from grapevine cv. Pinot gris, exhibiting mottling and deformation of the leaves. The objective of this study was to investigate the prevalence and genetic variability of GPGV isolates obtained from different local and imported grapevine cultivars in Turkey based on partial coat protein, movement protein and RNA-dependent RNA polymerase (RdRp) domain of the replicase (Rep) gene. Two hundred and one grapevine samples from different provinces were tested by RT-PCR assays, approximately 25% of which were found to be infected by GPGV. The PCR products were sequenced and based on the phylogenetic analysis, RdRp gene was found to be most conserved region. The phylograms of three genomic regions revealed correlation between geography and genetic structure. Furthermore, nucleotide diversity studies revealed a low divergence from the homologous sequences from GenBank and some variations within the groups were detected. The results presented in this study provide a better understanding of genetic variation and phylogenetic of GPGV isolates worldwide.

Survey of Grapevine Pinot gris virus in certified grapevine stocks in Ukraine

Eighteen grapevine mother plants used by nurseries for propagation in Ukraine were tested for the presence of Grapevine Pinot gris virus (GPGV) and other viruses by simplex and multiplex RT-PCR (reverse transcription polymerase chain reaction). GPGV was found in 10 grapevines, which were also co-infected with Grapevine virus A (GVA) and Grapevine fleck virus (GFkV). We sequenced coding regions of the movement and coat protein and a region of the RdRp domain in twelve isolates. Phylogenetic analyses of the two genes revealed that the Ukrainian GPGV isolates grouped with previously described asymptomatic isolates. This study provides the first detailed survey of GPGV occurrence in Ukraine.

Occurrence of Grapevine Pinot gris virus in Poland and description of asymptomatic exhibitions in grapevines

Sixty five grapevines in productive areas from southern regions in Poland were tested for the presence of Grapevine Pinot gris virus (GPGV) by RT-PCR. Twenty two percent of the tested plants were infected by GPGV. GPGV positive grapevines were also tested for the presence of other viruses by multiplex and simplex RT-PCR. Part of the movement and coat protein coding regions and a part of RdRp domain were sequenced. Phylogenetic analyses of the 2 genes revealed that south Polish GPGV isolates grouped with already described asymptomatic isolates. This study provides the first survey of the GPGV occurrence in Poland.

Association between genetic variability and titre of Grapevine Pinot gris virus with disease symptoms

The present work was carried out in order to verify the possible association between a new grapevine disease, characterized by leaf mottling and deformation, and the genetic variability and concentration of Grapevine Pinot gris virus (GPGV), a recently identified virus tentatively associated with the pathology. After vineyard surveys and the establishment of real‐time qPCR assays, characterization of GPGV isolates and evaluation of GPGV titre were assessed in more than 100 samples of grapevine Glera, collected from plants regardless of whether or not they showed the symptomatology. Results showed that there was an important association between the GPGV variants and manifestation of the symptoms, and that grapevines with symptoms harboured significantly higher GPGV titre than symptomless vines. Moreover, an interesting relationship among the phylogenetic clustering of the isolates originating from plants with symptoms and some epidemiological characteristics of the disease was found. The current study confirmed the role of GPGV in the emergent disease characterized by grapevine leaf mottling and deformation.

First report of Grapevine Pinot gris virus in Georgia

Grapevine Pinot gris virus (GPGV), a Thricovirus (Be- taflexiviridae) inducing grapevine mottling and deformation in Vitis vinifera L., has been reported in Europe and Korea (Martelli, 2014). During autumn 2013, a survey on the sani- tary status of native V. vinifera cultivars was carried out in Georgia, collecting leaf samples from 37 vines of 25 white- and red-berried cultivars. To detect GPGV, total RNAs were extracted from leaf tissues and RT-PCR reactions were performed with specific primer pairs amplifying dis- tinct genomic regions (GPG-14F/GPG-632R, GPG-5637F/ GPG-5939R, GPG-6609F/GPG-7020R, DetF/DetR) (Glasa et al., 2014; Morelli et al., 2014). DetF/DetR PCR products were sequenced (coverage 4X) and compared with Gen- Bank sequences. Phylogenetic analysis was done using the software MEGA6. GPGV was detected in eight plants of white-berried cvs Goruli mtsvane, Khikvi, Mtsvane kviteli and red-berried cvs Saperavi pachkha, Tavkveri, Korkaula using primer pairs GPG-5637F/GPG-5939R and DetF/ DetR. GPGV detection sensitiveness of the other primer pairs was lower. Blast comparison with GenBank showed that the Georgian GPGV isolates share the highest sequence identity at the nucleotide level (98%) with the isolate GPGV SK107 from Slovakia (GenBank accession No. KF134126). Phylogenetic analysis performed by MEGA6 showed that the Georgian GPGV isolates grouped with the Slovakian isolates in a distinct cluster separated from the Italian, French, and Slovenian isolates. To our knowledge, this is the first report of GPGV in Georgia. As response of Georgian grapevine varieties to pathogens has not been described accurately, fur- ther investigation will be crucial to determine the symptoms associated with GPGV presence and to evaluate its potential effects on yield and wine quality.

DETECTION OF GRAPEVINE PINOT GRIS VIRUS IN CERTIFIED GRAPEVINE STOCKS IN MORAVIA, CZECH REPUBLIC

Twenty one grapevine mother plants used by nurseries for propagation in South Moravia, Czech Republic, were tested for the presence of Grapevine Pinot gris virus (GPGV) and other viruses by simplex and multiplex RT-PCR. GPGV was found in all vines tested and Grapevine virus A, Grapevine fanleaf virus and Grapevine fleck virus were detected only in some of them. Part of the movement and coat protein coding regions of 21 GPGV isolates was sequenced. Phylogenetic analysis revealed that south Moravian GPGV isolates grouped with isolates from other regions and countries. This study provides the first comprehensive survey of the GPGV occurrence in South Moravia.