First report of grapevine Pinot gris virus infecting grapevine in Iran

The use of high-throughput sequencing (HTS) technology has led to significant progress in the identification of many viruses and their genetic variants. In this study, we used the HTS platform to sequence small RNAs (sRNAs) of grapevine to study the virome. Isolation of RNA was performed using symptomatic grapevines collected from commercial vineyards in Krasnodar Krai in 2017–2018. To determine the viromes of vineyards, we used an integrated approach that included a bioinformatic analysis of the results of sRNA HTS and the molecular method RT-PCR, which made it possible to identify 13 viruses and 4 viroids. Grapevine leafroll-associated virus 4 (GLRaV-4), Grapevine Syrah Virus-1 (GSyV-1), Raspberry bushy dwarf virus (RBDV), Australian grapevine viroid (AGVd), and Grapevine yellow speckle viroid 2 (GYSVd-2) were identified for the first time in Russia. Out of 38 samples analyzed, 37 had mixed infections with 4–11 viruses, indicating a high viral load. Analysis of the obtained sequences of fragments of virus genomes made it possible to identify recombination events in GLRaV-1, GLRaV-2, GLRaV-3, GLRaV-4, GVT, GPGV, GRSPaV, GVA, and GFLV. The obtained results indicate a wide spread of the viruses and a high genetic diversity in the vineyards of Krasnodar Krai and emphasize the urgent need to develop and implement long-term strategies for the control of viral grapevine diseases.

Section: Validation Of the Results Of Srna Hts By Rt-pcr And The Phylogenetic Analysis Of Detected Virusesmentioning

confidence: 99%

High-Throughput Sequencing of Small RNAs for Diagnostics of Grapevine Viruses and Viroids in Russia

Navrotskaya

Porotikova

Yurchenko

et al. 2021

“…It was not until 2019 that GPGV’s causal role in GLMD was established for the first time [ 3 ]. GPGV was reported in different Vitis vinifera cultivars from various grape-growing regions such as Algeria [ 4 ], Armenia [ 5 ], Argentina [ 6 ], Australia [ 7 ], Belgium [ 8 ], Brazil [ 9 ], Bulgaria [ 10 ], Canada [ 11 ], Chile [ 12 ], China [ 13 ], France [ 14 ], Germany [ 15 ], Greece [ 16 ], Iran [ 17 ], Italy [ 16 ], Japan [ 18 ], Lebanon and the Middle East [ 19 ], Moldavia [ 20 ], Pakistan [ 21 ], Poland [ 22 ], Slovakia and the Czech Republic [ 23 ], Slovenia [ 24 ], South Korea [ 25 ], Spain [ 26 ], Turkey [ 27 ] and the USA [ 28 ].…”

Section: Introductionmentioning

confidence: 99%

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

Vemulapati

McFadden-Smith

et al. 2023

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.

“…In the present study, GLRaV1, GFLV, GDefV, ArMV, GV-Sat, GPGV, GRBV, GRGV, and GVA from the seven genera of plant viruses and GYSVd1, GYSVd2, HSVd, and AGVd from the two viroid genera of the family Pospiviroidae were identified from six libraries of five grapevine cultivars in Iran ( Figure 3 and Figure 4 , Table 4 ). ArMV [ 57 ], GdefV [ 58 ], GFLV [ 59 ], GLRaV1 [ 40 ], GPGV [ 60 ], GRGV [ 61 ], and grapevine viroids (GYSVd1, GYSVd2, HSVd, and AGVd) [ 38 ] have been previously reported from Iran; however, GRBV and GV-Sat are two new species for Iranian grapevine virome reported for the first time. These viruses comprise 1.24, 0.62, and 0.1 percent of the populations in the virome, respectively.…”

Section: Discussionmentioning

confidence: 99%

Application of High-Throughput Sequencing for Comprehensive Virome Profiling in Grapevines Shows Yellows in Iran

Gholampour,

Zakiaghl,

Asquini

et al. 2024

A comprehensive study on the whole spectrum of viruses and viroids in five Iranian grapevine cultivars was carried out using sRNA libraries prepared from phloem tissue. A comparison of two approaches to virus detection from sRNAome data indicated a significant difference in the results and performance of the aligners in viral genome reconstruction. The results showed a complex virome in terms of viral composition, abundance, and richness. Thirteen viruses and viroids were identified in five Iranian grapevine cultivars, among which the grapevine red blotch virus and grapevine satellite virus were detected for the first time in Iranian vineyards. Grapevine leafroll-associated virus 1 (GLRaV1) and grapevine fanleaf virus (GFLV) were highly dominant in the virome. However, their frequency and abundance were somewhat different among grapevine cultivars. The results revealed a mixed infection of GLRaV1/grapevine yellow speckle viroid 1 (GYSVd1) and GFLV/GYSVd1 in grapevines that exhibited yellows and vein banding. We also propose a threshold of 14% of complete reconstruction as an appropriate threshold for detection of grapevine viruses that can be used as indicators for reliable grapevine virome profiling or in quarantine stations and certification programs.