First report of Australian grapevine viroid in grapevine in Greece

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: Viroidsmentioning

confidence: 88%

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

Navrotskaya

Porotikova

Yurchenko

et al. 2021

“…Unlike HSVd and GYSVd-1, which are characterized by their widespread presence, AGVd is found only sporadically [148]; its presence has been reported in the vineyards of Iran [149], Tunisia [150], India [151], Turkey [152], Australia [153], the USA [114], Thailand [142], China [154], Greece [155], and Russia [35]. In addition, AGVd was found in the Grapevine Germplasm Resources Garden in Beijing [146] and the germplasm collections in Italy [144]; to our knowledge, these are the only records of the presence of this viroid in grapevine collections.…”

Section: Family: Pospiviroidaementioning

confidence: 99%

Virome of Grapevine Germplasm from the Anapa Ampelographic Collection (Russia)

Shvets

Porotikova

Sandomirsky

et al. 2022

Grapevine germplasm collections are unique repositories of grape cultivars; therefore, it is necessary to minimize their infection with pathogens, including viruses, and develop various programs to maintain them in a virus-free state. In our study, we examined the virome of the largest Russian grapevine germplasm collection, the Anapa Ampelographic Collection, using high-throughput sequencing of total RNAs. As a result of bioinformatics analysis and validation of its results by reverse transcription PCR (RT-PCR) and quantitative RT-PCR (RT-qPCR), we identified 20 viruses and 3 viroids in 47 libraries. All samples were infected with 2 to 12 viruses and viroids, including those that cause economically significant diseases: leafroll, fleck, and rugose wood complex. For the first time in Russia, we detected Grapevine virus B (GVB), Grapevine virus F (GVF), Grapevine asteroid mosaic-associated virus (GAMaV), Grapevine Red Globe virus (GRGV), Grapevine satellite virus (GV-Sat), Grapevine virga-like virus (GVLV), Grapevine-associated jivivirus 1 (GaJV-1) and Vitis cryptic virus (VCV). A new putative representative of the genus Umbravirus with the provisional name Grapevine umbra-like virus (GULV) was also identified in Russian grape samples.

“…The subsequent tests also revealed the presence of grapevine rupestris stem pitting-associated virus (GRSPaV), grapevine leafroll-associated virus-3 (GLRaV-3), GYSVd-1, GYSVd-2, and HSVd. Grapevine fanleaf virus, GLRaV-3, and GYSVd-2 were also detected in symptomatic AGVd-positive plants showing bright yellow and chlorotic discolorations, not allowing for the observed symptoms to be directly correlated with the AGVd infection [ 25 , 79 ]. In another case, GYSVd-1 and HSVd together with a badnavirus were identified by NGS in a Greek vineyard showing leaf discoloration symptoms [ 169 ].…”

Section: Incidence Of Viroids and Viroid Diseases In Countries Of The...mentioning

confidence: 99%

“…One of cv. ‘Mandilaria’ [VIVC 7300] from Heraklion) gave 29 AGVd sequences that shared 100% identity [ 25 ].…”

Section: Origin Evolution and Spread Of Viroids In The Mediterranean ...mentioning

confidence: 99%

“…Table 1 shows the geographical distribution and host range of these viroids. Lebanon apple [10] Israel, Spain pomegranate [11] Greece, Turkey fig [12][13][14] AHVd Italy, Spain apple, loquat [15][16][17] ASSVd Greece apple, sweet cherry, pear, wild pear, wild apple [18][19][20][21][22][23] Italy pear [19] Turkey apple [24] AGVd Greece, Italy, Tunisia, Turkey grapevine [25][26][27][28] ASBVd Greece, Israel, Spain, Turkey avocado [29][30][31][32] CChMVd France chrysanthemum [33] Table 1. Cont.…”

Section: Geographical Distribution and Host Range Of Viroids In The M...mentioning

confidence: 99%

See 1 more Smart Citation

Viroids of the Mediterranean Basin

Kaponi,

Kyriakopoulou,

Hadidi

2024

There has been substantial progress in the Mediterranean countries regarding research on viroids. Twenty-nine viroid species, all belonging to Pospiviroidae and Avsunviroidae genera, have been detected in the Mediterranean Basin. Not only have detection methods, such as reverse transcription-quantitative polymerase chain reaction and next-generation sequencing, been used for viroid detection, along with molecular hybridization techniques allowing for rapid detection, identification, and characterization of known and novel viroids in these countries, but eradication measures have also been taken that allowed for the efficient elimination of certain viroids in a number of Mediterranean countries. The eradication measures were followed as recommended by the European and Mediterranean Plant Protection Organization, which is known by its abbreviation, EPPO. The Mediterranean Region has been a niche for viroids since ancient times due to the warm climate and the socio-cultural conditions that facilitate viroid transmission among different host plant species.