Distribution and Genetic Diversity of Grapevine Viruses in Russia

Abstract

Viral diseases can seriously damage the vineyard productivity and the quality of grape and wine products. Therefore, the study of the species composition and range of grapevine viruses is important for the development and implementation of strategies and tactics to limit their spread and increase the economic benefits of viticulture. In 2014–2019, we carried out a large-scale phytosanitary monitoring of Russian commercial vineyards in the Krasnodar region, Stavropol region and Republic of Crimea. A total of 1857 samples were collected and tested for the presence of Grapevine rupestris stem pitting-associated virus (GRSPaV), Grapevine virus A (GVA), Grapevine leafroll-associated virus-1 (GLRaV-1), Grapevine leafroll-associated virus-2 (GLRaV-2), Grapevine leafroll-associated virus-3 (GLRaV-3), Grapevine fanleaf virus (GFLV), and Grapevine fleck virus (GFkV) using RT-PCR. Out of all samples tested, 54.5% were positive for at least one of the viruses (GRSPaV, GVA, GLRaV-1, GLRaV-2, GLRaV-3, GFLV, GFkV) in the Stavropol region, 49.8% in the Krasnodar region and 49.5% in the Republic of Crimea. Some plants were found to be infected with several viruses simultaneously. In the Republic of Crimea, for instance, a number of plants were infected with five viruses. In the Krasnodar region and the Republic of Crimea, 4.7% and 3.3% of the samples were predominantly infected with both GFkV and GRSPaV, whereas in the Stavropol region, 6% of the selected samples had both GLRaV-1 and GVA infections. We carried out a phylogenetic analysis of the coat protein genes of the detected viruses and identified the presence of GVA of groups I and IV, GRSPaV of groups BS and SG1, GLRaV-1 of group III, GLRaV-2 of groups PN and H4, GLRaV-3 of groups I and III. The results obtained make it possible to assess the viral load and the distribution of the main grapevine viruses on plantations in the viticultural zones of Russia, emphasizing the urgent need to develop and implement long-term strategies for the control of viral diseases of grapes.

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

“…At the same time, we were unable to confirm the presence of the GLRaV-2RG strain, the contigs of which were mapped to GRSLaV NC_004724.1 using two pairs of primers. Using the restrictions of the GLR2CP1/GLR2CP2 fragment, we established that MZ065369 belongs to group 3, like other Russian isolates that we found earlier in Krasnodar Krai [29]. Phylogenetic analysis of the complete nucleotide sequence of the coat protein gene of the detected isolate showed that it is 87.9% identical to the sequence of the reference genome GLRaV-2 NC_007448.…”

“…The presence of this pathogen has been confirmed on all continents where grapes are grown [53]. In the Russian territory, this virus was previously detected in Krasnodar Krai and the Republic of Crimea [29,54].…”

“…According to the literature, GVA is found in almost all regions of the world where grapes are grown [55,56]. In Russia, we previously detected GVA in vineyards in the Republic of Crimea and Krasnodar Krai [29,57].…”

“…Along with GFLV, GLRaV causes one of the most important viral grapevine diseases, affecting grapevines worldwide [44]. Previously, we identified GLRaV-1, GLRaV-2, and GLRaV-3 in Russia [29,[45][46][47]. In this work, we were able to detect four Grapevine leafroll-associated viruses, namely GLRaV-1, GLRaV-2, GLRaV-3, and GLRaV-4; it should be noted that this was the first detection of GLRaV-4 in Russia.…”

“…The amplicons were sequenced bidirectionally using the Sanger method, and the nucleotide sequence was assembled using the Finch TV 1.4.0 program and submitted to GenBank (www.ncbi.nlm.nih.gov/genbank/) (accessed on 30 November 2021) [27] (Supplementary Table S4). Moreover, to determine the GLRaV-2 group, we used in silico RFLP analysis [28,29]. Multiple sequence alignment was performed using the Geneious Alignment tool of the Geneious Prime program.…”