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Grapevine viruses are found throughout the viticultural world and have detrimental effects on vine productivity and grape and wine quality. This report provides a comprehensive and up-to-date review on grapevine viruses in Australia with a focus on "Shiraz Disease" (SD) and its two major associated viruses, grapevine virus A (GVA) and grapevine leafroll-associated virus 3 (GLRaV-3). Sensitive grapevine cultivars like Shiraz infected with GVA alone or with a co-infection of a leafroll virus, primarily GLRaV-3, show symptoms of SD leading to significant yield and quality reductions in Australia and in South Africa. Symptom descriptors for SD will be outlined and a phylogenetic tree will be presented indicating the SD-associated isolates of GVA in both countries belong to the same clade. Virus transmission, which occurs through infected propagation material, grafting, and naturally vectored by mealybugs and scale insects, will be discussed. Laboratory and field-based indexing will also be discussed along with management strategies including rogueing and replanting certified stock that decrease the incidence and spread of SD. Finally, we present several cases of SD incidence in South Australian vineyards and their effects on vine productivity. We conclude by offering strategies for virus detection and management that can be adopted by viticulturists. Novel technologies such as high throughput sequencing and remote sensing for virus detection will be outlined.

A new genetic variant of grapevine virus A (GVA) of phylogenetic group I was identified during comparative analysis of the viruses infecting two sibling grapevines cv. Shiraz. The grapevines were propagated from a single mother plant. One of them become infected with Shiraz disease (SD), which is highly destructive on noble grapevine cultivars Shiraz and Merlot in South Africa. The new variant was not associated with SD, as it was present in both SD-affected and SD-free plants. However, unlike in an earlier study of grapevines affected by this disease, this GVA variant of group I strongly dominated over a coinfecting variant of group II associated with SD and a variant of group III. The variant, named I327-5, was mechanically transmitted from SD-affected grapevine to Nicotiana benthamiana, and its genome was fully sequenced. The sequence data revealed that the most distinctive genomic feature of variant I327-5 is the deletion of three nucleotides in the region where the ORF2 and ORF3 genes overlap. These genes of GVA encode a 19.8-kDa protein, the function of which remains unknown, and a 31-kDa protein that is indispensable for the movement of the virus in plants. An alignment of the amino acid sequences of these proteins encoded by variant I327-5 with the corresponding proteins encoded by other members of group I suggested that, as the result of mutations, a neutral threonine or alanine and a negatively charged glutamic acid, respectively, were removed from the proteins of GVA variant I327-5.

Three genetic variants of grapevine leafroll-associated virus 3 (GLRaV-3) were identified in vineyards of the Western Cape, South Africa. The GLRaV-3 variants were identified by single-strand conformation polymorphism (SSCP) profiles generated from a region amplified in ORF5. ORF5 sequence data confirmed the three genetic variant groups, and a specific SSCP profile was assigned to each variant group. The results of SSCP analysis of this region in ORF5 showed that this method gives a fast and reliable indication of the GLRaV-3 variant status of a plant, which in many instances showed mixed infections. The full genome sequence of one representative of each variant group i.e. isolates 621 (group I), 623 (group II) and PL-20 (group III), was determined by sequencing overlapping cloned fragments of these isolates. The sequences of genomic 5' ends of these isolates were determined by RLM-RACE. Sequence alignment of the 5'UTRs indicated significant sequence and length variation in this region between the three South African variant groups. Alignment of the Hsp70h and CP gene regions of these isolates with those of isolates from elsewhere in the world, followed by phylogenetic analysis, further supported the presence of three variants of GLRaV-3 in South Africa and the presence of two or three additional variant groups elsewhere in the world.

The presence of rugose-wood-associated viruses of the genera Foveavirus and Vitivirus in the family Betaflexiviridae was investigated in various clones of own-rooted and grafted Vitis vinifera cv. Shiraz that were affected, or not, by Shiraz decline, and in rootstocks. RT nested-PCR amplification of double-stranded RNA using degenerate primers for the simultaneous detection of foveaviruses and vitiviruses (Dovas CI, Katis NI in J Virol Meth 170:99-106, 2003), cloning of DNA amplicons, SSCP analysis of clones, sequencing and computer-assisted analysis of sequences was used to characterize viral genetic variability. A total of 1,137 clones were analysed by SSCP, and, of those, 371 clones were sequenced. The results revealed that variants of five molecular groups belonging to the species Grapevine rupestris stem pitting-associated virus (GRSPaV), including highly divergent variants related to strain SY (Lima MF et al. in Arch Virol 151:1889-1894, 2006) were present in plants of various clones of Shiraz regardless of their Shiraz decline status, and in rootstocks. Grapevine virus A (GVA) and grapevine virus B (GVB) were detected in a relatively small number of plants. This study suggested no involvement of GRSPaV, GVA or GVB in Shiraz decline.

Shiraz disease (SD) is a highly destructive, insect-transmitted disease of noble grapevine cultivars, such as Shiraz and Merlot, in South Africa. Earlier studies revealed that, of the three molecular groups of GVA that were detected in local vineyards, variants of group II are closely associated with expression of this disease, and variants of group III are commonly present in GVA-infected SD-negative plants [Goszczynski, D.E., 2007. Single-strand conformation polymorphism (SSCP), cloning and sequencing of Grapevine virus A (GVA) reveal a close association between related molecular variants of the virus and Shiraz disease in South Africa. Plant Pathol. 56, 755-762]. Among many GVA variants transmitted to Nicotiana benthamiana from various grapevines with different SD status, a variant of group II, referred to here as GTR1-2, was also isolated from a consistently SD-negative Shiraz plant. The genome of this variant, along with 7 other GVA variants of the 3 molecular groups, including 4 variants of molecular group II associated with strong symptoms of SD, were sequenced. Results of comparative analysis of these genomes, with emphasis on differences between GTR1-2 and other variants of molecular group II, are presented. Among the many differences that were found, a 119 nt ORF2-related fragment was discovered within the native ORF2 of a GVA variant, P163-M5. This variant was isolated from a grapevine used by local industry as a reliable positive control for SD in woody indexing. The variant induced symptoms in N. benthamina that were significantly more severe than those of other variants of molecular group II.