A Chronological Study on Grapevine Leafroll-Associated Virus 2 in Australia

Abstract

Grapevine leafroll disease affects the health status of grapevines worldwide. Most studies in Australia have focused on grapevine leafroll-associated viruses 1 and 3, while little attention has been given to other leafroll virus types, in particular, grapevine leafroll-associated virus 2 (GLRaV-2). A chronological record of the temporal occurrence of GLRaV-2 in Australia since 2001 is reported. From a total of 11,257 samples, 313 tested positive, with an overall incidence of 2.7%. This virus has been detected in 18 grapevine varieties and Vitis rootstocks in different regions of Australia. Most varieties were symptomless on their own roots, while Chardonnay showed a decline in virus-sensitive rootstocks. An isolate of GLRaV-2, on own-rooted Vitis vinifera cv. Grenache, clone SA137, was associated with severe leafroll symptoms after veraison with abnormal leaf necrosis. The metagenomic sequencing results of the virus in two plants of this variety confirmed the presence of GLRaV-2, as well as two inert viruses, grapevine rupestris stem pitting-associated virus (GRSPaV) and grapevine rupestris vein feathering virus (GRVFV). No other leafroll-associated viruses were detected. Among the viroids, hop stunt viroid and grapevine yellow speckle viroid 1 were detected. Of the six phylogenetic groups identified in GLRaV-2, we report the presence of four groups in Australia. Three of these groups were detected in two plants of cv. Grenache, without finding any recombination event. The hypersensitive reaction of certain American hybrid rootstocks to GLRaV-2 is discussed. Due to the association of GLRaV-2 with graft incompatibility and vine decline, the risk from this virus in regions where hybrid Vitis rootstocks are used cannot be overlooked.

Keywords: Closterovirus; RNA silencing suppressor; graft incompatibility; grapevine leafroll-associated virus 2; hypersensitive reaction.

Figure 1

A vineyard of Vitis vinifera cv. Chardonnay grafted on Paulsen 1103 (Table 2, Batch 5). Vines infected with grapevine leafroll-associated virus 2 (GLRaV-2) show retarded growth and decline. The symptomatic vines were infected with GLRaV-2, and grapevine rupestris stem pitting-associated virus (GRSPaV), while healthy vines had only the inert virus, GRSPaV.

Figure 2

Severe symptoms of grapevine leafroll-associated virus 2 on Vitis vinifera cv. Grenache clone SA137. A severe leaf reddening and vein yellowing in late autumn. Note the necrosis of infected leaf starts from one side of the leaf, which will later expand to the whole leaf.

Figure 3

Mild leafroll symptoms on Vitis vinifera cv. Shiraz 1654 grafted on cv. Viognier tested positive for grapevine leafroll-associated virus 2 and grapevine rupestris stem pitting-associated virus (January 2015, Barossa Valley, South Australia). The pair of leaves on the right are healthy controls.

Figure 4

Phylogenetic mapping of the grapevine leafroll-associated virus 2 (GLRaV-2) variants from Australia and those selected from NCBI. Phylogenetic analysis was carried out using partial nt sequence of CP in Australian-grown Grenache, Chardonnay and Red Globe grapevine varieties. (A) The complete sequence of p24, (B) of selected isolates of GLRaV-2 in Grenache, and (C) nearly full-length virus genome from Vine 2 (V2) and Vine 5 (V5) of Grenache clone SA137. The sequences of the international isolates were obtained from the Genbank NCBI database. The p24 gene sequence of the PV20 phylogroup was not available in the NCBI database. The co-existence of three phylogenetic groups in V2 and V5 is shown by blue asterisks. Neighbour-Joining with bootstrap values of more than 50% (with 1000 repeats) was used for tree construction. Previously classified phylogenetic group names [12] are shown to the right of each clade. For further information on each contig, see Tables S2 and S3. For a clear comparative analysis, the outgroups were not used.