A Metagenomic Investigation of the Viruses Associated with Shiraz Disease in Australia

Qi Wu; Nuredin Habili; Wycliff M Kinoti; Stephen D Tyerman; Amy Rinaldo; Linda Zheng; Fiona E Constable

doi:10.3390/v15030774

A Metagenomic Investigation of the Viruses Associated with Shiraz Disease in Australia

Viruses. 2023 Mar 17;15(3):774. doi: 10.3390/v15030774.

Authors

Qi Wu^{1

2}, Nuredin Habili^{1

2}, Wycliff M Kinoti³, Stephen D Tyerman¹, Amy Rinaldo², Linda Zheng³, Fiona E Constable^{3

4}

Affiliations

¹ School of Agriculture, Food and Wine, University of Adelaide, Waite Precinct, PMB 1, Glen Osmond, SA 5064, Australia.
² Australian Wine Research Institute, Wine Innovation Central Building, Hartley Grove crn Paratoo Road, Urrbrae, SA 5064, Australia.
³ Agriculture Victoria Research, Department of Energy, Environment and Climate Action, AgriBio, Centre for AgriBioscience, 5 Ring Road, Bundoora, VIC 3083, Australia.
⁴ School of Applied Systems Biology, La Trobe University, Bundoora, VIC 3086, Australia.

Abstract

Shiraz disease (SD) is an economically important virus-associated disease that can significantly reduce yield in sensitive grapevine varieties and has so far only been reported in South Africa and Australia. In this study, RT-PCR and metagenomic high-throughput sequencing was used to study the virome of symptomatic and asymptomatic grapevines within vineyards affected by SD and located in South Australia. Results showed that grapevine virus A (GVA) phylogroup II variants were strongly associated with SD symptoms in Shiraz grapevines that also had mixed infections of viruses including combinations of grapevine leafroll-associated virus 3 (GLRaV-3) and grapevine leafroll-associated virus 4 strains 5, 6 and 9 (GLRaV-4/5, GLRaV-4/6, GLRaV-4/9). GVA phylogroup III variants, on the other hand, were present in both symptomatic and asymptomatic grapevines, suggesting no or decreased virulence of these strains. Similarly, only GVA phylogroup I variants were found in heritage Shiraz grapevines affected by mild leafroll disease, along with GLRaV-1, suggesting this phylogroup may not be associated with SD.

Keywords: Australia; Shiraz disease; dsRNA; grapevine leafroll-associated virus 3; grapevine leafroll-associated virus 4; grapevine virus A; metagenomic sequencing; phylogenetic groups.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Australia / epidemiology
Flexiviridae* / genetics
Metagenome
Plant Diseases
Vitis*

Grants and funding

This work was supported by Wine Australia under the project WAPh1706, with levies from Australia’s grapegrowers and winemakers and matching funds from the Australian Government. It was also supported by funding from Agriculture Victoria Research, the University of Adelaide and the Australian Wine Research Institute.