Identification and distribution of multiple virus infections in Grapevine leafroll diseased vineyards

A survey of viruses affecting grapevine in the wine regions of the Western Cape Province in South Africa was conducted. The survey determined the relative abundance of five different Grapevine leafroll-associated virus 3 (GLRaV-3) variants. Virus profiles were also determined for individual vines. A total of 315 plants were sampled and analysed over two growing seasons. Five GLRaV-3 variants were detected as either single or mixed infections, with GLRaV-3 variant groups II and VI being the most prominent as single infections and in combinations with each other and other variants. An analysis of the distribution of variants per region showed that single infections of variant groups II and VI occurred predominantly in certain regions, and were equally distributed in the red and white cultivars studied. The distribution of a recently identified, unclassified variant of GLRaV-3 (represented by isolates GH24 and GTG10) was included in the study. The overall analysis showed that infection with variant groups II and VI were the most abundant among the samples with 49.8 and 47.6 %, respectively, followed by variant group I, variants similar to isolate GH24 and variant group III with 16.2, 13.3 and 2.5 % infection, respectively. Mixed infections, representing 36 virus combinations, were found in 251 plants. The most abundant virus combination was GLRaV-3 with Grapevine virus E (GVE), found in 28 % of the plants. GLRaV-3 was the predominant virus detected in the samples with a frequency of 80 % detection, followed by GVE (57.4 %), Grapevine rupestris stem pitting-associated virus (GRSPaV) (36.8 %), Grapevine virus A (GVA) (19.3 %), Grapevine virus F (GVF) (16.25 %), Grapevine leafroll-associated virus 2 (GLRaV-2) (8.25 %), Grapevine leafroll-associated virus 1 (GLRaV-1) (1.58 % infection) and Grapevine leafroll-associated virus 4 (GLRaV-4 like) (0.6 %). Most of the plants tested were infected with multiple viruses. The complexity of virus populations detected in this study, highlights the need for detection methods able to identify all viruses and their variants in vineyards. The information generated in this study will assist in the development of reliable detection assays that will benefit the monitoring of disease spread and aid in the efficient management of Grapevine leafroll disease (GLD).