Detection and diversity of grapevine virus L from a Vitis cultivar collection in Stellenbosch, South Africa

A total of 229 Vitis cultivars were sampled from a collection in Stellenbosch, Western Cape, South Africa and subjected to an RNAtag-seq workflow and Illumina HiSeq 2500 sequencing. Following de novo assembly and initial BLASTn analysis of the resulting reads showed that 85 cultivars were infected with grapevine virus L (GVL), with a total of 96 complete/near complete genomes. This is the first time that GVL has been detected in South Africa. Phylogenetic analyses of the amino acid sequences of ORF1 showed that GVL from this study is diverse, grouping with references from Croatia, USA and China, as well as forming a unique South African phylogroup.