Diversity and distribution of turnip yellows virus infecting Brassica napus L. (canola) in the Western Cape, South Africa

Abstract Turnip yellows virus (TuYV), (genus: Polerovirus ), poses a significant threat to brassicaceous crops, particularly Brassica napus L. (canola). In Australia and the United Kingdom, TuYV has caused substantial grain yield reductions of up to 50%. This study documents the first extensive survey of TuYV on canola in South Africa, specifically in the Swartland and Overberg regions of the Western Cape. Using RNAseq-derived metaviromes generated from 38 symptomatic plants in 2021, complete TuYV genomes, spanning approximately 5650 nucleotides, were assembled from 30 datasets. Phylogenetic (ORF 5) and phylogenomic analyses revealed two genetically distinct yet geographically undifferentiated populations. For samples collected in the 2022 and 2023 seasons, RT-PCR targeting a 1,284 nucleotide fragment, including ORF 3a, confirmed TuYV presence in a further 245 samples, with phylogenetic analyses again indicating two distinct phylogroups, based on ORF 3a. These findings suggest a widespread TuYV distribution in the Western Cape, with spread potentially facilitated by various aphid vectors. The existence of distinct, widely distributed variants, implies a longstanding presence in the region, underscoring the need for continued monitoring, management, and resistance testing to mitigate potential severe yield losses.