Diversity of viroids infecting grapevines in South Africa

Abstract

Seven viroid species have been reported to infect grapevine namely, hop stunt viroid (HSVd), grapevine yellow speckle viroid 1 (GYSVd-1), grapevine yellow speckle viroid 2 (GYSVd-2), Australian grapevine viroid (AGVd), Japanese grapevine viroid (JGVd), grapevine latent viroid (GLVd), and citrus exocortis viroid (CEVd). In this study, RNA sequence (RNA-Seq) data, from 229 Vitis accessions from the field maintained South African Vitis germplasm collection vineyard, were analysed to determine the diversity of the viroids present. Five of the seven known grapevine infecting viroids were very commonly found, with 214 of the 229 samples containing at least one viroid species. HSVd, GYSVd-1, GYSVd-2, AGVd, and JGVd were identified in the RNA-Seq data of the samples and confirmed with RT-PCR detection and Sanger sequencing. The HSVd sequences indicated the presence of two variants, with one showing multiple nucleotide insertions. AGVd and GYSVd-2 did not display significant sequence diversity, confirming past international studies. GYSVd-1 occurred as four major variants worldwide and representatives of all four were identified in this vineyard. This is first report on the diversity of viroids infecting grapevine in South Africa and the first report of JGVd outside of Japan. Further studies are needed to fully assess the population and to identify potentially new viroid species.