Metaviromic Characterization of Betaflexivirus Populations Associated with a Vitis cultivar Collection in South Africa.

South Africa is associated with a centuries-old viticultural industry, accompanied by a diverse range of wine and table grape cultivars and an extensive history of pervasive introductions of vine material and associated viruses. The Vitis D2 collection in Stellenbosch represents the most comprehensive collection of Vitis species, hybrids, and cultivars in South Africa. We collected leaf petiole material from 229 accessions from this collection. Our metaviromic analyses revealed a total of 406 complete/near complete genomes of various betaflexiviruses. Among these, we identified the presence of grapevine rupestris stem pitting-associated virus and grapevine viruses A, B, E, F, H (GVH), I (GVI), and M (GVM). Notably, this study marks the first report of GVH, GVI, and GVM in South Africa, which were confirmed via RT-PCR. This research significantly contributes to our understanding of viral diversity and introductions in South African viticulture and emphasizes the need for vigilant monitoring and management of viral infections. Our findings lay the groundwork for strategies that mitigate the impact of viruses on South Africa's wine industry, which generates an annual revenue of approximately 500 million USD.

Genomic and phylogenetic characterization of wheat yellows virus, a novel tenuivirus infecting wheat in South Africa.

During the 2019 winter wheat season, symptoms of severe chlorosis and stunting were observed on wheat in the irrigation production areas of South Africa. RNAtag-seq data were generated for seven samples from KwaZulu-Natal province and one from Limpopo. Analysis of assembled contigs indicated the presence of a putatively novel member of the genus Tenuivirus, tentatively named "wheat yellows virus" (WhYV). The genome is made up of four segments, which are 8952, 3451, 2338, and 2045 nucleotides in length and code for a total of seven ORFs. Phylogenies of each segment (nucleotide) and the polymerase gene (amino acid), as well as amino acid sequence comparisons of each gene product, showed that WhYV is most closely related to rice stripe virus.

Genomic characterization of grapevine viruses N and O: novel vitiviruses from South Africa.

A survey was performed on a Vitis cultivar collection in Stellenbosch, South Africa. Metaviromes were generated for each cultivar, using an RNAtag-seq workflow. Analysis of assembled contigs indicated the presence of two putatively novel members of the genus Vitivirus, provisionally named "grapevine virus N" (GVN) and "grapevine virus O" (GVO). Comparisons of amino acid sequences showed that GVN and GVO are most closely related to grapevine virus G and grapevine virus E, respectively. The incidence of these novel viruses within the sampling site was low, with GVO and GVN associated with only five and two cultivars, respectively, of the 229 sampled.

Novel viruses associated with plants of the family Amaryllidaceae in South Africa.

Nineteen samples from members of the plant genera Agapanthus, Clivia, Hippeastrum, and Scadoxus were collected from gardens in the Gauteng and Western Cape provinces of South Africa. The plants displayed highly variable symptoms of viral disease, including chlorosis, necrosis, streaking, and ringspot. RNAtag-seq was used to characterize the associated viral populations. Plants of the genus Agapanthus were found to be associated with three novel viruses from the families Caulimoviridae, Closteroviridae, and Betaflexiviridae; plants of the genus Clivia were associated with novel members of the families Potyviridae and Betaflexiviridae; and plants of the genus Scadoxus were associated with a novel member of the family Tospoviridae. Nerine latent virus was associated with plants of the genera Agapanthus, Clivia, and Hippeastrum, while hippeastrum mosaic virus was associated exclusively with a Hippeastrum cultivar.

Cultivation shapes genetic novelty in a globally important invader.

Acacia saligna is a species complex that has become invasive in a number of countries worldwide where it has caused substantial environmental and economic impacts. Understanding genetic and other factors contributing to its success may allow managers to limit future invasions of closely related species. We used three molecular markers to compare the introduced range (South Africa) to the native range (Western Australia). Nuclear markers showed that invasive populations are divergent from native populations and most closely related to a cultivated population in Western Australia. We also found incongruence between nuclear and chloroplast data that, together with the long history of cultivation of the species, suggest that introgressive hybridization (coupled with chloroplast capture) may have occurred within A. saligna. While we could not definitively prove introgression, the genetic distance between cultivated and native A. saligna populations was comparable to known interspecific divergences among other Acacia species. Therefore, cultivation, multiple large-scale introductions and possibly introgressive hybridization have rapidly given rise to the divergent genetic entity present in South Africa. This may explain the known global variation in invasiveness and inaccuracy of native bioclimatic models in predicting potential distributions.