Read, David AlanThompson, Genevieve D.Swanevelder, Dirk Z.H.Pietersen, Gerhard2024-04-162024-04-162023-06-29Read, D.A.; Thompson, G.D.; Swanevelder, D.Z.H.; Pietersen, G. Metaviromic Characterization of Betaflexivirus Populations Associated with a Vitis cultivar Collection in South Africa. Viruses 2023, 15, 1474. https://DOI.org/10.3390/v15071474.1999-4915 (online)10.3390/v15071474http://hdl.handle.net/2263/95558DATA AVAILABILITY STATEMENT : All RNAseq datasets are available at National Center for Biotechnology Information’s (NCBI) Sequence Read Archive (SRA), accession PRJNA626577. All assembled sequences have been submitted to NCBI GenBank, listed in Table S1.SUPPLEMENTARY MATERIALS : FIGURE S1: RNA-dependent RNA polymerase (RdRP) gene phylogeny of GRSPaV variants; FIGURE S2: pairwise ANI values shared between GRSPaV variants; FIGURE S3: RNA-dependent RNA polymerase (RdRP) gene phylogeny of GVA variants; FIGURE S4: pairwise ANI values shared between GVA variants; FIGURE S5: RNA-dependent RNA polymerase (RdRP) gene phylogeny of GVB variants; FIGURE S6: pairwise ANI values shared between GVB variants; FIGURE S7: RNA-dependent RNA polymerase (RdRP) gene phylogeny of GVE variants; FIGURE S8: pairwise ANI values shared between GVE variants; FIGURE S9: RNA-dependent RNA polymerase (RdRP) gene phylogeny of GVF variants; FIGURE S10: pairwise ANI values shared between GVF variants; FIGURE S11: RNA-dependent RNA polymerase (RdRP) gene phylogeny of GVH variants; FIGURE S12: pairwise ANI values shared between GVH variants; FIGURE S13: RNA-dependent RNA polymerase (RdRP) gene phylogeny of GVI variants; FIGURE S14: pairwise ANI values shared between GVI variants; FIGURE S15: RNA-dependent RNA polymerase (RdRP) gene phylogeny of GVM variants; FIGURE S16: pairwise ANI values shared between GVM variants; TABLE S1: sample information, number of reads, and BioSample and GenBank accession numbers for each accession; TABLE S2: mixed infections for cultivar accessions with more than one betaflexivirus present.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.en© 2023 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license.ViticultureGrapevine cultivarsGrapevine virusesBetaflexivirusesSouth Africa (SA)SDG-15: Life on landArticle