Diversity of viroids infecting grapevines in the South African Vitis germplasm collection

Morgan, Seamus W.; Read, David Alan; Burger, Johan T.; Pietersen, Gerhard

doi:10.1007/s11262-023-01971-7

Cited by 4 publications

(3 citation statements)

References 48 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…These differences between nucleotide sequences of HSVd isolates suggest that it displays a quasispecies nature (Eiras et al, 2006;Kofalvi et al, 1997). A previous study into viroid diversity in South Africa has shown that the rst and third group are present in South African vineyards (Morgan et al, 2023) (Chap. 4).…”

Section: Discussionmentioning

confidence: 86%

Next generation RNA sequencing analysis of nuclear grapevines to identify viruses and viroids

Morgan,

Burger,

Pietersen

2023

Preprint

Self Cite

View full text Add to dashboard Cite

The use of next generation sequencing technology has allowed for greater elucidation of viruses infecting grapevine, which number more than 85. Many of these viruses can result in disease symptoms and it is therefore vital to the industry that they be supplied with healthy plant material. This is done through grapevine certification schemes. In this study, 97 nuclear grapevine vines subjected to a virus elimination process and maintained in vector-free conditions, were subjected to total RNA sequencing using the Ion-Torrent platform to determine the presence of viruses and viroids. In total, five virus species, four viroid species, and a further putative viroid species were identified in these nuclear grapevines through NGS analysis and confirmed using RT-PCR and Sanger sequencing. Grapevine Rupestris stem pitting-associated virus was identified in six nuclear accessions, while grapevine fleck virus, grapevine Syrah virus, grapevine leafroll-associated virus 4, and grapevine Rupestris vein feathering virus were identified in one nuclear accession each. Viroids were identified in 73 of the 97 nuclear accessions, with hop stunt viroid present in 63 of the 97 samples followed by grapevine yellow speckle viroid 1, present in 52 of the 97 samples, grapevine yellow speckle viroid 2, present in 17 of the 97 samples, Australian grapevine viroid present in three of the 97 samples and grapevine hammerhead viroid-like RNA was identified in two of the 97 samples. These findings suggest that some viruses, especially GRSPaV, and viroids are recalcitrant to currently employed virus elimination techniques, and how advantageous the use of NGS is to grapevine certification schemes.

show abstract

Section: Discussionmentioning

confidence: 86%

Next generation RNA sequencing analysis of nuclear grapevines to identify viruses and viroids

Morgan,

Burger,

Pietersen

2023

Preprint

Self Cite

View full text Add to dashboard Cite

show abstract

“…The Biosample accession number of each individual dataset is presented in Table S1 . Blastn analysis of the resulting metaSPAdes-derived contigs indicated the presence of several different grapevine leafroll-associated viruses, grapevine virus L (GVL) [ 22 ], grapevine virus N (GVN), and O (GVO) [ 15 ], as well as six different viroids [ 43 ]. Additional betaflexiviruses were identified, namely GRSPaV, GVA, GVB, GVE, GVF, GVH, GVI, and GVM.…”

Section: Resultsmentioning

confidence: 99%

“…Similar to many grapevine germplasm collections worldwide, the D2 vineyard at Nietvoorbij clearly consists of materials collected over a long period from various global sources, and as such includes a diverse range of viruses. Previous studies by Read et al [ 15 , 22 ] and Morgan et al [ 43 ] have contributed to our understanding of the virology of this vineyard. The findings of this study confirm previous observations, including the high diversity and incidence of GRSPaV and the presence of the IId phylogroup, as initially identified by Mostert et al [ 46 ].…”

Section: Discussionmentioning

confidence: 99%

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

Read

Thompson²,

Swanevelder

et al. 2023

Viruses

Self Cite

View full text Add to dashboard Cite

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.

show abstract

Naturally occurring viroid diseases of economically important plants in Africa

Elleuch,

Hamdi

2024

Fundamentals of Viroid Biology

View full text Add to dashboard Cite

Diversity of viroids infecting grapevines in the South African Vitis germplasm collection

Cited by 4 publications

References 48 publications

Next generation RNA sequencing analysis of nuclear grapevines to identify viruses and viroids

Next generation RNA sequencing analysis of nuclear grapevines to identify viruses and viroids

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

Naturally occurring viroid diseases of economically important plants in Africa

Contact Info

Product

Resources

About