Genetic diversity and identification of putative recombination events in grapevine rupestris stem pitting-associated virus

Mostert, Ilani; Burger, Johan T.; Maree, Hans J.

doi:10.1007/s00705-018-3883-x

Cited by 9 publications

(5 citation statements)

References 114 publications

(244 reference statements)

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“…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 ]. Additionally, this study also confirms a high diversity of GVA and GVB without any geographical clustering, as well as homogeneity of GVE in South Africa, as initially shown by Coetzee et al [ 20 ].…”

Section: Discussionsupporting

confidence: 93%

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

Read

Thompson²,

Swanevelder

et al. 2023

Viruses

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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.

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Section: Discussionsupporting

confidence: 93%

“…GRSPaV has previously been reported in South Africa [ 20 , 46 ] and can be classified into at least seven subgroups [ 45 , 46 ]. It is one of the most frequently reported viruses in commercial vineyards and has pronounced genetic diversity [ 44 ].…”

Section: Resultsmentioning

confidence: 99%

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

Read

Thompson²,

Swanevelder

et al. 2023

Viruses

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“…Variants of group IIa are associated with grapevine vein necrosis, group IIc are associated with RSP, and group I are associated with Syrah decline (Habili et al, 2006;Lima et al, 2006;Meng et al, 2005). Phylogenetic analyses of the coat protein gene of the isolates from this study reveal that four of the isolates fall into GRSPaV group I and two isolates fall into the recently identi ed group IId (Mostert et al, 2018). GRSPaV group IId was initially identi ed in South Africa and this nuclear block is potentially the original source of this variant in South African vineyards.…”

Section: Discussionmentioning

confidence: 68%

“…GRSPaV, a virus of the genus Foveavirus of the family Beta exiviridae, was shown to be associated with Rupestris stem pitting (RSP), though the disease aetiology has not been clearly de ned (Goheen, 1988;Meng and Rowhani, 2017). Currently, seven distinctive variant groups (I, IIa, IIb, IIc, IId, III, and IV) are recognised for GRSPaV (Glasa et al, 2017;Hily et al, 2018;Mostert et al, 2018). The symptoms associated with GRSPaV differ among variants and depend on the cultivar which is infected (Habili et al, 2006;Meng et al, 2005).…”

Section: Discussionmentioning

confidence: 99%

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

Morgan,

Burger,

Pietersen

2023

Preprint

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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.

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“…Molecular groups of GRSPaV are identified both on the basis of CP and RdRp sequences [78,79,[81][82][83] and on the basis of complete genomes [78,82]. In both cases, it is customary to distinguish phylogroups 1, 2a, 2b, 2c, 3, and 4 that are divided into subgroups.…”

Section: Grapevine Rupestris Stem Pitting-associated Virusmentioning

confidence: 99%

Grapevine Virome of the Don Ampelographic Collection in Russia Has Concealed Five Novel Viruses

Belkina,

Karpova,

Porotikova

et al. 2023

Viruses

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In this study, an analysis of the virome of 51 grapevines from the Don ampelographic collection named after Ya. I. Potapenko (Russia) was performed using high-throughput sequencing of total RNA. A total of 20 previously described grapevine viruses and 4 viroids were identified. The most detected were grapevine rupestris stem pitting-associated virus (98%), hop stunt viroid (98%), grapevine Pinot gris virus (96%), grapevine yellow speckle viroid 1 (94%), and grapevine fleck virus (GFkV, 80%). Among the economically significant viruses, the most present were grapevine leafroll-associated virus 3 (37%), grapevine virus A (24%), and grapevine leafroll-associated virus 1 (16%). For the first time in Russia, a grapevine-associated tymo-like virus (78%) was detected. After a bioinformatics analysis, 123 complete or nearly complete viral genomes and 64 complete viroid genomes were assembled. An analysis of the phylogenetic relationships with reported global isolates was performed. We discovered and characterized the genomes of five novel grapevine viruses: bipartite dsRNA grapevine alphapartitivirus (genus Alphapartitivirus, family Partitiviridae), bipartite (+) ssRNA grapevine secovirus (genus Fabavirus, family Secoviridae) and three (+) ssRNA grapevine umbra-like viruses 2, -3, -4 (which phylogenetically occupy an intermediate position between representatives of the genus Umbravirus and umbravirus-like associated RNAs).

show abstract

Genetic diversity and identification of putative recombination events in grapevine rupestris stem pitting-associated virus

Cited by 9 publications

References 114 publications

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

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

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

Grapevine Virome of the Don Ampelographic Collection in Russia Has Concealed Five Novel Viruses

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