Abstract
Abstract The use of high-throughput sequencing technology (HTS) has allowed for greater elucidation of viruses infecting grapevine, which number around 100. Many of these viruses can result in disease—it is therefore vital to the industry that it be supplied with virus-free (VF) plant material. This is generally done through grapevine certification schemes. In this study, 97 nucleus grapevine plants of the South African Virus Improvement Association (VIA) were subjected to total RNA extraction and high-throughput sequencing using the Ion Torrent platform to determine the presence of any viruses and viroids. Nucleus plants are the initial source of all propagation material of Vitis clones in South Africa, and are subjected to a virus elimination process, tested for several disease-inducing viruses, and maintained under vector-excluded conditions. Of the 97 nucleus accessions, 21 were free of any detectable viruses or viroids. Five viruses were detected in eight nuclear accessions; grapevine Rupestris stem pitting-associated virus was identified in six nuclear accessions, while grapevine fleck virus, grapevine Syrah virus 1, grapevine leafroll-associated virus 4, and grapevine Rupestris vein feathering virus were identified in one nuclear accession each. Four viroids and one putative viroid were identified in 76 accessions by HTS analysis. Hop stunt viroid was identified in 63 of the 97 samples, followed by grapevine yellow speckle viroid 1, identified in 52 samples, grapevine yellow speckle viroid 2, identified in 17 samples, and Australian grapevine viroid in three samples. The putative viroid grapevine hammerhead viroid-like RNA was identified in two samples. All virus and viroid infections were confirmed using virus/viroid-specific RT-PCR and Sanger sequencing. These findings highlight the need for more diverse testing virus/viroid detection techniques in nuclear plants of the grapevine certification scheme, and suggest that some viruses, especially GRSPaV, and viroids are recalcitrant to currently employed virus elimination techniques.
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Claims 16
Claim · model-written summary
Twenty-one of 97 nucleus grapevine accessions had no detectable viruses or viroids.
VitisOrganisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Of the 97 nucleus accessions, 21 were free of any detectable viruses or viroids.”
t0“grapevine”
Claim · model-written summary
Five viruses occurred in eight nuclear accessions.
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Five viruses were detected in eight nuclear accessions;”
t0“grapevine”
Claim · model-written summary
Rupestris stem pitting-associated virus occurred in six nuclear accessions.
- Interactor
- grapevine Rupestris stem pitting-associated virusGrapevine rupestris stem pitting-associated viruse0pathogen
- Outcome
- identifiede0
- Value
- sixe0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“grapevine Rupestris stem pitting-associated virus was identified in six nuclear accessions”
t0“grapevine”
Claim · model-written summary
Grapevine fleck virus occurred in one nuclear accession.
- Interactor
- grapevine fleck virusGrapevine fleck viruse0pathogen
- Outcome
- identifiede0
- Value
- onee0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“while grapevine fleck virus, grapevine Syrah virus 1, grapevine leafroll-associated virus 4, and grapevine Rupestris vein feathering virus were identified in one nuclear accession each.”
t0“grapevine”
Claim · model-written summary
Grapevine Syrah virus 1 occurred in one nuclear accession.
- Interactor
- grapevine Syrah virus 1Grapevine Syrah virus 1e0pathogen
- Outcome
- identifiede0
- Value
- onee0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“while grapevine fleck virus, grapevine Syrah virus 1, grapevine leafroll-associated virus 4, and grapevine Rupestris vein feathering virus were identified in one nuclear accession each.”
t0“grapevine”
Claim · model-written summary
Grapevine leafroll-associated virus 4 occurred in one nuclear accession.
- Interactor
- grapevine leafroll-associated virus 4Grapevine leafroll-associated virus 4e0pathogen
- Outcome
- identifiede0
- Value
- onee0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“while grapevine fleck virus, grapevine Syrah virus 1, grapevine leafroll-associated virus 4, and grapevine Rupestris vein feathering virus were identified in one nuclear accession each.”
t0“grapevine”
Claim · model-written summary
Grapevine Rupestris vein feathering virus occurred in one nuclear accession.
- Interactor
- grapevine Rupestris vein feathering virusGrapevine rupestris vein feathering viruse0pathogen
- Outcome
- identifiede0
- Value
- onee0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“while grapevine fleck virus, grapevine Syrah virus 1, grapevine leafroll-associated virus 4, and grapevine Rupestris vein feathering virus were identified in one nuclear accession each.”
t0“grapevine”
Claim · model-written summary
HTS identified four viroids and one putative viroid in 76 accessions.
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Four viroids and one putative viroid were identified in 76 accessions by HTS analysis.”
t0“grapevine”
Claim · model-written summary
Hop stunt viroid occurred in 63 of 97 samples.
- Interactor
- Hop stunt viroidHop stunt viroide0pathogen
- Outcome
- identifiede0
- Value
- 63e0
- Qualifier
- 97 samplese0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Hop stunt viroid was identified in 63 of the 97 samples”
t0“grapevine”
Claim · model-written summary
Grapevine yellow speckle viroid 1 occurred in 52 samples.
- Interactor
- grapevine yellow speckle viroid 1Grapevine yellow speckle viroid 1e0pathogen
- Outcome
- identifiede0
- Value
- 52e0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“grapevine yellow speckle viroid 1, identified in 52 samples”
t0“grapevine”
Claim · model-written summary
Grapevine yellow speckle viroid 2 occurred in 17 samples.
- Interactor
- grapevine yellow speckle viroid 2Grapevine yellow speckle viroid 2e0pathogen
- Outcome
- identifiede0
- Value
- 17e0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“grapevine yellow speckle viroid 2, identified in 17 samples”
t0“grapevine”
Claim · model-written summary
Australian grapevine viroid occurred in three samples.
- Interactor
- Australian grapevine viroidAustralian grapevine viroide0pathogen
- Outcome
- Australian grapevine viroide0
- Value
- threee0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“and Australian grapevine viroid in three samples.”
t0“grapevine”
Claim · model-written summary
Putative grapevine hammerhead viroid-like RNA occurred in two samples.
- Interactor
- grapevine hammerhead viroid-like RNAGrapevine hammerhead viroid-like RNAe0other
- Outcome
- identifiede0
- Value
- twoe0
- Qualifier
- putative viroide0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“The putative viroid grapevine hammerhead viroid-like RNA was identified in two samples.”
t0“grapevine”
Claim · model-written summary
Specific RT-PCR and Sanger sequencing confirmed all virus and viroid infections.
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“All virus and viroid infections were confirmed using virus/viroid-specific RT-PCR and Sanger sequencing.”
t0“grapevine”
Claim · model-written summary
The authors recommend more diverse virus and viroid detection techniques for nuclear certification plants.
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“These findings highlight the need for more diverse testing virus/viroid detection techniques in nuclear plants of the grapevine certification scheme”
Claim · model-written summary
Some viruses, especially GRSPaV, and viroids appear recalcitrant to current elimination techniques.
- Interactor
- GRSPaVGrapevine rupestris stem pitting-associated viruse0pathogen
- Outcome
- recalcitrant to currently employed virus elimination techniquese0
- Qualifier
- some virusese0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“suggest that some viruses, especially GRSPaV, and viroids are recalcitrant to currently employed virus elimination techniques.”
t0“grapevine”