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Detection of grapevine fleck virus in South Africa
Thesis (MScAgric)--Stellenbosch University, 2022.
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| Format: | Thesis |
| Language: | en_ZA |
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Stellenbosch : Stellenbosch University
2022
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| _version_ | 1867613893806784512 |
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| access_status_str | Open Access |
| author | Usher, Katherine Alice |
| author2 | Pietersen, Gerhard |
| author_browse | Pietersen, Gerhard Usher, Katherine Alice |
| author_facet | Pietersen, Gerhard Usher, Katherine Alice |
| author_sort | Usher, Katherine Alice |
| collection | Thesis |
| dc_rights_str_mv | Stellenbosch University |
| description | Thesis (MScAgric)--Stellenbosch University, 2022. |
| format | Thesis |
| id | oai:scholar.sun.ac.za:10019.1/125909 |
| institution | Stellenbosch University (South Africa) |
| language | en_ZA |
| last_indexed | 2026-06-10T12:43:23.129Z |
| license_str | Other — see source repository |
| provenance_str_mv | Harvested via OAI-PMH from SUNScholar — Stellenbosch University Repository |
| publishDate | 2022 |
| publishDateRange | 2022 |
| publishDateSort | 2022 |
| publisher | Stellenbosch : Stellenbosch University |
| publisherStr | Stellenbosch : Stellenbosch University |
| record_format | dspace |
| source_str | SUNScholar — Stellenbosch University Repository |
| spelling | oai:scholar.sun.ac.za:10019.1/125909 Detection of grapevine fleck virus in South Africa Usher, Katherine Alice Pietersen, Gerhard Stellenbosch University. Faculty of AgriSciences. Dept. of Genetics. Grapevine fleck virus (GFkV)-- South Africa Grapevine (Vitis spp.) -- Diseases and pests Enzyme-linked immunosorbent assay (ELISA)-- Technique Virus diseases of plants -- Genetic aspects Reverse transcription-polymerase chain reaction -- Testing Viral genomes Grapevine fanleaf virus UCTD Thesis (MScAgric)--Stellenbosch University, 2022. ENGLISH ABSTRACT: Grapevine (Vitis spp.) is one of the oldest and most widely cultivated crops, however, it is highly susceptible to viral diseases, which result in significant crop losses. It is therefore necessary to gain insight into the pathogens and diseases that can impact vine health. Although grapevine fleck virus (GFkV) is not known to cause significant damage, it is a requirement to test for the virus within the South African certification scheme. Moreover, very little information regarding the genetic diversity and spread of the virus exists. The aim of the study was to investigate the genetic diversity of South African isolates of GFkV, validate the ELISA tests required for the certification schemes, and ascertain whether field spread of the virus is naturally occurring. Illumina data sets of 230 Grapevine samples were analyzed for the presence of Grapevine fleck virus (GFkV) infections using reference mapping under various stringencies, as well as de novo assembly. Consensus sequences of 75 GFkV sources were obtained. The presence of these infections was confirmed using one-step RT-PCR and ELISA tests. A subset of 11 variants were selected for further characterization and primers designed to characterize the variants. Three genomic areas, the methyl-transferase region, coat protein and replicase domains were ascertained. This represents the most comprehensive study of the variation of this virus in South Africa to date. Validation of ELISA for use in industry was conducted, whereby the optimal time of year and tissue for sampling for ELISA detection of the virus was established. A confirmation of the efficacy of pooled samples for ELISA testing was also performed. Finally, the presence, incidence, and spatial distribution of GFkV in 19 vineyards was determined. AFRIKAANSE OPSOMMING: Wingerd (Vitis spp.) is een van die oudste en mees aangeplante gewasse. Dit is egter uiters vatbaar vir virale siektes wat lei tot merkwaardige gewas verliese. Dit is daarom noodsaaklik om beter insig te verkry van die patogene en siektes wat ’n invloed het op wingerd gesondheid. Alhoewel die wingerdvlek virus nie bekend is daarvoor dat dit merkwaardige skade veroorsaak nie, is dit ’n vereiste van die Suid-Afrikaanse sertifiseringskema om te toets vir die virus. Boonop is baie min inligting tans beskikbaar oor die genetiese diversiteit en verspreiding van die virus. Die doel van hierdie studie was om die genetiese diversiteit van Suid-Afrikaanse isolate van wingerdvlek te ondersoek, om die Gekoppelde Immunosorbent toets (ELISA) toetse wat vereis word vir sertifiseringskemas te bekragtig, asook om te bepaal of die verspreiding van die virus in die veld natuurlik plaasvind. Illumina datastelle van 230 wingerd monsters was geanaliseer vir die teenwoordigheid van wingerdvlek virus infeksies deur gebruik te maak van verwysingskartering met verskeie strenghede, sowel as de novo samestelling. Konsensus volgordes was verkry vir 75 wingerdvlek virus bronne, waarvan infeksie bevestig was deur een-stap RT-PCR en ELISA toetse. ’n Substel van 11 variante was geselekteer vir verdere karakterisering en inleiers was ontwerp om die variante te karakteriseer. Drie genomiese areas, die metiel-transferase- , kapsied proteïen- en replikasedomeine, was vasgestel. Hierdie verteenwoordig die mees omvattende studie van die variasie van die virus in Suid-Afrika tot op hede. Validering van ELISA toetse vir gebruik in die industrie was uitgevoer deur die optimale tyd van die jaar, asook die optimale weefsel vir monsterneming vas te stel vir die opspoor van die virus met ELISA. ’n Bevestiging van die effektiwiteit van die gebruik van saamgevoegde monsters vir ELISA toetse was ook uitgevoer. Laastens was die teenwoordigheid, voorkoms en ruimtelike verspreiding van wingerdvlek virus in 19 wingerde bepaal. Masters 2022-10-20T07:14:15Z 2023-01-16T12:40:51Z 2022-10-20T07:14:15Z 2023-01-16T12:40:51Z 2022-12 Thesis http://hdl.handle.net/10019.1/125909 en_ZA Stellenbosch University xv, 88 pages : illustrations (some color) application/pdf Stellenbosch : Stellenbosch University |
| spellingShingle | Grapevine fleck virus (GFkV)-- South Africa Grapevine (Vitis spp.) -- Diseases and pests Enzyme-linked immunosorbent assay (ELISA)-- Technique Virus diseases of plants -- Genetic aspects Reverse transcription-polymerase chain reaction -- Testing Viral genomes Grapevine fanleaf virus UCTD Usher, Katherine Alice Detection of grapevine fleck virus in South Africa |
| title | Detection of grapevine fleck virus in South Africa |
| title_full | Detection of grapevine fleck virus in South Africa |
| title_fullStr | Detection of grapevine fleck virus in South Africa |
| title_full_unstemmed | Detection of grapevine fleck virus in South Africa |
| title_short | Detection of grapevine fleck virus in South Africa |
| title_sort | detection of grapevine fleck virus in south africa |
| topic | Grapevine fleck virus (GFkV)-- South Africa Grapevine (Vitis spp.) -- Diseases and pests Enzyme-linked immunosorbent assay (ELISA)-- Technique Virus diseases of plants -- Genetic aspects Reverse transcription-polymerase chain reaction -- Testing Viral genomes Grapevine fanleaf virus UCTD |
| url | http://hdl.handle.net/10019.1/125909 |
| work_keys_str_mv | AT usherkatherinealice detectionofgrapevinefleckvirusinsouthafrica |