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The application of Next-Generation Sequencing technology for the detection and diagnosis of non-culturable organisms: viruses and viroids (NGSdetect)

Ziebell, Heiko; De Jonghe, Kris; Rott, Mike; Nicolaisen, Mogens; Gentit, Pascal; Renvoise, Jean-Philippe; Candresse, Thierry; Fox, Adrian; Varveri, Christina; Melika, George; Krizbai, Laszlo; Angelini, Elisa; Ferretti, Luca; Westenberg, Marcel; Roenhorst, Annelien; Shneyder, Yury; Kornev, Konstantin; Olmos, Antonio; Kreuze, Jan; Ravnikar, Maja; Mehle, Natasa; Maree, Hans J


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    "description": "<p>High-throughput sequencing (HTS, formerly also known as next-generation sequencing or pyrosequecing) technologies have seen a tremendous evolution in terms of technical developments. These technologies are more and more used for plant virus discovery, metagenomic and ecological studies but are also increasingly being used in plant virus diagnostic settings, post-entry quarantine investigations or pre-export diagnostics. Conventional virus detection methods based on serology (i.e., enzyme-linked immunosorbent assays) or nucleic acids (polymerase chain reaction (PCR), real-time PCR), requires in depth knowledge for the target pathogen to develop antisera or primers limiting these methods to the detection of mostly known viruses.</p>\n\n<p>The use of HTS for virus detection is not dependent on <em>a priori</em> knowledge about the viruses to be detected which is a major advance in diagnostic testing.</p>\n\n<p>This project aimed to harmonise sample enrichment strategies and HTS workflows for plant virus and viroid detection within a diagnostic framework. Existing bioinformatics approaches were investigated during a proficiency test and a test performance study which demonstrated the power of HTS for diagnostics but also the limitations if diagnosticians are not experienced with the analyses of HTS data. HTS and newly developed sequencing technologies such as Oxford Nanopore Sequencing have a great potential for diagnostics but further work is required to set up guidelines for validation of HTS workflows.</p>", 
    "language": "eng", 
    "title": "The application of Next-Generation Sequencing technology for the detection and diagnosis of non-culturable organisms: viruses and viroids (NGSdetect)", 
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    "notes": "Report of the Euphresco project 2015-F-172 'The application of Next-Generation Sequencing technology for the detection and diagnosis of non-culturable organisms: viruses and viroids (NGSdetect)'", 
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    "keywords": [
      "Euphresco, plant health, diagnostics, high-throughput sequencing, HTS, next generation sequencing, NGS, pipeline, proficiency test, test performance study"
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    "publication_date": "2021-01-26", 
    "creators": [
      {
        "affiliation": "Julius K\u00fchn-Institut (JKI), Braunschweig, Germany", 
        "name": "Ziebell, Heiko"
      }, 
      {
        "affiliation": "Institute for AgriculturaI and Fisheries Research (ILVO), Merelbeke, Belgium", 
        "name": "De Jonghe, Kris"
      }, 
      {
        "affiliation": "Canadian Food Inspection Agency (CFIA), North Saanich, Canada", 
        "name": "Rott, Mike"
      }, 
      {
        "affiliation": "Aarhus University (AU), Slagelse, Denmark", 
        "name": "Nicolaisen, Mogens"
      }, 
      {
        "affiliation": "French Agency for Food, Environmental and Occupational Health and Safety (ANSES), Angers, France", 
        "name": "Gentit, Pascal"
      }, 
      {
        "affiliation": "French Agency for Food, Environmental and Occupational Health and Safety (ANSES), Angers, France", 
        "name": "Renvoise, Jean-Philippe"
      }, 
      {
        "affiliation": "National Research Institute for Agriculture, Food and Environment (INRA), Bordeaux, France", 
        "name": "Candresse, Thierry"
      }, 
      {
        "affiliation": "Fera Science Ltd (Fera), Sand Hutton, United Kingdom", 
        "name": "Fox, Adrian"
      }, 
      {
        "affiliation": "Benaki Phytopathological Institute (BPI), Athens, Greece", 
        "name": "Varveri, Christina"
      }, 
      {
        "affiliation": "National Food Chain Safety Office Directorate of Plant Protection (NEBIH), Budapest, Hungary", 
        "name": "Melika, George"
      }, 
      {
        "affiliation": "National Food Chain Safety Office Directorate of Plant Protection (NEBIH), Budapest, Hungary", 
        "name": "Krizbai, Laszlo"
      }, 
      {
        "affiliation": "Council for agronomic research and bioeconomy (CREA), Rome, Italy", 
        "name": "Angelini, Elisa"
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        "affiliation": "Council for agronomic research and bioeconomy (CREA), Rome, Italy", 
        "name": "Ferretti, Luca"
      }, 
      {
        "affiliation": "National Plant Protection Organization, Netherlands Food and Consumer Products Safety Authority (NVWA), Wageningen, The Netherlands", 
        "name": "Westenberg, Marcel"
      }, 
      {
        "affiliation": "National Plant Protection Organization, Netherlands Food and Consumer Products Safety Authority (NVWA), Wageningen, The Netherlands", 
        "name": "Roenhorst, Annelien"
      }, 
      {
        "affiliation": "All-Russian Plant Quarantine Centre (VNIIKR), Bykovo, Russia", 
        "name": "Shneyder, Yury"
      }, 
      {
        "affiliation": "All-Russian Plant Quarantine Centre (VNIIKR), Bykovo, Russia", 
        "name": "Kornev, Konstantin"
      }, 
      {
        "affiliation": "Instituto Valenciano de Investigaciones Agrarias (IVIA), Valencia, Spain", 
        "name": "Olmos, Antonio"
      }, 
      {
        "affiliation": "International Potato Center (CIP), Lima, Peru", 
        "name": "Kreuze, Jan"
      }, 
      {
        "affiliation": "National Institute of Biology (NIB), Ljubljana, Slovenia", 
        "name": "Ravnikar, Maja"
      }, 
      {
        "affiliation": "National Institute of Biology (NIB), Ljubljana, Slovenia", 
        "name": "Mehle, Natasa"
      }, 
      {
        "affiliation": "Stellenbosch University (SU), Stellenbosh, South Africa", 
        "name": "Maree, Hans J"
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