4467914
doi
10.5281/zenodo.4467914
oai:zenodo.org:4467914
De Jonghe, Kris
Institute for AgriculturaI and Fisheries Research (ILVO), Merelbeke, Belgium
Rott, Mike
Canadian Food Inspection Agency (CFIA), North Saanich, Canada
Nicolaisen, Mogens
Aarhus University (AU), Slagelse, Denmark
Gentit, Pascal
French Agency for Food, Environmental and Occupational Health and Safety (ANSES), Angers, France
Renvoise, Jean-Philippe
French Agency for Food, Environmental and Occupational Health and Safety (ANSES), Angers, France
Candresse, Thierry
National Research Institute for Agriculture, Food and Environment (INRA), Bordeaux, France
Fox, Adrian
Fera Science Ltd (Fera), Sand Hutton, United Kingdom
Varveri, Christina
Benaki Phytopathological Institute (BPI), Athens, Greece
Melika, George
National Food Chain Safety Office Directorate of Plant Protection (NEBIH), Budapest, Hungary
Krizbai, Laszlo
National Food Chain Safety Office Directorate of Plant Protection (NEBIH), Budapest, Hungary
Angelini, Elisa
Council for agronomic research and bioeconomy (CREA), Rome, Italy
Ferretti, Luca
Council for agronomic research and bioeconomy (CREA), Rome, Italy
Westenberg, Marcel
National Plant Protection Organization, Netherlands Food and Consumer Products Safety Authority (NVWA), Wageningen, The Netherlands
Roenhorst, Annelien
National Plant Protection Organization, Netherlands Food and Consumer Products Safety Authority (NVWA), Wageningen, The Netherlands
Shneyder, Yury
All-Russian Plant Quarantine Centre (VNIIKR), Bykovo, Russia
Kornev, Konstantin
All-Russian Plant Quarantine Centre (VNIIKR), Bykovo, Russia
Olmos, Antonio
Instituto Valenciano de Investigaciones Agrarias (IVIA), Valencia, Spain
Kreuze, Jan
International Potato Center (CIP), Lima, Peru
Ravnikar, Maja
National Institute of Biology (NIB), Ljubljana, Slovenia
Mehle, Natasa
National Institute of Biology (NIB), Ljubljana, Slovenia
Maree, Hans J
Stellenbosch University (SU), Stellenbosh, South Africa
The application of Next-Generation Sequencing technology for the detection and diagnosis of non-culturable organisms: viruses and viroids (NGSdetect)
Ziebell, Heiko
Julius Kühn-Institut (JKI), Braunschweig, Germany
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Euphresco, plant health, diagnostics, high-throughput sequencing, HTS, next generation sequencing, NGS, pipeline, proficiency test, test performance study
<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>
<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>
<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>
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)'
Zenodo
2021-01-26
info:eu-repo/semantics/report
4467913
1611839842.119912
382877
md5:06837cbdb0453b7152a6c8e7e60ad2ff
https://zenodo.org/records/4467914/files/2015-F-172_FINAL.pdf
public
10.5281/zenodo.4467913
isVersionOf
doi