Objectives
The main aim of this research focus is to develop new methods for high-throughput sequencing of full viral genome and virus sequence analysis web platforms, that can be instrumental to better characterize natural resistance mechanisms, identify emerging and fast spreading virus threats, and design isolates for cross-protection. Specifically, VIRTIGATION seeks to develop new tools for the large-scale analysis and monitoring of plant virus outbreaks and their transmission routes between European countries.
The specific objectives of the viral genome sequencing and monitoring of virus outbreaks component are to:
• Facilitate the standardization of full genome sequencing procedures;
• Link virus diversity to entry and transmission
• Monitor virus diversity and evolution in the EU
• Risk assessment of possible disease outbreaks
• Assessment of virus control methods
Find out more >>
Approach
VIRTIGATION will build on proven protocols such as CIDER-Seq for begomoviruses and easy-to-use and affordable technologies like e.g. the Oxford Nanopore Sequencing Technology in order to increase the precision of these existing diagnostics methods. This approach will contribute to expand European capacity to investigate and exploit natural resistance and other mechanisms such as cross-protection to provide sustainable measures against plant virus attacks.
Specifically, the tools developed by VIRTIGATION will include new web-based software to study virus diversity and evolution, based on datasets of full-length viral genome sequences obtained through application of HTS (high throughput)-nanopore sequencing. The exploitation of HTS dataset for genomic surveillance and epidemiological studies will allow for overcoming the currently limited characterization of virus diversity done through existing databases such as the Q-bank of the European and Mediterranean Plant Protection Organization (EPPO). Moreover, the tools produced by the project will also allow for a more precise identification of virus introduction and transmission routes, and will thus aid in determining factors that currently drive virus outbreaks (i.e. trade routes, spreading of insect vectors such as whiteflies).
Key partners involved
The VIRTIGATION project coordinator KU Leuven will be leading the efforts of this research focus, benefitting from its longstanding expertise in cutting-edge sequencing technologies and access to highly integrated, high-performance research computing environment.
KU Leuven will be closely supported by Emweb and its Genome Detective, a web-based platform for analysis, storage and collaboration tools related to genotypic virus and bacterial sequence data.
Other project partners involved include WR – Wageningen Research, CSIC – the Spanish National Research Council, INRAE – the French National Research Institute for Agriculture, Food and the Environment, CRAG – the Centre for Research in Agricultural Genomics, and LIST – the Luxembourg Institute of Science and Technology.
