Diagnostic, Surveillance and Epidemiology

(Manager : Sébastien Massart)

A reliable diagnostic of plant pathogens is an essential step for developing integrated control strategies against plant diseases and for monitoring their evolution in space and time. A reliable diagnostic therefore allows proper study of the epidemiology and ecology of plant pathogens.

For more than 30 years, the laboratory has been developing, validating and applying innovative methods for plant pathogen diagnostics. The current developments aim to apply high-throughput sequencing techniques (HTS) rationally for the characterisation of known or unknown plant-pathogens at the plant, ecosystem or national level. In this context, bioinformatic analyses of HTS data has taken an important place in the research and development carried out within the laboratory.

An international team of 13 researchers are working within this axis : Yves Bisimwa (PhD Student), Arnaud Blouin (postdoc), Nuria Fontdevila (PhD Student), Marwa Hanafi (PhD Student), Bénédicte Lebas (postdoc), Angelo Locicero (technicien), François Maclot (PhD Student), Liu Shangwu (PhD Student), Rachid Tahzima (PhD Student), Lucie Tamisier (postdoc), Coline Temple (PhD Student) and Rong Wei (postdoc).

Several projects are currently ongoing in collaboration with national and international partners (see map):

  • ByPOP (2017-2019): study of the impact of host plants on the genetic diversity of Barley yellow dwarf virus (BYDV) and its fitness
  • Inextvir (2019-2023): an international network for the training of doctoral students focusing on the virology of fruit trees and vegetable crops integrating the development of bioinformatic tools
  • Valitest (2018-2021): new standards are written to improve the reliability of diagnostic methods, including statistical analysis of validation data and the use of HTS in diagnostics
  • Ecovir (2016-2019): the diversity of Poaceae viruses is compared in contrasting biodiversity ecosystems of Burdinale-Mehaigne natural park
  • Diagnosis of banana viruses (2017 – 2021): in support of the activities of the Germplasm Health Unit of Bioversity International Genebank, new diagnostic protocols are developed
  • Etiology – Identification of new phytoviruses (2017 – …): International training schools are organized to identify viruses present in symptomatic samples of unknown etiology. The viruses present in these samples are identified by HTS
  • SEVIPLANT (2018-2021): a study of the Solanaceae virome nationwide, more than 10,000 plants will be sequenced
  • VIRFAST (2018-2020): Evaluation of Oxford Nanopore Technology (Minion) for quick on-site virus detection
  • iCARE (2017-2021): a study of viruses infesting cassava plantations and of the cassava seed sector in Rwanda and the Democratic Republic of Congo
  • Plant Health Bioinformatic Network (2019-2021): A project to federate bioinformatic efforts for the analysis of high-throughput sequencing data and pathogen detection
  • Doctoral program on virology (2015 – 2022): fruit tree and potato viruses are studied by the HTS in collaboration with the Chinese Academy of Agricultural Sciences

Researchers are currently collaborating with many countries around the world: