Phytopathogenic viruses are obligate parasites associated with diseases that can cause considerable agricultural losses, due to their biological characteristics (host ranges, various modes of transmission, high genetic diversity and rapid evolution) and the difficulty of implementing effective management measures. Phytoviruses are responsible for almost half of all diseases associated with microorganisms affecting plants.
The team's research activities are mainly focused on the study of phytopathogenic viruses affecting vegetable crops in the Mediterranean basin, in particular Solanaceae (tomato, pepper, eggplant), Cucurbitaceae (melon, zucchini, watermelon, cucumber), lettuce and ornamental crops. For vegetable crops, it is estimated that one new virus is described per year for the last 25 years in France.
OUR SKILLS
Our team brings together multidisciplinary skills in plant virology, molecular biology, metagenomics, epidemiology, ecology, evolution, statistics and spatio-temporal modeling.
OUR OBJECTIVES
Our main objectives are to characterize emerging viruses, estimate viral diversity, characterize the ecological, demographic and evolutionary processes leading to the emergence of epidemics, and develop sustainable control methods.
OUR MODELS
The main viral models studied are potato virus Y (PVY), cucumber mosaic virus (CMV), watermelon mosaic virus (WMV), zucchini yellow mosaic virus (ZYMV) and tomato spotted wilt virus (TSWV). The regular and successive emergence or re-emergence of new viral species or variants harmful to crops has led the team to extend its expertise to other viral models, in particular whitefly-transmitted viruses such as tomato leaf curl New Delhi virus (ToLCNDV) in cucurbits, or aphid-transmitted viruses in other cultivated species (e.g. peas). The team is also interested in the role of bacteriophages in the ecology and evolution of phytopathogenic bacteria, for a possible use as biocontrol agents.
OUR RESOURCES
To carry out these studies, the Virology team has access to a large collection of viruses and appropriate infrastructure such as greenhouses with different levels of containment (S2, S3) and experimental plots (open fields or under tunnels) managed by the experimental facilities section of the PROPHYLE platform, insect vector rearing (aphids, whiteflies), laboratories (etiology, vection, serology) housing useful virology equipment (centrifuge and ultracentrifuge, hood, grinders, titration plate reader, spectrophotometer, etc.).
The team also relies on the microscopy section of the PROPHYLE platform and the laboratories and equipment hosted by the regional molecular biology platform (LBM): PCR and quantitative PCR, thermocyclers, sequencers, etc.
The team invests in the development of R packages for epidemiological analysis and simulation: the landsepi package, for simulating epidemics in time and space in relation to the deployment of control strategies and/or the structure of the agro-ecological landscape; and the mapi package, for characterizing the spatial genetic structures of populations and comparing them with the structure of the environment.
OUR RESEARCH
The Virology team's research belongs to the 3 thematic areas of the Plant pathology unit:
Area 1 Etiology and diagnosis of plant diseases associated with emerging pathogens
In order to better anticipate the risks associated with viral diseases, the team studies viruses associated with emerging, damaging or atypical diseases. It focuses on identifying viral species and better characterizing their biological (host range, transmission) and molecular (genome, phylogeny) properties. The team relies on the development and use of a wide range of complementary tools: biological investigations (mechanical or biolistic inoculation, inoculation by insect vectors such as aphids or whiteflies), electron microscopy, serological (ELISA) and molecular tests (PCR, quantitative PCR, conventional sequencing, high-throughput sequencing). Depending on the project's objectives, these investigations can lead to targeted detection of viral species, or to more generic approaches, such as virome exploration (high-throughput sequencing). This expertise in viral etiology feeds into the research carried out in the unit's two other thematic areas, and enables the PROPHYLE platform to offer diagnostic advice to agricultural professional sectors.
Area 2 Epidemiology, ecology, evolution
The team studies ecological, epidemiological and evolutionary processes by investigating the interactions of viruses with their environment at different spatial scales: crop, plot, production basin, continent. The aim is to identify the main determinants of epidemic dynamics by combining different approaches such as estimating disease incidence, prevalence and severity, analyzing viral genetic diversity, the role of reservoir plants, identifying insect vector species (in particular aphids), estimating dispersal processes and the link between demographic processes and environmental variability. The team focuses on emerging and/or model pathosystems, mainly aphid-borne viruses (CABYV, CMV, WMV), and is involved in field sampling campaigns on cultivated and wild plants and vector trapping. It uses a dedicated information system (Virobase) to ensure the traceability of samples from the field, through diagnosis and collection management, to molecular analysis. The identification and spatio-temporal tracking of viruses and viral variants are carried out using metagenomic approaches to answer viral ecology questions for the understanding of epidemics. The team also relies on laboratory experiments to characterize epidemio-evolutionary processes under controlled conditions, such as viral vection and transmission.
Area 3 Efficiency and sustainability of plant health management strategies
An important aspect of the team's work concerns the characterization of new types of mechanisms or genes controlling plant immunity: quantitative resistances and tolerances, genes controlling the robustness of immunity to environmental stresses. The team is also committed to understanding the evolutionary mechanisms involved in the durability of immunity, in particular by looking at the consequences of genetic drift controlled by the host plant.
To achieve this, the team uses a variety of approaches such as functional genetics, quantitative genetics (GWAS: genome-wide association studies) and experimental evolution. The team evaluates various strategies for deploying resistant varieties in terms of their effectiveness and sustainability at the level of the agricultural production basin. To do this, it uses mathematical modeling tools such as the R package landsepi, which simulates the propagation and evolution of pathogens (viruses and fungi) in a diversified agricultural landscape. The team is also involved in the development and evaluation of management strategies combining several control methods (e.g. genetic control, biological control, nitrogen fertilization
OUR TEAM
Link to Virology team member profiles
