APHIDS - Phylodynamic analysis of the effect of agricultural landscape diversity and seasonality on the spread of a vector-borne plant virus

Background and challenge

Agri-ecosystems are characterised by semi-artificial biodiversity and spatio-temporal heterogeneity, which shape the epidemiology of plant viruses. Within these dynamic landscapes, barley yellow dwarf virus (BYDV), transmitted in particular by the aphid vector Rhopalosiphum padi, poses a major challenge to plant health and the agroecological transition. These viruses exploit a wide range of hosts, including cultivated cereals and various wild grasses. 

The latter potentially function as reservoirs or ‘green bridges’, ensuring the continuity of the infection cycle and the persistence of viral isolates during fallow periods. Nevertheless, the mechanisms governing viral flows between natural and anthropised compartments remain poorly understood, particularly the existence of biological or ecological barriers limiting exchanges within the interaction network. Understanding these dynamics requires the development of « phylodynamic » inference tools capable of integrating the evolutionary and discontinuous nature of contact networks. Anchored in the Zone Atelier Plaine & Val de Sèvre research infrastructure, the APHIDS project aims to address these gaps. The challenge lies in modelling these complex ecological processes to define sustainable management strategies at the regional level.
 

Objectives 

The APHIDS project aims to explore the pathways of virus transmission within a changing landscape. Its main objective is to develop innovative mathematical tools, based on « phylodynamics », capable of reconstructing the history of an epidemic from viral genetic sequences. Unlike traditional models, these new tools will incorporate the dynamic nature of ecosystems, taking into account the fact that crops appear or disappear over the course of the seasons. 

To achieve this, the team will adopt an interdisciplinary approach combining mathematics, virology, and ecology. The work will begin with numerical simulations to optimise field sampling strategies. Subsequently, intensive campaigns will be conducted to collect wild plants, crops, and aphids within the Zone Atelier. High-throughput sequencing of viral genomes will then provide a precise map of circulating variants. By cross-referencing this genetic data with geographical and botanical information, the project will be able to quantify the relative importance of each plant reservoir in the spread of the disease. 

Ultimately, this knowledge will enable the refinement of models capable of predicting epidemic risks at a regional scale. The ultimate aim is to translate these advances into practical solutions, such as decision-support tools for farmers, promoting landscape management that naturally limits viral spread without affecting biodiversity.

Involved research units and partnership

Partners

Contacts / coordination