Spatio-temporal dynamics of viral populations associated to rice in West Africa – SPADYVA

The emergent crop diseases, a high proportion of which are caused by viruses, are a significant burden on food security and economic stability of societies, especially in developing countries. Rice is the most important human food crop in the world, and it is becoming increasingly important in Africa. During the last decades, rice cultivation has been drastically intensified in West Central Africa, which renders the rice production more exposed to epidemics and new pathogen emergences.

While viruses correspond to the most abundant biological entity in nature, the virus diversity remains largely unexplored compared to other microorganisms. This lack of knowledge has inevitable consequences on the risk valuation of new virus emergence and the management of epidemics, for human, animals and crops. The key to evaluate and to map the risk of virus emergence that threatens the crop production is to associate the exploration of the plant virus diversity in the agro-ecosystems with phytopathologic, epidemiological and experimental studies.

The aim of the SPADYVA project is to understand the impact of the biotic, abiotic and historical factors on the diversity, the emergence, the dispersion and the virulence of rice viruses in Africa combining viral metagenomics, molecular epidemiology, phylodynamics and experimental validations.

For that, we will analyse thousands of rice samples collected at 100 years apart in West-Central Africa to explore the viral diversity associated to rice cultivation, using the most recent high-throughput sequencing technologies (Illumina and Oxford Nanopore technology). Then, contrary to most of metagenomics studies, we will determine the distribution, the prevalence, the host range, the virulence and the fitness of viruses identified in rice, some of them might be at an early stage of emergence. Finally, we will use phylogeographic and phylodynamics modelling, scarcely implemented for plant viruses, to reconstruct finely the evolution history of a rice virus with a significant epidemic success in Africa, the Rice yellow mottle virus (RYMV).

Hence, through an integrative and multidisciplinary approach, the SPADYVA project will contribute to understand the shape and the dynamics of the plant virus diversity in the agro-ecosystems, from the emergence to the global dispersion, and will assess the long-term impact of agricultural changes and human history on the diversity, the emergence, the dispersal and the virulence of viral populations associated to rice cultivation in West-Central Africa.

The results generated during this project will greatly contribute i) to support epidemiological surveillance of viral disease affecting rice in Africa, ii) to identify unknown rice viruses and to develop efficient diagnostic tools to detect these emerging rice viruses, and iii) to design sustainable control strategies against rice viruses once the genetic and environmental factors involved in virus epidemics will be identified.

Altogether, this project will gather plant material, data and knowledge accumulated over the last century on rice and rice viruses in West-Central Africa to understand why and how some viral strains emerge and disperse and others do not, i.e. to decipher the balance and the interplay between genetic determinants and stochasticity in plant virus epidemiology, an innovative and ambitious question that goes beyond virology.