Résumé
Pathogens actually share their hosts with a myriad of other microbes, some of them being pathogenic. Multiple infections, or ‘co-infection’, occur when a single host is infected by various pathogen species, or genotypes. This is known to affect symptom expression and pathogen multiplication in many systems. However, the population-scale consequences remain poorly explored, and this will be discussed in the introduction, focusing on evolutionary and epidemiological consequences of multiple infections.I will then illustrate by our work (IRD-INERA-PathoBios team) on plant diseases in Burkina Faso. Through a multi-pathogen epidemiological survey, we documented the dynamics of various rice diseases jointly. Symptom monitoring showed high levels of co-occurrences were found between the four rice diseases under study, particularly in irrigated areas. The epidemiology of rice yellow mottle disease, due to the RYMV, is not affected by the rice production system, but instead by the specific site. A very high RYMV genetic diversity, with the co-occurrence of four distinct lineages, was found at the small geographical scale of one irrigated perimeter. Temporal dynamics suggest an evolution of the frequencies of each genetic lineage within the studied period. Experimentally, we found differences between isolates in terms of viral load post inoculation, and this may contribute to explain observed RYMV population evolution. Finally, we found reciprocal interactions between the RYMV and the bacteria Xanthomonas oryzae under controlled conditions. Because these two pathogens are known to co-occur in the same rice fields, these interactions evidenced experimentally may have consequences for the evolution of pathogen populations and the maintenance of viral genetic diversity in the field. More generally, I will present an ongoing project that aims to investigate the impact of multiple infections on evolutionary trajectories of this rice virus, with applied consequences for food safety in West Africa.