Résumé
Multiple infections, or ‘co-infections’, occur when a single host is infected by different pathogen species, or genotypes. This is known to affect symptom expression and pathogen multiplication in many pathosystems. However, the population-scale consequences remain poorly explored.Rice grown in Burkina Faso is affected by multiple pests, of which the rice yellow mottle virus (RYMV) and the bacteria Xanthomonas oryzae (Xo) are known to interact in experimental co-infections. In addition, several lineages of the RYMV co-circulate locally, and were evidenced as mixed infections. In this project, we aimed to investigate the evolutionary consequences of multiple infections (both within and between species) and their role in maintaining viral genetic diversity, for the RYMV in Burkina Faso.To this end, a stratified random sampling was performed in two sites, during two consecutive years (2021 and 2022). Molecular detection applied jointly to RYMV and Xo revealed a much higher frequency of samples co-infected by the two pathogens, than inferred from the observations of the two types of specific symptoms on the same plants. We then characterised the genetic diversity of RYMV in collected samples revealing a locally high diversity within fields, and significant structuration between the two sites. In addition, we found some evidence for an association of some RYMV lineages with the presence of Xo, suggesting reciprocal influence of co-infecting pathogens on the genetic structuration of other pathogen species. Further research could confirm such consequences of multiple infections on the evolution of viral populations.