Résumé
Co-occurrence of multiple diseases and co-infection of individual plants by various pathogens have potential epidemiological implications. Based on data on the co-occurrence of the rice yellow mottle disease (caused by the rice yellow mottle virus, RYMV) and bacterial leaf streak (BLS, due to Xanthomonas oryzae pv. oryzicola, Xoc) in Burkina Faso, and experimental evidence of interactions between the pathogens causing these two diseases, we monitored the two pathogens more intensively in farmer's rice fields. We selected fields showing both types of symptoms to maximize chances of observing co-infections at the plant scale. We performed observations and sampling in two sites over two consecutive years, resulting in 1666 samples. 1341 plants were symptomatic for any of the two diseases. Although the sampling design was biased towards observing co-infections, only 37 of these samples (2.8%) were annotated as presenting both yellow mottle and BLS symptoms. The samples were then subjected to a newly designed molecular detection test that specifically amplifies both the virus (RYMV) and the bacteria (Xo). This revealed that 166 samples, i.e. 12.4% of the symptomatic samples, were co-infected by RYMV and Xo, hence showing that symptom observation in the field greatly underestimated co-infection levels in this dataset. Combining these data with a previously published dataset, we estimated that at least 1-5% of all plants in disease hotspots may be simultaneously infected by the two pathogens. Further research on multiple infections would benefit from longitudinal surveys over the growing season rather than such a cross-sectional study.