Geminivirus diversity and community structure at the scale of agro-ecological systems in two localities of Burkina Faso

Circular replication-associated protein encoding single stranded (CRESS) DNA viruses have emerged to become one of the largest and most devastating groups of crops-infecting viruses in tropical and subtropical regions of the world. In West Africa, renewed outbreaks of disease-like symptoms in the field have prompted surveys that revealed the circulation of multiple CRESS DNA virus species. Recognizing that plant viral diseases may be best understood at the ecosystem scale, we conducted a survey of plant-associated CRESS DNA virus communities in two localities of Burkina Faso (1,068 plant samples). CRESS DNA viruses were detected in 41% and 13% of samples from cultivated and uncultivated plants respectively. Virus community maps constructed from the 30 uncovered species of geminivirus and associated satellites revealed strong modularity. Whereas few co-infections involving viruses belonging to different host-virus modules were observed, evidence of recombination was nevertheless detected between viruses belonging to different modules. This suggests that co-infections between viruses in different modules does at least occasionally occur: possibly as a consequence of seasonal variations in virus-host community structures with the inter-cropping period in particular promoting such “inter-module” co-infections.