Solanaceous crops fields are severely affected by the emerging virus Pepper yellow vein Mali virus (PepYVMLV) in West Africa. It belongs to the genus Begomovirus (family Geminiviridae) and is transmitted by Bemisia tabaci. African begomoviruses described on crops are mainly monopartite (DNA-A component), except cassava-infecting bipartite begomoviruses (DNA-A and DNA-B components). Up to now, the PepYVMLV was described as a monopartite Begomovirus. In order to better understand the epidemiology of this virus in West Africa, particularly in Burkina Faso, two surveys were undertaken in the whole country and 1,614 solanaceous plants were collected to be checked for the presence of the virus. The deep characterization allowed to discover the presence of a typical DNA-B associated with the pepper yellow vein disease. This DNA-B is different from those of currently described cassava mosaic Geminiviruses. The discovery of the association of a newly described DNA-B component with the PepYVMLV also leads to the study of the epidemiological parameters of this co-infection. Although this association is relaxed, we demonstrated that disease virulence, viral accumulation and transmission by Bemisia tabaci were increased in co-infection with the DNA-B component. All these factors are probably related to the success of this association in the field. Because of the extreme severity of the resulting disease, the dispersal of this new DNA-B component at a larger scale would represent a major threat to tomato and pepper cultivation in Burkina Faso, Africa and the world in general.