Surveillance and molecular characterization of banana viruses and their association with Musa germplasm in Malawi.

Malawi has local banana germplasm preferred by its population. However, the epidemics of banana bunchy top disease, caused by the banana bunchy top virus (BBTV), is wiping out the most preferred germplasm and limiting its plantation. On the other hand, there needs to be more knowledge on viruses present in Malawi on banana crops. Therefore, a survey was conducted country-wide to characterize banana germplasm and evaluate the presence, incidence and prevalence of banana viruses. The survey covered four country zones, combined farmers structured questionnaire and plant sampling. PCR products from infected germplasm were sequenced and aligned for each detected virus to build a phylogenetic tree. BBTV, BanMMV and BSV species were detected in Malawi. Malawis BBTV isolates belonged to the Pacific Indian Ocean group only and BanMMV isolates clustered to three sub-branches. All the BSV species present in Malawi belonged to clade 1. Among the genetic groups of Musa, the identified banana germplasm belonged to AA, AAA, AB, AAB, and ABB groups with some germplasms unique compared to already genotyped germplasms. The ABB group was dominant in Malawi and was often infected by BSV species (probably originating from endogenous viral sequences), while BBTV more often infected the AAA group. Banana propagule sharing was the primary source of banana planting materials with a higher risk of spreading virus diseases. The survey underlined the need to set up a banana seed industry and policies that promote farmers access to virus-tested planting materials, which will consequently prevent future virus epidemics.