Exploring the Diversity of Cacao Swollen Shoot Virus, an Emergent Badnavirus of Theobromus cacao Endemic to West Africa

Cacao swollen shoot virus (CSSV), a plant pararetrovirus (genus, Badnavirus; family, Caulimoviridae), has become pandemic in West Africa where over 70% of the world’s cocoa production is centered. Disease incidence has increased and the distribution has expanded substantially during the last 15 years. Following infection, trees may remain asymptomatic at the outset, but then lose vigor and die as they approach production age (~4 yrs).  Sensitive detection and accurate identification of CSSV has become essential for conducting epidemiological studies, to assist breeding programs, and for implementation of integrated management programs. Preliminary studies have indicated that CSSV isolates are more genetically variable and possibly more divergent than expected, rendering current diagnostic tests ineffective. To improve virus detection and enable differentiation of CSSV isolates, strains, and related species that may be associated with cacao and wild plant hosts, and the mealybug vectors, a multi-pronged approach was implemented. PCR primers were designed based on coding and non-coding regions of 7 available genome (~7.2 kb) sequences, and used together with rolling circle amplification, cloning, and DNA sequencing with primer walking to explore CSSV genomic diversity. Results thus far indicate that isolates from Cote d’Ivoire samples were highly variable in certain regions and conserved in others. Detailed studies are needed to understand the basis for the recent pandemic in which CSSV has spread rapidly throughout West Africa cocoa producing countries. In addition to a number of mealybug species that transmit the virus between plants, human-mediated movement of infected germplasm is suspected to be exacerbating long-distance movement of CSSV, an outcome owing to the shortage of virus-free planting materials, as production has expanded to meet the high demand for cocoa beans.