Geographical Distribution of Cacao swollen shoot virus Molecular Variability in Côte d'Ivoire

Kouakou, K., Kebe, B. I., Kouassi, N., Ake, S., Cilas, C., and Muller, E. 2012. Geographical distribution of Cacao swollen shoot virus molecular variability in Cote d’Ivoire. Plant Dis. 96:1445-1450. The discovery of new outbreaks caused by Cacao swollen shoot virus (CSSV) in Cote d’Ivoire in 2003, when this disease seemed to have been eradicated since the end of the 1950s in that country, casts doubt on the sustainability of Ivorian cocoa production. The aims of this study were, first, to carry out a molecular characterization of CSSV isolates from the main outbreaks in Cote d’Ivoire; second, determine their phylogenetic position in relation to isolates already discovered in Togo and Ghana; and, finally, study their geographical distribution to understand the dispersal of the virus. Additionally, this study was intended to enable the implementation and validation of a polyvalent molecular diagnosis assay for CSSV. Sequences analyses, corresponding to a fragment located at the 5′ end of open reading frame (ORF)3 of the CSSV genome, revealed three new CSSV groups (D, E, and F) distinct from the A, B, and C groups already identified in Togo. Only group B was detected in all the outbreaks, whereas groups A and C were not identified in Cote d’Ivoire. In addition, a polymerase chain reaction diagnostic using the ORF3A F/R primer pair was polyvalent, because it enabled the detection of CSSV in 90% of the plots in all the cocoa regions analyzed by this study. The sustainability of cocoa production in Cote d’Ivoire, the world’s leading producer, has been under threat since the discovery of cocoa swollen shoot disease outbreaks in the Centre West of the country, notably at Bouafle and Sinfra (12). This disease, which was described for the first time in Ghana by Steven in 1936 (29), is primarily confined to the countries of West Africa. It severely reduces the yields of an affected cocoa tree and kills the tree in under 5 years (23). However, between these two extreme phases (reduced yields and tree death), the leaves gradually turn yellow and fall, then the branches dry out from their tips (die-back). The typical symptoms of the disease are a red vein banding of young leaves, mosaic on older leaves, and, above all, swelling of the orthotropic shoots (23). The pathogen responsible for the disease is Cacao swollen shoot virus (CSSV) belonging to the genus Badnavirus and family Caulimoviridae (15). Natural transmission of the virus is via mealybugs of the family Pseudococcidae in a semipersistent manner (7). The only effective way of controlling swollen shoot disease is to remove infected cocoa trees and their nearest neighbors, then replant with healthy hybrids selected for their partial resistance to the virus (32). However, the cocoa hybrids selected thus far display low resistance against CSSV under conditions of high viral pressure. In fact, not only are CSSV resistance levels low in the cocoa tree (1,26) but, especially, the genetic diversity of CSSV has not yet been taken into account in breeding programs. Six CSSV isolates from Ghana and Togo have been entirely sequenced thus far (10,19) and are genetically structured in three groups: A, B, and C (17). Swollen shoot disease has always been described as a disease endemic to West Africa, because it has never been reported in