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Background Cacao swollen shoot virus (CSSV), Cacao swollen shoot CD virus (CSSCDV), and Cacao swollen shoot Togo A virus (CSSTAV) cause cacao swollen shoot disease (CSSD) in West Africa. During 2000–2003, leaf and shoot-swelling symptoms and rapid tree death were observed in cacao in Cote d’Ivoire and Ghana. Molecular tests showed positive infection in only ~50–60% of symptomatic trees, suggesting the possible emergence of an unknown badnavirus.MethodsThe DNA virome was determined from symptomatic cacao samples using Illumina-Hi Seq, and sequence accuracy was verified by Sanger sequencing. The resultant 14, and seven previously known, full-length badnaviral genomic and RT-RNase H sequences were analyzed by pairwise distance analysis to resolve species relationships, and by Maximum likelihood (ML) to reconstruct phylogenetic relationships. The viral coding and non-coding sequences, genome organization, and predicted conserved protein domains (CPDs) were identified and characterized at the species level.ResultsThe 21 CSSD-badnaviral genomes and RT-RNase H sequences shared 70–100% and 72–100% identity, respectively. The RT-RNase H analysis predicted four species, based on an ≥80% species cutoff. The ML genome sequence tree resolved three well-supported clades, with ≥70% bootstrap, whereas, the RT-RNase H phylogeny was poorly resolved, however, both trees grouped CSSD isolates within one large clade, including the newly discovered Cacao red vein virus (CRVV) proposed species. The genome arrangement of the four species consists of four, five, or six predicted open reading frames (ORFs), and the CPDs have similar architectures. By comparison, two New World cacao-infecting badnaviruses encode four ORFs, and harbor CPDs like the West African species.ConclusionsThree previously recognized West African cacao-infecting badnaviral species were identified, and a fourth, previously unidentified species, CRVV, is described for the first time. The CRVV is a suspect causal agent of the rapid decline phenotype, however Koch’s Postulates have not been proven. To reconcile viral evolutionary with epidemiology considerations, more detailed information about CSSD-genomic variability is essential. Also, the functional basis for the multiple genome arrangements and subtly distinct CPD architectures among cacao-infecting badnaviruses is poorly understood. New knowledge about functional relationships may help explain the diverse symptomatologies observed in affected cacao trees.Electronic supplementary materialThe online version of this article (10.1186/s12985-017-0866-6) contains supplementary material, which is available to authorized users.

From 2013 to 2018, surveys were conducted in counties not previously surveyed in order to determine species of mealybugs present in the cocoa orchard in Côte d'Ivoire as well as their abundance according to the age of cocoa trees. Immature and mature cocoa trees were inspected to hand‐height in 5 and 29 counties infected with Cacao swollen shoot virus (CSSV). In each cocoa farm, mealybugs were searched for on fruits, leaves, flowers, twigs and trunks. Mealybug species were identified, and colonies were counted. Five mealybug species were identified on immature cocoa trees: Ferrisia virgata, Formicococcus njalensis, Planococcus citri, Planococcus kenyae and Pseudococcus longispinus. In addition to these species, four species, Dysmicoccus brevipes, Maconellicoccus hirsutus, Phenacoccus hargreavesi and Pseudococcus jackbeardsleyi were identified on mature cocoa trees. On immature cocoa trees, Fo. Njalensis, Pl. citri and Ps. longispinus comprised were, respectively, 35%, 33% and 19% of colonies, respectively. On mature cocoa trees, Fo. Njalensis and Pl. citri comprised 63.2% and 21.0%, and others species 15.8%. Nevertheless, the abundance of mealybug species varied according to the age of cocoa trees. The preferred organs of mealybugs were pods (74.1%) followed by twigs (13.4%) and flowers (7.4%). Previously, the mealybug Paracoccus burnerae (Brain) was found on Theobroma cacao, which is the first record for this species in Côte d'Ivoire and on this host‐plant.