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. The 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. The 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. Three 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.

The cacao swollen shoot disease (CSSD) caused by a complex of badnavirus species presents a major challenge for cacao production in West Africa, especially Ghana and Côte d’Ivoire. In this study, CSSD species detection efficiency, diversity, and geographic distribution patterns in cacao plantations in Ghana and Côte d’Ivoire were investigated through field surveillance, PCR detection assays, sequencing of positive amplicons, and phylogeographic clustering. Cumulatively, the detection efficiency of the tested CSSD primer sets that were targeting the movement protein domain of the virus ranged from 0.15% (CSSD-3 primer) to 66.91% (CSSD-1 primer) on all the symptomatic cacao leaf samples assessed. The identified CSSD species differed phylogenetically and overlapped in distribution, with the cacao swollen shoot Togo B virus (CSSTBV) (n = 588 sequences) being the most prevalent and widely distributed compared to the other CSSD species that were encountered in both countries. Geographically, the cacao swollen shoot CE virus (CSSCEV) species (n = 124 sequences) that was identified was largely restricted to the bordering regions of Ghana and Côte d’Ivoire. These results provide updated knowledge of the geographic distribution of the key CSSD species and their diagnostic efficiency and, thus, provide guidance in identifying locations for structured testing of cacao germplasm and optimal diagnostics for the predominant CSSD species in Ghana and Côte d’Ivoire.

This study was conducted to understand the reinfection pattern of cocoa swollen shoot disease (CSSD) in rehabilitation pilot plots in the cocoa landscape on Nawa region (Soubre) in Côte d’Ivoire. For that, the monitoring of CSSD was carried out on a ran-domly selected representative sample size of rehabilitating trials over time by assessing the epidemiological parameters of the disease through field observations combined with molecular samples analysis on-farm and at landscape level. Results showed that the reinfection appeared earlier than expected with high speed of incidence estimated to 6.95 % from 2020 to 2022. Grafting technology with clones on matures cocoa trees seems more susceptible to reinfection compared to grafting on seedling and hybrids. The use of PCR as molecular diagnostic indicated some miss infections in the removal strategy when considering the buffer zone recommended in the cutting out process currently in force. Recommendations for an efficient protection of rehabilitated farms after the cutting out campaigns were highlighted.

This study was conducted to understand the reinfection pattern of cocoa swollen shoot disease (CSSD) in rehabilitated plots in the cocoa landscape of the Nawa region (Soubré) in Côte d’Ivoire. CSSD was monitored over time on a sample of 200 farms randomly selected from 1200 rehabilitated cocoa farms. Disease epidemiological parameters were assessed through field observations and molecular diagnostic analysis at farm and landscape levels. The results of this study showed that reinfection occurred earlier than expected, with a high disease incidence estimated at 6.95% from 2020 to 2022. Grafting with clones on mature cocoa trees was more susceptible to reinfection than grafting on seedlings and hybrids. The use of PCR as a molecular diagnostic tool indicated missed infections in the current removal strategy when considering the buffer zone recommended in the cutting out process currently in place. Recommendations for the efficient protection of rehabilitated farms after cutting out campaigns are highlighted.