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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.

The cacao swollen shoot virus disease (CSSVD) is among the most economically damaging diseases of cacao trees and accounts for almost 15-50% of harvest losses in Ghana. This virus is transmitted by several species of mealybugs (Pseudococcidae, Homoptera) when they feed on cacao plants. One of the mitigation strategies for CSSVD investigated at the Cocoa Research Institute of Ghana (CRIG) is the use of mild-strain cross-protection of cacao trees against the effects of severe strains. In this study, simple deterministic, delay, and stochastic ordinary differential equation-based models to describe the dynamic of the disease and spread of the virus are suggested. Model parameters are estimated using detailed empirical data from CRIG. The modeling outcomes demonstrate a remarkable resemblance between real and simulated dynamics. We have found that models with delay approximate the data better and this agrees with the knowledge that CSSVD epidemics develop slowly. Also, since there are large variations in the data, stochastic models lead to better results. We show that these models can be used to gain useful informative insights about the nature of disease spread., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Agusto et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Cacao swollen shoot disease (CSSD) caused by complexes of cacao swollen shoot badnaviruses (family Caulimoviridae , genus Badnavirus ) remains highly prevalent and devastating in West Africa. The disease continues to impact substantially on cacao yield loss, cacao tree mortality, and decline in foreign exchange income from cacao bean sales. Currently, the disease is estimated to have a prevalence rate of over 30% in Ghana, as assessed in the ongoing third country-wide surveillance program. Although achievements from past research interventions have greatly elucidated the etiology, biology, epidemiology, diagnostics, and management of the disease, there are some outstanding knowledge gaps. The role of these information gaps and their effect on CSSD epidemiology and prevalence remain unanswered. This paper summarizes existing scientific knowledge from past research achievements that have provided elucidation on CSSD epidemiology, management options, and guided future research. The discussion highlights the need for multidisciplinary research with modern tools and institutional collaborators to holistically bring clarity on knowledge gaps on pathogen biology, virus-host--vector interactions, role of environmental and soil nutrient effects on CSSD severity, evolution pattern, role of alternative hosts on virus species diversity, vector population dynamics, and their overall impact on CSSD prevalence and integrated management in cacao plantations.

Cacao swollen shoot virus causes cacao swollen shoot disease of Theobroma cacao (cacao) plants. At least six cacao-infecting Badnavirus species- Cacao swollen shoot Togo A virus , Cacao swollen shoot Togo B virus (previously known as Cacao swollen shoot virus ), Cacao swollen shoot CE virus , Cacao swollen shoot Ghana M virus , Cacao swollen shoot Ghana N virus , and Cacao swollen shoot Ghana Q virus -are responsible for the swollen shoot disease of cacao in Ghana. Each of these species consists of a multiplicity of strains. The New Juaben strain, the most virulent cacao swollen shoot virus strain in Ghana, belongs to the Cacao swollen shoot Togo B virus species, and is a commonly used strain in laboratory transmission assays. Infection of cacao trees with multiple strains of the virus is common and new evidence suggests that these coinfections may have resulted in the emergence of recombinant strains of the virus. The impact of these emerging recombinant strains on disease severity is uncertain. This review focuses largely on the discovery of cacao swollen shoot virus in Ghana, diversity of the virus strains, molecular characterization, propagation of virus infection in cacao plants, emergence of recombinant virus strains, vector-mediated transmission of the virus, and the management of the cacao swollen shoot disease in Ghana. It also contains sections on the botany and origin of the cacao tree, its introduction to Ghana, the role of cacao swollen shoot disease in facilitating Ghana's independence from Britain, and a brief history of chocolate., Competing Interests: The author(s) declare no conflict of interest.

Cocoa swollen shoot virus disease (CSSVD) is a major disease of cacao (Theobroma cacao L.) in Ghana and other West African countries that grow the crop. Attempts to develop resistant varieties since the discovery of the disease in 1936 have yielded little success. Recently, planting materials that are tolerant to the disease have been recommended for planting in areas with high CSSVD prevalence. However, the effect of CSSVD on yield component traits of most cacao clones including the tolerant varieties has not been well studied. To investigate the impact of CSSVD on these traits, reduction in bean weight (BW), number of beans per pod (NoBP) and dry bean yield (DBY) between symptomless and symptomatic trees, and disease incidence (DI) among 210 different cacao clones were evaluated. The clones were transplanted in June 2010 following a randomised complete block design with four replications consisting of three trees per clone per block. Response of the clones to CSSVD incidence had 180 of the genotypes having < 50% symptoms. Clones of Contanama, Iquitos, Marañon, Nanay and unknown derived from Upper Amazon parentage had less DI at the end of the study. The CSSVD effect (symptomless vs. symptomatic) was significant (p < 0.05) for DBY and NoBP, and the symptomless trees surpassed on average their symptomatic trees by 21.17% for DBY. Some of the best-performing clones identified under natural CSSVD infection were; COCA 3348/52 and GU 219/V among the underrepresented clones, B 36, ICS 40, NA 33 x IMC 67, T30/628, T60/887, T63/971, T 81/1879 and T 82/503 among those that combine high DBY with low yield reduction, and NA 124, T17/358, T35/78, T57/305, T63/971 x SCA 6, T65/239, T76/1835 and T82/2294 among those that combine high DBY with no disease incidence. Their inclusion in breeding programs that seek to develop resistant CSSVD varieties or deployment as planting materials in endemic areas to improve yield production in Ghana is recommended on the basis of the present observations., Competing Interests: The authors have declared that no competing interests exist.