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The cacao swollen shoot disease complex in West Africa comprises at least five divergent badnavirus species

Judith Brown: School of Plant Sciences, University of Arizona

<div>The cacao swollen shoot disease (CSSD) of <em>Theobroma cacao</em> in West Africa is characterized by diverse foliar symptoms, swollen shoots, and tree death. CSSD was previously thought to be caused by a single virus, <em>Cacao swollen shoot virus</em> (CSSV). Current molecular tests confirm positive infection in <70% of symptomatic trees, suggesting presence of uncharacterized viruses. Molecular characterization of 61 full-length genome virus sequences from symptomatic trees in Ghana, Togo, Cote d’Ivoire and Nigeria indicated that at least five badnavirus species are associated with CSSD. Analysis of the taxonomic RT-RNase H region confirmed that <em>Cacao swollen shoot CD virus</em> (CSSCDV), <em>Cacao swollen shoot Togo A virus</em> (CSSTAV), and the recently proposed Cacao red vein virus (CRVV) and Cacao red vein-banding virus (CRVBV), are also found in cacao trees exhibiting characteristic CSSD symptoms. All 61 genomes showed similar conserved protein domain architectures, despite the differences in genome arrangement and 70 – 100% shared nucleotide identity. CSSV is found in all four countries, except Nigeria, whereas CSSCDV, CSSTAV, and CRVBV appear to be confined to Cote d’Ivoire, Togo, and Nigeria, respectively. In contrast, CRVV has been reported in Ghana and Cote d’Ivoire. Genome sequences and geographical distributions of the CSSD viruses will facilitate development of virus diagnostics, epidemiology studies, and breeding programs for virus-resistant cacao varieties.</div>