Abstract
Cocoa (Theobroma cacao L.) is a major agricultural commodity, essential for the global chocolate industry and the livelihoods of millions of farmers. However, viral diseases pose a significant threat to cocoa production, with Badnavirus species causing severe losses in Africa. Despite its economic importance, the overall virome of T. cacao remains poorly characterized, limiting our understanding of viral diversity and potential disease interactions. This study aims to assess the cocoa-associated virome by analyzing 109 publicly available RNA-seq libraries from nine BioProjects, covering diverse conditions and geographic regions. We implemented a comprehensive bioinformatics pipeline integrating multiple viral sequence enrichment steps, a hybrid assembly strategy using different assemblers, and sequence similarity searches against NCBI non-redundant databases. Our approach identified ten putative novel viruses associated with the cocoa microbiome and a novel Badnavirus species. These findings provide new insights into the viral landscape of T. cacao, characterizing the diversity of cacao-associated viruses and their potential ecological roles. Expanding the catalog of viruses associated with cocoa plants not only enhances our understanding of plant-virus-microbiome interactions but also contributes to the development of more effective disease surveillance and management strategies, ultimately supporting sustainable cocoa production.