Unveiling Common Bean ( <i>Phaseolus vulgaris</i> L) RNA‐ and DNA‐Based Virome in Western Kenya: Insights From Metatranscriptomic and Metagenomic Signatures

Common bean (<i>Phaseolus vulgaris</i> L) is Kenya's second most important agricultural product after maize, serving as a vital source of protein for many rural families in Western Kenya. However, viral diseases caused by RNA and DNA viruses greatly impair bean productivity, often leading to yield losses of up to 100%, thus contributing to food insecurity. Global research has isolated 168 viruses of plants that have detrimental effects on common beans; however, no extensive profiling of these viruses has been done in Western Kenya. The scope of this study was to delineate the whole virome that infects common beans through a comprehensive disease diagnostic survey. Sixty-one diseased samples were collected, and nucleic acids were extracted using standard extraction protocols (DNA &RNA Qiagen) and sequenced on the Illumina platform. Metagenomic analysis revealed several DNA-based viruses, such as <i>Badnavirus</i> spp, <i>Caulimovirus maculatractylodei</i>, <i>Pandanus badnavirus</i>, <i>Okra enation leaf curl virus</i>, and <i>Paper mulberry vein-banding virus</i>, while metatranscriptomic analysis uncovered viruses like <i>Tomato leaf curl Cameroon alphasatellite</i>, <i>Physalis Rugose Mosaic Virus</i>, Citrus endogenous paretrovirus, <i>Natevirus nate</i>, and <i>Bracoviriform facetosae</i>. To the best of our knowledge, this study provides a comprehensive inventory of viral entities associated with common beans not documented in Africa. This information is essential for defining plant defense mechanisms, guiding crop protection strategies, lowering agriculture-related risks, strengthening resistance, and advancing resilience.