Comparative Virome Profiling and Discovery of Novel Viruses in Managed and Wild Bees using RNA-seq

Insect pollinators face growing challenges from viral pathogens that may contribute to population declines, yet comparative data on virome composition in managed versus wild bees remain limited. Using RNA-Seq-based metatranscriptomic analysis, we compared the virome of Apis mellifera L. and Ceratina calcarata Robertson collected from agricultural and non-agricultural landscapes. We identified multiple known bee pathogens including Black Queen Cell Virus and Deformed Wing Virus in A. mellifera , and discovered three novel insect viruses—two iflaviruses and one entomopoxvirus—associated with C. calcarata . Notably, one novel iflavirus was identified in A. mellifera . Our findings reveal species- and landscape-specific viral prevalence, highlight viral diversity beyond canonical bee pathogens, and provide genomic resources for future functional studies. These data offer new insights into virus-host dynamics and underscore the utility of virome profiling in understanding pollinator health at the molecular level.