Metagenomic Characterization of Aedes aegypti Virome in Kwale County, Kenya

Abstract Background Aedes aegypti is a primary vector of arboviruses, including dengue, chikungunya, yellow fever, and Zika, and is widespread along the Kenyan coast, a region with recurrent outbreaks. In addition to human-pathogenic arboviruses, Ae. aegypti harbors insect-specific viruses (ISVs) that replicate exclusively in arthropods and may influence mosquito physiology, immunity, and vector competence. However, data on ISVs in Kenyan Ae. aegypti populations are limited. Methods Twenty-nine mosquito pools containing 20 individual mosquitoes from Kwale County were homogenized, combined into a superpool, and subjected to total RNA extraction. Libraries were sequenced on an Illumina MiSeq platform. Initial analysis was done on CZ-ID platform. Reads were quality-filtered using PrinseqLite and assembled de novo with MEGAHIT. Phylogenetic analyses was performed with IQ-TREE using the Maximum Likelihood method. Results Metagenomic analysis revealed diverse ISVs in Ae. aegypti . Complete genomes of Fako virus and Tesano Aedes virus, and partial genomes of Aedes partiti-like virus, Cell fusing agent virus, and Formosus virus, were recovered. Genome lengths ranged from 1,149 to 10,146 nucleotides, with 91–99.5% identity to reference strains. Phylogenetic analysis placed the viruses within established ISV lineages, showing close evolutionary relationships with strains previously reported from Africa and other regions. Conclusions This study provides comprehensive characterization of ISVs in Ae. aegypti from Kwale County. The recovery of complete and near-complete genomes demonstrates the diversity and active circulation of ISVs, establishing a baseline for future studies on mosquito viromes, virus–mosquito interactions, and potential impacts on vector competence. Importance Insect-specific viruses (ISVs) are widespread in mosquitoes and replicate exclusively in arthropods, influencing mosquito physiology, immunity, and potentially vector competence for human-pathogenic arboviruses. Despite recurrent arboviral outbreaks along the Kenyan coast, the diversity and ecological roles of ISVs in Aedes aegypti remain poorly understood. This study provides a comprehensive metagenomic characterization of ISVs in Ae. aegypti from Kwale County, revealing complete genomes of Fako virus and Tesano Aedes virus, along with near-complete genomes of Aedes partiti-like virus, Cell fusing agent virus, and Formosus virus. These findings establish a baseline for mosquito virome composition in this region and underscore the active circulation of diverse ISVs in natural populations. Understanding these virus–mosquito interactions is critical for interpreting arbovirus ecology, assessing the potential impacts of ISVs on vector competence, and informing future vector surveillance and biological control strategies.