Genome-wide Characterization of Endogenous Viral Elements Reveals Extensive Viral Diversity in Culicinae Mosquitoes

Abstract Endogenous viral elements (EVEs) are viral sequences integrated into host genomes that shape genome evolution, antiviral immunity, and gene regulation; however, their diversity and evolutionary significance in mosquitoes remain insufficiently characterized. A genome-wide analysis of EVEs was conducted across 19 RefSeq Culicinae mosquito genomes, identifying 77,141 putative EVEs representing 1,538 viral species, although these elements occupy less than 1% of mosquito genomes. EVE abundance varied significantly among species, with Aedes koreicus exhibiting the highest EVE burden. Approximately 62% of EVEs were homologous to Trichoplusia ni TED-like and Cladosporium fulvum T1-like retroviral elements. EVEs demonstrated non-random chromosomal distributions, integration hotspots, and frequent associations with transposable element-related domains. Phylogenetic analyses revealed multiple previously unrecognized EVE clades, while transcriptomic and PCR analyses confirmed the expression and conservation of dominant EVEs in Indian Aedes aegypti. This study provides the most comprehensive catalog of mosquito EVEs to date and establishes a foundation for understanding their roles in mosquito evolution, antiviral immunity, and vector biology.