Metagenomic Analysis Reveals Viral Diversity in Phlebotomine Sand Flies from Caribbean Region in Colombia

Phlebotomine sand flies are dipterans that transmit leishmaniasis, bartonellosis, and arboviruses of public health importance. Colombia is a tropical country with high annual incidences of arboviruses, such as dengue and, more recently, yellow fever, all of which have similar symptoms. This study characterized the viruses circulating in phlebotomine sand flies in two departments in the Colombian Caribbean. Between August 2023 and December 2024, a descriptive study was conducted in the Departments of Córdoba and Cesar in Colombia. Four municipalities were selected per department, and four insect captures were performed using CDC light traps. Specimens were taxonomically identified and organized into groups according to species and study area, and total RNA was extracted for NGS analysis. Short sequences were quality-assessed, assembled using MEGAHIT to obtain contigs, and classified using DIAMOND-MEGAN6 to select viral genomic sequences for phylogenetic analysis. Thirteen viral families were identified, including a virus from the family Rhabdoviridae in Pi. evansi in the department of Cesar and another from the family Dicistroviridae in Lutzomyia gomezi in both departments. Two genome segments of the family Phenuiviridae were found in Lutzomyia gomezi in the department of Córdoba, Colombia. Sand flies harbor a diverse range of viral families, some of which are previously undescribed, and can be studied to determine their taxonomy and assess their potential to infect vertebrate cells or their interactions with medically important pathogens such as Leishmania spp.