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West Nile virus is a mosquito borne flavivirus endemic over a large geographic area including Africa, Asia, and the Middle East. Although the virus generally causes a mild, self-limiting febrile illness in humans, it has sporadically caused central nervous system infections during epidemics. An isolate of West Nile virus was obtained from a pool of four male Culex univittatus complex mosquitoes while we were conducting an investigation of Rift Valley fever along the Kenya-Uganda border in February-March 1998. This represents the first field isolation of West Nile virus from male mosquitoes and strongly suggests that vertical transmission of the virus occurs in the primary maintenance mosquito vector in Kenya. A phylogenetic analysis of the complete amino acid sequence of the viral envelope glycoprotein demonstrated a sister relationship with a Culex pipiens mosquito isolate from Romania made in 1996. This unexpected finding probably reflects the role of migratory birds in disseminating West Nile virus between Africa and Europe.