Re-emergence of chikungunya and o'nyong-nyong viruses: evidence for distinct geographical lineages and distant evolutionary relationships

Chikungunya (CHIK) virus is a member of the genus Alphavirus in the family Togaviridae, Serologically, it is most closely related to o'nyong-nyong (ON N) virus and is a member of the Semliki Forest antigenic complex. CHIK viru s is believed to be enzootic throughout much of Africa and historical evide nce indicates that it spread to other parts of the world from this origin. Strains from Africa and Asia are reported to differ biologically, indicatin g that distinct lineages may exist. To examine the relatedness of CHIK and ONN viruses using genetic data, we conducted phylogenetic studies on isolat es obtained throughout Africa and Southeast Asia. Analyses revealed that ON N virus is indeed distinct from CHIK viruses, and these viruses probably di verged thousands of years ago. Two distinct CHIK virus lineages were deline ated, one containing all isolates from western Africa and the second compri sing all southern and East African strains, as well as isolates from Asia. Phylogenetic trees corroborated historical evidence that CHIK virus origina ted in Africa and subsequently was introduced into Asia. Within the eastern Africa and southern Africa/Asia lineage, Asian strains grouped together in a genotype distinct from the African groups. These different geographical genotypes exhibit differences in their transmission cycles: in Asia, the vi rus appears to be maintained in an urban cycle with Aedes aegypti mosquito vectors, while CHIK virus transmission in Africa involves a sylvatic cycle, primarily with Ae. furcifer and Ae. africanus mosquitoes.