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Published March 1990 | public
Journal Article

Complete sequence of the genomic RNA of O'Nyong-Nyong virus and its use in the construction of alphavirus phylogenetic trees


The alphaviruses are a group of about 25 positive-strand RNA viruses that are important human and veterinary pathogens and that are geographically dispersed. We report here the complete nucleotide sequence of the genomic RNA of the alphavirus, O'nyong-nyong virus. The RNA is 11,835 nucleotides in length and the organization of the genome is typical of alphaviruses. Phylogenetic trees were constructed from the protein sequences of O'nyong-nyong and six other alphaviruses. Trees were constructed for each nonstructural and structural viral protein individually in order to detect any possible recombination events, as well as to examine the differential divergence among the various proteins. The members of each tree can be divided into three subgroups: the Semliki Forest virus subgroup (Semliki Forest, O'nyong-nyong, and Ross River viruses), the eastern equine encephalitis virus subgroup (eastern equine encephalitis and Venezuelan equine encephalitis viruses), and the Sindbis virus subgroup. Sindbis virus, which is geographically restricted to the Old World, is more closely related to the eastern equine encephalitis subgroup, which are New World viruses, than it is to the Semliki Forest virus subgroup, which are mostly Old World viruses. Western equine encephalitis virus is a special case because it is a recombinant virus. Its nonstructural and capsid proteins are most closely related to those of eastern equine encephalitis virus while its glycoproteins are most closely related to those of Sindbis virus. All members of a given subgroup have diverged the same amount from their common node point. However, the structural proteins of the Semliki Forest virus subgroup are more closely related to one another than those of the eastern equine encephalitis virus subgroup. This difference probably indicates that the members of the eastern equine encephalitis virus subgroup diverged earlier than the members of the Semliki Forest virus subgroup, which suggests that the alphaviruses originated in the New World.

Additional Information

© 1990 Academic Press, Inc. Received September 29, 1989; accepted November 14, 1989. We thank J. Dalrymple for kindly supplying us with O'nyong-nyong virus RNA and with the Mayaro virus sequence prior to its publication, E. Lenches for her expert technical assistance, and C. Hahn for all his help and advice during the sequencing. We also thank T. Hunkapiller and L. Hood for their advice and the use of their computer facilities. Finally, we give special thanks to G. Zabetakis, D.-F. Feng, and R. Doolittle for their kind cooperation in the generation of the trees for the structural proteins and the use of their facilities. This work was supported by Grants AI 10793 and AI 20612 from the National Institutes of Health and Grant DMB 86-17372 from the National Science Foundation.

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