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400 Å diameter nucleocapsid, is penetrated by 80 spikes arranged in a T = 4 lattice. Each spike is a trimer of heterodimers consisting of glycoproteins Ell and E2. Cryoelectron microscopy and image reconstruction of Ross River virus showed that the T=4 quaternary structure of the nucleocapsid consists of pentamerand hexamer clusters of the capsid protein, but not dimers, as have been observed in several crystallographic studies. The E1–E2 heterodimers form one-to-one associations with the nucleocapsid monomers across the lipid bilayer. Knowledge of the atomic structure of the capsid protein and our reconstruction allows us to identify capsid-protein residues that interact with the RNA, the glycoproteins, and adjacent capsid-proteins.
doi:10.1016/0042-6822(90)90191-S 
Copyright © 1990 Published by Elsevier Science (USA).
Complete sequence of the genomic RNA of O'Nyong-Nyong virus and its use in the construction of alphavirus phylogenetic trees
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Randy S. Levinson1, James H. Strauss
and Ellen G. Strauss
Received 29 September 1989;
Abstract
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.
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Corresponding author. To whom requests for reprints should be addressed.
1 Current address: Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94143.
