title: A comparison of the nucleotide sequences of eastern and western equine encephalomyelitis viruses with those of other alphaviruses and related RNA viruses.
abstract: The complete nucleotide sequence of a 1982 Florida strain of eastern equine encephalomyelitis (EEE) virus, and partial sequence of the nonstructural protein genes of western equine encephalomyelitis (WEE) virus, were determined. The EEE virus genome was 11,678 nucleotides in length, excluding the cap nucleotide and poly(A) tail, and the nucleotide composition was 28% A, 24% G, 25% C, and 23% U. The organization of both EEE and WEE virus genomes was like that of other alphaviruses and included a termination codon between the nsP3 and nsP4 genes. Codon usage for 10 of 20 amino acids was nonrandom in the EEE genome, and dinucleotide CpG-containing codons were underutilized in both genomes. The slight CpG deficiency was similar to that seen in other alphaviruses and plant viruses in the alphavirus-like group, but less than that of poliovirus and yellow fever virus. This slight deficiency may reflect adaptation for replication in both CpG-deficient vertebrates, as well as insects which do not have CpG-deficient genomes. Phylogenetic analyses using nonstructural protein amino acid sequences indicated that alphaviruses evolved from a common ancestor which existed a few thousand years ago. An intercontinental introduction of an ancestral virus from the Old to New World, or vice versa, probably resulted in two main extant groups: one includes New World (EEE and Venezuelan equine encephalitis) viruses, while the other includes Old World (Sindbis, Middelburg, O'nyong-nyong, Ross River, and Semliki Forest) viruses. The position of WEE virus in the phylogenetic trees indicated that, in addition to its capsid gene (C. S. Hahn et al. (1988) Proc. Natl. Acad. Sci. USA 85, 5997-6001), WEE virus acquired its nonstructural genes from an EEE-like ancestor during recombination.
authors.affiliation: Department of Biology, University of California, San Diego, La Jolla 92093.
authors.forename: S C
authors.initials: SC
authors.lastname: Weaver
authors.forename: A
authors.initials: A
authors.lastname: Hagenbaugh
authors.forename: L A
authors.initials: LA
authors.lastname: Bellew
authors.forename: S V
authors.initials: SV
authors.lastname: Netesov
authors.forename: V E
authors.initials: VE
authors.lastname: Volchkov
authors.forename: G J
authors.initials: GJ
authors.lastname: Chang
authors.forename: D K
authors.initials: DK
authors.lastname: Clarke
authors.forename: L
authors.initials: L
authors.lastname: Gousset
authors.forename: T W
authors.initials: TW
authors.lastname: Scott
authors.forename: D W
authors.initials: DW
authors.lastname: Trent
mesh_terms: D000524:Alphavirus / Q000737:chemistry / Q000235:genetics*; D000595:Amino Acid Sequence; D000818:Animals; D001483:Base Sequence; D002460:Cell Line; D003001:Cloning, Molecular; D003062:Codon / Q000235:genetics; D009033:Culicidae / Q000382:microbiology; D017931:DNA Primers; D004663:Encephalitis Virus, Eastern Equine / Q000737:chemistry / Q000235:genetics*; D004667:Encephalitis Virus, Western Equine / Q000737:chemistry / Q000235:genetics*; D016679:Genome, Viral; D008969:Molecular Sequence Data; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D012328:RNA Viruses / Q000737:chemistry / Q000235:genetics*; D012367:RNA, Viral / Q000737:chemistry / Q000235:genetics*
chemical_list: D003062:Codon; D017931:DNA Primers; D012367:RNA, Viral