A Comparison of the Nucleotide Sequences of Eastern and Western Equine Encephalomyelitis Viruses with Those of Other Alphaviruses and Related RNA Viruses

Scott Weaver, Amy Hagenbaugh, Liz Anne Bellew, Sergey V. Netesov, Victor E. Volchkov, Gwong Jen J Chang, David K. Clarke, Laurent Gousset, Thomas W. Scott, Dennis W. Trent, John J. Holland

Research output: Contribution to journalArticle

73 Citations (Scopus)

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 WE E 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.

Original languageEnglish (US)
Pages (from-to)375-390
Number of pages16
JournalVirology
Volume197
Issue number1
DOIs
StatePublished - Nov 1993
Externally publishedYes

Fingerprint

Western Equine Encephalitis Viruses
Eastern equine encephalitis virus
Alphavirus
Eastern Equine Encephalomyelitis
RNA Viruses
Genome
Nucleotides
Codon
Venezuelan Equine Encephalitis Viruses
Yellow fever virus
Semliki forest virus
Genes
Viruses
Plant Viruses
Poliovirus
Terminator Codon
Capsid
Rivers
Genetic Recombination
Insects

ASJC Scopus subject areas

  • Infectious Diseases
  • Virology

Cite this

A Comparison of the Nucleotide Sequences of Eastern and Western Equine Encephalomyelitis Viruses with Those of Other Alphaviruses and Related RNA Viruses. / Weaver, Scott; Hagenbaugh, Amy; Bellew, Liz Anne; Netesov, Sergey V.; Volchkov, Victor E.; Chang, Gwong Jen J; Clarke, David K.; Gousset, Laurent; Scott, Thomas W.; Trent, Dennis W.; Holland, John J.

In: Virology, Vol. 197, No. 1, 11.1993, p. 375-390.

Research output: Contribution to journalArticle

Weaver, S, Hagenbaugh, A, Bellew, LA, Netesov, SV, Volchkov, VE, Chang, GJJ, Clarke, DK, Gousset, L, Scott, TW, Trent, DW & Holland, JJ 1993, 'A Comparison of the Nucleotide Sequences of Eastern and Western Equine Encephalomyelitis Viruses with Those of Other Alphaviruses and Related RNA Viruses', Virology, vol. 197, no. 1, pp. 375-390. https://doi.org/10.1006/viro.1993.1599
Weaver, Scott ; Hagenbaugh, Amy ; Bellew, Liz Anne ; Netesov, Sergey V. ; Volchkov, Victor E. ; Chang, Gwong Jen J ; Clarke, David K. ; Gousset, Laurent ; Scott, Thomas W. ; Trent, Dennis W. ; Holland, John J. / A Comparison of the Nucleotide Sequences of Eastern and Western Equine Encephalomyelitis Viruses with Those of Other Alphaviruses and Related RNA Viruses. In: Virology. 1993 ; Vol. 197, No. 1. pp. 375-390.
@article{a79f0b843151469a9e49dd57046a1817,
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 WE E 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.",
author = "Scott Weaver and Amy Hagenbaugh and Bellew, {Liz Anne} and Netesov, {Sergey V.} and Volchkov, {Victor E.} and Chang, {Gwong Jen J} and Clarke, {David K.} and Laurent Gousset and Scott, {Thomas W.} and Trent, {Dennis W.} and Holland, {John J.}",
year = "1993",
month = "11",
doi = "10.1006/viro.1993.1599",
language = "English (US)",
volume = "197",
pages = "375--390",
journal = "Virology",
issn = "0042-6822",
publisher = "Academic Press Inc.",
number = "1",

}

TY - JOUR

T1 - A Comparison of the Nucleotide Sequences of Eastern and Western Equine Encephalomyelitis Viruses with Those of Other Alphaviruses and Related RNA Viruses

AU - Weaver, Scott

AU - Hagenbaugh, Amy

AU - Bellew, Liz Anne

AU - Netesov, Sergey V.

AU - Volchkov, Victor E.

AU - Chang, Gwong Jen J

AU - Clarke, David K.

AU - Gousset, Laurent

AU - Scott, Thomas W.

AU - Trent, Dennis W.

AU - Holland, John J.

PY - 1993/11

Y1 - 1993/11

N2 - 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 WE E 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.

AB - 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 WE E 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.

UR - http://www.scopus.com/inward/record.url?scp=0027358384&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=0027358384&partnerID=8YFLogxK

U2 - 10.1006/viro.1993.1599

DO - 10.1006/viro.1993.1599

M3 - Article

VL - 197

SP - 375

EP - 390

JO - Virology

JF - Virology

SN - 0042-6822

IS - 1

ER -