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Home / Equine Research Bank / Virology / The full-length nucleotide sequences of the virulent Trinida...
Virology1989; 170(1); 19-30; doi: 10.1016/0042-6822(89)90347-4

The full-length nucleotide sequences of the virulent Trinidad donkey strain of Venezuelan equine encephalitis virus and its attenuated vaccine derivative, strain TC-83.

Abstract: Nucleotide sequence analysis of cDNA clones covering the entire genomes of Trinidad donkey (TRD) Venezuelan equine encephalitis (VEE) virus and its vaccine derivative, TC-83, has revealed 11 differences between the genomes of TC-83 virus and its parent. One nucleotide substitution and a single nucleotide deletion occurred in the 5'- and 3'-noncoding regions of the TC-83 genome, respectively. The deduced amino acid sequences of the nonstructural polypeptides of the two viruses differed only in a conservative Ser(TRD) to Thr(TC-83) substitution in nonstructural protein (nsP) three at amino acid position 260. The two silent mutations (one each in E1 and E2), one amino acid substitution in the E1 glycoprotein, and five substitutions in the E2 envelope glycoprotein of TC-83 virus were reported previously (B.J.B. Johnson, R.M. Kinney, C.L. Kost, and D.W. Trent, 1986, J. Gen. Virol. 67, 1951-1960). The genome of TRD virus was 11,444 nucleotides long with a 5'-noncoding region of 44 nucleotides. The carboxyl terminal portion of VEE nsP3 contained two peptide segments (7 and 34 amino acids long) that were repeated with high fidelity. The open reading frame of the nonstructural polyprotein was interrupted by an in-frame opal termination codon between nsP3 and nsP4, as has been reported for Sindbis, Ross River, and Middelburg viruses. The deduced amino acid sequences of the VEE TRD nsP1, nsP2, nsP3, and nsP4 polypeptides showed 60-66%, 57-58%, 35-44%, and 73-71% identity with the aligned sequences of the cognate polypeptides of Sindbis and Semliki Forest viruses, respectively. The lack of homology in the nsP3 of the viruses is due to sequence variation in the carboxyl terminal half of this polypeptide.
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Publication Date: 1989-05-01 PubMed ID: 2524126DOI: 10.1016/0042-6822(89)90347-4Google Scholar: Lookup
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  • Comparative Study
  • Journal Article
  • Research Support
  • U.S. Gov't
  • Non-P.H.S.

Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

This research studied the full DNA sequences of a strain of the Trinidad donkey Venezuelan equine encephalitis virus and its TC-83 vaccine variant, identifying 11 differences between their genomes, including various substitutions and mutations.

Identified Differences in Genome

  • The researchers sequenced the complete genomes of the Trinidad donkey strain of the Venezuelan equine encephalitis virus and its vaccine derivative, strain TC-83.
  • In the process, they discovered a total of 11 differences between the two genomes. This included nucleotide substitutions and deletions, as well as singular and multiple amino acid substitutions.

Specific Changes in Genome

  • Specifically, there was a single nucleotide substitution and a single nucleotide deletion in the noncoding regions of the TC-83 genome.
  • The nonstructural proteins of the two viruses were almost identical barring a single conservative amino acid substitution in the nonstructural protein three.
  • Other mutations identified included two silent mutations in E1 and E2, an amino acid substitution in the E1 glycoprotein, and five substitutions in the E2 envelope glycoprotein of the TC-83 virus. These changes were previously reported in earlier studies.

TRD Virus Genome and Proteins

  • The analysis also revealed that the genome of the Trinidad Donkey (TRD) virus was 11,444 nucleotides long and had a noncoding region of 44 nucleotides.
  • The research also identified that the carboxyl terminal segment of the virus’s nonstructural protein 3 (nsP3) included two parts that were repeated with high fidelity.
  • The nonstructural polyprotein’s open reading frame was interrupted by an in-frame termination codon between nsP3 and nsP4, similar to Sindbis, Ross River, and Middelburg viruses.
  • Comparing the amino acid sequences of the nonstructural proteins of the VEE TRD virus to that of Sindbis and Semliki Forest viruses revealed percent identity ranges from 35% to 66%. The lowest homology was found in nsP3 due to sequence variation in the carboxyl terminal half of this polypeptide.

Significance of the Study

  • This research will help in understanding the fundamental DNA differences between the virulent strain of the Venezuelan equine encephalitis virus and its vaccine variant. This can aid in the development or improvement of vaccines for this and possibly other viruses.

Cite This Article

APA
Kinney RM, Johnson BJ, Welch JB, Tsuchiya KR, Trent DW. (1989). The full-length nucleotide sequences of the virulent Trinidad donkey strain of Venezuelan equine encephalitis virus and its attenuated vaccine derivative, strain TC-83. Virology, 170(1), 19-30. https://doi.org/10.1016/0042-6822(89)90347-4

Publication

Virology
ISSN: 0042-6822
NlmUniqueID: 0110674
Country: United States
Language: English
Volume: 170
Issue: 1
Pages: 19-30

Researcher Affiliations

Kinney, R M
  • Division of Vector-Borne Viral Diseases, Centers for Disease Control, Fort Collins, Colorado.
Johnson, B J
    Welch, J B
      Tsuchiya, K R
        Trent, D W

          MeSH Terms

          • Amino Acid Sequence
          • Animals
          • Base Sequence
          • Capsid / genetics
          • Encephalitis Virus, Venezuelan Equine / genetics
          • Genes, Viral
          • Molecular Sequence Data
          • Perissodactyla / microbiology
          • RNA, Viral / genetics
          • Viral Core Proteins / genetics
          • Viral Nonstructural Proteins
          • Viral Vaccines / genetics

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