Complete genomic RNA sequence of western equine encephalitis virus and expression of the structural genes

• Published in: Journal of general virology 2000-01, Vol.81 (1), p.151-159
• Main Authors: Netolitzky, Donald J, Schmaltz, Fay L, Parker, Michael D, Rayner, George A, Fisher, Glen R, Trent, Dennis W, Bader, Douglas E, Nagata, Les P
• Format: Article
• Language: English
• Subjects: 5' Untranslated Regions - genetics; Base Sequence; Cell Line; Eastern equine encephalitis virus; Encephalitis Virus, Western Equine - genetics; Encephalitis Virus, Western Equine - growth & development; Gene Expression Profiling; Genes, Viral; Genome, Viral; Molecular Sequence Data; NS1 protein; NS4 protein; Phylogeny; Reverse Transcriptase Polymerase Chain Reaction; RNA, Ribosomal - genetics; RNA, Viral - genetics; Sequence Analysis, DNA; Viral Nonstructural Proteins - genetics; Viral Structural Proteins - genetics; Western equine encephalitis virus
• ISSN: 0022-1317; 1350-0872; 1465-2099; 1465-2080
• DOI: 10.1099/0022-1317-81-1-151

Defence Research Establishment Suffield, Medical Countermeasures Section, PO Box 4000 Station Main, Medicine Hat, Alberta, Canada T1A 8K6 1 Virology Division, US Army Medical Research Institute for Infectious Diseases, Fort Detrick, Frederick, MD, USA 2 Regulatory Division, Pasteur Merieux Connaught, Swiftwater, PA, USA 3 Author for correspondence: Les Nagata. Fax [phone]. e-mail les.nagata{at}dres.dnd.ca The complete nucleotide sequence of the 71V-1658 strain of western equine encephalitis virus (WEE) was determined (minus 25 nucleotides from the 5' end). A 5' RACE reaction was used to sequence the 5' terminus from WEE strain CBA87. The deduced WEE genome was 11508 nucleotides in length, excluding the 5' cap nucleotide and 3' poly(A) tail. The nucleotide composition was 28% A, 25% C, 25% G and 22% U. Comparison with partial WEE sequences of strain 5614 (nsP2–nsP3 of the nonstructural region) and strain BFS1703 (26S structural region) revealed comparatively little variation; a total of 149 nucleotide differences in 8624 bases (1·7% divergence), of which only 28% (42 nucleotides) altered the encoded amino acids. Comparison of deduced nsP1 and nsP4 amino acid sequences from WEE with the corresponding proteins from eastern equine encephalitis virus (EEE) yielded identities of 84·9 and 83·8%, respectively. Previously uncharacterized stem–loop structures were identified in the nontranslated terminal regions. A cDNA clone of the 26S region encoding the structural polyprotein of WEE strain 71V-1658 was placed under the control of a cytomegalovirus promoter and transfected into tissue culture cells. The viral envelope proteins were functionally expressed in tissue culture, as determined by histochemical staining with monoclonal antibodies that recognize WEE antigens, thus, forming the initial step in the investigation of subunit vaccines to WEE.