Molecular characterization of the first Australian isolate of Japanese encephalitis virus, the FU strain

• Published in: Journal of general virology Vol. 81; no. 10; pp. 2471 - 2480
• Main Authors: Williams, David T, Wang, Lin-Fa, Daniels, Peter W, Mackenzie, John S
• Format: Journal Article
• Language: English
• Published: England Soc General Microbiol 01.10.2000
• Subjects: AE gene; Amino Acid Sequence; Amino Acid Substitution; Australia; Base Sequence; Codon; DNA, Viral - chemistry; E gene; Encephalitis Virus, Japanese - genetics; Encephalitis Virus, Japanese - isolation & purification; Genome, Viral; Genotype; Humans; Japanese encephalitis virus; Molecular Sequence Data; neurovirology; Open Reading Frames; Phylogeny; prM gene; Sequence Alignment; Viral Envelope Proteins - genetics; Australia
• ISSN: 0022-1317; 1465-2099
• DOI: 10.1099/0022-1317-81-10-2471

CSIRO, Australian Animal Health Laboratory, 5 Portarlington Road, Geelong, Victoria 3220, Australia 1 Department of Microbiology and Parasitology, University of Queensland, Brisbane, Queensland 4072, Australia 2 Author for correspondence: David Williams at CSIRO. Fax +61 3 5227 5555. e-mail david.williams{at}dah.csiro.au The complete genomic and predicted amino acid sequence of the Japanese encephalitis virus (JEV) FU strain, a human isolate recovered from the first outbreak of Japanese encephalitis in Australian territory, was determined. Comparison of the FU genome with 15 fully sequenced JEV genomes revealed high levels of sequence identity, ranging from 88·7% (GP78) to 89·7% (K94P05) for nucleotides and 96·8% (K94P05) to 98·0% (JaGAr01) for amino acid sequences. A total of 39 unique amino acid differences were found in the FU strain polyprotein. Phylogenetic analyses were performed on all available full-length JEV genomes and a selection of 64 E gene sequences from temporally and geographically diverse JEV strains. For comparison with the E gene phylogeny, phylogenetic analysis using cognate prM gene sequences was also carried out. The FU strain was found to be most closely related to Korean isolate K94P05 in the full-length analysis and to Southeast Asian strains in the E and prM gene analyses. The E gene analysis corresponded well with the prM gene analysis and with previous genotyping studies using the prM gene. The epidemiological implications of this investigation are discussed.