Molecular characterization of the Japanese encephalitis virus representative immunotype strain JaGAr 01

We determined the full genomic sequence of the Japanese encephalitis virus JaGAr 01 strain and its predicted amino acid sequence. Nucleotide sequence comparison with ten fully sequenced JE strains shows a homology range from 89.62 to 99.49%. Amino acid sequence homologies range from 96.85 to 99.74%. Comparison of amino acid sequences shows a unique amino acid, arginine, fo r JaGAr 01 at position 123 of the E-protein, while the eight other strains contained serine. Secondary structure prediction by free energy minimizatio n shows a unique structure for JaGAr 01 that includes an RNA segment that i s conserved for all flaviviruses. Speculation is made about the role these results may play in the replication and antigenic characteristics of JaGAr 01. Phylogenetic analyses of the E-protein of JaGAr 01 together with 35 oth er JE strains showed diversity in amino acid characteristics between the pr ototype strains Nakayama, JaGAr 01 and Beijing-l. Phylogenetic trees comput ed by neighbor joining and Fitch-Margoliash analysis of nucleic acid and pr otein sequences showed Nakayama and Beijing in one cluster different from J aGAr 01. (C) 1999 Published by Elsevier Science B.V. All rights reserved.