COMPLETE NUCLEOTIDE-SEQUENCE OF THE GENOME OF JAPANESE ENCEPHALITIS-VIRUS LING STRAIN - THE PRESENCE OF A 25-NUCLEOTIDE DELETION IN THE 3'-NONTRANSLATED REGION

The complete sequence of the genome of the Japanese encephalitis virus (JEV) Ling strain isolated from the brain of a patient in Taiwan in 1 965 was cloned by using the reverse transcription-polymerase chain rea ction method. Seven overlapping cDNA clones that span the entire virus genome were isolated and sequenced to determine the complete nucleoti de sequence, which is 10,951 nucleotides in length. As reported for th ree other JEV strains (Beijing-1, SA-14, and JaOArS982), the Ling stra in contains 95 nucleotides in the 5' nontranslated region (NTR), follo wed by a single open reading frame of 10,296 nucleotides. However, the length of the 3' NTR of JEV Ling is 560 nucleotides, 25 nucleotides s horter than that of other JEV strains sequenced to date. Comparison of nucleotide and amino acid sequences among these four JEV strains show ed that nucleotide (amino acid) sequence divergence in the translated region varied from 1.25% to 3.27% (0.49-1.63%). The nucleotide (amino acid) divergences between the Ling and Beijing-l strains were 1.25% (0 .87%) and between the SA-14 and JaOArS982 strains were 1.42% (0.49%). These values are lower than those found between the Ling and SA-14 [2. 44% (1.02%)] or the Ling and JaOArS982 strains [2.84% (0.93%)], as wel l as those between Beijing-l and SA-14 [3.14% (1.60%)] or Beijing-l an d JaOArS982 [3.27% (1.63%)] strains. Sequence comparisons of subregion s of the genomes i.e., structural genes, nonstructural genes, or indiv idual genes, showed divergence similar to that obtained by comparing t he entire sequence. It is likely that the JEV sequence divergence betw een two human isolates or between two mosquito isolates is lower than that between a human isolate and a mosquito isolate.