High level of sequence variation in the 3' noncoding region of Japanese encephalitis viruses isolated in Korea.
The 3' noncoding region (NCR) of Japanese encephalitis (JE) viruses isolated in Korea and Nakayama-NIH strain have been sequenced and compared with the 3' NCR sequences of other JE isolates reported previously. Sequence alignment of about 60 nucleotides (based on consensus sequence number) immediately downstream of the open reading frame (ORF) stop codon in the 3' NCR of the Korean isolates showed high degree of sequence variation and deletion; thus, this region was termed as the variable region. However, in the predicted RNA secondary structures, a similar type loop exists at the 5'-terminus of the 3' NCR of JE viruses, despite low level of sequence homology (22%) and deletion in the variable region. The phylogenetic tree based on the 3' NCR sequences of JE viruses including the variable region showed a similar pattern to that based on envelope genes; in that, there are two genetically different types of JE viruses in Korea. Therefore, the variable region would be a useful genetic marker for JE viruses.
Nam
Jae-Hwan
JH
Department of Virology, Korea National Institute of Health, Seoul.
Chae
Soo-Lim
SL
Park
Sun-Hee
SH
Jeong
Yong-Seok
YS
Joo
Myung-Soo
MS
Kang
Chil-Yong
CY
Cho
Hae-Wol
HW
D024509:3' Flanking Region / Q000235:genetics*; D001483:Base Sequence; D004664:Encephalitis Virus, Japanese / Q000235:genetics*; D005819:Genetic Markers; D014644:Genetic Variation; D016679:Genome, Viral; D007723:Korea / Q000453:epidemiology; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D010802:Phylogeny; D022661:RNA, Untranslated / Q000235:genetics; D012367:RNA, Viral / Q000737:chemistry* / Q000235:genetics; D017384:Sequence Deletion
D005819:Genetic Markers; D022661:RNA, Untranslated; D012367:RNA, Viral