[Molecular characterization of full-length genome of Japanese encephalitis virus strain patient's cerebrospinal fluid in China].
OBJECTIVE
To sequence and analyze the whole genome of Japanese encephalitis virus (JEV) strain named 47 which was isolated from patient's cerebrospinal fluid sample in Heilongjiang province in 1950.


METHODS
RNA was extracted from the recovery strain 47 and amplified with self-designed JEV genome sequencing primers. The differentiation analysis for nucleotides and coding amino acids and phylogenetic analysis were performed by the software of DNAStar, Modeltest, and Phylip.


RESULTS
The whole genome of strain 47 has 10,977 nucleotides. An open reading frame from 95 to 10,391 including 10,296 nucleotides is capable of coding a 3432 amino acid polyprotein. The nucleotide difference between strain 47 and 5 vaccine strains is 2.4%-4.4%, the amino acid difference between strain 47 and 5 vaccine strains is 0.3%-1.1%. The best evolution model for the whole genome is GTR + I + G. Based on the phylogenetic analysis, strain 47 belongs to the genotype III JEV.


CONCLUSIONS
Strain 47 is highly conserved on whole genome nucleotide and amino acid sequence. And it is belongs to the genotype III JEV.
Institution for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Bejing 100052, China.
Xiao-Ling
XL
Pan
Huan-Yu
HY
Wang
Shi-Hong
SH
Fu
Na
N
Hian
Hai-Zhou
HZ
Liu
Simon
S
Rayner
Guo-Dong
GD
Hang
D002681:China; D004664:Encephalitis Virus, Japanese / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D004672:Encephalitis, Japanese / Q000821:virology*; D016679:Genome, Viral; D006801:Humans; D008969:Molecular Sequence Data; D016366:Open Reading Frames; D010802:Phylogeny; D012367:RNA, Viral / Q000134:cerebrospinal fluid* / Q000235:genetics / Q000302:isolation & purification
D012367:RNA, Viral