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Virus Genes

, Volume 24, Issue 1, pp 21–27 | Cite as

High Level of Sequence Variation in the 3′ Noncoding Region of Japanese Encephalitis Viruses Isolated in Korea

  • Jae-Hwan Nam
  • Soo-Lim Chae
  • Sun-Hee Park
  • Yong-Seok Jeong
  • Myung-Soo Joo
  • Chil-Yong Kang
  • Hae-Wol ChoEmail author
Article

Abstract

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.

Japanese encephalitis virus 3′ NCR variable region 

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Copyright information

© Kluwer Academic Publishers 2002

Authors and Affiliations

  • Jae-Hwan Nam
    • 1
    • 2
    • 3
  • Soo-Lim Chae
    • 1
    • 2
    • 3
  • Sun-Hee Park
    • 1
    • 2
    • 3
  • Yong-Seok Jeong
    • 1
    • 2
    • 3
  • Myung-Soo Joo
    • 1
    • 2
    • 3
  • Chil-Yong Kang
    • 1
    • 2
    • 3
  • Hae-Wol Cho
    • 1
    • 2
    • 3
    Email author
  1. 1.Department of VirologyKorea National Institute of HealthSeoulKorea
  2. 2.Department of BiologyKyung Hee UniversitySeoulKorea
  3. 3.Siebens-Drake Research InstituteThe University of Western OntarioLondonCanada

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