Journal of Microbiology

The Microbiological Society of Korea (한국미생물학회)
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Molecular Phylogenetic Analysis of HIV -1 vif Gene from Korean Isolates

  • Park, Chan-Seung (School of Life Sciences, Chungbuk National University) ;
  • Kim, Mi-Sook (School of Life Sciences, Chungbuk National University) ;
  • Lee, Sung-Duk (Department of Statistics, Chungbuk National University) ;
  • Kim, Sung-Soo (School of Electrical and Computer Engineering, Chungbuk National University) ;
  • Lee, Keon-Myung (School of Electrical and Computer Engineering, Chungbuk National University) ;
  • Lee, Chan-Hee (School of Life Sciences, Chungbuk National University)
  • Published : 2006.12.31
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Abstract

Phylogenetic studies of nef, pol, and env gene sequences of HIV-1 isolated from Koreans suggested the presence of a Korean clade in which Korean sequences are clustered to the exclusion of foreign sequences. We attempted to identify and characterize the Korean clade using all vif gene sequences isolated from Koreans registered in the NCBI GenBank database (n = 233). Most (77 %) of the Korean isolates belonged to the Korean clade as a large subcluster in subtype B, designated the Korean clade subtype B ($K_{C}B$). $K_{C}B$ sequences were relatively homogenous compared to Korean subtype B sequences that did not belong to the $K_{C}B$ (non-Korean clade subtype B; $NK_{C}B$). Comparison of amino acid frequencies of $K_{C}B$ and $NK_{C}B$ sequences revealed several positions where the amino acid frequencies were significantly different. These amino acid residues were critical in separating $K_{C}B$ from $NK_{C}B$ or from foreign sequences, since substitution of these amino acids in $K_{C}B$ with the $NK_{C}B$ amino acids relocated the $K_{C}B$ sequences to $NK_{C}B$, and vice versa. Further analyses of $K_{C}B$ will help us to understand the origin and evolutionary history of $K_{C}B$.

Keywords

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