Journal of Microbiology

Research Support, Non-U.S. Gov'ts

Timing and Evolution of the Most Recent Common Ancestor of the Korean Clade HIV Subtype B Based on Nef and Vif Sequences: Mi-Suk Kim , So-Young Jang , Chan-Seung Park , Keon-Myung Lee , Dong-Hun Lee , Chan-Hee Lee; J. Microbiol. 2009;47(1):85-90. Published online February 20, 2009; DOI: https://doi.org/10.1007/s12275-008-0240-x

Abstract: Molecular phylogenetic studies of the HIV-1 isolated from Koreans have suggested the presence of the so- called “Korean clade”, which can be defined as a cluster free of foreign isolates. The Korean clade accounts for more than 60% of Korean isolates and exerts characteristic amino acid sequences. Thus, it is merited to estimate when this Korean clade first emerged in order to understand the evolutionary pattern of the Korean clade. We analyzed and reconstructed the most recent common ancestor (MRCA) sequences from nef (n=229) and vif (n=179) Korean clade sequences. Linear regression analyses of sequence divergence estimates were plotted against sampling years to infer the year in which there was zero divergence from the MRCA sequences. MRCA sequences suggested the Korean clade was first emerged around 1984, before the first detection of HIV-1 in Korea in 1985. Further studies on synonymous and nonsynonymous substitution rates suggested positive selection event for the Korean clade, while other subtype B had undergone negative to neutral evolution.

Analysis of Substitution Events in HIV-1 vif Gene of the Korean Clade: Chan Seung Park , Mi Sook Kim , Hyun Ah Yi , Dong Hun Lee , Keon Myung Lee , Chan Hee Lee; J. Microbiol. 2007;45(1):75-78.; DOI: https://doi.org/2487 [pii]

Abstract: Nucleotide and amino acid substitution pattern in vif gene of the Korean clade of HIV-1 isolated from Koreans were analyzed using consensus sequences. At nucleotide level, transition/transversion substitution ratio was 1.88, and nonsynonymous/synonymous substitution ratio was 2.67, suggesting a divergent <br>evolution in the Korean clade. At amino acid level, there were 17 substitutions and G→E substitution at position 37 may be responsible for change in predicted secondary structure.

Molecular Phylogenetic Analysis of HIV-1 vif Gene from Korean Isolates: Chan Seung Park , Mi Sook Kim , Sung Duk Lee , Sung Soo Kim , Keon Myung Lee , Chan-Hee Lee; J. Microbiol. 2006;44(6):655-659.; DOI: https://doi.org/2461 [pii]

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 (KCB). KCB sequences were relatively homogenous compared to Korean subtype B sequences that did not belong to the KCB (non-Korean clade subtype B; NKCB). Comparison of amino acid frequencies of KCB and NKCB sequences revealed several positions where the amino acid frequencies were significantly different. These amino acid residues were critical in separating KCB from NKCB or from foreign sequences, since substitution of these amino acids in KCB with the NKCB amino acids relocated the KCB sequences to NKCB, and vice versa. Further analyses of KCB will help us to understand the origin and evolutionary history of KCB.

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