Journal of Microbiology

Chan Seung Park

3 Articles

Characterization and Signature Pattern Analysis of Korean Clade HIV-1 Using nef Gene Sequences: Chan Seung Park , Dong Hun Lee , Keon Myung Lee , Chan-Hee Lee; J. Microbiol. 2008;46(1):88-94.; DOI: https://doi.org/10.1007/s12275-007-0156-x

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Phylogenetic studies of the HIV-1 gene sequences isolated from Korean patients have suggested that most of Korean isolates belong to the subtype B strain. This study aims to characterize the Korean clade by molecular phylogenetic analysis using all of the Korean nef gene sequences registered in the NCBI GenBank (N=422), in addition to 41 reference strains and 94 foreign isolates. Through phylogenetic analyses, we verified that most of the Korean isolates belonged to the subtype B, where 78.8% are clustered exclusively of foreign isolates. This cluster has been named the Korean clade subtype B (KCB) in order to distinguish it from other subtype B clusters. Genetic distance analysis suggested that the KCB cluster was more homogeneous and clearly distinctive from the non-Korean clade subtype B (NKCB). Comparison of consensus amino acid sequences from KCB and NKCB revealed that characteristic KCB signature amino acid patterns composed of 11 amino acid residues, whose frequencies in the KCB were significantly higher than in the NKCB. The KCB signature amino acid residues were critical in identifying KCB from NKCB, since substitution of the NKCB sequences with KCB signature amino acids relocated them to the Koran clade, and vice versa.

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Sequence Length of HIV-1 Subtype B Increases over Time: Analysis of a Cohort of Patients with Hemophilia over 30 Years
Young-Keol Cho, Jung-Eun Kim, Brian T. Foley
Viruses.2021; 13(5): 806. CrossRef
Characterization and phylogenetic analysis of Varicella-zoster virus strains isolated from Korean patients
Min Ho Kim, Jeong Seon Jeon, In Kyo Kim, Ji Seon Park, Hosun Park, Ok Sarah Shin, Chan Hee Lee
Journal of Microbiology.2017; 55(8): 665. CrossRef
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
The Journal of Microbiology.2009; 47(1): 85. CrossRef

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]

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Abstract PDF: 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]

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Abstract PDF: 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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