Journal of Microbiology

Chan-Hee Lee

6 Articles

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

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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.

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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
Genetic Analysis of the Full-Length gag Gene from the Earliest Korean Subclade B of HIV-1: An Outbreak among Korean Hemophiliacs
Young-Keol Cho, Jung-Eun Kim, Brian T. Foley
Viruses.2019; 11(6): 545. CrossRef
Phylogenetic and Temporal Dynamics of Human Immunodeficiency Virus Type 1B in China: Four Types of B Strains Circulate in China
Jingrong Ye, Hongyan Lu, Xueli Su, Ruolei Xin, Lishi Bai, Ke Xu, Shuangqing Yu, Xia Feng, Hong Yan, Xiong He, Yi Zeng
AIDS Research and Human Retroviruses.2014; 30(9): 920. CrossRef
The origin and diversity of the HIV-1 pandemic
Joris Hemelaar
Trends in Molecular Medicine.2012; 18(3): 182. CrossRef
Full Genome Analysis of an Emerging Cluster of Human Immunodeficiency Virus Type 1 Subtype B Infection in Hong Kong
Stephen K.W. Tsui, Nga-Yin Fong, Sai-Kam Li, Ka-Kit Leung, Denise P.C. Chan, Paul K.S. Chan, Ka-Hing Wong, Shui-Shan Lee
AIDS Research and Human Retroviruses.2010; 26(1): 117. CrossRef

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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Abstract PDF

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

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.

Phylogenetic Analysis of the HIV-1 nef Gene from Korean Isolates: Dong-Hun Lee , Yeup Yoon , Chan-Hee Lee; J. Microbiol. 2003;41(3):232-238.

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Abstract PDF: Previous phylogenetic studies on human immunodeficiency virus type 1 (HIV-1) isolated from Korean patients suggest that the major subtype of Korean isolate is subtype B. In this subtype, some of the Korean isolates seem to be clustered exclusively of foreign isolates. Presence of this so-called “Korean clade” among Korean isolates is unique but needs verification since the number of Korean isolates used in previous studies was limited. This study aimed to identify the presence of the “Korean clade” by molecular phylogenetic analysis using all the Korean nef gene sequences registered in the NCBI GenBank (N=243) together with 32 reference strains and 77 foreign isolates. Extensive analysis of the nef gene nucleotide sequences by neighbor-joining method revealed the following. Most (83.1%) of the Korean isolates belonged to subtype B, and 81.2% of subtype B were clustered together and excluded foreign isolates (bootstrap value=91.9%). Within Korean subtype B cluster, no characteristic subcluster formation was evident since the bootstrap values for the subcluster were very low. Due to limited information, the phylogenetic analysis failed to identify the epidemiological linkage among specific groups such as homosexuals and hemophiliacs within the Korean subtype B cluster. Detailed analysis and epidemiological information are needed to clarify the origin and significance of the Korean subtype B cluster.

Measurement of Antiviral Activities Using Recombinant Human Cytomegalovirus: Byung-Hak Song , Gyu-Cheol Lee , Chan-Hee Lee; J. Microbiol. 2000;38(4):255-259.

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Abstract PDF: For rapid and sensitive measurement of antiviral activities, application of a recombinant virus containing firefly luciferase gene was attempted. Recombinant human cytomegalovirus (HCMV) containing luciferase gene driven by HCMV late gene pp28 promoter (HCMV/pp28-luc) was used to test the antiviral activities of three known compounds and the result was compared with results from the conventional plaque assay for measuring the production of infectious viruses. When human fibroblast cells were infected with HCMV/pp28-luc, luciferase activity was observed at 2 days after infection and reached maximum at 6 days after infection, whereas the production of infectious virus was maximal at 4 days after infection. The antiviral activities of ganciclovir, acyclovir, and papaverine were measured in HFF cells infected with HCMV/pp28-luc and the luciferase activity was compared with the infectious virus titers. Luciferase activity decreased as the concentration of ganciclovir or papaverine increased, while there was a slight decrease in luciferase activity with acyclovir. The level of the decrease in luciferase activity was comparable to the level of decrease in the production of infectious virus. Therefore, the antiviral assay using recombinant virus HCMV/pp28-luc resulted in sensitivity similar to the conventional plaque assay with a significant reduction in assay time.

Expression of Human Cytomegalovirus Immediate Early US3 Gene in Human Fibroblast Cells: Gyu-Cheol Lee , Chong-Kyo Lee , Jin-Hyun Ahn , Chan-Hee Lee; J. Microbiol. 2000;38(1):24-30.

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Abstract PDF: US3 gene is a member of the human cytomegalovirus (HCMV) immediate early gene. Although the precise functions of the US3 gene in HCMV replication and pathogenesis are not known, it has been reported to play a role in inhibiting major histocompatibility class I antigen presentation. For further knowledge of US3 gene expression, rabbit polyclonal antiserum of the US3 gene product was used for indirect immunofluorescence assay. In permissive human foreskin fibroblast (HFF) cells, US3 gene expression was detectable as crescent or half-moon shape in the perinuclear region at immediate early times after virus infection. HFF cells infected with mutant HCMV lacking US3 open reading frames were negative for US3 immunofluorescence assay. Double immunofluorescence assay using monoclonal antibody to gamma adaptin (specific for the Golgi complex) and rabbit anti-US3 antiserum revealed that US3 gene product could be localized to the Golgi complex. At later time after HCMV infection, US3 gene products were detected as globular aggregates in the cytosol. These aggregates were positive for gamma adaptin and stained with preimmune serum, suggesting a nonspecific reaction to the Golgi complex. Northern blot analysis revealed that transcription of US3 was observed only during immediate early times after virus infection (until 6 h postinfection). Therefore US3 gene expression appears to be confined to immediate early time and its gene products are localized to the Golgi complex as cres-cent shaped forms in the perinuclear cytoplasm.

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