title: Timing and evolution of the most recent common ancestor of the Korean clade HIV subtype B based on nef and vif sequences.
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.
authors.affiliation: School of Life Sciences, Chungbuk National University, Chungbuk 361-763, Republic of Korea.
authors.forename: Mi-Suk
authors.initials: MS
authors.lastname: Kim
authors.forename: So-Young
authors.initials: SY
authors.lastname: Jang
authors.forename: Chan-Seung
authors.initials: CS
authors.lastname: Park
authors.forename: Keon-Myung
authors.initials: KM
authors.lastname: Lee
authors.forename: Dong-Hun
authors.initials: DH
authors.lastname: Lee
authors.forename: Chan-Hee
authors.initials: CH
authors.lastname: Lee
mesh_terms: D004279:DNA, Viral / Q000032:analysis; D019143:Evolution, Molecular; D040961:Genetic Drift; D015658:HIV Infections / Q000235:genetics / Q000821:virology*; D015497:HIV-1 / Q000235:genetics*; D006801:Humans; D007723:Korea; D012044:Regression Analysis; D017422:Sequence Analysis, DNA; D013997:Time Factors; D054311:nef Gene Products, Human Immunodeficiency Virus / Q000235:genetics*; D054320:vif Gene Products, Human Immunodeficiency Virus / Q000235:genetics*
chemical_list: D004279:DNA, Viral; D054311:nef Gene Products, Human Immunodeficiency Virus; C514837:nef protein, Human immunodeficiency virus 1; D054320:vif Gene Products, Human Immunodeficiency Virus; C514847:vif protein, Human immunodeficiency virus 1