Phylogenetic analysis of the nef gene reveals a distinctive monophyletic clade in Korean HIV-1 cases
To study the genetic variation of the HIV-1 strains prevalent in South Korea, we analyzed the nef sequences derived from 46 HIV-1-positive individuals living in various geographic regions in Korea. Phylogenetic analysis revealed four subtypes of HIV-1: A (3 patients), B (41 patients), D (1 patient),...
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| Veröffentlicht in: | Journal of acquired immune deficiency syndromes (1999) 1998, Vol.17 (1), p.58-68 |
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| creator | MI RAN KANG CHO, Y.-K JUNE MYUNG KIM SHIN, Y.-O KANG, C JOO SHIL LEE KANG WON CHOI KIM, D.-G FITCH, W. M KIM, S CHUN, J KIM, Y.-B LEE, I.-S HEE JUNG LEE SEON HEE KIM KIM, Y.-K YOON, K YANG, J.-M |
| description | To study the genetic variation of the HIV-1 strains prevalent in South Korea, we analyzed the nef sequences derived from 46 HIV-1-positive individuals living in various geographic regions in Korea. Phylogenetic analysis revealed four subtypes of HIV-1: A (3 patients), B (41 patients), D (1 patient), and a type that could not be clearly classified to any known subtype (1 patient). Thirty-five of the 41 Korean subtype B isolates formed a distinct monophyletic clade that is not related to any of the international sequences from the Los Alamos Database or GenBank as of June 1997. Indeed, the presence of unique conserved sequences was identified among the Korean isolates in this Korean subtype B group. The variations in the nucleotide sequences of a majority (32 of 35) subtype B samples within the Korean clade were 1.9% to 8.8%, and amino acid sequences varied from 3.9% to 15.5%. These results suggest that HIV-1 strains currently present in South Korea might have originated from a few sources or might be developing through a certain selective pressure. This is the first report on the molecular nature of the HIV-1 infection present in South Korea. |
| doi_str_mv | 10.1097/00042560-199801010-00009 |
| format | Article |
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M ; KIM, S ; CHUN, J ; KIM, Y.-B ; LEE, I.-S ; HEE JUNG LEE ; SEON HEE KIM ; KIM, Y.-K ; YOON, K ; YANG, J.-M</creator><creatorcontrib>MI RAN KANG ; CHO, Y.-K ; JUNE MYUNG KIM ; SHIN, Y.-O ; KANG, C ; JOO SHIL LEE ; KANG WON CHOI ; KIM, D.-G ; FITCH, W. M ; KIM, S ; CHUN, J ; KIM, Y.-B ; LEE, I.-S ; HEE JUNG LEE ; SEON HEE KIM ; KIM, Y.-K ; YOON, K ; YANG, J.-M</creatorcontrib><description>To study the genetic variation of the HIV-1 strains prevalent in South Korea, we analyzed the nef sequences derived from 46 HIV-1-positive individuals living in various geographic regions in Korea. Phylogenetic analysis revealed four subtypes of HIV-1: A (3 patients), B (41 patients), D (1 patient), and a type that could not be clearly classified to any known subtype (1 patient). Thirty-five of the 41 Korean subtype B isolates formed a distinct monophyletic clade that is not related to any of the international sequences from the Los Alamos Database or GenBank as of June 1997. Indeed, the presence of unique conserved sequences was identified among the Korean isolates in this Korean subtype B group. The variations in the nucleotide sequences of a majority (32 of 35) subtype B samples within the Korean clade were 1.9% to 8.8%, and amino acid sequences varied from 3.9% to 15.5%. These results suggest that HIV-1 strains currently present in South Korea might have originated from a few sources or might be developing through a certain selective pressure. This is the first report on the molecular nature of the HIV-1 infection present in South Korea.</description><identifier>ISSN: 1077-9450</identifier><identifier>ISSN: 1525-4135</identifier><identifier>EISSN: 2331-6993</identifier><identifier>EISSN: 1944-7884</identifier><identifier>DOI: 10.1097/00042560-199801010-00009</identifier><identifier>PMID: 9436760</identifier><language>eng</language><publisher>New York, NY: Raven Press</publisher><subject>Adolescent ; Adult ; Amino Acid Sequence ; Biological and medical sciences ; Child ; Child, Preschool ; Cloning, Molecular ; Epidemiology ; Genes ; Genes, nef ; Genetic Variation ; Genetics ; HIV ; HIV Infections - epidemiology ; HIV Infections - virology ; HIV-1 - classification ; HIV-1 - genetics ; Human immunodeficiency virus ; Human viral diseases ; Humans ; Infectious diseases ; Korea - epidemiology ; Male ; Medical research ; Medical sciences ; Molecular Sequence Data ; Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; Tropical medicine ; Viral diseases ; Viral diseases of the lymphoid tissue and the blood. Aids</subject><ispartof>Journal of acquired immune deficiency syndromes (1999), 1998, Vol.17 (1), p.58-68</ispartof><rights>1998 INIST-CNRS</rights><rights>Copyright Lippincott Williams & Wilkins Jan 1, 1998</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c385t-51cd3b2a53ee7b1b0624a1c2be4177b576577b08424a85c19db8f76c8a9291c23</citedby><cites>FETCH-LOGICAL-c385t-51cd3b2a53ee7b1b0624a1c2be4177b576577b08424a85c19db8f76c8a9291c23</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>314,780,784,4021,27921,27922,27923</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=2142599$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/9436760$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>MI RAN KANG</creatorcontrib><creatorcontrib>CHO, Y.-K</creatorcontrib><creatorcontrib>JUNE MYUNG KIM</creatorcontrib><creatorcontrib>SHIN, Y.-O</creatorcontrib><creatorcontrib>KANG, C</creatorcontrib><creatorcontrib>JOO SHIL LEE</creatorcontrib><creatorcontrib>KANG WON CHOI</creatorcontrib><creatorcontrib>KIM, D.-G</creatorcontrib><creatorcontrib>FITCH, W. M</creatorcontrib><creatorcontrib>KIM, S</creatorcontrib><creatorcontrib>CHUN, J</creatorcontrib><creatorcontrib>KIM, Y.-B</creatorcontrib><creatorcontrib>LEE, I.-S</creatorcontrib><creatorcontrib>HEE JUNG LEE</creatorcontrib><creatorcontrib>SEON HEE KIM</creatorcontrib><creatorcontrib>KIM, Y.-K</creatorcontrib><creatorcontrib>YOON, K</creatorcontrib><creatorcontrib>YANG, J.-M</creatorcontrib><title>Phylogenetic analysis of the nef gene reveals a distinctive monophyletic clade in Korean HIV-1 cases</title><title>Journal of acquired immune deficiency syndromes (1999)</title><addtitle>J Acquir Immune Defic Syndr Hum Retrovirol</addtitle><description>To study the genetic variation of the HIV-1 strains prevalent in South Korea, we analyzed the nef sequences derived from 46 HIV-1-positive individuals living in various geographic regions in Korea. Phylogenetic analysis revealed four subtypes of HIV-1: A (3 patients), B (41 patients), D (1 patient), and a type that could not be clearly classified to any known subtype (1 patient). Thirty-five of the 41 Korean subtype B isolates formed a distinct monophyletic clade that is not related to any of the international sequences from the Los Alamos Database or GenBank as of June 1997. Indeed, the presence of unique conserved sequences was identified among the Korean isolates in this Korean subtype B group. The variations in the nucleotide sequences of a majority (32 of 35) subtype B samples within the Korean clade were 1.9% to 8.8%, and amino acid sequences varied from 3.9% to 15.5%. These results suggest that HIV-1 strains currently present in South Korea might have originated from a few sources or might be developing through a certain selective pressure. This is the first report on the molecular nature of the HIV-1 infection present in South Korea.</description><subject>Adolescent</subject><subject>Adult</subject><subject>Amino Acid Sequence</subject><subject>Biological and medical sciences</subject><subject>Child</subject><subject>Child, Preschool</subject><subject>Cloning, Molecular</subject><subject>Epidemiology</subject><subject>Genes</subject><subject>Genes, nef</subject><subject>Genetic Variation</subject><subject>Genetics</subject><subject>HIV</subject><subject>HIV Infections - epidemiology</subject><subject>HIV Infections - virology</subject><subject>HIV-1 - classification</subject><subject>HIV-1 - genetics</subject><subject>Human immunodeficiency virus</subject><subject>Human viral diseases</subject><subject>Humans</subject><subject>Infectious diseases</subject><subject>Korea - epidemiology</subject><subject>Male</subject><subject>Medical research</subject><subject>Medical sciences</subject><subject>Molecular Sequence Data</subject><subject>Phylogeny</subject><subject>Sequence Alignment</subject><subject>Sequence Analysis, DNA</subject><subject>Tropical medicine</subject><subject>Viral diseases</subject><subject>Viral diseases of the lymphoid tissue and the blood. Aids</subject><issn>1077-9450</issn><issn>1525-4135</issn><issn>2331-6993</issn><issn>1944-7884</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>1998</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNo9kV1LwzAUhoMoc05_ghDE2-pJ0zTNpQx1w4FeqLchTU9dRtfOpBvs35t9OHJx4LwfcJ4QQhk8MFDyEQCyVOSQMKUKYPElcQXqjAxTzlmSK8XPyZCBlInKBFySqxAWAExyDgMyUBnPZQ5DUn3Mt033gy32zlLTmmYbXKBdTfs50hZrutOoxw2aJlBDKxd619rebZAuu7Zbxfw-axtTIXUtfes8mpZOpt8Jo9YEDNfkoo5pvDnOEfl6ef4cT5LZ--t0_DRLLC9EnwhmK16mRnBEWbIS8jQzzKYlZkzKUshcxAFFFteFsExVZVHL3BZGpSr6-IjcHXpXvvtdY-j1olv7eFPQkUouRMaLaCoOJuu7EDzWeuXd0vitZqB3cPU_XH2Cq_dwY_T22L8ul1idgkeaUb8_6iZY09TetNaFky1lsTZ-zB-ko4CI</recordid><startdate>1998</startdate><enddate>1998</enddate><creator>MI RAN KANG</creator><creator>CHO, Y.-K</creator><creator>JUNE MYUNG KIM</creator><creator>SHIN, Y.-O</creator><creator>KANG, C</creator><creator>JOO SHIL LEE</creator><creator>KANG WON CHOI</creator><creator>KIM, D.-G</creator><creator>FITCH, W. 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M ; KIM, S ; CHUN, J ; KIM, Y.-B ; LEE, I.-S ; HEE JUNG LEE ; SEON HEE KIM ; KIM, Y.-K ; YOON, K ; YANG, J.-M</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c385t-51cd3b2a53ee7b1b0624a1c2be4177b576577b08424a85c19db8f76c8a9291c23</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>1998</creationdate><topic>Adolescent</topic><topic>Adult</topic><topic>Amino Acid Sequence</topic><topic>Biological and medical sciences</topic><topic>Child</topic><topic>Child, Preschool</topic><topic>Cloning, Molecular</topic><topic>Epidemiology</topic><topic>Genes</topic><topic>Genes, nef</topic><topic>Genetic Variation</topic><topic>Genetics</topic><topic>HIV</topic><topic>HIV Infections - epidemiology</topic><topic>HIV Infections - virology</topic><topic>HIV-1 - classification</topic><topic>HIV-1 - genetics</topic><topic>Human immunodeficiency virus</topic><topic>Human viral diseases</topic><topic>Humans</topic><topic>Infectious diseases</topic><topic>Korea - epidemiology</topic><topic>Male</topic><topic>Medical research</topic><topic>Medical sciences</topic><topic>Molecular Sequence Data</topic><topic>Phylogeny</topic><topic>Sequence Alignment</topic><topic>Sequence Analysis, DNA</topic><topic>Tropical medicine</topic><topic>Viral diseases</topic><topic>Viral diseases of the lymphoid tissue and the blood. 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Phylogenetic analysis revealed four subtypes of HIV-1: A (3 patients), B (41 patients), D (1 patient), and a type that could not be clearly classified to any known subtype (1 patient). Thirty-five of the 41 Korean subtype B isolates formed a distinct monophyletic clade that is not related to any of the international sequences from the Los Alamos Database or GenBank as of June 1997. Indeed, the presence of unique conserved sequences was identified among the Korean isolates in this Korean subtype B group. The variations in the nucleotide sequences of a majority (32 of 35) subtype B samples within the Korean clade were 1.9% to 8.8%, and amino acid sequences varied from 3.9% to 15.5%. These results suggest that HIV-1 strains currently present in South Korea might have originated from a few sources or might be developing through a certain selective pressure. 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| ispartof | Journal of acquired immune deficiency syndromes (1999), 1998, Vol.17 (1), p.58-68 |
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| subjects | Adolescent Adult Amino Acid Sequence Biological and medical sciences Child Child, Preschool Cloning, Molecular Epidemiology Genes Genes, nef Genetic Variation Genetics HIV HIV Infections - epidemiology HIV Infections - virology HIV-1 - classification HIV-1 - genetics Human immunodeficiency virus Human viral diseases Humans Infectious diseases Korea - epidemiology Male Medical research Medical sciences Molecular Sequence Data Phylogeny Sequence Alignment Sequence Analysis, DNA Tropical medicine Viral diseases Viral diseases of the lymphoid tissue and the blood. Aids |
| title | Phylogenetic analysis of the nef gene reveals a distinctive monophyletic clade in Korean HIV-1 cases |
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