Identification and Characterization of CRF02_AG, CRF06_cpx, and CRF09_cpx Recombinant Subtypes in Mali, West Africa
Abstract Multiple HIV-1 subtypes and circulating recombinant forms (CRFs) are known to cocirculate in Africa. In West Africa, the high prevalence of CRF02_AG, and cocirculation of subtype A, CRF01_AE, CRF06_cpx, and other complex intersubtype recombinants has been well documented. Mali, situated in...
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| Veröffentlicht in: | AIDS research and human retroviruses 2009, Vol.25 (1), p.45-55 |
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| creator | IMAMICHI, Hiromi KOITA, Ousmane WASHINGTON, Janice A POLIS, Michael A LANE, H. Clifford TOUNKARA, Anatole DABITAO, Djeneba DAO, Sounkalo IBRAH, Mahamadou SOGOBA, Dramane DEWAR, Robin L BERG, Steve C JIANG, Min-Kang PARTA, Mark |
| description | Abstract Multiple HIV-1 subtypes and circulating recombinant forms (CRFs) are known to cocirculate in Africa. In West Africa, the high prevalence of CRF02_AG, and cocirculation of subtype A, CRF01_AE, CRF06_cpx, and other complex intersubtype recombinants has been well documented. Mali, situated in the heart of West Africa, is likely to be affected by the spread of recombinant subtypes. However, the dynamics of the spread of HIV-1 recombinant subtypes as well as nonrecombinant HIV-1 group M subtypes in this area have not been systematically assessed. Herein, we undertook genetic analyses on full-length env sequences derived from HIV-1-infected individuals living in the capital city of Mali, Bamako. Of 23 samples we examined, 16 were classified as CRF02_AG and three had a subsubtype A3. Among the remaining HIV-1 strains, CRF06_cpx and CRF09_cpx were each found in two patients. Comparison of phylogenies for six matched pol and full-length env sequences revealed that two strains had discordant subtype/CRF designations between the pol and env regions: one had A3(pol)CRF02_AG(env) and the other had CRF02_AG(pol)A3(env). Taken together, our study demonstrated the high prevalence of CRF02_AG and complexity of circulating HIV-1 strains in Mali. It also provided evidence of ongoing virus evolution of CRF02_AG, as illustrated by the emergence of more complex CRF02_AG/A3 intersubtype recombinants in this area. |
| doi_str_mv | 10.1089/aid.2008.0111 |
| format | Article |
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Clifford ; TOUNKARA, Anatole ; DABITAO, Djeneba ; DAO, Sounkalo ; IBRAH, Mahamadou ; SOGOBA, Dramane ; DEWAR, Robin L ; BERG, Steve C ; JIANG, Min-Kang ; PARTA, Mark</creator><creatorcontrib>IMAMICHI, Hiromi ; KOITA, Ousmane ; WASHINGTON, Janice A ; POLIS, Michael A ; LANE, H. Clifford ; TOUNKARA, Anatole ; DABITAO, Djeneba ; DAO, Sounkalo ; IBRAH, Mahamadou ; SOGOBA, Dramane ; DEWAR, Robin L ; BERG, Steve C ; JIANG, Min-Kang ; PARTA, Mark</creatorcontrib><description>Abstract Multiple HIV-1 subtypes and circulating recombinant forms (CRFs) are known to cocirculate in Africa. In West Africa, the high prevalence of CRF02_AG, and cocirculation of subtype A, CRF01_AE, CRF06_cpx, and other complex intersubtype recombinants has been well documented. Mali, situated in the heart of West Africa, is likely to be affected by the spread of recombinant subtypes. However, the dynamics of the spread of HIV-1 recombinant subtypes as well as nonrecombinant HIV-1 group M subtypes in this area have not been systematically assessed. Herein, we undertook genetic analyses on full-length env sequences derived from HIV-1-infected individuals living in the capital city of Mali, Bamako. Of 23 samples we examined, 16 were classified as CRF02_AG and three had a subsubtype A3. Among the remaining HIV-1 strains, CRF06_cpx and CRF09_cpx were each found in two patients. Comparison of phylogenies for six matched pol and full-length env sequences revealed that two strains had discordant subtype/CRF designations between the pol and env regions: one had A3(pol)CRF02_AG(env) and the other had CRF02_AG(pol)A3(env). Taken together, our study demonstrated the high prevalence of CRF02_AG and complexity of circulating HIV-1 strains in Mali. It also provided evidence of ongoing virus evolution of CRF02_AG, as illustrated by the emergence of more complex CRF02_AG/A3 intersubtype recombinants in this area.</description><identifier>ISSN: 0889-2229</identifier><identifier>EISSN: 1931-8405</identifier><identifier>DOI: 10.1089/aid.2008.0111</identifier><identifier>PMID: 19182920</identifier><identifier>CODEN: ARHRE7</identifier><language>eng</language><publisher>New Rochelle, NY: Liebert</publisher><subject>Adolescent ; Adult ; AIDS/HIV ; Biological and medical sciences ; Cluster Analysis ; DNA sequencing ; env Gene Products, Human Immunodeficiency Virus - genetics ; Epidemiology ; Female ; Fundamental and applied biological sciences. Psychology ; Gene mutations ; Genetic aspects ; Genotype ; Health aspects ; HIV (Viruses) ; HIV Infections - epidemiology ; HIV Infections - virology ; HIV-1 - classification ; HIV-1 - genetics ; HIV-1 - isolation & purification ; Human immunodeficiency virus 1 ; Human viral diseases ; Humans ; Infectious diseases ; Male ; Mali - epidemiology ; Medical sciences ; Methods ; Microbiology ; Middle Aged ; Miscellaneous ; Molecular Epidemiology ; Molecular Sequence Data ; Nucleotide sequencing ; Phylogeny ; Polymorphism, Genetic ; Prevalence ; Prevalence studies (Epidemiology) ; Recombination, Genetic ; Retrovirus ; Sequence Analysis, DNA ; Sequence Homology ; Viral diseases ; Virology</subject><ispartof>AIDS research and human retroviruses, 2009, Vol.25 (1), p.45-55</ispartof><rights>2009 INIST-CNRS</rights><rights>COPYRIGHT 2009 Mary Ann Liebert, Inc.</rights><rights>Copyright 2009, Mary Ann Liebert, Inc.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c513t-248e681c9aa2b25f5dc17bd6ec2ad92abacd23be8d4bc27c2c1fda0f65211ea33</citedby><cites>FETCH-LOGICAL-c513t-248e681c9aa2b25f5dc17bd6ec2ad92abacd23be8d4bc27c2c1fda0f65211ea33</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>230,314,776,780,881,3029,4010,27902,27903,27904</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=21171669$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/19182920$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>IMAMICHI, Hiromi</creatorcontrib><creatorcontrib>KOITA, Ousmane</creatorcontrib><creatorcontrib>WASHINGTON, Janice A</creatorcontrib><creatorcontrib>POLIS, Michael A</creatorcontrib><creatorcontrib>LANE, H. Clifford</creatorcontrib><creatorcontrib>TOUNKARA, Anatole</creatorcontrib><creatorcontrib>DABITAO, Djeneba</creatorcontrib><creatorcontrib>DAO, Sounkalo</creatorcontrib><creatorcontrib>IBRAH, Mahamadou</creatorcontrib><creatorcontrib>SOGOBA, Dramane</creatorcontrib><creatorcontrib>DEWAR, Robin L</creatorcontrib><creatorcontrib>BERG, Steve C</creatorcontrib><creatorcontrib>JIANG, Min-Kang</creatorcontrib><creatorcontrib>PARTA, Mark</creatorcontrib><title>Identification and Characterization of CRF02_AG, CRF06_cpx, and CRF09_cpx Recombinant Subtypes in Mali, West Africa</title><title>AIDS research and human retroviruses</title><addtitle>AIDS Res Hum Retroviruses</addtitle><description>Abstract Multiple HIV-1 subtypes and circulating recombinant forms (CRFs) are known to cocirculate in Africa. In West Africa, the high prevalence of CRF02_AG, and cocirculation of subtype A, CRF01_AE, CRF06_cpx, and other complex intersubtype recombinants has been well documented. Mali, situated in the heart of West Africa, is likely to be affected by the spread of recombinant subtypes. However, the dynamics of the spread of HIV-1 recombinant subtypes as well as nonrecombinant HIV-1 group M subtypes in this area have not been systematically assessed. Herein, we undertook genetic analyses on full-length env sequences derived from HIV-1-infected individuals living in the capital city of Mali, Bamako. Of 23 samples we examined, 16 were classified as CRF02_AG and three had a subsubtype A3. Among the remaining HIV-1 strains, CRF06_cpx and CRF09_cpx were each found in two patients. Comparison of phylogenies for six matched pol and full-length env sequences revealed that two strains had discordant subtype/CRF designations between the pol and env regions: one had A3(pol)CRF02_AG(env) and the other had CRF02_AG(pol)A3(env). Taken together, our study demonstrated the high prevalence of CRF02_AG and complexity of circulating HIV-1 strains in Mali. It also provided evidence of ongoing virus evolution of CRF02_AG, as illustrated by the emergence of more complex CRF02_AG/A3 intersubtype recombinants in this area.</description><subject>Adolescent</subject><subject>Adult</subject><subject>AIDS/HIV</subject><subject>Biological and medical sciences</subject><subject>Cluster Analysis</subject><subject>DNA sequencing</subject><subject>env Gene Products, Human Immunodeficiency Virus - genetics</subject><subject>Epidemiology</subject><subject>Female</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>Gene mutations</subject><subject>Genetic aspects</subject><subject>Genotype</subject><subject>Health aspects</subject><subject>HIV (Viruses)</subject><subject>HIV Infections - epidemiology</subject><subject>HIV Infections - virology</subject><subject>HIV-1 - classification</subject><subject>HIV-1 - genetics</subject><subject>HIV-1 - isolation & purification</subject><subject>Human immunodeficiency virus 1</subject><subject>Human viral diseases</subject><subject>Humans</subject><subject>Infectious diseases</subject><subject>Male</subject><subject>Mali - epidemiology</subject><subject>Medical sciences</subject><subject>Methods</subject><subject>Microbiology</subject><subject>Middle Aged</subject><subject>Miscellaneous</subject><subject>Molecular Epidemiology</subject><subject>Molecular Sequence Data</subject><subject>Nucleotide sequencing</subject><subject>Phylogeny</subject><subject>Polymorphism, Genetic</subject><subject>Prevalence</subject><subject>Prevalence studies (Epidemiology)</subject><subject>Recombination, Genetic</subject><subject>Retrovirus</subject><subject>Sequence Analysis, DNA</subject><subject>Sequence Homology</subject><subject>Viral diseases</subject><subject>Virology</subject><issn>0889-2229</issn><issn>1931-8405</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2009</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFks9rFDEUx4Modq0evcqA2NPOmrzZmUkuwrK0tVARquIxvMmPNjKTbJNZsf71ZpylWhAkh-S9fN5PvoS8ZHTFKBdv0ekVUMpXlDH2iCyYqFjJ17R-TBaUc1ECgDgiz1L6RikVAPVTcsQE4yCALki60MaPzjqFowu-QK-L7Q1GVKOJ7ufsDLbYXp1RkJvz5e9XI9Xux3KGsykms7gyKgyd8-jH4tO-G-92JhXOFx-wd8viq0ljsbExF3pOnljsk3lxuI_Jl7PTz9v35eXH84vt5rJUNavGEtbcNJwpgQgd1LbWirWdbowC1AKwQ6Wh6gzX605Bq0Axq5HapgbGDFbVMXk3593tu8FolQeN2MtddAPGOxnQyYc_3t3I6_BdguCs4jQnODkkiOF2nweQg0vK9D16E_ZJNg1vgVP4Lwi0WreUTS29nsFr7I103oZcWE2w3DDR0LqircjU6h9UPtoMTgVvrMv-BwHlHKBiSCkaez8ko3KSicwykZNM5CSTzL_6ezN_6IMuMvDmAGBS2NuIXrl0z-UFt6xpRPUL0inEWQ</recordid><startdate>2009</startdate><enddate>2009</enddate><creator>IMAMICHI, Hiromi</creator><creator>KOITA, Ousmane</creator><creator>WASHINGTON, Janice A</creator><creator>POLIS, Michael A</creator><creator>LANE, H. Clifford</creator><creator>TOUNKARA, Anatole</creator><creator>DABITAO, Djeneba</creator><creator>DAO, Sounkalo</creator><creator>IBRAH, Mahamadou</creator><creator>SOGOBA, Dramane</creator><creator>DEWAR, Robin L</creator><creator>BERG, Steve C</creator><creator>JIANG, Min-Kang</creator><creator>PARTA, Mark</creator><general>Liebert</general><general>Mary Ann Liebert, Inc</general><scope>IQODW</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7U9</scope><scope>H94</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>2009</creationdate><title>Identification and Characterization of CRF02_AG, CRF06_cpx, and CRF09_cpx Recombinant Subtypes in Mali, West Africa</title><author>IMAMICHI, Hiromi ; KOITA, Ousmane ; WASHINGTON, Janice A ; POLIS, Michael A ; LANE, H. Clifford ; TOUNKARA, Anatole ; DABITAO, Djeneba ; DAO, Sounkalo ; IBRAH, Mahamadou ; SOGOBA, Dramane ; DEWAR, Robin L ; BERG, Steve C ; JIANG, Min-Kang ; PARTA, Mark</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c513t-248e681c9aa2b25f5dc17bd6ec2ad92abacd23be8d4bc27c2c1fda0f65211ea33</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2009</creationdate><topic>Adolescent</topic><topic>Adult</topic><topic>AIDS/HIV</topic><topic>Biological and medical sciences</topic><topic>Cluster Analysis</topic><topic>DNA sequencing</topic><topic>env Gene Products, Human Immunodeficiency Virus - genetics</topic><topic>Epidemiology</topic><topic>Female</topic><topic>Fundamental and applied biological sciences. Psychology</topic><topic>Gene mutations</topic><topic>Genetic aspects</topic><topic>Genotype</topic><topic>Health aspects</topic><topic>HIV (Viruses)</topic><topic>HIV Infections - epidemiology</topic><topic>HIV Infections - virology</topic><topic>HIV-1 - classification</topic><topic>HIV-1 - genetics</topic><topic>HIV-1 - isolation & purification</topic><topic>Human immunodeficiency virus 1</topic><topic>Human viral diseases</topic><topic>Humans</topic><topic>Infectious diseases</topic><topic>Male</topic><topic>Mali - epidemiology</topic><topic>Medical sciences</topic><topic>Methods</topic><topic>Microbiology</topic><topic>Middle Aged</topic><topic>Miscellaneous</topic><topic>Molecular Epidemiology</topic><topic>Molecular Sequence Data</topic><topic>Nucleotide sequencing</topic><topic>Phylogeny</topic><topic>Polymorphism, Genetic</topic><topic>Prevalence</topic><topic>Prevalence studies (Epidemiology)</topic><topic>Recombination, Genetic</topic><topic>Retrovirus</topic><topic>Sequence Analysis, DNA</topic><topic>Sequence Homology</topic><topic>Viral diseases</topic><topic>Virology</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>IMAMICHI, Hiromi</creatorcontrib><creatorcontrib>KOITA, Ousmane</creatorcontrib><creatorcontrib>WASHINGTON, Janice A</creatorcontrib><creatorcontrib>POLIS, Michael A</creatorcontrib><creatorcontrib>LANE, H. 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Clifford</au><au>TOUNKARA, Anatole</au><au>DABITAO, Djeneba</au><au>DAO, Sounkalo</au><au>IBRAH, Mahamadou</au><au>SOGOBA, Dramane</au><au>DEWAR, Robin L</au><au>BERG, Steve C</au><au>JIANG, Min-Kang</au><au>PARTA, Mark</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Identification and Characterization of CRF02_AG, CRF06_cpx, and CRF09_cpx Recombinant Subtypes in Mali, West Africa</atitle><jtitle>AIDS research and human retroviruses</jtitle><addtitle>AIDS Res Hum Retroviruses</addtitle><date>2009</date><risdate>2009</risdate><volume>25</volume><issue>1</issue><spage>45</spage><epage>55</epage><pages>45-55</pages><issn>0889-2229</issn><eissn>1931-8405</eissn><coden>ARHRE7</coden><abstract>Abstract Multiple HIV-1 subtypes and circulating recombinant forms (CRFs) are known to cocirculate in Africa. In West Africa, the high prevalence of CRF02_AG, and cocirculation of subtype A, CRF01_AE, CRF06_cpx, and other complex intersubtype recombinants has been well documented. Mali, situated in the heart of West Africa, is likely to be affected by the spread of recombinant subtypes. However, the dynamics of the spread of HIV-1 recombinant subtypes as well as nonrecombinant HIV-1 group M subtypes in this area have not been systematically assessed. Herein, we undertook genetic analyses on full-length env sequences derived from HIV-1-infected individuals living in the capital city of Mali, Bamako. Of 23 samples we examined, 16 were classified as CRF02_AG and three had a subsubtype A3. Among the remaining HIV-1 strains, CRF06_cpx and CRF09_cpx were each found in two patients. Comparison of phylogenies for six matched pol and full-length env sequences revealed that two strains had discordant subtype/CRF designations between the pol and env regions: one had A3(pol)CRF02_AG(env) and the other had CRF02_AG(pol)A3(env). Taken together, our study demonstrated the high prevalence of CRF02_AG and complexity of circulating HIV-1 strains in Mali. It also provided evidence of ongoing virus evolution of CRF02_AG, as illustrated by the emergence of more complex CRF02_AG/A3 intersubtype recombinants in this area.</abstract><cop>New Rochelle, NY</cop><pub>Liebert</pub><pmid>19182920</pmid><doi>10.1089/aid.2008.0111</doi><tpages>11</tpages><oa>free_for_read</oa></addata></record> |
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| ispartof | AIDS research and human retroviruses, 2009, Vol.25 (1), p.45-55 |
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| subjects | Adolescent Adult AIDS/HIV Biological and medical sciences Cluster Analysis DNA sequencing env Gene Products, Human Immunodeficiency Virus - genetics Epidemiology Female Fundamental and applied biological sciences. Psychology Gene mutations Genetic aspects Genotype Health aspects HIV (Viruses) HIV Infections - epidemiology HIV Infections - virology HIV-1 - classification HIV-1 - genetics HIV-1 - isolation & purification Human immunodeficiency virus 1 Human viral diseases Humans Infectious diseases Male Mali - epidemiology Medical sciences Methods Microbiology Middle Aged Miscellaneous Molecular Epidemiology Molecular Sequence Data Nucleotide sequencing Phylogeny Polymorphism, Genetic Prevalence Prevalence studies (Epidemiology) Recombination, Genetic Retrovirus Sequence Analysis, DNA Sequence Homology Viral diseases Virology |
| title | Identification and Characterization of CRF02_AG, CRF06_cpx, and CRF09_cpx Recombinant Subtypes in Mali, West Africa |
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