Characterization of subtype A HIV-1 from Africa by full genome sequencing
To improve our understanding of the genetic complexity of HIV-1 subtype A by increasing the number of subtype A isolates that have been sequenced in their entirety. Nine HIV-1-seropositive patients from Africa living in Sweden contributed peripheral blood mononuclear cells (PBMC) for this study. Seq...
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| Veröffentlicht in: | AIDS (London) 1999-10, Vol.13 (14), p.1819-1826 |
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| creator | CARR, J. K LAUKKANEN, T SALMINEN, M. O ALBERT, J ALAEUS, A KIM, B SANDERS-BUELL, E BIRX, D. L MCCUTCHAN, F. E |
| description | To improve our understanding of the genetic complexity of HIV-1 subtype A by increasing the number of subtype A isolates that have been sequenced in their entirety.
Nine HIV-1-seropositive patients from Africa living in Sweden contributed peripheral blood mononuclear cells (PBMC) for this study. Sequencing of the C2-V3 region of env had shown them to be subtype A. DNA from virus cultures was used for the amplification of virtually full-length proviral sequences, and the resulting fragment was sequenced.
Six of the nine viral isolates were subtype A throughout the genome, or non-recombinant, and all of these were from east Africa. One virus from the Ivory Coast had the AG(IbNG) genetic form, a recombinant form common in west Africa. Two of the isolates were novel recombinants: one was an A/C recombinant and the other was A/D. Analysis of gag reveals three subclusters within the A subtype: one containing the AG(IbNG) subtype viruses, one containing the AE(CM240) viruses and one containing the non-recombinant A viruses. These genetic clusters have different geographical distributions in Africa.
The prevailing view of HIV-1 subtype A forming a uniform band across the center of sub-Saharan Africa needs revision. In all probability, the most common subtype in west Africa and west central Africa is the AG recombinant, AG(IbNG), whereas in east central Africa it is the non-recombinant subtype A. |
| doi_str_mv | 10.1097/00002030-199910010-00003 |
| format | Article |
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Nine HIV-1-seropositive patients from Africa living in Sweden contributed peripheral blood mononuclear cells (PBMC) for this study. Sequencing of the C2-V3 region of env had shown them to be subtype A. DNA from virus cultures was used for the amplification of virtually full-length proviral sequences, and the resulting fragment was sequenced.
Six of the nine viral isolates were subtype A throughout the genome, or non-recombinant, and all of these were from east Africa. One virus from the Ivory Coast had the AG(IbNG) genetic form, a recombinant form common in west Africa. Two of the isolates were novel recombinants: one was an A/C recombinant and the other was A/D. Analysis of gag reveals three subclusters within the A subtype: one containing the AG(IbNG) subtype viruses, one containing the AE(CM240) viruses and one containing the non-recombinant A viruses. These genetic clusters have different geographical distributions in Africa.
The prevailing view of HIV-1 subtype A forming a uniform band across the center of sub-Saharan Africa needs revision. In all probability, the most common subtype in west Africa and west central Africa is the AG recombinant, AG(IbNG), whereas in east central Africa it is the non-recombinant subtype A.</description><identifier>ISSN: 0269-9370</identifier><identifier>EISSN: 1473-5571</identifier><identifier>DOI: 10.1097/00002030-199910010-00003</identifier><identifier>PMID: 10513639</identifier><language>eng</language><publisher>Hagerstown, MD: Lippincott Williams & Wilkins</publisher><subject>Africa ; AIDS/HIV ; Biological and medical sciences ; DNA, Viral ; env gene ; Epidemiology ; Female ; Fundamental and applied biological sciences. Psychology ; gag gene ; Genome, Viral ; HIV Envelope Protein gp120 - genetics ; HIV Seropositivity - blood ; HIV Seropositivity - virology ; HIV-1 - classification ; HIV-1 - genetics ; HIV-1 - isolation & purification ; Human immunodeficiency virus 1 ; Humans ; Male ; Microbiology ; Peptide Fragments - genetics ; Phylogeny ; Recombination, Genetic ; Sequence Analysis, DNA ; Virology</subject><ispartof>AIDS (London), 1999-10, Vol.13 (14), p.1819-1826</ispartof><rights>1999 INIST-CNRS</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c554t-b09a7bdae48d6d7fda5a06396ac3a0db76bac5e61c6879a7de6d3f27ccfd58a83</citedby><cites>FETCH-LOGICAL-c554t-b09a7bdae48d6d7fda5a06396ac3a0db76bac5e61c6879a7de6d3f27ccfd58a83</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>230,314,776,780,881,27901,27902</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=1983900$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/10513639$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink><backlink>$$Uhttp://kipublications.ki.se/Default.aspx?queryparsed=id:1938086$$DView record from Swedish Publication Index$$Hfree_for_read</backlink></links><search><creatorcontrib>CARR, J. K</creatorcontrib><creatorcontrib>LAUKKANEN, T</creatorcontrib><creatorcontrib>SALMINEN, M. O</creatorcontrib><creatorcontrib>ALBERT, J</creatorcontrib><creatorcontrib>ALAEUS, A</creatorcontrib><creatorcontrib>KIM, B</creatorcontrib><creatorcontrib>SANDERS-BUELL, E</creatorcontrib><creatorcontrib>BIRX, D. L</creatorcontrib><creatorcontrib>MCCUTCHAN, F. E</creatorcontrib><title>Characterization of subtype A HIV-1 from Africa by full genome sequencing</title><title>AIDS (London)</title><addtitle>AIDS</addtitle><description>To improve our understanding of the genetic complexity of HIV-1 subtype A by increasing the number of subtype A isolates that have been sequenced in their entirety.
Nine HIV-1-seropositive patients from Africa living in Sweden contributed peripheral blood mononuclear cells (PBMC) for this study. Sequencing of the C2-V3 region of env had shown them to be subtype A. DNA from virus cultures was used for the amplification of virtually full-length proviral sequences, and the resulting fragment was sequenced.
Six of the nine viral isolates were subtype A throughout the genome, or non-recombinant, and all of these were from east Africa. One virus from the Ivory Coast had the AG(IbNG) genetic form, a recombinant form common in west Africa. Two of the isolates were novel recombinants: one was an A/C recombinant and the other was A/D. Analysis of gag reveals three subclusters within the A subtype: one containing the AG(IbNG) subtype viruses, one containing the AE(CM240) viruses and one containing the non-recombinant A viruses. These genetic clusters have different geographical distributions in Africa.
The prevailing view of HIV-1 subtype A forming a uniform band across the center of sub-Saharan Africa needs revision. In all probability, the most common subtype in west Africa and west central Africa is the AG recombinant, AG(IbNG), whereas in east central Africa it is the non-recombinant subtype A.</description><subject>Africa</subject><subject>AIDS/HIV</subject><subject>Biological and medical sciences</subject><subject>DNA, Viral</subject><subject>env gene</subject><subject>Epidemiology</subject><subject>Female</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>gag gene</subject><subject>Genome, Viral</subject><subject>HIV Envelope Protein gp120 - genetics</subject><subject>HIV Seropositivity - blood</subject><subject>HIV Seropositivity - 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>Humans</subject><subject>Male</subject><subject>Microbiology</subject><subject>Peptide Fragments - genetics</subject><subject>Phylogeny</subject><subject>Recombination, Genetic</subject><subject>Sequence Analysis, DNA</subject><subject>Virology</subject><issn>0269-9370</issn><issn>1473-5571</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>1999</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFkUuPEzEQhC0EYsPCX0A-IG6G9nj8OkYRy0ZaiQtwtXr8WAbmEewZofDrcUhYuOGLrdLX1SUXIZTDGw5Wv4V6GhDAuLWWA3BgJ0k8IhveasGk1Pwx2UCjLLNCwxV5VsrXSkgw5im54iC5UMJuyH73BTP6Jeb-Jy79PNE50bJ2y_EQ6Zbe7j8zTlOeR7pNufdIuyNN6zDQ-zjNY6Qlfl_j5Pvp_jl5knAo8cXlviafbt593N2yuw_v97vtHfNStgvrwKLuAsbWBBV0CigRahSFXiCETqsOvYyKe2V0RUNUQaRGe5-CNGjENWFn3_IjHtbOHXI_Yj66GXt3kb7VV3QKWmiayr8-84c816xlcWNffBwGnOK8FqfBNEJr-1-Q6xaU1CdHcwZ9nkvJMT1k4OBO_bg__biHfn5Loo6-vOxYuzGGfwbPhVTg1QXA4nFIGevnlr-cNcJWo1_Th5gT</recordid><startdate>19991001</startdate><enddate>19991001</enddate><creator>CARR, J. K</creator><creator>LAUKKANEN, T</creator><creator>SALMINEN, M. O</creator><creator>ALBERT, J</creator><creator>ALAEUS, A</creator><creator>KIM, B</creator><creator>SANDERS-BUELL, E</creator><creator>BIRX, D. L</creator><creator>MCCUTCHAN, F. E</creator><general>Lippincott Williams & Wilkins</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>ADTPV</scope><scope>AOWAS</scope></search><sort><creationdate>19991001</creationdate><title>Characterization of subtype A HIV-1 from Africa by full genome sequencing</title><author>CARR, J. K ; LAUKKANEN, T ; SALMINEN, M. O ; ALBERT, J ; ALAEUS, A ; KIM, B ; SANDERS-BUELL, E ; BIRX, D. L ; MCCUTCHAN, F. E</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c554t-b09a7bdae48d6d7fda5a06396ac3a0db76bac5e61c6879a7de6d3f27ccfd58a83</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>1999</creationdate><topic>Africa</topic><topic>AIDS/HIV</topic><topic>Biological and medical sciences</topic><topic>DNA, Viral</topic><topic>env gene</topic><topic>Epidemiology</topic><topic>Female</topic><topic>Fundamental and applied biological sciences. Psychology</topic><topic>gag gene</topic><topic>Genome, Viral</topic><topic>HIV Envelope Protein gp120 - genetics</topic><topic>HIV Seropositivity - blood</topic><topic>HIV Seropositivity - 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>Humans</topic><topic>Male</topic><topic>Microbiology</topic><topic>Peptide Fragments - genetics</topic><topic>Phylogeny</topic><topic>Recombination, Genetic</topic><topic>Sequence Analysis, DNA</topic><topic>Virology</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>CARR, J. K</creatorcontrib><creatorcontrib>LAUKKANEN, T</creatorcontrib><creatorcontrib>SALMINEN, M. O</creatorcontrib><creatorcontrib>ALBERT, J</creatorcontrib><creatorcontrib>ALAEUS, A</creatorcontrib><creatorcontrib>KIM, B</creatorcontrib><creatorcontrib>SANDERS-BUELL, E</creatorcontrib><creatorcontrib>BIRX, D. L</creatorcontrib><creatorcontrib>MCCUTCHAN, F. E</creatorcontrib><collection>Pascal-Francis</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Virology and AIDS Abstracts</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>MEDLINE - Academic</collection><collection>SwePub</collection><collection>SwePub Articles</collection><jtitle>AIDS (London)</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>CARR, J. K</au><au>LAUKKANEN, T</au><au>SALMINEN, M. O</au><au>ALBERT, J</au><au>ALAEUS, A</au><au>KIM, B</au><au>SANDERS-BUELL, E</au><au>BIRX, D. L</au><au>MCCUTCHAN, F. E</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Characterization of subtype A HIV-1 from Africa by full genome sequencing</atitle><jtitle>AIDS (London)</jtitle><addtitle>AIDS</addtitle><date>1999-10-01</date><risdate>1999</risdate><volume>13</volume><issue>14</issue><spage>1819</spage><epage>1826</epage><pages>1819-1826</pages><issn>0269-9370</issn><eissn>1473-5571</eissn><abstract>To improve our understanding of the genetic complexity of HIV-1 subtype A by increasing the number of subtype A isolates that have been sequenced in their entirety.
Nine HIV-1-seropositive patients from Africa living in Sweden contributed peripheral blood mononuclear cells (PBMC) for this study. Sequencing of the C2-V3 region of env had shown them to be subtype A. DNA from virus cultures was used for the amplification of virtually full-length proviral sequences, and the resulting fragment was sequenced.
Six of the nine viral isolates were subtype A throughout the genome, or non-recombinant, and all of these were from east Africa. One virus from the Ivory Coast had the AG(IbNG) genetic form, a recombinant form common in west Africa. Two of the isolates were novel recombinants: one was an A/C recombinant and the other was A/D. Analysis of gag reveals three subclusters within the A subtype: one containing the AG(IbNG) subtype viruses, one containing the AE(CM240) viruses and one containing the non-recombinant A viruses. These genetic clusters have different geographical distributions in Africa.
The prevailing view of HIV-1 subtype A forming a uniform band across the center of sub-Saharan Africa needs revision. In all probability, the most common subtype in west Africa and west central Africa is the AG recombinant, AG(IbNG), whereas in east central Africa it is the non-recombinant subtype A.</abstract><cop>Hagerstown, MD</cop><pub>Lippincott Williams & Wilkins</pub><pmid>10513639</pmid><doi>10.1097/00002030-199910010-00003</doi><tpages>8</tpages><oa>free_for_read</oa></addata></record> |
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| identifier | ISSN: 0269-9370 |
| ispartof | AIDS (London), 1999-10, Vol.13 (14), p.1819-1826 |
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| source | Journals@Ovid Complete - AutoHoldings; MEDLINE; EZB-FREE-00999 freely available EZB journals |
| subjects | Africa AIDS/HIV Biological and medical sciences DNA, Viral env gene Epidemiology Female Fundamental and applied biological sciences. Psychology gag gene Genome, Viral HIV Envelope Protein gp120 - genetics HIV Seropositivity - blood HIV Seropositivity - virology HIV-1 - classification HIV-1 - genetics HIV-1 - isolation & purification Human immunodeficiency virus 1 Humans Male Microbiology Peptide Fragments - genetics Phylogeny Recombination, Genetic Sequence Analysis, DNA Virology |
| title | Characterization of subtype A HIV-1 from Africa by full genome sequencing |
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