Near full-length genomic characterization of a HIV type 1 BC recombinant strain from Manipur, India
Genetic complexity of HIV-1 is brought about by recombination between HIV-1 subtypes which leads to the development of epidemiologically significant founder strains. In the present study, the near full-length genome sequence of an HIV-1 isolate from an injecting drug user of Manipur (India) was dete...
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| Veröffentlicht in: | Virus genes 2012-10, Vol.45 (2), p.201-206 |
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| creator | Sarkar, Roni Sarkar, Kamalesh Singh, N. Brajachand Singh, Y. Manihar Chakrabarti, Sekhar |
| description | Genetic complexity of HIV-1 is brought about by recombination between HIV-1 subtypes which leads to the development of epidemiologically significant founder strains. In the present study, the near full-length genome sequence of an HIV-1 isolate from an injecting drug user of Manipur (India) was determined, which evidenced the presence of a novel HIV-1 BC recombinant strain. Near full-length genome was amplified by polymerase chain reaction using primer walking approach. The recombination break points were detected using bootscan and simplot analyses. This isolate exhibited a mosaic structure consisting of subtype C backbone with subtype B insertions at the upstream of pol gene (3026–3259) and the downstream of env gene which spanned till the nef gene (8183–8961). Phylogenetic relationships determined with neighbor-joining trees, revealed that the subtype C sequences clustered with sequences from Indian subtype C HIV-1 strains, and the subtype B sequences clustered with HIV-1 subtype B strains from Thailand. This finding may create a complex scenario of HIV-1 epidemic among the injecting drug users of Manipur in near future. |
| doi_str_mv | 10.1007/s11262-012-0768-z |
| format | Article |
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Phylogenetic relationships determined with neighbor-joining trees, revealed that the subtype C sequences clustered with sequences from Indian subtype C HIV-1 strains, and the subtype B sequences clustered with HIV-1 subtype B strains from Thailand. This finding may create a complex scenario of HIV-1 epidemic among the injecting drug users of Manipur in near future.</description><identifier>ISSN: 0920-8569</identifier><identifier>EISSN: 1572-994X</identifier><identifier>DOI: 10.1007/s11262-012-0768-z</identifier><identifier>PMID: 22710995</identifier><language>eng</language><publisher>Boston: Springer-Verlag</publisher><subject>Biomedical and Life Sciences ; Biomedicine ; Cluster Analysis ; Drug abuse ; drugs ; Env protein ; Epidemics ; Gene mapping ; genes ; Genome, Viral ; Genomes ; genomics ; Genotype ; HIV Infections - virology ; HIV-1 - genetics ; HIV-1 - isolation & purification ; Human immunodeficiency virus 1 ; Humans ; India ; Insertion ; Medical Microbiology ; Molecular Sequence Data ; Mosaics ; Nef protein ; Nucleotide sequence ; nucleotide sequences ; Phylogeny ; Plant Sciences ; pol gene ; Polymerase chain reaction ; Primers ; Recombination ; Recombination, Genetic ; RNA, Viral - genetics ; Sequence Analysis, DNA ; Thailand ; Virology</subject><ispartof>Virus genes, 2012-10, Vol.45 (2), p.201-206</ispartof><rights>Springer Science+Business Media, LLC 2012</rights><rights>Springer Science+Business Media New York 2012</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c496t-8d66d65e8cba4ebf781b7c4d635d976a4c4a19478d0e15e71da44bce9d5ef0123</citedby><cites>FETCH-LOGICAL-c496t-8d66d65e8cba4ebf781b7c4d635d976a4c4a19478d0e15e71da44bce9d5ef0123</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1007/s11262-012-0768-z$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1007/s11262-012-0768-z$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>314,776,780,27903,27904,41467,42536,51298</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/22710995$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Sarkar, Roni</creatorcontrib><creatorcontrib>Sarkar, Kamalesh</creatorcontrib><creatorcontrib>Singh, N. Brajachand</creatorcontrib><creatorcontrib>Singh, Y. Manihar</creatorcontrib><creatorcontrib>Chakrabarti, Sekhar</creatorcontrib><title>Near full-length genomic characterization of a HIV type 1 BC recombinant strain from Manipur, India</title><title>Virus genes</title><addtitle>Virus Genes</addtitle><addtitle>Virus Genes</addtitle><description>Genetic complexity of HIV-1 is brought about by recombination between HIV-1 subtypes which leads to the development of epidemiologically significant founder strains. In the present study, the near full-length genome sequence of an HIV-1 isolate from an injecting drug user of Manipur (India) was determined, which evidenced the presence of a novel HIV-1 BC recombinant strain. Near full-length genome was amplified by polymerase chain reaction using primer walking approach. The recombination break points were detected using bootscan and simplot analyses. This isolate exhibited a mosaic structure consisting of subtype C backbone with subtype B insertions at the upstream of pol gene (3026–3259) and the downstream of env gene which spanned till the nef gene (8183–8961). Phylogenetic relationships determined with neighbor-joining trees, revealed that the subtype C sequences clustered with sequences from Indian subtype C HIV-1 strains, and the subtype B sequences clustered with HIV-1 subtype B strains from Thailand. This finding may create a complex scenario of HIV-1 epidemic among the injecting drug users of Manipur in near future.</description><subject>Biomedical and Life Sciences</subject><subject>Biomedicine</subject><subject>Cluster Analysis</subject><subject>Drug abuse</subject><subject>drugs</subject><subject>Env protein</subject><subject>Epidemics</subject><subject>Gene mapping</subject><subject>genes</subject><subject>Genome, Viral</subject><subject>Genomes</subject><subject>genomics</subject><subject>Genotype</subject><subject>HIV Infections - virology</subject><subject>HIV-1 - genetics</subject><subject>HIV-1 - isolation & purification</subject><subject>Human immunodeficiency virus 1</subject><subject>Humans</subject><subject>India</subject><subject>Insertion</subject><subject>Medical Microbiology</subject><subject>Molecular Sequence Data</subject><subject>Mosaics</subject><subject>Nef protein</subject><subject>Nucleotide sequence</subject><subject>nucleotide sequences</subject><subject>Phylogeny</subject><subject>Plant Sciences</subject><subject>pol gene</subject><subject>Polymerase chain reaction</subject><subject>Primers</subject><subject>Recombination</subject><subject>Recombination, Genetic</subject><subject>RNA, Viral - genetics</subject><subject>Sequence Analysis, DNA</subject><subject>Thailand</subject><subject>Virology</subject><issn>0920-8569</issn><issn>1572-994X</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2012</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><recordid>eNqFkc1u1DAUhS0EotPCA7ABS2xYkGI7jh0vYUTpSC0soIid5dg3U1eJPdjJovP0eJS2QkjAwroLf-fcn4PQC0pOKSHyXaaUCVYRWp4UbbV_hFa0kaxSiv94jFZEMVK1jVBH6DjnG0JI2zL-FB0xJilRqlkh-xlMwv08DNUAYTtd4y2EOHqL7bVJxk6Q_N5MPgYce2zw-eY7nm53gCn-sMYJbBw7H0yYcJ6S8QH3KY740gS_m9NbvAnOm2foSW-GDM_v6gm6Ovv4bX1eXXz5tFm_v6gsV2KqWieEEw20tjMcul62tJOWO1E3TklhuOWGKi5bR4A2IKkznHcWlGugLzeoT9CbxXeX4s8Z8qRHny0MgwkQ56wppTWr6aH8FyWSl4vyui3o6z_QmzinUBYpFFe1bJgghaILZVPMOUGvd8mPJt0WSB_C0ktYugyqD2HpfdG8vHOeuxHcg-I-nQKwBcjlK2wh_d76766vFlFvojbb5LO--soI5SV-TphU_yQYK1D9CzgOsHo</recordid><startdate>20121001</startdate><enddate>20121001</enddate><creator>Sarkar, Roni</creator><creator>Sarkar, Kamalesh</creator><creator>Singh, N. 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Brajachand</au><au>Singh, Y. Manihar</au><au>Chakrabarti, Sekhar</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Near full-length genomic characterization of a HIV type 1 BC recombinant strain from Manipur, India</atitle><jtitle>Virus genes</jtitle><stitle>Virus Genes</stitle><addtitle>Virus Genes</addtitle><date>2012-10-01</date><risdate>2012</risdate><volume>45</volume><issue>2</issue><spage>201</spage><epage>206</epage><pages>201-206</pages><issn>0920-8569</issn><eissn>1572-994X</eissn><abstract>Genetic complexity of HIV-1 is brought about by recombination between HIV-1 subtypes which leads to the development of epidemiologically significant founder strains. In the present study, the near full-length genome sequence of an HIV-1 isolate from an injecting drug user of Manipur (India) was determined, which evidenced the presence of a novel HIV-1 BC recombinant strain. Near full-length genome was amplified by polymerase chain reaction using primer walking approach. The recombination break points were detected using bootscan and simplot analyses. This isolate exhibited a mosaic structure consisting of subtype C backbone with subtype B insertions at the upstream of pol gene (3026–3259) and the downstream of env gene which spanned till the nef gene (8183–8961). Phylogenetic relationships determined with neighbor-joining trees, revealed that the subtype C sequences clustered with sequences from Indian subtype C HIV-1 strains, and the subtype B sequences clustered with HIV-1 subtype B strains from Thailand. This finding may create a complex scenario of HIV-1 epidemic among the injecting drug users of Manipur in near future.</abstract><cop>Boston</cop><pub>Springer-Verlag</pub><pmid>22710995</pmid><doi>10.1007/s11262-012-0768-z</doi><tpages>6</tpages><oa>free_for_read</oa></addata></record> |
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| subjects | Biomedical and Life Sciences Biomedicine Cluster Analysis Drug abuse drugs Env protein Epidemics Gene mapping genes Genome, Viral Genomes genomics Genotype HIV Infections - virology HIV-1 - genetics HIV-1 - isolation & purification Human immunodeficiency virus 1 Humans India Insertion Medical Microbiology Molecular Sequence Data Mosaics Nef protein Nucleotide sequence nucleotide sequences Phylogeny Plant Sciences pol gene Polymerase chain reaction Primers Recombination Recombination, Genetic RNA, Viral - genetics Sequence Analysis, DNA Thailand Virology |
| title | Near full-length genomic characterization of a HIV type 1 BC recombinant strain from Manipur, India |
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