{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,6]],"date-time":"2026-10-06T14:20:47Z","timestamp":1791296447638,"version":"4.1.0"},"reference-count":93,"publisher":"American Society for Microbiology","issue":"12","license":[{"start":{"date-parts":[[2011,6,15]],"date-time":"2011-06-15T00:00:00Z","timestamp":1308096000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["J Virol"],"published-print":{"date-parts":[[2011,6,15]]},"abstract":"<jats:title>ABSTRACT<\/jats:title><jats:p>HIV-1 circulates within an infected host as a genetically heterogeneous viral population. Viral intrahost diversity is shaped by substitutional evolution and recombination. Although many studies have speculated that recombination could have a significant impact on viral phenotype, this has never been definitively demonstrated. We report here phylogenetic and subsequent phenotypic analyses of envelope genes obtained from HIV-1 populations present in different anatomical compartments. Assessment of<jats:italic>env<\/jats:italic>compartmentalization from immunologically discrete tissues was assessed utilizing a single genome amplification approach, minimizing<jats:named-content content-type=\"genus-species\">in vitro<\/jats:named-content>-generated artifacts. Genetic compartmentalization of variants was frequently observed. In addition, multiple incidences of intercompartment recombination, presumably facilitated by low-level migration of virus or infected cells between different anatomic sites and coinfection of susceptible cells by genetically divergent strains, were identified. These analyses demonstrate that intercompartment recombination is a fundamental evolutionary mechanism that helps to shape HIV-1<jats:italic>env<\/jats:italic>intrahost diversity in natural infection. Analysis of the phenotypic consequences of these recombination events showed that genetic compartmentalization often correlates with phenotypic compartmentalization and that intercompartment recombination results in phenotype modulation. This represents definitive proof that recombination can generate novel combinations of phenotypic traits which differ subtly from those of parental strains, an important phenomenon that may have an impact on antiviral therapy and contribute to HIV-1 persistence<jats:named-content content-type=\"genus-species\">in vivo<\/jats:named-content>.<\/jats:p>","DOI":"10.1128\/jvi.00131-11","type":"journal-article","created":{"date-parts":[[2011,4,7]],"date-time":"2011-04-07T12:45:22Z","timestamp":1302180322000},"page":"6024-6037","update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":50,"title":["Intercompartmental Recombination of HIV-1 Contributes to<i>env<\/i>Intrahost Diversity and Modulates Viral Tropism and Sensitivity to Entry Inhibitors"],"prefix":"10.1128","volume":"85","author":[{"given":"Richard J. P.","family":"Brown","sequence":"first","affiliation":[{"name":"School of Molecular Medical Sciences, The University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Paul J.","family":"Peters","sequence":"additional","affiliation":[{"name":"Center for AIDS Research, Program in Molecular Medicine and Department of Molecular Genetics and Microbiology, 373 Plantation Street, University of Massachusetts Medical School, Worcester, Massachusetts 01605"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Catherine","family":"Caron","sequence":"additional","affiliation":[{"name":"Center for AIDS Research, Program in Molecular Medicine and Department of Molecular Genetics and Microbiology, 373 Plantation Street, University of Massachusetts Medical School, Worcester, Massachusetts 01605"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maria Paz","family":"Gonzalez-Perez","sequence":"additional","affiliation":[{"name":"Center for AIDS Research, Program in Molecular Medicine and Department of Molecular Genetics and Microbiology, 373 Plantation Street, University of Massachusetts Medical School, Worcester, Massachusetts 01605"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Leanne","family":"Stones","sequence":"additional","affiliation":[{"name":"School of Molecular Medical Sciences, The University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chiambah","family":"Ankghuambom","sequence":"additional","affiliation":[{"name":"School of Molecular Medical Sciences, The University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kemebradikumo","family":"Pondei","sequence":"additional","affiliation":[{"name":"School of Molecular Medical Sciences, The University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"C. Patrick","family":"McClure","sequence":"additional","affiliation":[{"name":"School of Molecular Medical Sciences, The University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"George","family":"Alemnji","sequence":"additional","affiliation":[{"name":"Faculty of Medicine and Bio-Medical Sciences, University of Yaounde I, Yaounde, Cameroon"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stephen","family":"Taylor","sequence":"additional","affiliation":[{"name":"Department of Sexual Health and HIV Medicine, Directorate of Infection, Birmingham Heartlands Hospital, Heart of England NHS Foundation Trust, Birmingham B9 5SS, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Paul M.","family":"Sharp","sequence":"additional","affiliation":[{"name":"Institute of Evolutionary Biology, University of Edinburgh, Kings Buildings, Edinburgh EH9 3JT, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Paul R.","family":"Clapham","sequence":"additional","affiliation":[{"name":"Center for AIDS Research, Program in Molecular Medicine and Department of Molecular Genetics and Microbiology, 373 Plantation Street, University of Massachusetts Medical School, Worcester, Massachusetts 01605"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jonathan K.","family":"Ball","sequence":"additional","affiliation":[{"name":"School of Molecular Medical Sciences, The University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","reference":[{"key":"e_1_3_3_2_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.meegid.2004.08.006"},{"key":"e_1_3_3_3_2","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.00463-07"},{"key":"e_1_3_3_4_2","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.01403-06"},{"issue":"4","key":"e_1_3_3_5_2","first-page":"67","article-title":"Genomic variation of human immunodeficiency virus type 1 (HIV-1): molecular analyses of HIV-1 in sequential blood samples and various organs obtained at autopsy","volume":"75","author":"Ball J. K.","year":"1994","unstructured":"BallJ. K. HolmesE. C. WhitwellH. DesselbergerU.. 1994. Genomic variation of human immunodeficiency virus type 1 (HIV-1): molecular analyses of HIV-1 in sequential blood samples and various organs obtained at autopsy. J. Gen. Virol. 75(Pt. 4):67\u201379.","journal-title":"J. Gen. Virol."},{"key":"e_1_3_3_6_2","doi-asserted-by":"publisher","DOI":"10.1016\/S1470-2045(02)00776-3"},{"key":"e_1_3_3_7_2","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.00872-07"},{"key":"e_1_3_3_8_2","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.80.5.2472-2482.2006"},{"key":"e_1_3_3_9_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0092-8674(00)81313-6"},{"key":"e_1_3_3_10_2","doi-asserted-by":"publisher","DOI":"10.1056\/NEJMra025195"},{"key":"e_1_3_3_11_2","doi-asserted-by":"publisher","DOI":"10.1002\/jmv.2186"},{"key":"e_1_3_3_12_2","doi-asserted-by":"publisher","DOI":"10.1128\/jvi.66.9.5642-5645.1992"},{"key":"e_1_3_3_13_2","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.72.1.617-623.1998"},{"key":"e_1_3_3_14_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bti607"},{"key":"e_1_3_3_15_2","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.49.11.4721-4732.2005"},{"key":"e_1_3_3_16_2","doi-asserted-by":"publisher","DOI":"10.1128\/mcb.7.1.379-387.1987"},{"key":"e_1_3_3_17_2","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.02133-08"},{"key":"e_1_3_3_18_2","doi-asserted-by":"publisher","DOI":"10.1186\/1742-4690-6-69"},{"key":"e_1_3_3_19_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0605513103"},{"key":"e_1_3_3_20_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1096-0031.1994.tb00181.x"},{"key":"e_1_3_3_21_2","doi-asserted-by":"publisher","DOI":"10.1128\/jvi.70.3.1651-1667.1996"},{"key":"e_1_3_3_22_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.1070441"},{"key":"e_1_3_3_23_2","doi-asserted-by":"publisher","DOI":"10.1097\/00002030-200402200-00011"},{"key":"e_1_3_3_24_2","doi-asserted-by":"publisher","DOI":"10.1080\/10635150390235520"},{"key":"e_1_3_3_25_2","doi-asserted-by":"publisher","DOI":"10.1086\/315644"},{"key":"e_1_3_3_26_2","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.74.3.1234-1240.2000"},{"key":"e_1_3_3_27_2","doi-asserted-by":"crossref","first-page":"298","DOI":"10.4049\/jimmunol.146.1.298","article-title":"Enhanced HIV replication in macrophage colony-stimulating factor-treated monocytes","volume":"146","author":"Kalter D. C.","year":"1991","unstructured":"KalterD. C. . 1991. Enhanced HIV replication in macrophage colony-stimulating factor-treated monocytes. J. Immunol. 146:298\u2013306.","journal-title":"J. Immunol."},{"key":"e_1_3_3_28_2","doi-asserted-by":"publisher","DOI":"10.1128\/jvi.68.11.7467-7481.1994"},{"key":"e_1_3_3_29_2","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msl051"},{"key":"e_1_3_3_30_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btl474"},{"key":"e_1_3_3_31_2","doi-asserted-by":"publisher","DOI":"10.1038\/31405"},{"key":"e_1_3_3_32_2","doi-asserted-by":"publisher","DOI":"10.1038\/nm992"},{"key":"e_1_3_3_33_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0306764101"},{"key":"e_1_3_3_34_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.virol.2009.05.023"},{"key":"e_1_3_3_35_2","doi-asserted-by":"publisher","DOI":"10.1038\/nature07159"},{"key":"e_1_3_3_36_2","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.73.1.152-160.1999"},{"key":"e_1_3_3_37_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0092-8674(01)00234-3"},{"key":"e_1_3_3_38_2","doi-asserted-by":"publisher","DOI":"10.1038\/nature01709"},{"key":"e_1_3_3_39_2","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.00598-07"},{"key":"e_1_3_3_40_2","doi-asserted-by":"publisher","DOI":"10.1128\/jvi.69.8.5087-5094.1995"},{"key":"e_1_3_3_41_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bth490"},{"key":"e_1_3_3_42_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0166-0934(00)00179-8"},{"key":"e_1_3_3_43_2","doi-asserted-by":"publisher","DOI":"10.1093\/brain\/awh695"},{"key":"e_1_3_3_44_2","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.02187-10"},{"key":"e_1_3_3_45_2","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.00083-07"},{"key":"e_1_3_3_46_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.virol.2008.09.017"},{"key":"e_1_3_3_47_2","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.74.21.10074-10080.2000"},{"key":"e_1_3_3_48_2","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.77.22.12336-12345.2003"},{"key":"e_1_3_3_49_2","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.78.13.6915-6926.2004"},{"key":"e_1_3_3_50_2","doi-asserted-by":"publisher","DOI":"10.1186\/1742-4690-5-5"},{"key":"e_1_3_3_51_2","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.02328-05"},{"key":"e_1_3_3_52_2","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.79.1.353-363.2005"},{"key":"e_1_3_3_53_2","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.79.3.1734-1742.2005"},{"key":"e_1_3_3_54_2","doi-asserted-by":"publisher","DOI":"10.1093\/brain\/awl136"},{"key":"e_1_3_3_55_2","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.72.4.2855-2864.1998"},{"key":"e_1_3_3_56_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/14.9.817"},{"key":"e_1_3_3_57_2","doi-asserted-by":"publisher","DOI":"10.1007\/BF00163230"},{"key":"e_1_3_3_58_2","doi-asserted-by":"publisher","DOI":"10.1038\/374124b0"},{"key":"e_1_3_3_59_2","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.02050-06"},{"key":"e_1_3_3_60_2","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.00056-10"},{"key":"e_1_3_3_61_2","first-page":"406","article-title":"The neighbor-joining method: a new method for reconstructing phylogenetic trees","volume":"4","author":"Saitou N.","year":"1987","unstructured":"SaitouN. NeiM.. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:406\u2013425.","journal-title":"Mol. Biol. Evol."},{"key":"e_1_3_3_62_2","doi-asserted-by":"publisher","DOI":"10.1128\/jvi.68.8.5280-5283.1994"},{"key":"e_1_3_3_63_2","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.02660-07"},{"key":"e_1_3_3_64_2","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.79.17.11343-11352.2005"},{"key":"e_1_3_3_65_2","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.76.14.7293-7305.2002"},{"key":"e_1_3_3_66_2","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.00823-10"},{"key":"e_1_3_3_67_2","doi-asserted-by":"publisher","DOI":"10.1038\/nature05818"},{"key":"e_1_3_3_68_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1000395"},{"key":"e_1_3_3_69_2","doi-asserted-by":"publisher","DOI":"10.1099\/0022-1317-77-5-1071"},{"key":"e_1_3_3_70_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.virol.2010.04.008"},{"key":"e_1_3_3_71_2","doi-asserted-by":"publisher","DOI":"10.1128\/jvi.64.12.5840-5850.1990"},{"key":"e_1_3_3_72_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1000418"},{"key":"e_1_3_3_73_2","doi-asserted-by":"publisher","DOI":"10.1007\/BF00182389"},{"key":"e_1_3_3_74_2","doi-asserted-by":"publisher","DOI":"10.1128\/jvi.69.1.422-429.1995"},{"key":"e_1_3_3_75_2","doi-asserted-by":"publisher","DOI":"10.1093\/oxfordjournals.molbev.a026045"},{"key":"e_1_3_3_76_2","volume-title":"PAUP*: phylogenetic analysis using parsimony (*and other methods), version 4","author":"Swofford D. L.","year":"2003","unstructured":"SwoffordD. L. 2003. PAUP*: phylogenetic analysis using parsimony (*and other methods), version 4. Sinauer Associates, Sunderland, MA."},{"key":"e_1_3_3_77_2","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msm092"},{"key":"e_1_3_3_78_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.virol.2009.02.020"},{"key":"e_1_3_3_79_2","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.02619-09"},{"key":"e_1_3_3_80_2","doi-asserted-by":"publisher","DOI":"10.1186\/1742-4690-4-87"},{"key":"e_1_3_3_81_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0000271"},{"key":"e_1_3_3_82_2","doi-asserted-by":"publisher","DOI":"10.1097\/00002030-199902250-00002"},{"key":"e_1_3_3_83_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.1152622"},{"key":"e_1_3_3_84_2","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.79.8.4828-4837.2005"},{"key":"e_1_3_3_85_2","doi-asserted-by":"publisher","DOI":"10.1038\/nature08237"},{"key":"e_1_3_3_86_2","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.46.6.1896-1905.2002"},{"key":"e_1_3_3_87_2","doi-asserted-by":"publisher","DOI":"10.1038\/nature01470"},{"key":"e_1_3_3_88_2","unstructured":"WHO\/UNAIDS. 2007. AIDS epidemic update. WHO\/UNAIDS Geneva Switzerland. http:\/\/data.unaids.org\/pub\/epislides\/2007\/2007_epiupdate_en.pdf."},{"key":"e_1_3_3_89_2","doi-asserted-by":"publisher","DOI":"10.1007\/BF00178256"},{"key":"e_1_3_3_90_2","doi-asserted-by":"publisher","DOI":"10.1007\/BF00160154"},{"key":"e_1_3_3_91_2","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.02268-06"},{"key":"e_1_3_3_92_2","doi-asserted-by":"publisher","DOI":"10.1038\/nature05580"},{"key":"e_1_3_3_93_2","doi-asserted-by":"publisher","DOI":"10.1038\/nature04817"},{"key":"e_1_3_3_94_2","doi-asserted-by":"publisher","DOI":"10.1128\/jvi.70.5.3098-3107.1996"}],"container-title":["Journal of Virology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/JVI.00131-11","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/JVI.00131-11","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,6,6]],"date-time":"2023-06-06T05:02:36Z","timestamp":1686027756000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.asm.org\/doi\/10.1128\/JVI.00131-11"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2011,6,15]]},"references-count":93,"journal-issue":{"issue":"12","published-print":{"date-parts":[[2011,6,15]]}},"alternative-id":["10.1128\/JVI.00131-11"],"URL":"https:\/\/doi.org\/10.1128\/jvi.00131-11","relation":{},"ISSN":["0022-538X","1098-5514"],"issn-type":[{"value":"0022-538X","type":"print"},{"value":"1098-5514","type":"electronic"}],"subject":[],"published":{"date-parts":[[2011,6,15]]},"assertion":[{"value":"2011-01-19","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2011-03-30","order":1,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2011-05-19","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}]}}