{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,31]],"date-time":"2025-10-31T14:26:46Z","timestamp":1761920806063,"version":"3.41.2"},"reference-count":98,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2020,11,9]],"date-time":"2020-11-09T00:00:00Z","timestamp":1604880000000},"content-version":"vor","delay-in-days":131,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Medical Research Fund, Oxford University (MRF 1090) (A.K.N.I.), the EPSRC"},{"name":"Hendrik Muller"},{"DOI":"10.13039\/501100004040","name":"KU Leuven","doi-asserted-by":"publisher","award":["OT\/14\/115"],"award-info":[{"award-number":["OT\/14\/115"]}],"id":[{"id":"10.13039\/501100004040","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Research Foundation \u2013 Flanders"},{"name":"\u2018Fonds voor Wetenschappelijk Onderzoek \u2013 Vlaanderen\u2019","award":["G066215N","G0D5117N","G0B9317N"],"award-info":[{"award-number":["G066215N","G0D5117N","G0B9317N"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,7,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Pathogen-driven selection and past interbreeding with archaic human lineages have resulted in differences in human leukocyte antigen (HLA)-allele frequencies between modern human populations. Whether or not this variation affects pathogen subtype diversification is unknown. Here we show a strong positive correlation between ethnic diversity in African countries and both human immunodeficiency virus (HIV)-1 p24gag and subtype diversity. We demonstrate that ethnic HLA-allele differences between populations have influenced HIV-1 subtype diversification as the virus adapted to escape common antiviral immune responses. The evolution of HIV Subtype B (HIV-B), which does not appear to be indigenous to Africa, is strongly affected by immune responses associated with Eurasian HLA variants acquired through adaptive introgression from Neanderthals and Denisovans. Furthermore, we show that the increasing and disproportionate number of HIV-infections among African Americans in the USA drive HIV-B evolution towards an Africa-centric HIV-1 state. Similar adaptation of other pathogens to HLA variants common in affected populations is likely.<\/jats:p>","DOI":"10.1093\/ve\/veaa085","type":"journal-article","created":{"date-parts":[[2020,10,30]],"date-time":"2020-10-30T20:13:21Z","timestamp":1604088801000},"source":"Crossref","is-referenced-by-count":8,"title":["HIV-1 p24Gag adaptation to modern and archaic HLA-allele frequency differences in ethnic groups contributes to viral subtype diversification"],"prefix":"10.1093","volume":"6","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1081-6594","authenticated-orcid":false,"given":"Nicolaas C","family":"Kist","sequence":"first","affiliation":[{"name":"Division of Clinical Neurology, Nuffield Department of Clinical Neurosciences, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK"},{"name":"Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ben","family":"Lambert","sequence":"additional","affiliation":[{"name":"Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK"},{"name":"Department of Infectious Disease Epidemiology, School of Public Health, Faculty of Medicine, Imperial College London, Medical School Building St Mary\u2019s Campus, Norfolk Place, London W2 1PG, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Samuel","family":"Campbell","sequence":"additional","affiliation":[{"name":"Division of Clinical Neurology, Nuffield Department of Clinical Neurosciences, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK"},{"name":"Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5665-4041","authenticated-orcid":false,"given":"Aris","family":"Katzourakis","sequence":"additional","affiliation":[{"name":"Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Daniel","family":"Lunn","sequence":"additional","affiliation":[{"name":"Department of Statistics, University of Oxford, St Giles\u2019, Oxford OX1 3LB, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2826-5353","authenticated-orcid":false,"given":"Philippe","family":"Lemey","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven - University of Leuven, Leuven B-3000, Belgium"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3507-5956","authenticated-orcid":false,"given":"Astrid K N","family":"Iversen","sequence":"additional","affiliation":[{"name":"Division of Clinical Neurology, Nuffield Department of Clinical Neurosciences, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2020,12,12]]},"reference":[{"key":"2020121305533509800_veaa085-B1","doi-asserted-by":"crossref","first-page":"89","DOI":"10.1126\/science.1209202","article-title":"The Shaping of Modern Human Immune Systems by Multiregional Admixture with Archaic Humans","volume":"334","author":"Abi-Rached","year":"2011","journal-title":"Science"},{"key":"2020121305533509800_veaa085-B2","doi-asserted-by":"crossref","first-page":"507","DOI":"10.1097\/QAD.0b013e32835cab64","article-title":"Rapid, Complex Adaptation of Transmitted HIV-1 Full-Length Genomes in Subtype C-Infected Individuals with Differing Disease Progression","volume":"27","author":"Abrahams","year":"2013","journal-title":"Aids (London, England)"},{"key":"2020121305533509800_veaa085-B3","doi-asserted-by":"crossref","first-page":"155","DOI":"10.1023\/A:1024471506938","article-title":"Fractionalization","volume":"8","author":"Alesina","year":"2003","journal-title":"Journal of Economic Growth"},{"key":"2020121305533509800_veaa085-B4","doi-asserted-by":"crossref","first-page":"471","DOI":"10.1089\/aid.2015.0380","article-title":"Phylogenetic Analysis of Ethiopian HIV-1 Subtype C near Full-Length Genomes Reveals High Intrasubtype Diversity and a Strong Geographical Cluster","volume":"32","author":"Amogne","year":"2016","journal-title":"AIDS Research and Human Retroviruses"},{"key":"2020121305533509800_veaa085-B5","doi-asserted-by":"crossref","first-page":"2157","DOI":"10.1093\/molbev\/mss084","article-title":"Improving the Accuracy of Demographic and Molecular Clock Model Comparison While Accommodating Phylogenetic Uncertainty","volume":"29","author":"Baele","year":"2012","journal-title":"Molecular Biology and Evolution"},{"key":"2020121305533509800_veaa085-B6","doi-asserted-by":"crossref","first-page":"239","DOI":"10.1093\/molbev\/mss243","article-title":"Accurate Model Selection of Relaxed Molecular Clocks in Bayesian Phylogenetics","volume":"30","author":"Baele","year":"2013","journal-title":"Molecular Biology and Evolution"},{"key":"2020121305533509800_veaa085-B7","doi-asserted-by":"crossref","first-page":"153","DOI":"10.1146\/annurev.med.042508.093728","article-title":"HIV-1 Vaccine Development after STEP","volume":"61","author":"Barouch","year":"2010","journal-title":"Annual Review of Medicine"},{"key":"2020121305533509800_veaa085-B8","doi-asserted-by":"crossref","first-page":"90","DOI":"10.1111\/j.1469-1809.2007.00398.x","article-title":"Admixture and Population Stratification in African Caribbean Populations","volume":"72","author":"Benn-Torres","year":"2008","journal-title":"Annals of Human Genetics"},{"key":"2020121305533509800_veaa085-B9","doi-asserted-by":"crossref","first-page":"1583","DOI":"10.1126\/science.1131528","article-title":"Founder Effects in the Assessment of HIV Polymorphisms and HLA Allele Associations","volume":"315","author":"Bhattacharya","year":"2007","journal-title":"Science"},{"key":"2020121305533509800_veaa085-B10","doi-asserted-by":"crossref","first-page":"1620","DOI":"10.1093\/infdis\/jiz368","article-title":"HLA-I Associated Adaptation Dampens CD8 T-Cell Responses in HIV Ad5-Vectored Vaccine Recipients","volume":"220","author":"Boppana","year":"2019","journal-title":"The Journal of Infectious Diseases"},{"key":"2020121305533509800_veaa085-B11","doi-asserted-by":"crossref","first-page":"434","DOI":"10.1080\/10618600.1998.10474787","article-title":"General Method for Monitoring Convergence of Iterative Simulations","volume":"7","author":"Brooks","year":"1998","journal-title":"Journal of Computational and Graphical Statistics"},{"year":"2017","author":"Busby","key":"2020121305533509800_veaa085-B12","doi-asserted-by":"publisher","DOI":"10.1101\/205252"},{"key":"2020121305533509800_veaa085-B13","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.15266","article-title":"Admixture into and within Sub-Saharan Africa","volume":"5","author":"Busby","year":"2016","journal-title":"eLife"},{"key":"2020121305533509800_veaa085-B14","doi-asserted-by":"crossref","first-page":"293","DOI":"10.1111\/j.0001-2815.2004.00192.x","article-title":"Differentiation between African Populations is Evidenced by the Diversity of Alleles and Haplotypes of HLA Class I Loci","volume":"63","author":"Cao","year":"2004","journal-title":"Tissue Antigens"},{"key":"2020121305533509800_veaa085-B15","doi-asserted-by":"crossref","first-page":"e1000225","DOI":"10.1371\/journal.pcbi.1000225","article-title":"Phylogenetic Dependency Networks: Inferring Patterns of CTL Escape and Codon Covariation in HIV-1 Gag","volume":"4","author":"Carlson","year":"2008","journal-title":"PLoS Computational Biology"},{"key":"2020121305533509800_veaa085-B16","doi-asserted-by":"crossref","first-page":"1254031","DOI":"10.1126\/science.1254031","article-title":"HIV Transmission. Selection Bias at the Heterosexual HIV-1 Transmission Bottleneck","volume":"345","author":"Carlson","year":"2014","journal-title":"Science"},{"key":"2020121305533509800_veaa085-B17","doi-asserted-by":"crossref","first-page":"212","DOI":"10.1016\/j.tim.2014.12.008","article-title":"HIV-1 Adaptation to HLA: A Window into Virus-Host Immune Interactions\u2019","volume":"23","author":"Carlson","year":"2015","journal-title":"Trends in Microbiology"},{"key":"2020121305533509800_veaa085-B18","doi-asserted-by":"crossref","first-page":"606","DOI":"10.1038\/nm.4100","article-title":"Impact of Pre-Adapted HIV Transmission","volume":"22","author":"Carlson","year":"2016","journal-title":"Nature Medicine"},{"key":"2020121305533509800_veaa085-B19","doi-asserted-by":"crossref","first-page":"1","DOI":"10.18637\/jss.v076.i01","article-title":"Stan: A Probabilistic Programming Language","volume":"76","author":"Carpenter","year":"2017","journal-title":"Journal of Statistical Software"},{"year":"2020","author":"Centers for Disease Control and Prevention","key":"2020121305533509800_veaa085-B20"},{"key":"2020121305533509800_veaa085-B21","doi-asserted-by":"crossref","first-page":"11253","DOI":"10.1038\/srep11253","article-title":"HIV-Infected Sex Workers with Beneficial HLA-Variants Are Potential Hubs for Selection of HIV-1 Recombinants That May Affect Disease Progression","volume":"5","author":"Chang","year":"2015","journal-title":"Scientific Reports"},{"key":"2020121305533509800_veaa085-B22","doi-asserted-by":"crossref","first-page":"677","DOI":"10.1016\/j.cell.2020.01.012","article-title":"Identifying and Interpreting Apparent Neanderthal Ancestry in African Individuals","volume":"180","author":"Chen","year":"2020","journal-title":"Cell"},{"key":"2020121305533509800_veaa085-B23","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1097\/QAD.0b013e32830e6d6d","article-title":"Post-Step Modifications for Research on HIV Vaccines","volume":"23","author":"Corey","year":"2009","journal-title":"AIDS"},{"key":"2020121305533509800_veaa085-B24","doi-asserted-by":"crossref","first-page":"e1004295","DOI":"10.1371\/journal.pgen.1004295","article-title":"Genotypic and Functional Impact of HIV-1 Adaptation to Its Host Population during the North American Epidemic","volume":"10","author":"Cotton","year":"2014","journal-title":"PLoS Genetics"},{"key":"2020121305533509800_veaa085-B25","doi-asserted-by":"crossref","first-page":"1384","DOI":"10.1128\/JVI.01879-10","article-title":"The Hypervariable HIV-1 Capsid Protein Residues Comprise HLA-Driven CD8+ T-Cell Escape Mutations and Covarying HLA-Independent Polymorphisms","volume":"85","author":"Crawford","year":"2011","journal-title":"Journal of Virology"},{"key":"2020121305533509800_veaa085-B26","doi-asserted-by":"crossref","first-page":"11530","DOI":"10.1073\/pnas.1105315108","article-title":"Coordinate Linkage of HIV Evolution Reveals Regions of Immunological Vulnerability","volume":"108","author":"Dahirel","year":"2011","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"key":"2020121305533509800_veaa085-B27","doi-asserted-by":"crossref","first-page":"102","DOI":"10.1186\/1471-2148-12-102","article-title":"Bayesian Models for Comparative Analysis Integrating Phylogenetic Uncertainty","volume":"12","author":"de Villemereuil","year":"2012","journal-title":"BMC Evolutionary Biology"},{"key":"2020121305533509800_veaa085-B28","doi-asserted-by":"crossref","first-page":"50","DOI":"10.1038\/256050a0","article-title":"Enhanced Immunological Surveillance in Mice Heterozygous at the H-2 Gene Complex","volume":"256","author":"Doherty","year":"1975","journal-title":"Nature"},{"year":"2017","author":"Erban","key":"2020121305533509800_veaa085-B29"},{"year":"2020","author":"Ethnologue","key":"2020121305533509800_veaa085-B30"},{"key":"2020121305533509800_veaa085-B31","doi-asserted-by":"crossref","first-page":"151","DOI":"10.1002\/ajpa.1330300510","article-title":"Genetics and the History of Sub-Saharan Africa","volume":"30","author":"Excoffier","year":"1987","journal-title":"American Journal of Physical Anthropology"},{"key":"2020121305533509800_veaa085-B32","first-page":"273","article-title":"Spatial Differentiation of RH and GM Haplotype Frequencies in Sub-Saharan Africa and Its Relation to Linguistic Affinities","volume":"63","author":"Excoffier","year":"1991","journal-title":"Human Biology"},{"key":"2020121305533509800_veaa085-B33","doi-asserted-by":"crossref","first-page":"56","DOI":"10.1126\/science.1256739","article-title":"HIV Epidemiology. The Early Spread and Epidemic Ignition of HIV-1 in Human Populations","volume":"346","author":"Faria","year":"2014","journal-title":"Science"},{"key":"2020121305533509800_veaa085-B34","doi-asserted-by":"crossref","first-page":"14145","DOI":"10.1073\/pnas.2334336100","article-title":"Lytic versus Stimulatory Synapse in Cytotoxic T Lymphocyte\/Target Cell Interaction: Manifestation of a Dual Activation Threshold","volume":"100","author":"Faroudi","year":"2003","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"key":"2020121305533509800_veaa085-B35","doi-asserted-by":"crossref","first-page":"861","DOI":"10.1016\/j.patrec.2005.10.010","article-title":"An Introduction to ROC Analysis","volume":"27","author":"Fawcett","year":"2006","journal-title":"Pattern Recognition Letters"},{"year":"2001","author":"Felix","key":"2020121305533509800_veaa085-B36"},{"key":"2020121305533509800_veaa085-B37","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1086\/284325","article-title":"Phylogenies and the Comparative Method","volume":"125","author":"Felsenstein","year":"1985","journal-title":"The American Naturalist"},{"key":"2020121305533509800_veaa085-B38","doi-asserted-by":"crossref","DOI":"10.2172\/1458915","volume-title":"HIV Sequence Compendium 2018 (Theoretical Biology and Biophysics)","author":"Foley","year":"2018"},{"key":"2020121305533509800_veaa085-B39","doi-asserted-by":"crossref","first-page":"173","DOI":"10.1038\/ni1281","article-title":"Control of Human Immunodeficiency Virus Replication by Cytotoxic T Lymphocytes Targeting Subdominant Epitopes","volume":"7","author":"Frahm","year":"2006","journal-title":"Nature Immunology"},{"key":"2020121305533509800_veaa085-B40","doi-asserted-by":"crossref","first-page":"712","DOI":"10.1086\/343873","article-title":"Phylogenetic Analysis and Comparative Data: A Test and Review of Evidence","volume":"160","author":"Freckleton","year":"2002","journal-title":"The American Naturalist"},{"key":"2020121305533509800_veaa085-B41","doi-asserted-by":"crossref","first-page":"8568","DOI":"10.1128\/JVI.07020-11","article-title":"Cytotoxic T-Lymphocyte Escape Mutations Identified by HLA Association Favor Those Which Escape and Revert Rapidly","volume":"86","author":"Fryer","year":"2012","journal-title":"Journal of Virology"},{"year":"2009","author":"Gelman","key":"2020121305533509800_veaa085-B42"},{"key":"2020121305533509800_veaa085-B43","doi-asserted-by":"crossref","first-page":"457","DOI":"10.1214\/ss\/1177011136","article-title":"Inference from Iterative Simulation Using Multiple Sequences","volume":"7","author":"Gelman","year":"1992","journal-title":"Statistical Science"},{"key":"2020121305533509800_veaa085-B44","doi-asserted-by":"crossref","first-page":"1360","DOI":"10.1214\/08-AOAS191","article-title":"A Weakly Informative Default Prior Distribution for Logistic and Other Regression Models","volume":"2","author":"Gelman","year":"2008","journal-title":"The Annals of Applied Statistics"},{"key":"2020121305533509800_veaa085-B45","doi-asserted-by":"crossref","first-page":"18566","DOI":"10.1073\/pnas.0705329104","article-title":"The Emergence of HIV\/AIDS in the Americas and Beyond","volume":"104","author":"Gilbert","year":"2007","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"volume-title":"The Tumultous History - From Pearl of the Caribbean to Broken Nation.","year":"2010","author":"Giraud","key":"2020121305533509800_veaa085-B46"},{"key":"2020121305533509800_veaa085-B47","doi-asserted-by":"crossref","first-page":"D784","DOI":"10.1093\/nar\/gku1166","article-title":"Allele Frequency Net 2015 Update: New Features for HLA Epitopes, KIR and Disease and HLA Adverse Drug Reaction Associations","volume":"43","author":"Gonzalez-Galarza","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2020121305533509800_veaa085-B48","doi-asserted-by":"crossref","first-page":"426","DOI":"10.1016\/j.immuni.2012.09.005","article-title":"HIV and HLA Class I: An Evolving Relationship","volume":"37","author":"Goulder","year":"2012","journal-title":"Immunity"},{"key":"2020121305533509800_veaa085-B49","doi-asserted-by":"crossref","first-page":"619","DOI":"10.1038\/nri2357","article-title":"Impact of MHC Class I Diversity on Immune Control of Immunodeficiency Virus Replication","volume":"8","author":"Goulder","year":"2008","journal-title":"Nature Reviews Immunology"},{"key":"2020121305533509800_veaa085-B50","doi-asserted-by":"crossref","first-page":"334","DOI":"10.1038\/35085576","article-title":"Evolution and Transmission of Stable CTL Escape Mutations in HIV Infection","volume":"412","author":"Goulder","year":"2001","journal-title":"Nature"},{"key":"2020121305533509800_veaa085-B51","doi-asserted-by":"crossref","first-page":"1313","DOI":"10.1016\/j.humimm.2013.06.025","article-title":"Six-Locus High Resolution HLA Haplotype Frequencies Derived from Mixed-Resolution DNA Typing for the Entire US Donor Registry","volume":"74","author":"Gragert","year":"2013","journal-title":"Human Immunology"},{"key":"2020121305533509800_veaa085-B52","doi-asserted-by":"crossref","first-page":"520","DOI":"10.1001\/jama.300.5.520","article-title":"Estimation of HIV Incidence in the United States","volume":"300","author":"Hall","year":"2008","journal-title":"JAMA"},{"key":"2020121305533509800_veaa085-B53","doi-asserted-by":"crossref","first-page":"679","DOI":"10.1097\/QAD.0b013e328342ff93","article-title":"Global Trends in Molecular Epidemiology of HIV-1 during 2000-2007","volume":"25","author":"Hemelaar","year":"2011","journal-title":"AIDS (London, England)"},{"key":"2020121305533509800_veaa085-B54","doi-asserted-by":"crossref","first-page":"456","DOI":"10.1126\/science.aap8369","article-title":"The Earliest Modern Humans outside Africa","volume":"359","author":"Hershkovitz","year":"2018","journal-title":"Science"},{"year":"2016","author":"HIV Molecular Immunology Compendium","key":"2020121305533509800_veaa085-B55"},{"key":"2020121305533509800_veaa085-B56","doi-asserted-by":"crossref","first-page":"291","DOI":"10.1101\/gr.196634.115","article-title":"Model-Based Analyses of Whole-Genome Data Reveal a Complex Evolutionary History Involving Archaic Introgression in Central African Pygmies","volume":"26","author":"Hsieh","year":"2016","journal-title":"Genome Research"},{"key":"2020121305533509800_veaa085-B57","doi-asserted-by":"crossref","first-page":"1010","DOI":"10.1016\/j.cell.2019.02.035","article-title":"Multiple Deeply Divergent Denisovan Ancestries in Papuans","volume":"177","author":"Jacobs","year":"2019","journal-title":"Cell"},{"key":"2020121305533509800_veaa085-B58","doi-asserted-by":"crossref","first-page":"e225","DOI":"10.1371\/journal.pone.0000225","article-title":"Sequential Broadening of CTL Responses in Early HIV-1 Infection is Associated with Viral Escape","volume":"2","author":"Karlsson","year":"2007","journal-title":"PLoS One"},{"key":"2020121305533509800_veaa085-B59","doi-asserted-by":"crossref","first-page":"641","DOI":"10.1038\/nature07746","article-title":"Adaptation of HIV-1 to Human Leukocyte Antigen Class I","volume":"458","author":"Kawashima","year":"2009","journal-title":"Nature"},{"key":"2020121305533509800_veaa085-B60","doi-asserted-by":"crossref","first-page":"7552","DOI":"10.1073\/pnas.0802203105","article-title":"Identification and Characterization of Transmitted and Early Founder Virus Envelopes in Primary HIV-1 Infection","volume":"105","author":"Keele","year":"2008","journal-title":"Proceedings of the National Academy of Sciences"},{"key":"2020121305533509800_veaa085-B61","doi-asserted-by":"crossref","first-page":"46","DOI":"10.1038\/nm1520","article-title":"CD8+ T-Cell Responses to Different HIV Proteins Have Discordant Associations with Viral Load","volume":"13","author":"Kiepiela","year":"2007","journal-title":"Nature Medicine"},{"key":"2020121305533509800_veaa085-B62","doi-asserted-by":"crossref","first-page":"1244","DOI":"10.1128\/JVI.02353-15","article-title":"Population-Level Immune-Mediated Adaptation in HIV-1 Polymerase during the North American Epidemic","volume":"90","author":"Kinloch","year":"2016","journal-title":"Journal of Virology"},{"volume-title":"International Joint Conference on Artificial Intelligence","year":"1995","author":"Kohavi","key":"2020121305533509800_veaa085-B63"},{"key":"2020121305533509800_veaa085-B64","doi-asserted-by":"crossref","first-page":"282","DOI":"10.1038\/nm992","article-title":"HIV Evolution: CTL Escape Mutation and Reversion after Transmission","volume":"10","author":"Leslie","year":"2004","journal-title":"Nature Medicine"},{"key":"2020121305533509800_veaa085-B65","doi-asserted-by":"crossref","first-page":"891","DOI":"10.1084\/jem.20041455","article-title":"Transmission and Accumulation of CTL Escape Variants Drive Negative Associations between HIV Polymorphisms and HLA","volume":"201","author":"Leslie","year":"2005","journal-title":"Journal of Experimental Medicine"},{"volume-title":"Ethnic Groups Worldwide, a Ready Reference Handbook.","year":"1998","author":"Levinson","key":"2020121305533509800_veaa085-B66"},{"key":"2020121305533509800_veaa085-B67","doi-asserted-by":"crossref","first-page":"8548","DOI":"10.1128\/JVI.00580-08","article-title":"Central Role of Reverting Mutations in HLA Associations with Human Immunodeficiency Virus Set Point","volume":"82","author":"Matthews","year":"2008","journal-title":"Journal of Virology"},{"key":"2020121305533509800_veaa085-B68","doi-asserted-by":"crossref","first-page":"4605","DOI":"10.1128\/JVI.02017-08","article-title":"HLA Footprints on Human Immunodeficiency Virus Type 1 Are Associated with Interclade Polymorphisms and Intraclade Phylogenetic Clustering","volume":"83","author":"Matthews","year":"2009","journal-title":"Journal of Virology"},{"key":"2020121305533509800_veaa085-B69","doi-asserted-by":"crossref","first-page":"786","DOI":"10.1126\/science.356262","article-title":"Synthetic Maps of Human Gene Frequencies in Europeans","volume":"201","author":"Menozzi","year":"1978","journal-title":"Science"},{"key":"2020121305533509800_veaa085-B70","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1007\/s00251-017-1017-3","article-title":"A Genomic Perspective on HLA Evolution","volume":"70","author":"Meyer","year":"2018","journal-title":"Immunogenetics"},{"key":"2020121305533509800_veaa085-B71","doi-asserted-by":"crossref","first-page":"6889","DOI":"10.1128\/JVI.77.12.6889-6898.2003","article-title":"The Differential Ability of HLA B5701+ Long-Term Nonprogressors and Progressors to Restrict Human Immunodeficiency Virus Replication is Not Caused by Loss of Recognition of Autologous Viral Gag Sequences","volume":"77","author":"Migueles","year":"2003","journal-title":"Journal of Virology"},{"key":"2020121305533509800_veaa085-B72","doi-asserted-by":"crossref","first-page":"1439","DOI":"10.1126\/science.1069660","article-title":"Evidence of HIV-1 Adaptation to HLA-Restricted Immune Responses at a Population Level","volume":"296","author":"Moore","year":"2002","journal-title":"Science"},{"key":"2020121305533509800_veaa085-B73","doi-asserted-by":"crossref","first-page":"302","DOI":"10.1038\/nature21347","article-title":"Tracing the Peopling of the World through Genomics","volume":"541","author":"Nielsen","year":"2017","journal-title":"Nature"},{"key":"2020121305533509800_veaa085-B74","doi-asserted-by":"crossref","first-page":"83","DOI":"10.1016\/j.ajhg.2012.05.015","article-title":"Ethiopian Genetic Diversity Reveals Linguistic Stratification and Complex Influences on the Ethiopian Gene Pool","volume":"91","author":"Pagani","year":"2012","journal-title":"The American Journal of Human Genetics"},{"key":"2020121305533509800_veaa085-B75","doi-asserted-by":"crossref","first-page":"543","DOI":"10.1126\/science.aal1988","article-title":"Dispersals and Genetic Adaptation of Bantu-Speaking Populations in Africa and North America","volume":"356","author":"Patin","year":"2017","journal-title":"Science"},{"key":"2020121305533509800_veaa085-B76","doi-asserted-by":"crossref","first-page":"80","DOI":"10.1016\/j.humimm.2011.10.013","article-title":"Human Leukocyte Antigen Class I (A, B, C) and II (DRB1) Diversity in the Black and Caucasian South African Population","volume":"73","author":"Paximadis","year":"2012","journal-title":"Human Immunology"},{"key":"2020121305533509800_veaa085-B77","doi-asserted-by":"crossref","first-page":"885","DOI":"10.1586\/14787210.2013.825443","article-title":"The Origin and Molecular Epidemiology of HIV","volume":"11","author":"Peeters","year":"2013","journal-title":"Expert Review of anti-Infective Therapy"},{"year":"2003","author":"Plummer","key":"2020121305533509800_veaa085-B78"},{"key":"2020121305533509800_veaa085-B79","first-page":"7","article-title":"CODA: Convergence Diagnosis and Output Analysis for MCMC","volume":"6","author":"Plummer","year":"2006","journal-title":"R News"},{"key":"2020121305533509800_veaa085-B80","doi-asserted-by":"crossref","first-page":"e17502","DOI":"10.1371\/journal.pone.0017502","article-title":"Estimated HIV Incidence in the United States, 2006-2009","volume":"6","author":"Prejean","year":"2011","journal-title":"PLoS One"},{"key":"2020121305533509800_veaa085-B81","doi-asserted-by":"crossref","first-page":"524","DOI":"10.1038\/ni1058","article-title":"T Cell Killing Does Not Require the Formation of a Stable Mature Immunological Synapse","volume":"5","author":"Purbhoo","year":"2004","journal-title":"Nature Immunology"},{"key":"2020121305533509800_veaa085-B82","doi-asserted-by":"crossref","first-page":"540","DOI":"10.1038\/nrg2583","article-title":"Evolutionary Analysis of the Dynamics of Viral Infectious Disease","volume":"10","author":"Pybus","year":"2009","journal-title":"Nature Reviews Genetics"},{"key":"2020121305533509800_veaa085-B83","doi-asserted-by":"crossref","first-page":"184","DOI":"10.1016\/j.cell.2019.02.033","article-title":"Human Immunology through the Lens of Evolutionary Genetics","volume":"177","author":"Quintana-Murci","year":"2019","journal-title":"Cell"},{"key":"2020121305533509800_veaa085-B84","doi-asserted-by":"crossref","first-page":"e1007167","DOI":"10.1371\/journal.ppat.1007167","article-title":"Evolution of HIV-1 within Untreated Individuals and at the Population Scale in Uganda","volume":"14","author":"Raghwani","year":"2018","journal-title":"PLoS Pathogens"},{"key":"2020121305533509800_veaa085-B85","doi-asserted-by":"crossref","first-page":"1047","DOI":"10.1038\/35074179","article-title":"Human Immunodeficiency Virus. Phylogeny and the Origin of HIV-1","volume":"410","author":"Rambaut","year":"2001","journal-title":"Nature"},{"key":"2020121305533509800_veaa085-B86","doi-asserted-by":"crossref","first-page":"52","DOI":"10.1038\/nrg1246","article-title":"The Causes and Consequences of HIV Evolution","volume":"5","author":"Rambaut","year":"2004","journal-title":"Nature Reviews Genetics"},{"volume-title":"Who We Are and How we Got Here","year":"2018","author":"Reich","key":"2020121305533509800_veaa085-B87"},{"year":"2016","author":"Saeb","key":"2020121305533509800_veaa085-B88"},{"key":"2020121305533509800_veaa085-B89","doi-asserted-by":"crossref","first-page":"79","DOI":"10.1016\/j.coi.2014.08.002","article-title":"Preserving Immune Diversity through Ancient Inheritance and Admixture","volume":"30","author":"Segurel","year":"2014","journal-title":"Current Opinion in Immunology"},{"key":"2020121305533509800_veaa085-B90","first-page":"331","volume-title":"Public Health Aspects of HIV\/AIDS in Low and Middle Income Countries","author":"Simmons","year":"2009"},{"key":"2020121305533509800_veaa085-B91","doi-asserted-by":"crossref","first-page":"e23469","DOI":"10.1371\/journal.pone.0023469","article-title":"Disparate Associations of HLA Class I Markers with HIV-1 Acquisition and Control of Viremia in an African Population","volume":"6","author":"Song","year":"2011","journal-title":"PLoS One"},{"key":"2020121305533509800_veaa085-B92","doi-asserted-by":"crossref","first-page":"636","DOI":"10.1038\/ni.1728","article-title":"Antigen Processing Influences HIV-Specific Cytotoxic T Lymphocyte Immunodominance","volume":"10","author":"Tenzer","year":"2009","journal-title":"Nature Immunology"},{"key":"2020121305533509800_veaa085-B93","doi-asserted-by":"crossref","first-page":"448","DOI":"10.1016\/j.celrep.2014.03.031","article-title":"HIV-1 Adaptation to Antigen Processing Results in Population-Level Immune Evasion and Affects Subtype Diversification","volume":"7","author":"Tenzer","year":"2014","journal-title":"Cell Reports"},{"key":"2020121305533509800_veaa085-B94","doi-asserted-by":"crossref","first-page":"1035","DOI":"10.1126\/science.1172257","article-title":"The Genetic Structure and History of Africans and African Americans","volume":"324","author":"Tishkoff","year":"2009","journal-title":"Science"},{"key":"2020121305533509800_veaa085-B95","doi-asserted-by":"crossref","first-page":"81","DOI":"10.1097\/00002030-199701000-00012","article-title":"An Association between HIV-1 Subtypes and Mode of Transmission in Cape Town, South Africa","volume":"11","author":"van Harmelen","year":"1997","journal-title":"AIDS (London, England)"},{"key":"2020121305533509800_veaa085-B96","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1097\/00007435-200201000-00007","article-title":"Reducing the Risk of Sexual HIV Transmission: Quantifying the per-Act Risk for HIV on the Basis of Choice of Partner, Sex Act, and Condom Use","volume":"29","author":"Varghese","year":"2002","journal-title":"Sexually Transmitted Diseases"},{"key":"2020121305533509800_veaa085-B97","doi-asserted-by":"crossref","first-page":"661","DOI":"10.1038\/nature07390","article-title":"Direct Evidence of Extensive Diversity of HIV-1 in Kinshasa by 1960","volume":"455","author":"Worobey","year":"2008","journal-title":"Nature"},{"key":"2020121305533509800_veaa085-B98","doi-asserted-by":"crossref","first-page":"98","DOI":"10.1038\/nature19827","article-title":"1970s and \u201cPatient 0\u201d HIV-1 Genomes Illuminate Early HIV\/AIDS History in North America","volume":"539","author":"Worobey","year":"2016","journal-title":"Nature"}],"container-title":["Virus Evolution"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/ve\/advance-article-pdf\/doi\/10.1093\/ve\/veaa085\/34178298\/veaa085.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"http:\/\/academic.oup.com\/ve\/article-pdf\/6\/2\/veaa085\/34886070\/veaa085.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"http:\/\/academic.oup.com\/ve\/article-pdf\/6\/2\/veaa085\/34886070\/veaa085.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,8,16]],"date-time":"2024-08-16T18:16:59Z","timestamp":1723832219000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/ve\/article\/doi\/10.1093\/ve\/veaa085\/5962043"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,7,1]]},"references-count":98,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2020,7,1]]}},"URL":"https:\/\/doi.org\/10.1093\/ve\/veaa085","relation":{},"ISSN":["2057-1577"],"issn-type":[{"type":"electronic","value":"2057-1577"}],"subject":[],"published-other":{"date-parts":[[2020,7]]},"published":{"date-parts":[[2020,7,1]]},"article-number":"veaa085"}}