{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,18]],"date-time":"2026-03-18T01:28:36Z","timestamp":1773797316892,"version":"3.50.1"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1010756","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2023,1,13]],"date-time":"2023-01-13T00:00:00Z","timestamp":1673568000000}}],"reference-count":42,"publisher":"Public Library of Science (PLoS)","issue":"1","license":[{"start":{"date-parts":[[2023,1,3]],"date-time":"2023-01-03T00:00:00Z","timestamp":1672704000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001732","name":"Danmarks Grundforskningsfond","doi-asserted-by":"publisher","award":["126"],"award-info":[{"award-number":["126"]}],"id":[{"id":"10.13039\/501100001732","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"abstract":"<jats:sec id=\"sec001\">\n<jats:title>Background<\/jats:title>\n<jats:p>Infection with human immunodeficiency virus type 1 (HIV) typically results from transmission of a small and genetically uniform viral population. Following transmission, the virus population becomes more diverse because of recombination and acquired mutations through genetic drift and selection. Viral intrahost genetic diversity remains a major obstacle to the cure of HIV; however, the association between intrahost diversity and disease progression markers has not been investigated in large and diverse cohorts for which the majority of the genome has been deep-sequenced. Viral load (VL) is a key progression marker and understanding of its relationship to viral intrahost genetic diversity could help design future strategies for HIV monitoring and treatment.<\/jats:p>\n<\/jats:sec>\n<jats:sec id=\"sec002\">\n<jats:title>Methods<\/jats:title>\n<jats:p>We analysed deep-sequenced viral genomes from 2,650 treatment-naive HIV-infected persons to measure the intrahost genetic diversity of 2,447 genomic codon positions as calculated by Shannon entropy. We tested for associations between VL and amino acid (AA) entropy accounting for sex, age, race, duration of infection, and HIV population structure.<\/jats:p>\n<\/jats:sec>\n<jats:sec id=\"sec003\">\n<jats:title>Results<\/jats:title>\n<jats:p>We confirmed that the intrahost genetic diversity is highest in the <jats:italic>env<\/jats:italic> gene. Furthermore, we showed that mean Shannon entropy is significantly associated with VL, especially in infections of &gt;24 months duration. We identified 16 significant associations between VL (p-value&lt;2.0x10<jats:sup>-5<\/jats:sup>) and Shannon entropy at AA positions which in our association analysis explained 13% of the variance in VL. Finally, equivalent analysis based on variation in HIV consensus sequences explained only 2% of VL variance.<\/jats:p>\n<\/jats:sec>\n<jats:sec id=\"sec004\">\n<jats:title>Conclusions<\/jats:title>\n<jats:p>Our results elucidate that viral intrahost genetic diversity is associated with VL and could be used as a better disease progression marker than HIV consensus sequence variants, especially in infections of longer duration. We emphasize that viral intrahost diversity should be considered when studying viral genomes and infection outcomes.<\/jats:p>\n<\/jats:sec>\n<jats:sec id=\"sec005\">\n<jats:title>Trial registration<\/jats:title>\n<jats:p>Samples included in this study were derived from participants who consented in the clinical trial, START (NCT00867048) (23), run by the International Network for Strategic Initiatives in Global HIV Trials (INSIGHT). All the participant sites are listed here: <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/www.insight-trials.org\/start\/my_phpscript\/participating.php?by=site\" xlink:type=\"simple\">http:\/\/www.insight-trials.org\/start\/my_phpscript\/participating.php?by=site<\/jats:ext-link><\/jats:p>\n<\/jats:sec>","DOI":"10.1371\/journal.pcbi.1010756","type":"journal-article","created":{"date-parts":[[2023,1,3]],"date-time":"2023-01-03T19:27:58Z","timestamp":1672774078000},"page":"e1010756","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":6,"title":["Deep-sequencing of viral genomes from a large and diverse cohort of treatment-naive HIV-infected persons shows associations between intrahost genetic diversity and viral load"],"prefix":"10.1371","volume":"19","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7959-8767","authenticated-orcid":true,"given":"Migle","family":"Gabrielaite","sequence":"first","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2753-5991","authenticated-orcid":true,"given":"Marc","family":"Bennedb\u00e6k","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2982-6258","authenticated-orcid":true,"given":"Malthe Sebro","family":"Rasmussen","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7569-2740","authenticated-orcid":true,"given":"Virginia","family":"Kan","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1375-3146","authenticated-orcid":true,"given":"Hansjakob","family":"Furrer","sequence":"additional","affiliation":[]},{"given":"Robert","family":"Flisiak","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4273-4833","authenticated-orcid":true,"given":"Marcelo","family":"Losso","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8901-7850","authenticated-orcid":true,"given":"Jens D.","family":"Lundgren","sequence":"additional","affiliation":[]},{"name":"INSIGHT START Study Group","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5267-3173","authenticated-orcid":true,"given":"Rasmus L.","family":"Marvig","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2023,1,3]]},"reference":[{"issue":"9","key":"pcbi.1010756.ref001","doi-asserted-by":"crossref","first-page":"e1002251","DOI":"10.1371\/journal.pbio.1002251","article-title":"Extremely High Mutation Rate of HIV-1","volume":"13","author":"JM Cuevas","year":"2015","journal-title":"In Vivo. 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Hightower","year":"2012","journal-title":"Virology"},{"issue":"2","key":"pcbi.1010756.ref011","doi-asserted-by":"crossref","first-page":"363","DOI":"10.1111\/j.2006.0030-1299.14714.x","article-title":"Entropy and diversity","volume":"113","author":"L Jost","year":"2006","journal-title":"Oikos"},{"issue":"5","key":"pcbi.1010756.ref012","doi-asserted-by":"crossref","first-page":"e0177281","DOI":"10.1371\/journal.pone.0177281","article-title":"Association of HIV diversity and virologic outcomes in early antiretroviral treatment: HPTN 052","volume":"12","author":"PJ Palumbo","year":"2017","journal-title":"PLoS ONE"},{"issue":"2","key":"pcbi.1010756.ref013","doi-asserted-by":"crossref","first-page":"e29","DOI":"10.1371\/journal.pcbi.0030029","article-title":"Synonymous substitution rates predict HIV disease progression as a result of underlying replication dynamics","volume":"3","author":"P Lemey","year":"2007","journal-title":"PLoS Comput 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Gabrielaite","year":"2022","journal-title":"Dryad Dataset"},{"issue":"1","key":"pcbi.1010756.ref027","doi-asserted-by":"crossref","first-page":"94","DOI":"10.1093\/bioinformatics\/btu587","article-title":"VirVarSeq: a low-frequency virus variant detection pipeline for Illumina sequencing using adaptive base-calling accuracy filtering","volume":"31","author":"BMP Verbist","year":"2015","journal-title":"Bioinformatics"},{"key":"pcbi.1010756.ref028","doi-asserted-by":"crossref","first-page":"337","DOI":"10.1016\/j.meegid.2013.04.032","article-title":"Automated subtyping of HIV-1 genetic sequences for clinical and surveillance purposes: performance evaluation of the new REGA version 3 and seven other tools","volume":"19","author":"A-C Pineda-Pe\u00f1a","year":"2013","journal-title":"Infect Genet Evol"},{"key":"pcbi.1010756.ref029","unstructured":"R: The R Project for Statistical Computing [Internet]. [cited 2020 Feb 10]. Available from: https:\/\/www.r-project.org\/"},{"issue":"12","key":"pcbi.1010756.ref030","doi-asserted-by":"crossref","first-page":"e190","DOI":"10.1371\/journal.pgen.0020190","article-title":"Population structure and eigenanalysis","volume":"2","author":"N Patterson","year":"2006","journal-title":"PLoS Genet"},{"key":"pcbi.1010756.ref031","unstructured":"Best-defined CTL\/CD8+ Epitope Summary [Internet]. [cited 2021 Mar 8]. Available from: https:\/\/www.hiv.lanl.gov\/content\/immunology\/tables\/optimal_ctl_summary.html"},{"issue":"8","key":"pcbi.1010756.ref032","doi-asserted-by":"crossref","first-page":"1335","DOI":"10.1097\/QAD.0000000000002219","article-title":"The benefit of immediate compared with deferred antiretroviral therapy on CD4+ cell count recovery in early HIV infection","volume":"33","author":"S Sharma","year":"2019","journal-title":"AIDS"},{"key":"pcbi.1010756.ref033","unstructured":"HIV mutation database [Internet]. [cited 2021 Mar 4]. Available from: https:\/\/hivmut.org\/index.php?page=structure&uniprot=P04585"},{"key":"pcbi.1010756.ref034","doi-asserted-by":"crossref","first-page":"e01123","DOI":"10.7554\/eLife.01123","article-title":"A genome-to-genome analysis of associations between human genetic variation, HIV-1 sequence diversity, and viral control","volume":"2","author":"I Bartha","year":"2013","journal-title":"eLife"},{"issue":"12","key":"pcbi.1010756.ref035","doi-asserted-by":"crossref","first-page":"1697","DOI":"10.1097\/01.aids.0000131395.14339.f5","article-title":"Differences in HIV RNA levels before the initiation of antiretroviral therapy among 1864 individuals with known HIV-1 seroconversion dates","volume":"18","author":"G Touloumi","year":"2004","journal-title":"AIDS"},{"issue":"1","key":"pcbi.1010756.ref036","first-page":"380","article-title":"Vertical T cell immunodominance and epitope entropy determine HIV-1 escape","volume":"123","author":"MKP Liu","year":"2013","journal-title":"J Clin Invest"},{"issue":"6","key":"pcbi.1010756.ref037","first-page":"1165","article-title":"Evolution of intrahost HIV-1 genetic diversity during chronic infection","volume":"60","author":"D Shriner","year":"2006","journal-title":"Evolution"},{"issue":"8","key":"pcbi.1010756.ref038","doi-asserted-by":"crossref","first-page":"e12303","DOI":"10.1371\/journal.pone.0012303","article-title":"Transmission of single HIV-1 genomes and dynamics of early immune escape revealed by ultra-deep sequencing","volume":"5","author":"W Fischer","year":"2010","journal-title":"PLoS ONE"},{"issue":"1","key":"pcbi.1010756.ref039","doi-asserted-by":"crossref","first-page":"22","DOI":"10.1186\/s12977-017-0343-8","article-title":"The HIV-1 transmission bottleneck","volume":"14","author":"SM Kariuki","year":"2017","journal-title":"Retrovirology"},{"issue":"7","key":"pcbi.1010756.ref040","doi-asserted-by":"crossref","first-page":"414","DOI":"10.1038\/nrmicro3471","article-title":"Bottlenecks in HIV-1 transmission: insights from the study of founder viruses","volume":"13","author":"SB Joseph","year":"2015","journal-title":"Nat Rev Microbiol"},{"key":"pcbi.1010756.ref041","doi-asserted-by":"crossref","first-page":"65","DOI":"10.1186\/1742-4690-4-65","article-title":"The HIV RNA setpoint theory revisited","volume":"4","author":"RB Geskus","year":"2007","journal-title":"Retrovirology"},{"issue":"12","key":"pcbi.1010756.ref042","doi-asserted-by":"crossref","first-page":"e0189999","DOI":"10.1371\/journal.pone.0189999","article-title":"HIV-1 envelope sequence-based diversity measures for identifying recent infections","volume":"12","author":"A Kafando","year":"2017","journal-title":"PLoS ONE"}],"updated-by":[{"DOI":"10.1371\/journal.pcbi.1010756","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2023,1,13]],"date-time":"2023-01-13T00:00:00Z","timestamp":1673568000000}}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1010756","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,13]],"date-time":"2023-01-13T18:47:06Z","timestamp":1673635626000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1010756"}},"subtitle":[],"editor":[{"given":"Nicola","family":"Segata","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2023,1,3]]},"references-count":42,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2023,1,3]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1010756","relation":{"new_version":[{"id-type":"doi","id":"10.1371\/journal.pcbi.1010756","asserted-by":"object"}]},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,1,3]]}}}