{"id":"https://openalex.org/W7204257682","doi":"https://doi.org/10.64898/2026.08.21.746200","title":"Ultrasensitive single-genome sequencing reveals strong purifying selection in acute HIV- 1 infection","display_name":"Ultrasensitive single-genome sequencing reveals strong purifying selection in acute HIV- 1 infection","publication_year":2026,"publication_date":"2026-08-26","ids":{"openalex":"https://openalex.org/W7204257682","doi":"https://doi.org/10.64898/2026.08.21.746200","pmid":"https://pubmed.ncbi.nlm.nih.gov/42827436","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/13628423"},"language":"en","primary_location":{"id":"doi:10.64898/2026.08.21.746200","doi":"https://doi.org/10.64898/2026.08.21.746200","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.08.21.746200","pdf_url":null,"source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"volume":null,"type":"preprint","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://doi.org/10.64898/2026.08.21.746200","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5064084308","display_name":"Adam A. Capoferri","orcid":"https://orcid.org/0000-0002-6048-2115","observed_orcids":["https://orcid.org/0000-0002-6048-2115"]},"institutions":[{"id":"https://openalex.org/I4210140884","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210140884"]},{"id":"https://openalex.org/I4210149717","display_name":"Center for Cancer Research","ror":"https://ror.org/05bjen692","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210140884","https://openalex.org/I4210149717"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Adam A. Capoferri","raw_affiliation_strings":["HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA"],"raw_orcid":"https://orcid.org/0000-0002-6048-2115","affiliations":[{"raw_affiliation_string":"HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA","institution_ids":["https://openalex.org/I4210140884","https://openalex.org/I4210149717"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040327077","display_name":"Valerie F. Boltz","orcid":"https://orcid.org/0000-0001-8872-5599","observed_orcids":["https://orcid.org/0000-0001-8872-5599"]},"institutions":[{"id":"https://openalex.org/I4210140884","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210140884"]},{"id":"https://openalex.org/I4210149717","display_name":"Center for Cancer Research","ror":"https://ror.org/05bjen692","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210140884","https://openalex.org/I4210149717"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Valerie F. Boltz","raw_affiliation_strings":["HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA","institution_ids":["https://openalex.org/I4210140884","https://openalex.org/I4210149717"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101923609","display_name":"Wei Shao","orcid":"https://orcid.org/0000-0002-3662-5753","observed_orcids":["https://orcid.org/0000-0002-3662-5753"]},"institutions":[{"id":"https://openalex.org/I4210130649","display_name":"Frederick National Laboratory for Cancer Research","ror":"https://ror.org/03v6m3209","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210130649","https://openalex.org/I4210140884"]},{"id":"https://openalex.org/I4396570585","display_name":"Leidos Biomedical Research Inc. (United States)","ror":"https://ror.org/00bardy64","country_code":"US","type":"company","lineage":["https://openalex.org/I114662689","https://openalex.org/I4396570585"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Wei Shao","raw_affiliation_strings":["Leidos Biomedical Research, Inc., Frederick National Laboratories for Cancer Research, Frederick, MD, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Leidos Biomedical Research, Inc., Frederick National Laboratories for Cancer Research, Frederick, MD, USA","institution_ids":["https://openalex.org/I4210130649","https://openalex.org/I4396570585"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5148278491","display_name":"Clarissa Halpern","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I4210140884","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210140884"]},{"id":"https://openalex.org/I4210149717","display_name":"Center for Cancer Research","ror":"https://ror.org/05bjen692","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210140884","https://openalex.org/I4210149717"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Clarissa Halpern","raw_affiliation_strings":["HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA","institution_ids":["https://openalex.org/I4210140884","https://openalex.org/I4210149717"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062482925","display_name":"Rasmi Thomas","orcid":"https://orcid.org/0000-0002-2116-2418","observed_orcids":["https://orcid.org/0000-0002-2116-2418"]},"institutions":[{"id":"https://openalex.org/I92664306","display_name":"Walter Reed Army Institute of Research","ror":"https://ror.org/0145znz58","country_code":"US","type":"government","lineage":["https://openalex.org/I106965489","https://openalex.org/I1304082316","https://openalex.org/I1330347796","https://openalex.org/I2802581893","https://openalex.org/I92664306"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Rasmi Thomas","raw_affiliation_strings":["US Military HIV Research Program, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Sliver Spring MD, USA"],"raw_orcid":"https://orcid.org/0000-0002-2116-2418","affiliations":[{"raw_affiliation_string":"US Military HIV Research Program, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Sliver Spring MD, USA","institution_ids":["https://openalex.org/I92664306"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052362702","display_name":"Nittaya Phanuphak","orcid":"https://orcid.org/0000-0002-0036-3165","observed_orcids":["https://orcid.org/0000-0002-0036-3165"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Nittaya Phanuphak","raw_affiliation_strings":["Institute of HIV Research and Innovation (IHRI), Bangkok, Thailand"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of HIV Research and Innovation (IHRI), Bangkok, Thailand","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077202736","display_name":"Lydie Trautmann","orcid":"https://orcid.org/0000-0002-3012-0009","observed_orcids":["https://orcid.org/0000-0002-3012-0009"]},"institutions":[{"id":"https://openalex.org/I1280259254","display_name":"Henry M. Jackson Foundation","ror":"https://ror.org/04q9tew83","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1280259254"]},{"id":"https://openalex.org/I92664306","display_name":"Walter Reed Army Institute of Research","ror":"https://ror.org/0145znz58","country_code":"US","type":"government","lineage":["https://openalex.org/I106965489","https://openalex.org/I1304082316","https://openalex.org/I1330347796","https://openalex.org/I2802581893","https://openalex.org/I92664306"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Lydie Trautmann","raw_affiliation_strings":["Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA","US Military HIV Research Program, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Sliver Spring MD, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA","institution_ids":["https://openalex.org/I1280259254"]},{"raw_affiliation_string":"US Military HIV Research Program, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Sliver Spring MD, USA","institution_ids":["https://openalex.org/I92664306"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039272834","display_name":"Sandhya Vasan","orcid":"https://orcid.org/0000-0002-6378-6288","observed_orcids":["https://orcid.org/0000-0002-6378-6288"]},"institutions":[{"id":"https://openalex.org/I1280259254","display_name":"Henry M. Jackson Foundation","ror":"https://ror.org/04q9tew83","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1280259254"]},{"id":"https://openalex.org/I92664306","display_name":"Walter Reed Army Institute of Research","ror":"https://ror.org/0145znz58","country_code":"US","type":"government","lineage":["https://openalex.org/I106965489","https://openalex.org/I1304082316","https://openalex.org/I1330347796","https://openalex.org/I2802581893","https://openalex.org/I92664306"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sandhya Vasan","raw_affiliation_strings":["Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA","US Military HIV Research Program, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Sliver Spring MD, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA","institution_ids":["https://openalex.org/I1280259254"]},{"raw_affiliation_string":"US Military HIV Research Program, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Sliver Spring MD, USA","institution_ids":["https://openalex.org/I92664306"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053087484","display_name":"Carlo Sacdalan","orcid":"https://orcid.org/0000-0002-5839-4837","observed_orcids":["https://orcid.org/0000-0002-5839-4837"]},"institutions":[{"id":"https://openalex.org/I158708052","display_name":"Chulalongkorn University","ror":"https://ror.org/028wp3y58","country_code":"TH","type":"education","lineage":["https://openalex.org/I158708052"]}],"countries":["TH"],"is_corresponding":false,"raw_author_name":"Carlo Sacdalan","raw_affiliation_strings":["Research Affairs, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand","SEARCH Research Foundation, Bangkok, Thailand"],"raw_orcid":"https://orcid.org/0000-0002-5839-4837","affiliations":[{"raw_affiliation_string":"Research Affairs, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand","institution_ids":["https://openalex.org/I158708052"]},{"raw_affiliation_string":"SEARCH Research Foundation, Bangkok, Thailand","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5059411570","display_name":"Somchai Sriplienchan","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Somchai Sriplienchan","raw_affiliation_strings":["SEARCH Research Foundation, Bangkok, Thailand"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"SEARCH Research Foundation, Bangkok, Thailand","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038307269","display_name":"John W. Mellors","orcid":"https://orcid.org/0000-0002-3737-9742","observed_orcids":["https://orcid.org/0000-0002-3737-9742"]},"institutions":[{"id":"https://openalex.org/I170201317","display_name":"University of Pittsburgh","ror":"https://ror.org/01an3r305","country_code":"US","type":"education","lineage":["https://openalex.org/I170201317"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"John W. Mellors","raw_affiliation_strings":["Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA","institution_ids":["https://openalex.org/I170201317"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065227576","display_name":"John M. Coffin","orcid":"https://orcid.org/0000-0003-3856-762X","observed_orcids":["https://orcid.org/0000-0003-3856-762X"]},"institutions":[{"id":"https://openalex.org/I121934306","display_name":"Tufts University","ror":"https://ror.org/05wvpxv85","country_code":"US","type":"education","lineage":["https://openalex.org/I121934306"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"John M. Coffin","raw_affiliation_strings":["Department of Molecular Biology and Microbiology, Tufts University, Boston, MA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Molecular Biology and Microbiology, Tufts University, Boston, MA, USA","institution_ids":["https://openalex.org/I121934306"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039741438","display_name":"Jason W. Rausch","orcid":"https://orcid.org/0000-0002-8377-425X","observed_orcids":["https://orcid.org/0000-0002-8377-425X"]},"institutions":[{"id":"https://openalex.org/I4210140884","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210140884"]},{"id":"https://openalex.org/I4210149717","display_name":"Center for Cancer Research","ror":"https://ror.org/05bjen692","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210140884","https://openalex.org/I4210149717"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jason W. Rausch","raw_affiliation_strings":["HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA","institution_ids":["https://openalex.org/I4210140884","https://openalex.org/I4210149717"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5029362932","display_name":"Mary F. Kearney","orcid":"https://orcid.org/0000-0003-3839-6576","observed_orcids":["https://orcid.org/0000-0003-3839-6576"]},"institutions":[{"id":"https://openalex.org/I4210140884","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210140884"]},{"id":"https://openalex.org/I4210149717","display_name":"Center for Cancer Research","ror":"https://ror.org/05bjen692","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210140884","https://openalex.org/I4210149717"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mary F. Kearney","raw_affiliation_strings":["HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA"],"raw_orcid":"https://orcid.org/0000-0003-3839-6576","affiliations":[{"raw_affiliation_string":"HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA","institution_ids":["https://openalex.org/I4210140884","https://openalex.org/I4210149717"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":9,"corresponding_author_ids":["https://openalex.org/A5064084308"],"corresponding_institution_ids":["https://openalex.org/I4210140884","https://openalex.org/I4210149717"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10112","display_name":"HIV Research and Treatment","score":0.9965999722480774,"subfield":{"id":"https://openalex.org/subfields/2406","display_name":"Virology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10112","display_name":"HIV Research and Treatment","score":0.9965999722480774,"subfield":{"id":"https://openalex.org/subfields/2406","display_name":"Virology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11764","display_name":"Evolution and Genetic Dynamics","score":0.002899999963119626,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10526","display_name":"HIV/AIDS drug development and treatment","score":9.999999747378752e-05,"subfield":{"id":"https://openalex.org/subfields/2725","display_name":"Infectious Diseases"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/acute-hiv-1-infection","display_name":"acute HIV-1 infection","score":0.9229999780654907},{"id":"https://openalex.org/keywords/purifying-selection","display_name":"purifying selection","score":0.9509999752044678},{"id":"https://openalex.org/keywords/hiv-quasispecies","display_name":"HIV quasispecies","score":0.6940000057220459},{"id":"https://openalex.org/keywords/viral-diversification","display_name":"viral diversification","score":0.6200000047683716},{"id":"https://openalex.org/keywords/de-novo-mutations","display_name":"de novo mutations","score":0.7250000238418579},{"id":"https://openalex.org/keywords/viral-evolution","display_name":"viral evolution","score":0.515999972820282},{"id":"https://openalex.org/keywords/single-genome-sequencing","display_name":"single-genome sequencing","score":0.6060000061988831}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.8269000053405762},{"id":"https://openalex.org/C7386963","wikidata":"https://www.wikidata.org/wiki/Q3954859","display_name":"Negative selection","level":4,"score":0.8181999921798706},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5108000040054321},{"id":"https://openalex.org/C189819185","wikidata":"https://www.wikidata.org/wiki/Q384283","display_name":"Subgenomic mRNA","level":4,"score":0.48420000076293945},{"id":"https://openalex.org/C159047783","wikidata":"https://www.wikidata.org/wiki/Q7215","display_name":"Virology","level":1,"score":0.47189998626708984},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4668999910354614},{"id":"https://openalex.org/C156719811","wikidata":"https://www.wikidata.org/wiki/Q28774","display_name":"Reverse transcriptase","level":4,"score":0.4108000099658966},{"id":"https://openalex.org/C761482","wikidata":"https://www.wikidata.org/wiki/Q118093","display_name":"Transmission (telecommunications)","level":2,"score":0.4002000093460083},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.3831999897956848},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.364300012588501},{"id":"https://openalex.org/C2522874641","wikidata":"https://www.wikidata.org/wiki/Q808","display_name":"Virus","level":2,"score":0.35040000081062317},{"id":"https://openalex.org/C132917006","wikidata":"https://www.wikidata.org/wiki/Q5250436","display_name":"Deep sequencing","level":4,"score":0.3402000069618225},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.32589998841285706},{"id":"https://openalex.org/C154317977","wikidata":"https://www.wikidata.org/wiki/Q376266","display_name":"Cytotoxic T cell","level":3,"score":0.29989999532699585},{"id":"https://openalex.org/C128526571","wikidata":"https://www.wikidata.org/wiki/Q619302","display_name":"Somatic hypermutation","level":4,"score":0.2915000021457672},{"id":"https://openalex.org/C24432333","wikidata":"https://www.wikidata.org/wiki/Q2068526","display_name":"Whole genome sequencing","level":4,"score":0.2903999984264374},{"id":"https://openalex.org/C8769409","wikidata":"https://www.wikidata.org/wiki/Q2066554","display_name":"Viral evolution","level":4,"score":0.2897999882698059},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.28209999203681946},{"id":"https://openalex.org/C81917197","wikidata":"https://www.wikidata.org/wiki/Q628760","display_name":"Selection (genetic algorithm)","level":2,"score":0.27390000224113464},{"id":"https://openalex.org/C2986302931","wikidata":"https://www.wikidata.org/wiki/Q764759","display_name":"Positive selection","level":3,"score":0.2736000120639801},{"id":"https://openalex.org/C75268714","wikidata":"https://www.wikidata.org/wiki/Q43478","display_name":"Natural selection","level":3,"score":0.2687999904155731},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.2669000029563904},{"id":"https://openalex.org/C68873052","wikidata":"https://www.wikidata.org/wiki/Q349856","display_name":"Genetic variation","level":3,"score":0.2599000036716461},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.258899986743927},{"id":"https://openalex.org/C90132467","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetics","level":3,"score":0.25609999895095825},{"id":"https://openalex.org/C501734568","wikidata":"https://www.wikidata.org/wiki/Q42918","display_name":"Mutation","level":3,"score":0.2533999979496002}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.64898/2026.08.21.746200","doi":"https://doi.org/10.64898/2026.08.21.746200","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.08.21.746200","pdf_url":null,"source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},{"id":"pmid:42827436","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/42827436","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"bioRxiv : the preprint server for biology","raw_type":"Journal Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:13628423","doi":null,"is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC13628423/","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"bioRxiv","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.64898/2026.08.21.746200","doi":"https://doi.org/10.64898/2026.08.21.746200","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.08.21.746200","pdf_url":null,"source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/3","score":0.8999999761581421,"display_name":"Good health and well-being"}],"sustainable_development_goals_aurora":[{"id":"https://metadata.un.org/sdg/3","score":0.726142168045044,"display_name":"Good health and well-being"}],"study_designs":[{"id":"https://openalex.org/study-designs/observational-study","display_name":"Observational Study"}],"awards":[{"id":"https://openalex.org/G307009047","display_name":"Ultrasensitive Single-Genome Sequencing to Study HIV Transmission and Evolution","funder_award_id":"1ziabc011699-05","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":100,"referenced_works":["https://openalex.org/W597876075","https://openalex.org/W1565428981","https://openalex.org/W1900729316","https://openalex.org/W1939559871","https://openalex.org/W1963704583","https://openalex.org/W1968107707","https://openalex.org/W1977279184","https://openalex.org/W1983466424","https://openalex.org/W1987554589","https://openalex.org/W1992194744","https://openalex.org/W1995598331","https://openalex.org/W1998238844","https://openalex.org/W2000620255","https://openalex.org/W2001800250","https://openalex.org/W2002574877","https://openalex.org/W2006847119","https://openalex.org/W2008351676","https://openalex.org/W2010452637","https://openalex.org/W2012564250","https://openalex.org/W2013914180","https://openalex.org/W2016582810","https://openalex.org/W2022098233","https://openalex.org/W2023035407","https://openalex.org/W2037793240","https://openalex.org/W2038110764","https://openalex.org/W2040139732","https://openalex.org/W2040681869","https://openalex.org/W2050839471","https://openalex.org/W2054437592","https://openalex.org/W2055187903","https://openalex.org/W2056832684","https://openalex.org/W2066295706","https://openalex.org/W2066480278","https://openalex.org/W2067925490","https://openalex.org/W2072752981","https://openalex.org/W2078847141","https://openalex.org/W2080653140","https://openalex.org/W2083283696","https://openalex.org/W2084197987","https://openalex.org/W2085464725","https://openalex.org/W2096193010","https://openalex.org/W2098439468","https://openalex.org/W2104559550","https://openalex.org/W2105565651","https://openalex.org/W2105712999","https://openalex.org/W2111550532","https://openalex.org/W2115879161","https://openalex.org/W2117439682","https://openalex.org/W2120315965","https://openalex.org/W2120915945","https://openalex.org/W2122936417","https://openalex.org/W2126141460","https://openalex.org/W2126515754","https://openalex.org/W2127398312","https://openalex.org/W2127774996","https://openalex.org/W2132692761","https://openalex.org/W2135691292","https://openalex.org/W2137417864","https://openalex.org/W2139311359","https://openalex.org/W2147413871","https://openalex.org/W2148245437","https://openalex.org/W2148686896","https://openalex.org/W2149445861","https://openalex.org/W2152365654","https://openalex.org/W2152534166","https://openalex.org/W2153180469","https://openalex.org/W2156178056","https://openalex.org/W2160378127","https://openalex.org/W2160412419","https://openalex.org/W2163576465","https://openalex.org/W2166692953","https://openalex.org/W2168776079","https://openalex.org/W2170614926","https://openalex.org/W2172297142","https://openalex.org/W2200798239","https://openalex.org/W2386785318","https://openalex.org/W2430671133","https://openalex.org/W2473595575","https://openalex.org/W2560986453","https://openalex.org/W2791212039","https://openalex.org/W2806154095","https://openalex.org/W2890205877","https://openalex.org/W2896671589","https://openalex.org/W2905334834","https://openalex.org/W2905503184","https://openalex.org/W2914383177","https://openalex.org/W2937781871","https://openalex.org/W2968277691","https://openalex.org/W2972082806","https://openalex.org/W3005077496","https://openalex.org/W3036613810","https://openalex.org/W3044215375","https://openalex.org/W3134697810","https://openalex.org/W3202242963","https://openalex.org/W4220959602","https://openalex.org/W4232273699","https://openalex.org/W4251751280","https://openalex.org/W4388405615","https://openalex.org/W4404235320","https://openalex.org/W4415235220"],"related_works":["https://openalex.org/W2038852567","https://openalex.org/W4415235220","https://openalex.org/W2952458008","https://openalex.org/W2093598506","https://openalex.org/W2098439468","https://openalex.org/W629882306","https://openalex.org/W7096034268","https://openalex.org/W7098645526","https://openalex.org/W2742086727","https://openalex.org/W7095374896"],"abstract_inverted_index":{"ABSTRACT":[0],"HIV":[1,391],"transmission":[2,49,77,128,302],"from":[3,92,101,375],"one":[4,10,79,256],"individual":[5],"to":[6,45,109,158,215,222,303,310],"another":[7],"occurs":[8],"by":[9,18,50,156,162,184,195,254,370,377],"or":[11,80,115,161,235,257,356],"a":[12,24,66,81,242,258,285,327,337,395],"small":[13],"number":[14,121],"of":[15,52,57,65,68,78,122,208,219,229,269,292,294,320,339,346,398],"virions":[16],"followed":[17],"spread":[19],"and":[20,87,186,267,393],"genetic":[21,341],"diversification":[22,153,331],"into":[23],"complex":[25],"quasispecies.":[26],"To":[27],"understand":[28,304],"the":[29,42,93,102,120,139,205,217,264,298,305,318,344,360,378],"early":[30,90,152,179,206,265,299,306,361],"events":[31,307],"in":[32,63,71,138,204,284,297,332],"this":[33,311],"process,":[34],"we":[35,289],"investigated":[36],"how":[37],"HIV-1":[38,110,180,209,330],"genomes":[39,62,281],"diversify":[40],"within":[41],"first":[43],"two":[44,279],"three":[46],"weeks":[47,207,300],"after":[48,127,301,401],"use":[51],"ultra-deep":[53],"single":[54,105],"subgenomic":[55],"sequencing":[56],"over":[58,263],"10,000":[59],"plasma":[60],"RNA":[61],"each":[64],"cohort":[67],"15":[69],"individuals":[70],"acute":[72,333],"infection.":[73],"This":[74],"approach":[75],"confirmed":[76],"few":[82,259],"transmitted/founder":[83],"(TF)":[84],"viral":[85,260,272,280,295,313,362,379,399],"lineages":[86,170],"very":[88],"limited":[89],"divergence":[91],"founder":[94],"sequences.":[95],"Most":[96],"observed":[97,125,203],"variants":[98,273,296],"that":[99,130,151,178,308,317,364],"differed":[100],"TF":[103],"included":[104],"nucleotide":[106],"changes":[107,126],"attributable":[108],"reverse":[111],"transcriptase":[112],"(RT)":[113],"error":[114],"host":[116,371],"APOBEC3G/F":[117],"activity.":[118],"Comparing":[119],"expected":[123],"versus":[124],"indicated":[129],"most":[131],"de":[132],"novo":[133],"mutations":[134,275,321,363],"do":[135],"not":[136],"persist":[137],"virus":[140],"population,":[141],"consistent":[142],"with":[143],"strong":[144,196,200],"purifying":[145,197,201],"selection.":[146,198],"We":[147,315],"found":[148,316],"little":[149],"evidence":[150],"is":[154,182,251],"driven":[155],"reversions":[157],"subtype":[159],"consensus":[160],"cytotoxic":[163],"T":[164],"lymphocyte":[165],"pressure,":[166],"although":[167],"rare":[168],"multi-mutation":[169],"suggest":[171],"occasional":[172],"influences.":[173],"Together,":[174],"these":[175,271],"findings":[176],"indicate":[177],"evolution":[181,392],"influenced":[183],"stochastic":[185],"host-mediated":[187],"mutational":[188],"processes":[189],"(":[190],"e.g.":[191],",":[192],"APOBEC3G/F)":[193],"filtered":[194],"The":[199],"selection":[202,328],"infection":[210,250],"may":[211],"provide":[212,386,394],"an":[213],"opportunity":[214],"investigate":[216],"potential":[218],"new":[220,347],"interventions":[221,348],"induce":[223],"viremic":[224,351],"control,":[225,352],"such":[226,353],"as":[227,354],"combinations":[228],"broadly":[230],"neutralizing":[231],"antibodies,":[232],"cellular":[233],"immunotherapy,":[234],"mRNA":[236,357],"therapeutic":[237],"vaccination.":[238,358],"AUTHOR":[239],"SUMMARY":[240],"When":[241],"person":[243],"acquires":[244],"HIV,":[245],"especially":[246],"through":[247],"sexual":[248],"transmission,":[249],"usually":[252],"established":[253],"just":[255],"variants.":[261],"However,":[262],"months":[266],"years":[268],"infection,":[270,334],"accumulate":[274],"until":[276],"almost":[277],"no":[278],"are":[282],"identical":[283],"typical":[286],"sample.":[287],"Here,":[288],"sequenced":[290],"tens":[291],"thousands":[293],"contribute":[309],"vast":[312],"diversification.":[314],"accumulation":[319],"was":[322],"slower":[323],"than":[324,374],"expected,":[325],"implying":[326],"against":[329],"potentially":[335],"leaving":[336],"window":[338],"low":[340],"diversity":[342,400],"for":[343,382,389],"study":[345],"towards":[349],"inducing":[350],"immunotherapy":[355],"Of":[359],"were":[365,368],"observed,":[366],"many":[367],"induced":[369],"enzymes,":[372],"rather":[373],"errors":[376],"enzyme":[380],"used":[381],"replication.":[383],"Our":[384],"results":[385],"more":[387],"context":[388],"understanding":[390],"deep":[396],"sampling":[397],"transmission.":[402]},"counts_by_year":[],"updated_date":"2026-10-29T09:56:32.521200","created_date":"2026-08-27T00:00:00"}
