{"id":"https://openalex.org/W3082372689","doi":"https://doi.org/10.25560/78479","title":"The role of HIV-1 transmitted/founder virus characteristics in driving pathogenesis","display_name":"The role of HIV-1 transmitted/founder virus characteristics in driving pathogenesis","publication_year":2019,"publication_date":"2019-03-01","ids":{"openalex":"https://openalex.org/W3082372689","doi":"https://doi.org/10.25560/78479","mag":"3082372689"},"language":"en","primary_location":{"id":"pmh:oai:spiral.imperial.ac.uk:10044/1/78479","doi":null,"is_oa":true,"landing_page_url":"http://hdl.handle.net/10044/1/78479","pdf_url":"http://hdl.handle.net/10044/1/78479","source":{"id":"https://openalex.org/S4306401396","display_name":"Spiral (Imperial College London)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I47508984","host_organization_name":"Imperial College London","host_organization_lineage":["https://openalex.org/I47508984"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Thesis or dissertation"},"volume":null,"type":"dissertation","is_traditional":true,"indexed_in":["datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"http://hdl.handle.net/10044/1/78479","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5022561453","display_name":"Gladys N. Macharia","orcid":"https://orcid.org/0000-0002-5605-5604","observed_orcids":["https://orcid.org/0000-0002-5605-5604"]},"institutions":[{"id":"https://openalex.org/I47508984","display_name":"Imperial College London","ror":"https://ror.org/041kmwe10","country_code":"GB","type":"education","lineage":["https://openalex.org/I47508984"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Macharia, Gladys Njeri","raw_affiliation_strings":["Imperial College London"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Imperial College London","institution_ids":["https://openalex.org/I47508984"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5022561453"],"corresponding_institution_ids":["https://openalex.org/I47508984"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"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":1.0,"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":1.0,"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/T10082","display_name":"HIV/AIDS Research and Interventions","score":0.0,"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"}},{"id":"https://openalex.org/T10526","display_name":"HIV/AIDS drug development and treatment","score":0.0,"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/transmission-bottlenecks","display_name":"transmission bottlenecks","score":0.8220000267028809},{"id":"https://openalex.org/keywords/hiv-1-subtypes","display_name":"HIV-1 subtypes","score":0.8399999737739563},{"id":"https://openalex.org/keywords/drug-resistance-mutations","display_name":"drug resistance mutations","score":0.6629999876022339},{"id":"https://openalex.org/keywords/viral-replicative-capacity","display_name":"viral replicative capacity","score":0.8650000095367432},{"id":"https://openalex.org/keywords/cell-to-cell-spread","display_name":"cell-to-cell transmission","score":0.7049999833106995},{"id":"https://openalex.org/keywords/cd4-t-cell-loss","display_name":"CD4+ T cell decline","score":0.7450000047683716},{"id":"https://openalex.org/keywords/set-point-viral-load","display_name":"viral load set point","score":0.8560000061988831},{"id":"https://openalex.org/keywords/chronic-immune-activation","display_name":"chronic immune activation","score":0.9319999814033508},{"id":"https://openalex.org/keywords/acute-hiv-1-infection","display_name":"acute HIV-1 infection","score":0.753000020980835},{"id":"https://openalex.org/keywords/men-who-have-sex-with-men","display_name":"men who have sex with men","score":0.7889999747276306},{"id":"https://openalex.org/keywords/chimeric-viruses","display_name":"chimeric viruses","score":0.7649999856948853}],"concepts":[{"id":"https://openalex.org/C3013748606","wikidata":"https://www.wikidata.org/wiki/Q15787","display_name":"Human immunodeficiency virus (HIV)","level":2,"score":0.6725778579711914},{"id":"https://openalex.org/C2780942790","wikidata":"https://www.wikidata.org/wiki/Q372016","display_name":"Pathogenesis","level":2,"score":0.5588165521621704},{"id":"https://openalex.org/C159047783","wikidata":"https://www.wikidata.org/wiki/Q7215","display_name":"Virology","level":1,"score":0.5509620308876038},{"id":"https://openalex.org/C195054827","wikidata":"https://www.wikidata.org/wiki/Q504568","display_name":"Founder effect","level":5,"score":0.5471895337104797},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4468138515949249},{"id":"https://openalex.org/C2522874641","wikidata":"https://www.wikidata.org/wiki/Q808","display_name":"Virus","level":2,"score":0.42373886704444885},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.3926101624965668},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.29187870025634766},{"id":"https://openalex.org/C203014093","wikidata":"https://www.wikidata.org/wiki/Q101929","display_name":"Immunology","level":1,"score":0.29141804575920105},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.10365036129951477},{"id":"https://openalex.org/C135763542","wikidata":"https://www.wikidata.org/wiki/Q106016","display_name":"Genotype","level":3,"score":0.05488300323486328},{"id":"https://openalex.org/C197754878","wikidata":"https://www.wikidata.org/wiki/Q80711","display_name":"Haplotype","level":4,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"pmh:oai:spiral.imperial.ac.uk:10044/1/78479","doi":null,"is_oa":true,"landing_page_url":"http://hdl.handle.net/10044/1/78479","pdf_url":"http://hdl.handle.net/10044/1/78479","source":{"id":"https://openalex.org/S4306401396","display_name":"Spiral (Imperial College London)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I47508984","host_organization_name":"Imperial College London","host_organization_lineage":["https://openalex.org/I47508984"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Thesis or dissertation"},{"id":"pmh:doi:10.25560/78479","doi":null,"is_oa":true,"landing_page_url":"http://hdl.handle.net/10044/1/78479","pdf_url":null,"source":null,"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"doi:10.25560/78479","doi":"https://doi.org/10.25560/78479","is_oa":true,"landing_page_url":"https://doi.org/10.25560/78479","pdf_url":null,"source":{"id":"https://openalex.org/S7407050757","display_name":"Imperial College Research Computing Service Data Repository","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I47508984","host_organization_name":"Imperial College London","host_organization_lineage":["https://openalex.org/I47508984"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article-journal"},{"id":"mag:3082372689","doi":null,"is_oa":false,"landing_page_url":"https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.806552","pdf_url":null,"source":null,"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null}],"best_oa_location":{"id":"pmh:oai:spiral.imperial.ac.uk:10044/1/78479","doi":null,"is_oa":true,"landing_page_url":"http://hdl.handle.net/10044/1/78479","pdf_url":"http://hdl.handle.net/10044/1/78479","source":{"id":"https://openalex.org/S4306401396","display_name":"Spiral (Imperial College London)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I47508984","host_organization_name":"Imperial College London","host_organization_lineage":["https://openalex.org/I47508984"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Thesis or dissertation"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being","score":0.9537000060081482}],"study_designs":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320306138","display_name":"International AIDS Vaccine Initiative","ror":"https://ror.org/05ayv2203"},{"id":"https://openalex.org/F4320320283","display_name":"Imperial College London","ror":"https://ror.org/041kmwe10"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3082372689.pdf","grobid_xml":"https://content.openalex.org/works/W3082372689.grobid-xml"},"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W3083679597","https://openalex.org/W4403856085","https://openalex.org/W2094193440","https://openalex.org/W1849393705","https://openalex.org/W2014281666","https://openalex.org/W1984645508","https://openalex.org/W4380303345","https://openalex.org/W4413229144","https://openalex.org/W7096722888","https://openalex.org/W7099574388"],"abstract_inverted_index":{"HIV-1":[0,49,71,143,260],"transmission":[1,80,228,286],"is":[2,64],"associated":[3],"with":[4,39,155,223],"a":[5,10,53,100,295],"severe":[6],"bottleneck":[7],"in":[8,198,226,244,265,298,307,315],"which":[9,107],"limited":[11],"number":[12],"of":[13,26,45,73,85,116,123,131,151,162,207,238,284,301],"variants":[14],"from":[15],"genetically":[16],"diverse":[17,48],"quasispecies":[18],"establish":[19],"infection.":[20],"The":[21,209],"IAVI":[22],"protocol":[23],"C":[24],"cohort":[25],"discordant":[27],"couples,":[28],"female":[29],"sex":[30,38],"workers,":[31],"other":[32],"heterosexuals":[33],"and":[34,51,83,89,114,141,166,177,186,191,212,234,247,262,280,291,312],"men":[35,40],"who":[36],"have":[37],"(MSM)":[41],"present":[42,52],"varying":[43],"risks":[44],"HIV":[46],"infection,":[47,87,172],"subtypes":[50],"unique":[54],"opportunity":[55],"to":[56,79,103,318],"characterize":[57],"transmitted/founder":[58],"viruses":[59,106,293],"(TFv)":[60],"where":[61,201],"disease":[62,132],"outcome":[63],"known.":[65],"To":[66],"identify":[67],"the":[68,70,125,135,282,285,289,299],"TFv,":[69],"repertoire":[72],"38":[74],"MSM":[75],"was":[76,145,148,181],"sequenced":[77],"close":[78],"(median":[81],"21dpi)":[82],"assessment":[84],"multivariant":[86,152,171,199],"subtype":[88],"genetic":[90],"polymorphisms":[91],"done.":[92,146],"Patient":[93],"derived":[94],"gag":[95],"genes":[96],"were":[97,108,129,203],"cloned":[98],"into":[99],"NL4.3":[101],"provirus":[102],"generate":[104],"chimeric":[105,292],"characterised":[109],"for":[110,304,313],"replicative":[111],"capacity":[112],"(RC)":[113],"mechanism":[115],"spread":[117,233],"between":[118,183],"cells.":[119],"Finally,":[120],"an":[121],"evaluation":[122],"how":[124],"virus":[126],"characteristics":[127,185],"that":[128,240,269,274],"predictors":[130,161],"progression":[133],"modified":[134],"immune":[136,189,254,321],"response":[137],"at":[138,251],"both":[139,187],"acute":[140],"chronic":[142,188],"infection":[144,153,200],"There":[147],"higher":[149],"incidence":[150],"compared":[154],"previously":[156],"described":[157],"heterosexual":[158],"cohorts.":[159],"TFv":[160,221,279,309],"CD4":[163],"T-cell":[164],"decline":[165,196],"set-point":[167],"viral":[168],"load":[169],"included":[170],"subtype,":[173],"drug":[174],"resistance":[175],"mutations":[176],"RC.":[178],"A":[179],"link":[180],"identified":[182],"these":[184],"activation":[190,255],"rapid":[192],"CD4+":[193,213],"T":[194,214],"cell":[195,210,215,231],"except":[197],"perturbations":[202],"restored":[204],"after":[205],"control":[206],"viremia.":[208],"entry":[211],"depletion":[216],"mechanisms":[217],"by":[218],"high":[219,277],"RC":[220,278],"overlapped":[222],"those":[224],"involved":[225,235,243],"cell-cell":[227],"but":[229],"not":[230],"free":[232],"increased":[236],"expression":[237],"RNA":[239],"encodes":[241],"proteins":[242],"apoptosis,":[245],"autophagy":[246],"necrosis.":[248],"Strategies":[249],"aimed":[250],"mitigating":[252],"persistent":[253],"could":[256],"contribute":[257],"toward":[258],"improving":[259],"prognosis":[261],"research":[263],"presented":[264],"this":[266,270],"thesis":[267],"suggests":[268],"may":[271],"involve":[272],"strategies":[273],"sieve":[275],"out":[276],"tighten":[281],"stringency":[283],"bottleneck.":[287],"Furthermore,":[288],"sequences":[290],"provide":[294],"useful":[296],"resource":[297],"field":[300],"immunogen":[302],"design,":[303],"their":[305],"utility":[306],"designing":[308],"peptide":[310],"sets":[311],"use":[314],"functional":[316],"assays":[317],"probe":[319],"effective":[320],"responses":[322],"against":[323],"TFv.":[324]},"counts_by_year":[],"updated_date":"2026-10-28T10:33:24.094632","created_date":"2020-09-08T00:00:00"}
