{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,10]],"date-time":"2026-07-10T14:10:42Z","timestamp":1783692642413,"version":"3.55.0"},"reference-count":34,"publisher":"Elsevier BV","license":[{"start":{"date-parts":[[2024,6,1]],"date-time":"2024-06-01T00:00:00Z","timestamp":1717200000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2024,6,1]],"date-time":"2024-06-01T00:00:00Z","timestamp":1717200000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2024,5,15]],"date-time":"2024-05-15T00:00:00Z","timestamp":1715731200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000923","name":"Australian Research Council","doi-asserted-by":"publisher","award":["FT220100629"],"award-info":[{"award-number":["FT220100629"]}],"id":[{"id":"10.13039\/501100000923","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000925","name":"National Health and Medical Research Council","doi-asserted-by":"publisher","award":["2017284"],"award-info":[{"award-number":["2017284"]}],"id":[{"id":"10.13039\/501100000925","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000925","name":"National Health and Medical Research Council","doi-asserted-by":"publisher","award":["GNT1172900"],"award-info":[{"award-number":["GNT1172900"]}],"id":[{"id":"10.13039\/501100000925","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000925","name":"National Health and Medical Research Council","doi-asserted-by":"publisher","award":["GNT1172873"],"award-info":[{"award-number":["GNT1172873"]}],"id":[{"id":"10.13039\/501100000925","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000925","name":"National Health and Medical Research Council","doi-asserted-by":"publisher","award":["GNT1174555"],"award-info":[{"award-number":["GNT1174555"]}],"id":[{"id":"10.13039\/501100000925","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["thelancet.com","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["The Lancet Regional Health - Western Pacific"],"published-print":{"date-parts":[[2024,6]]},"DOI":"10.1016\/j.lanwpc.2024.101103","type":"journal-article","created":{"date-parts":[[2024,6,7]],"date-time":"2024-06-07T17:52:00Z","timestamp":1717782720000},"page":"101103","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":3,"special_numbering":"C","title":["Characterising HIV-1 transmission in Victoria, Australia: a molecular epidemiological study"],"prefix":"10.1016","volume":"47","author":[{"given":"George","family":"Taiaroa","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Doris","family":"Chibo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sophie","family":"Herman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3820-5338","authenticated-orcid":false,"given":"Mona L.","family":"Taouk","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Megan","family":"Gooey","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jodie","family":"D'Costa","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rizmina","family":"Sameer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nicole","family":"Richards","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elaine","family":"Lee","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lydya","family":"Macksabo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nasra","family":"Higgins","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David J.","family":"Price","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Soo","family":"Jen Low","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eike","family":"Steinig","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5142-7440","authenticated-orcid":false,"given":"Genevieve E.","family":"Martin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael A.","family":"Moso","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Leon","family":"Caly","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jacqueline","family":"Prestedge","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christopher K.","family":"Fairley","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1766-0657","authenticated-orcid":false,"given":"Eric P.F.","family":"Chow","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marcus Y.","family":"Chen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sebastian","family":"Duchene","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jane S.","family":"Hocking","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sharon R.","family":"Lewin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Deborah A.","family":"Williamson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.lanwpc.2024.101103_bib1","series-title":"National update on HIV, viral hepatitis and sexually transmissible infections in Australia: 2009\u20132018. Sydney: kirby Institute","year":"2020"},{"issue":"5","key":"10.1016\/j.lanwpc.2024.101103_bib2","doi-asserted-by":"crossref","first-page":"835","DOI":"10.1097\/QAD.0000000000002797","article-title":"Increasing preexposure prophylaxis use and \u2018net prevention coverage\u2019in behavioural surveillance of Australian gay and bisexual men","volume":"35","author":"Holt","year":"2021","journal-title":"AIDS"},{"issue":"12","key":"10.1016\/j.lanwpc.2024.101103_bib3","doi-asserted-by":"crossref","first-page":"e831","DOI":"10.1016\/S2352-3018(19)30196-1","article-title":"Global, regional, and national incidence, prevalence, and mortality of HIV, 1980\u20132017, and forecasts to 2030, for 195 countries and territories: a systematic analysis for the global burden of diseases, Injuries, and risk factors study 2017","volume":"6","author":"Frank","year":"2019","journal-title":"Lancet HIV"},{"issue":"2","key":"10.1016\/j.lanwpc.2024.101103_bib5","doi-asserted-by":"crossref","first-page":"e0212268","DOI":"10.1371\/journal.pone.0212268","article-title":"HIV diagnoses in migrant populations in Australia\u2014a changing epidemiology","volume":"14","author":"Gunaratnam","year":"2019","journal-title":"PLoS One"},{"issue":"3","key":"10.1016\/j.lanwpc.2024.101103_bib6","doi-asserted-by":"crossref","first-page":"e1003044","DOI":"10.1371\/journal.pmed.1003044","article-title":"Gaps in the HIV diagnosis and care cascade for migrants in Australia, 2013\u20132017: a cross-sectional study","volume":"17","author":"Marukutira","year":"2020","journal-title":"PLoS Med"},{"issue":"6","key":"10.1016\/j.lanwpc.2024.101103_bib7","doi-asserted-by":"crossref","first-page":"622","DOI":"10.1111\/1753-6405.13158","article-title":"Sexual health service adaptations to the coronavirus disease 2019 (COVID-19) pandemic in Australia: a nationwide online survey","volume":"45","author":"Phillips","year":"2021","journal-title":"Aust N Z J Public Health"},{"key":"10.1016\/j.lanwpc.2024.101103_bib8","series-title":"HIV, viral hepatitis and sexually transmissible infections in Australia: annual surveillance report 2021","year":"2022"},{"issue":"7","key":"10.1016\/j.lanwpc.2024.101103_bib10","doi-asserted-by":"crossref","first-page":"951","DOI":"10.1086\/512088","article-title":"High rates of forward transmission events after acute\/early HIV-1 infection","volume":"195","author":"Brenner","year":"2007","journal-title":"J\u00a0Infect Dis"},{"issue":"16","key":"10.1016\/j.lanwpc.2024.101103_bib11","doi-asserted-by":"crossref","first-page":"1657","DOI":"10.1001\/jama.2018.1513","article-title":"Molecular epidemiology and the transformation of HIV prevention","volume":"319","author":"Oster","year":"2018","journal-title":"JAMA"},{"issue":"3","key":"10.1016\/j.lanwpc.2024.101103_bib12","doi-asserted-by":"crossref","first-page":"229","DOI":"10.1056\/NEJMoa1515195","article-title":"HIV infection linked to injection use of oxymorphone in Indiana, 2014\u20132015","volume":"375","author":"Peters","year":"2016","journal-title":"N\u00a0Engl J Med"},{"issue":"12","key":"10.1016\/j.lanwpc.2024.101103_bib13","doi-asserted-by":"crossref","first-page":"1875","DOI":"10.1093\/infdis\/jiy130","article-title":"Recent and rapid transmission of HIV among people who inject drugs in Scotland revealed through phylogenetic analysis","volume":"217","author":"Ragonnet-Cronin","year":"2018","journal-title":"J\u00a0Infect Dis"},{"issue":"5","key":"10.1016\/j.lanwpc.2024.101103_bib14","doi-asserted-by":"crossref","first-page":"482","DOI":"10.3390\/v11050482","article-title":"Limited sustained local transmission of HIV-1 CRF01_AE in New South Wales, Australia","volume":"11","author":"Di Giallonardo","year":"2019","journal-title":"Viruses"},{"issue":"12","key":"10.1016\/j.lanwpc.2024.101103_bib15","doi-asserted-by":"crossref","first-page":"1402","DOI":"10.3390\/v12121402","article-title":"Increased HIV subtype diversity reflecting demographic changes in the HIV epidemic in New South Wales, Australia","volume":"12","author":"Di Giallonardo","year":"2020","journal-title":"Viruses"},{"issue":"9","key":"10.1016\/j.lanwpc.2024.101103_bib16","doi-asserted-by":"crossref","first-page":"e0237469","DOI":"10.1371\/journal.pone.0237469","article-title":"Phylogenetic clustering networks among heterosexual migrants with new HIV diagnoses post-migration in Australia","volume":"15","author":"Sacks-Davis","year":"2020","journal-title":"PLoS One"},{"issue":"5","key":"10.1016\/j.lanwpc.2024.101103_bib17","doi-asserted-by":"crossref","first-page":"e0170601","DOI":"10.1371\/journal.pone.0170601","article-title":"A\u00a0national study of the molecular epidemiology of HIV-1 in Australia 2005\u20132012","volume":"12","author":"Castley","year":"2017","journal-title":"PLoS One"},{"issue":"10","key":"10.1016\/j.lanwpc.2024.101103_bib18","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1080\/15265161.2020.1809550","article-title":"We are people, not clusters","volume":"20","author":"Bernard","year":"2020","journal-title":"Am J Bioeth"},{"issue":"12","key":"10.1016\/j.lanwpc.2024.101103_bib19","doi-asserted-by":"crossref","first-page":"1997","DOI":"10.1093\/infdis\/jiaa107","article-title":"Addressing ethical challenges in US-based HIV phylogenetic research","volume":"222","author":"Dawson","year":"2020","journal-title":"J\u00a0Infect Dis"},{"issue":"1","key":"10.1016\/j.lanwpc.2024.101103_bib20","doi-asserted-by":"crossref","DOI":"10.1093\/ve\/veac045","article-title":"Epidemiological inference from pathogen genomes: a review of phylodynamic models and applications","volume":"8","author":"Featherstone","year":"2022","journal-title":"Virus Evolution"},{"issue":"2","key":"10.1016\/j.lanwpc.2024.101103_bib21","doi-asserted-by":"crossref","first-page":"233","DOI":"10.1093\/infdis\/jiz085","article-title":"Tracing the impact of public health interventions on HIV-1 transmission in Portugal using molecular epidemiology","volume":"220","author":"Vasylyeva","year":"2019","journal-title":"J\u00a0Infect Dis"},{"issue":"3","key":"10.1016\/j.lanwpc.2024.101103_bib22","doi-asserted-by":"crossref","first-page":"e4724","DOI":"10.1371\/journal.pone.0004724","article-title":"Drug resistance mutations for surveillance of transmitted HIV-1 drug-resistance: 2009 update","volume":"4","author":"Bennett","year":"2009","journal-title":"PLoS One"},{"issue":"2","key":"10.1016\/j.lanwpc.2024.101103_bib23","doi-asserted-by":"crossref","first-page":"e1008537","DOI":"10.1371\/journal.pcbi.1008537","article-title":"Factors influencing estimates of HIV-1 infection timing using BEAST","volume":"17","author":"Dearlove","year":"2021","journal-title":"PLoS Comput Biol"},{"issue":"6","key":"10.1016\/j.lanwpc.2024.101103_bib26","doi-asserted-by":"crossref","first-page":"445","DOI":"10.1310\/YHGE-07Y8-T3XF-F6VT","article-title":"Baseline antiretroviral drug susceptibility influences treatment response in\u00a0patients receiving saquinavir-enhancing therapy","volume":"2","author":"Middleton","year":"2001","journal-title":"HIV Clin Trials"},{"issue":"2","key":"10.1016\/j.lanwpc.2024.101103_bib27","doi-asserted-by":"crossref","first-page":"98","DOI":"10.1159\/000331998","article-title":"The HIVdb system for HIV-1 genotypic resistance interpretation","volume":"55","author":"Tang","year":"2012","journal-title":"Intervirology"},{"key":"10.1016\/j.lanwpc.2024.101103_bib28","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":"Pineda-Pe\u00f1a","year":"2013","journal-title":"Infect Genet Evol"},{"issue":"7","key":"10.1016\/j.lanwpc.2024.101103_bib29","doi-asserted-by":"crossref","first-page":"1812","DOI":"10.1093\/molbev\/msy016","article-title":"HIV-TRACE (TRAnsmission Cluster Engine): a tool for large scale molecular epidemiology of HIV-1 and other rapidly evolving pathogens","volume":"35","author":"Pond","year":"2018","journal-title":"Mol Biol Evol"},{"issue":"4","key":"10.1016\/j.lanwpc.2024.101103_bib30","doi-asserted-by":"crossref","first-page":"e1006650","DOI":"10.1371\/journal.pcbi.1006650","article-title":"Beast 2.5: an advanced software platform for Bayesian evolutionary analysis","volume":"15","author":"Bouckaert","year":"2019","journal-title":"PLoS Comput Biol"},{"issue":"1","key":"10.1016\/j.lanwpc.2024.101103_bib32","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s41467-020-19801-x","article-title":"Reduced efficacy of HIV-1 integrase inhibitors in patients with drug resistance mutations in reverse transcriptase","volume":"11","author":"Siedner","year":"2020","journal-title":"Nat Commun"},{"issue":"6580","key":"10.1016\/j.lanwpc.2024.101103_bib33","doi-asserted-by":"crossref","first-page":"540","DOI":"10.1126\/science.abk1688","article-title":"A\u00a0highly virulent variant of HIV-1 circulating in The Netherlands","volume":"375","author":"Wymant","year":"2022","journal-title":"Science"},{"issue":"9","key":"10.1016\/j.lanwpc.2024.101103_bib34","doi-asserted-by":"crossref","first-page":"1053","DOI":"10.1093\/infdis\/jix307","article-title":"Detailed transmission network analysis of a large opiate-driven outbreak of HIV infection in the United States","volume":"216","author":"Campbell","year":"2017","journal-title":"J\u00a0Infect Dis"},{"issue":"10","key":"10.1016\/j.lanwpc.2024.101103_bib35","doi-asserted-by":"crossref","first-page":"4600","DOI":"10.1128\/JCM.41.10.4600-4604.2003","article-title":"Segregation of human immunodeficiency virus type 1 subtypes by risk factor in Australia","volume":"41","author":"Herring","year":"2003","journal-title":"J\u00a0Clin Microbiol"},{"issue":"11","key":"10.1016\/j.lanwpc.2024.101103_bib36","doi-asserted-by":"crossref","first-page":"1735","DOI":"10.1093\/infdis\/jiu666","article-title":"Global dispersal pattern of HIV type 1 subtype CRF01_AE: a genetic trace of human mobility related to heterosexual sexual activities centralized in Southeast Asia","volume":"211","author":"Angelis","year":"2015","journal-title":"J\u00a0Infect Dis"},{"issue":"5","key":"10.1016\/j.lanwpc.2024.101103_bib37","doi-asserted-by":"crossref","first-page":"505","DOI":"10.1097\/01.qai.0000186361.42834.61","article-title":"Prevalence of transmitted HIV-1 drug resistance and the role of resistance algorithms: data from seroconverters in the CASCADE collaboration from 1987 to 2003","volume":"40","author":"Masquelier","year":"2005","journal-title":"JAcquir Immune Defic Syndr"},{"issue":"1","key":"10.1016\/j.lanwpc.2024.101103_bib38","doi-asserted-by":"crossref","first-page":"3988","DOI":"10.1038\/s41467-019-12053-4","article-title":"Bridging of Neisseria gonorrhoeae lineages across sexual networks in the HIV pre-exposure prophylaxis era","volume":"10","author":"Williamson","year":"2019","journal-title":"Nat Commun"},{"issue":"1","key":"10.1016\/j.lanwpc.2024.101103_bib39","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s41467-022-28529-9","article-title":"AusTrakka: fast-tracking nationalized genomics surveillance in response to the COVID-19 pandemic","volume":"13","author":"Hoang","year":"2022","journal-title":"Nat Commun"}],"container-title":["The Lancet Regional Health - Western Pacific"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S266660652400097X?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S266660652400097X?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2024,7,3]],"date-time":"2024-07-03T06:35:16Z","timestamp":1719988516000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S266660652400097X"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,6]]},"references-count":34,"alternative-id":["S266660652400097X"],"URL":"https:\/\/doi.org\/10.1016\/j.lanwpc.2024.101103","relation":{},"ISSN":["2666-6065"],"issn-type":[{"value":"2666-6065","type":"print"}],"subject":[],"published":{"date-parts":[[2024,6]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Characterising HIV-1 transmission in Victoria, Australia: a molecular epidemiological study","name":"articletitle","label":"Article Title"},{"value":"The Lancet Regional Health - Western Pacific","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.lanwpc.2024.101103","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2024 The Author(s). Published by Elsevier Ltd.","name":"copyright","label":"Copyright"}],"article-number":"101103"}}