{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,14]],"date-time":"2026-10-14T18:33:29Z","timestamp":1792002809671,"version":"4.4.0"},"reference-count":61,"publisher":"Elsevier BV","license":[{"start":{"date-parts":[[2025,7,1]],"date-time":"2025-07-01T00:00:00Z","timestamp":1751328000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2025,7,1]],"date-time":"2025-07-01T00:00:00Z","timestamp":1751328000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2025,7,1]],"date-time":"2025-07-01T00:00:00Z","timestamp":1751328000000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-017"},{"start":{"date-parts":[[2025,7,1]],"date-time":"2025-07-01T00:00:00Z","timestamp":1751328000000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-037"},{"start":{"date-parts":[[2025,7,1]],"date-time":"2025-07-01T00:00:00Z","timestamp":1751328000000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-012"},{"start":{"date-parts":[[2025,7,1]],"date-time":"2025-07-01T00:00:00Z","timestamp":1751328000000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-029"},{"start":{"date-parts":[[2025,7,1]],"date-time":"2025-07-01T00:00:00Z","timestamp":1751328000000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-004"}],"funder":[{"DOI":"10.13039\/501100001711","name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung","doi-asserted-by":"publisher","award":["883"],"award-info":[{"award-number":["883"]}],"id":[{"id":"10.13039\/501100001711","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001711","name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung","doi-asserted-by":"publisher","award":["33FI-0_229621"],"award-info":[{"award-number":["33FI-0_229621"]}],"id":[{"id":"10.13039\/501100001711","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003921","name":"Department of Health and Aged Care, Australian Government","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100003921","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001773","name":"University of New South Wales","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001773","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100008902","name":"Los Alamos National Laboratory","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100008902","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["clinicalkey.com","clinicalkey.com.au","clinicalkey.es","clinicalkey.fr","clinicalkey.jp","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Virology"],"published-print":{"date-parts":[[2025,7]]},"DOI":"10.1016\/j.virol.2025.110558","type":"journal-article","created":{"date-parts":[[2025,4,29]],"date-time":"2025-04-29T20:23:25Z","timestamp":1745958205000},"page":"110558","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":2,"special_numbering":"C","title":["Threshold sensitivity analysis for HIV-1 transmission cluster detection using different genomic regions and subtypes"],"prefix":"10.1016","volume":"608","author":[{"given":"Billal M.","family":"Obeng","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Roger D.","family":"Kouyos","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Katharina","family":"Kusejko","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Luisa","family":"Salazar-Vizcaya","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Huldrych F.","family":"G\u00fcnthard","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anthony D.","family":"Kelleher","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Francesca","family":"Di Giallonardo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"issue":"3","key":"10.1016\/j.virol.2025.110558_bib1","doi-asserted-by":"crossref","first-page":"380","DOI":"10.1016\/j.meegid.2009.09.020","article-title":"Comparative performance of the REGA subtyping tool version 2 versus version 1","volume":"10","author":"Abecasis","year":"2010","journal-title":"Infect. Genet. Evol."},{"key":"10.1016\/j.virol.2025.110558_bib2","doi-asserted-by":"crossref","first-page":"52","DOI":"10.1007\/s11904-011-0107-3","article-title":"The HIV-1 env protein: a coat of many colors","volume":"9","author":"Arrildt","year":"2012","journal-title":"Curr. HIV AIDS Rep."},{"issue":"6","key":"10.1016\/j.virol.2025.110558_bib3","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pbio.2001855","article-title":"Viral genetic variation accounts for a third of variability in HIV-1 set-point viral load in Europe","volume":"15","author":"Blanquart","year":"2017","journal-title":"PLoS Biol."},{"issue":"3","key":"10.1016\/j.virol.2025.110558_bib4","doi-asserted-by":"crossref","first-page":"211","DOI":"10.1016\/j.dci.2004.07.007","article-title":"Using models of nucleotide evolution to build phylogenetic trees","volume":"29","author":"Bos","year":"2005","journal-title":"Dev. Comp. Immunol."},{"issue":"8","key":"10.1016\/j.virol.2025.110558_bib5","doi-asserted-by":"crossref","first-page":"1643","DOI":"10.3390\/v13081643","article-title":"The role of phylogenetics in unravelling patterns of HIV transmission towards epidemic control: the Quebec experience (2002\u20132020)","volume":"13","author":"Brenner","year":"2021","journal-title":"Viruses"},{"issue":"9","key":"10.1016\/j.virol.2025.110558_bib6","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1009300","article-title":"MicrobeTrace: retooling molecular epidemiology for rapid public health response","volume":"17","author":"Campbell","year":"2021","journal-title":"PLoS Comput. Biol."},{"key":"10.1016\/j.virol.2025.110558_bib7","series-title":"Detecting and responding to HIV transmission clusters: a guide for health departments","year":"2019"},{"issue":"11","key":"10.1016\/j.virol.2025.110558_bib8","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1010745","article-title":"Optimized phylogenetic clustering of HIV-1 sequence data for public health applications","volume":"18","author":"Chato","year":"2022","journal-title":"PLoS Comput. Biol."},{"issue":"1","key":"10.1016\/j.virol.2025.110558_bib9","doi-asserted-by":"crossref","DOI":"10.1093\/ve\/veaa011","article-title":"Public health in genetic spaces: a statistical framework to optimize cluster-based outbreak detection","volume":"6","author":"Chato","year":"2020","journal-title":"Virus Evol."},{"issue":"1","key":"10.1016\/j.virol.2025.110558_bib10","doi-asserted-by":"crossref","DOI":"10.1093\/ve\/vex013","article-title":"Rising prevalence of non-B HIV-1 subtypes in North Carolina and evidence for local onward transmission","volume":"3","author":"Dennis","year":"2017","journal-title":"Virus Evol."},{"key":"10.1016\/j.virol.2025.110558_bib11","series-title":"Time Series and Statistics","first-page":"126","article-title":"Likelihood","author":"Edwards","year":"1972"},{"issue":"8","key":"10.1016\/j.virol.2025.110558_bib12","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0135325","article-title":"Recent transmission clustering of HIV-1 C and CRF17_BF strains characterized by NNRTI-related mutations among newly diagnosed men in central Italy","volume":"10","author":"Fabeni","year":"2015","journal-title":"PLoS One"},{"issue":"5","key":"10.1016\/j.virol.2025.110558_bib14","doi-asserted-by":"crossref","first-page":"696","DOI":"10.1080\/10635150390235520","article-title":"A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood","volume":"52","author":"Guindon","year":"2003","journal-title":"Syst. Biol."},{"issue":"9","key":"10.1016\/j.virol.2025.110558_bib15","doi-asserted-by":"crossref","first-page":"1211","DOI":"10.1097\/QAD.0000000000001470","article-title":"Defining HIV-1 transmission clusters based on sequence data","volume":"31","author":"Hassan","year":"2017","journal-title":"AIDS"},{"issue":"2","key":"10.1016\/j.virol.2025.110558_bib16","doi-asserted-by":"crossref","first-page":"182","DOI":"10.1093\/sysbio\/42.2.182","article-title":"An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis","volume":"42","author":"Hillis","year":"1993","journal-title":"Syst. Biol."},{"issue":"6","key":"10.1016\/j.virol.2025.110558_bib17","doi-asserted-by":"crossref","DOI":"10.1002\/rmv.70001","article-title":"Next\u2010Generation sequencing methods for near\u2010real\u2010time molecular epidemiology of HIV and HCV","volume":"34","author":"Horsburgh","year":"2024","journal-title":"Rev. Med. Virol."},{"issue":"5","key":"10.1016\/j.virol.2025.110558_bib18","doi-asserted-by":"crossref","first-page":"719","DOI":"10.1097\/00002030-200403260-00002","article-title":"HIV-1 pol gene variation is sufficient for reconstruction of transmissions in the era of antiretroviral therapy","volume":"18","author":"Hu\u00e9","year":"2004","journal-title":"AIDS"},{"issue":"17","key":"10.1016\/j.virol.2025.110558_bib19","doi-asserted-by":"crossref","first-page":"9479","DOI":"10.1002\/ece3.5425","article-title":"Effects of taxon sampling and tree reconstruction methods on phylodiversity metrics","volume":"9","author":"Jantzen","year":"2019","journal-title":"Ecol. Evol."},{"issue":"4","key":"10.1016\/j.virol.2025.110558_bib20","doi-asserted-by":"crossref","first-page":"225","DOI":"10.1016\/j.tig.2006.02.003","article-title":"Phylogenomics: the beginning of incongruence?","volume":"22","author":"Jeffroy","year":"2006","journal-title":"Trends Genet."},{"issue":"3","key":"10.1016\/j.virol.2025.110558_bib21","doi-asserted-by":"crossref","first-page":"161","DOI":"10.1097\/COH.0000000000000540","article-title":"Factors influencing HIV-1 phylogenetic clustering","volume":"14","author":"Junqueira","year":"2019","journal-title":"Curr. Opin. HIV AIDS"},{"issue":"6","key":"10.1016\/j.virol.2025.110558_bib22","doi-asserted-by":"crossref","first-page":"587","DOI":"10.1038\/nmeth.4285","article-title":"ModelFinder: fast model selection for accurate phylogenetic estimates","volume":"14","author":"Kalyaanamoorthy","year":"2017","journal-title":"Nat. Methods"},{"issue":"7","key":"10.1016\/j.virol.2025.110558_bib23","doi-asserted-by":"crossref","first-page":"428","DOI":"10.1038\/s41576-020-0233-0","article-title":"Phylogenetic tree building in the genomic age","volume":"21","author":"Kapli","year":"2020","journal-title":"Nat. Rev. Genet."},{"issue":"14","key":"10.1016\/j.virol.2025.110558_bib24","doi-asserted-by":"crossref","first-page":"3059","DOI":"10.1093\/nar\/gkf436","article-title":"MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform","volume":"30","author":"Katoh","year":"2002","journal-title":"Nucleic Acids Res."},{"issue":"7","key":"10.1016\/j.virol.2025.110558_bib25","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":"Kosakovsky Pond","year":"2018","journal-title":"Mol. Biol. Evol."},{"issue":"1","key":"10.1016\/j.virol.2025.110558_bib26","doi-asserted-by":"crossref","first-page":"85","DOI":"10.3390\/biology3010085","article-title":"R-based software for the integration of pathway data into bioinformatic algorithms","volume":"3","author":"Kramer","year":"2014","journal-title":"Biology"},{"issue":"14","key":"10.1016\/j.virol.2025.110558_bib28","doi-asserted-by":"crossref","first-page":"1551","DOI":"10.1097\/01.aids.0000182519.92030.ce","article-title":"Exploring full-genome sequences for phylogenetic support of HIV-1 transmission events","volume":"19","author":"Lemey","year":"2005","journal-title":"AIDS"},{"issue":"7702","key":"10.1016\/j.virol.2025.110558_bib29","doi-asserted-by":"crossref","first-page":"452","DOI":"10.1038\/s41586-018-0043-0","article-title":"Renewing Felsenstein's phylogenetic bootstrap in the era of big data","volume":"556","author":"Lemoine","year":"2018","journal-title":"Nature"},{"issue":"6","key":"10.1016\/j.virol.2025.110558_bib30","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0098443","article-title":"Using HIV networks to inform real time prevention interventions","volume":"9","author":"Little","year":"2014","journal-title":"PLoS One"},{"key":"10.1016\/j.virol.2025.110558_bib31","volume":"vol. 1","author":"Lycett","year":"2013"},{"key":"10.1016\/j.virol.2025.110558_bib32","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.72657","article-title":"Deep-sequence phylogenetics to quantify patterns of HIV transmission in the context of a universal testing and treatment trial\u2013BCPP\/Ya Tsie trial","volume":"11","author":"Magosi","year":"2022","journal-title":"Elife"},{"issue":"1","key":"10.1016\/j.virol.2025.110558_bib33","doi-asserted-by":"crossref","first-page":"115","DOI":"10.1093\/cid\/civ732","article-title":"HIV-1 transmission during recent infection and during treatment interruptions as major drivers of new infections in the Swiss HIV Cohort Study","volume":"62","author":"Marzel","year":"2016","journal-title":"Clin. Infect. Dis."},{"issue":"9","key":"10.1016\/j.virol.2025.110558_bib34","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1009336","article-title":"Incorporating metadata in HIV transmission network reconstruction: a machine learning feasibility assessment","volume":"17","author":"Mazrouee","year":"2021","journal-title":"PLoS Comput. Biol."},{"issue":"5","key":"10.1016\/j.virol.2025.110558_bib35","doi-asserted-by":"crossref","first-page":"1530","DOI":"10.1093\/molbev\/msaa015","article-title":"IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era","volume":"37","author":"Minh","year":"2020","journal-title":"Mol. Biol. Evol."},{"issue":"9","key":"10.1016\/j.virol.2025.110558_bib36","doi-asserted-by":"crossref","first-page":"1689","DOI":"10.3390\/v13091689","article-title":"Large evolutionary rate heterogeneity among and within HIV-1 subtypes and CRFs","volume":"13","author":"Nasir","year":"2021","journal-title":"Viruses"},{"issue":"12","key":"10.1016\/j.virol.2025.110558_bib37","doi-asserted-by":"crossref","first-page":"1226","DOI":"10.1089\/aid.2014.0173","article-title":"Impact of sampling density on the extent of HIV clustering","volume":"30","author":"Novitsky","year":"2014","journal-title":"AIDS Res. Hum. Retrovir."},{"issue":"5","key":"10.1016\/j.virol.2025.110558_bib38","doi-asserted-by":"crossref","first-page":"531","DOI":"10.1089\/aid.2014.0211","article-title":"Importance of viral sequence length and number of variable and informative sites in analysis of HIV clustering","volume":"31","author":"Novitsky","year":"2015","journal-title":"AIDS Res. Hum. Retrovir."},{"issue":"1","key":"10.1016\/j.virol.2025.110558_bib39","doi-asserted-by":"crossref","DOI":"10.1038\/s41598-020-75560-1","article-title":"Empirical comparison of analytical approaches for identifying molecular HIV-1 clusters","volume":"10","author":"Novitsky","year":"2020","journal-title":"Sci. Rep."},{"key":"10.1016\/j.virol.2025.110558_bib40","doi-asserted-by":"crossref","DOI":"10.1016\/j.virusres.2024.199310","article-title":"Molecular epidemiology to aid virtual elimination of HIV transmission in Australia","volume":"341","author":"Obeng","year":"2024","journal-title":"Virus Res."},{"key":"10.1016\/j.virol.2025.110558_bib41","series-title":"Geneious R7: a Bioinformatics Platform for Biologists. International Plant and Animal Genome Conference Xxii","author":"Olsen","year":"2014"},{"issue":"5","key":"10.1016\/j.virol.2025.110558_bib42","doi-asserted-by":"crossref","first-page":"543","DOI":"10.1097\/QAI.0000000000001856","article-title":"Identifying clusters of recent and rapid HIV transmission through analysis of molecular surveillance data","volume":"79","author":"Oster","year":"2018","journal-title":"J. Acquir. Immune Defic. Syndr."},{"issue":"2","key":"10.1016\/j.virol.2025.110558_bib43","doi-asserted-by":"crossref","first-page":"31","DOI":"10.1093\/ve\/vew031","article-title":"Impacts and shortcomings of genetic clustering methods for infectious disease outbreaks","volume":"2","author":"Poon","year":"2016","journal-title":"Virus Evol."},{"issue":"8","key":"10.1016\/j.virol.2025.110558_bib44","doi-asserted-by":"crossref","first-page":"1035","DOI":"10.1097\/QAD.0b013e3283467020","article-title":"Time-measured phylogenies of gag, pol and env sequence data reveal the direction and time interval of HIV-1 transmission","volume":"25","author":"Rachinger","year":"2011","journal-title":"AIDS"},{"issue":"1","key":"10.1016\/j.virol.2025.110558_bib45","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/1471-2105-14-317","article-title":"Automated analysis of phylogenetic clusters","volume":"14","author":"Ragonnet-Cronin","year":"2013","journal-title":"BMC Bioinf."},{"issue":"9","key":"10.1016\/j.virol.2025.110558_bib46","doi-asserted-by":"crossref","first-page":"1410","DOI":"10.1093\/infdis\/jiv758","article-title":"Transmission of non-B HIV subtypes in the United Kingdom is increasingly driven by large non-heterosexual transmission clusters","volume":"213","author":"Ragonnet-Cronin","year":"2016","journal-title":"JID (J. Infect. Dis.)"},{"issue":"9","key":"10.1016\/j.virol.2025.110558_bib47","doi-asserted-by":"crossref","first-page":"921","DOI":"10.3390\/v12090921","article-title":"Employing molecular phylodynamic methods to identify and forecast HIV transmission clusters in public health settings: a qualitative study","volume":"12","author":"Rich","year":"2020","journal-title":"Viruses"},{"issue":"8","key":"10.1016\/j.virol.2025.110558_bib48","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0135367","article-title":"Combining the estimated date of HIV infection with a phylogenetic cluster study to better understand HIV spread: application in a Paris neighbourhood","volume":"10","author":"Robineau","year":"2015","journal-title":"PLoS One"},{"issue":"3","key":"10.1016\/j.virol.2025.110558_bib49","doi-asserted-by":"crossref","first-page":"211","DOI":"10.1089\/aid.2016.0205","article-title":"Identifying transmission clusters with cluster picker and HIV-TRACE","volume":"33","author":"Rose","year":"2017","journal-title":"AIDS Res. Hum. Retrovir."},{"key":"10.1016\/j.virol.2025.110558_bib50","first-page":"410","article-title":"V-measure: a conditional entropy-based external cluster evaluation measure","author":"Rosenberg","year":"2007","journal-title":"methods in natural language processing and computational natural language learning"},{"issue":"5","key":"10.1016\/j.virol.2025.110558_bib51","doi-asserted-by":"crossref","first-page":"1261","DOI":"10.1093\/molbev\/msu061","article-title":"Novel information theory-based measures for quantifying incongruence among phylogenetic trees","volume":"31","author":"Salichos","year":"2014","journal-title":"Mol. Biol. Evol."},{"issue":"1","key":"10.1016\/j.virol.2025.110558_bib52","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1093\/ije\/dyab141","article-title":"Cohort profile update: the Swiss HIV cohort study (SHCS)","volume":"51","author":"Scherrer","year":"2022","journal-title":"Int. J. Epidemiol."},{"key":"10.1016\/j.virol.2025.110558_bib53","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1007\/s00203-011-0677-x","article-title":"Phylogenetics","volume":"193","author":"Sleator","year":"2011","journal-title":"Arch. Microbiol."},{"issue":"1","key":"10.1016\/j.virol.2025.110558_bib54","doi-asserted-by":"crossref","first-page":"1928","DOI":"10.1038\/s41467-018-04217-5","article-title":"Tracking HIV-1 recombination to resolve its contribution to HIV-1 evolution in natural infection","volume":"9","author":"Song","year":"2018","journal-title":"Nat. Commun."},{"issue":"9","key":"10.1016\/j.virol.2025.110558_bib55","doi-asserted-by":"crossref","first-page":"1312","DOI":"10.1093\/bioinformatics\/btu033","article-title":"RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies","volume":"30","author":"Stamatakis","year":"2014","journal-title":"Bioinformatics"},{"key":"10.1016\/j.virol.2025.110558_bib56","first-page":"1","article-title":"Incongruence in the phylogenomics era","author":"Steenwyk","year":"2023","journal-title":"Nat. Rev. Genet."},{"issue":"2","key":"10.1016\/j.virol.2025.110558_bib57","doi-asserted-by":"crossref","first-page":"134","DOI":"10.1159\/000332010","article-title":"Description of two commercially available assays for genotyping of HIV-1","volume":"55","author":"St\u00fcrmer","year":"2012","journal-title":"Intervirology"},{"issue":"10","key":"10.1016\/j.virol.2025.110558_bib58","doi-asserted-by":"crossref","first-page":"2286","DOI":"10.3390\/v14102286","article-title":"Comparative HIV-1 phylogenies characterized by pr\/rt, pol and near-full-length genome sequences","volume":"14","author":"Topcu","year":"2022","journal-title":"Viruses"},{"key":"10.1016\/j.virol.2025.110558_bib60","doi-asserted-by":"crossref","DOI":"10.3389\/fbinf.2024.1400003","article-title":"AUTO-TUNE: selecting the distance threshold for inferring HIV transmission clusters","volume":"4","author":"Weaver","year":"2024","journal-title":"Frontiers in Bioinformatics"},{"issue":"6","key":"10.1016\/j.virol.2025.110558_bib61","doi-asserted-by":"crossref","first-page":"961","DOI":"10.1016\/j.jmoldx.2019.06.003","article-title":"Prospective evaluation of the vela diagnostics next-generation sequencing platform for HIV-1 genotypic resistance testing","volume":"21","author":"Weber","year":"2019","journal-title":"J. Mol. Diagn."},{"issue":"3","key":"10.1016\/j.virol.2025.110558_bib62","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1097\/COH.0000000000000539","article-title":"Comparative analysis of HIV sequences in real time for public health","volume":"14","author":"Wertheim","year":"2019","journal-title":"Curr. Opin. HIV AIDS"},{"issue":"10","key":"10.1016\/j.virol.2025.110558_bib64","doi-asserted-by":"crossref","first-page":"1327","DOI":"10.1089\/aid.2008.0101","article-title":"Identification of new CRF43_02G and CRF25_cpx in Saudi Arabia based on full genome sequence analysis of six HIV type 1 isolates","volume":"24","author":"Yamaguchi","year":"2008","journal-title":"AIDS Res. Hum. Retrovir."},{"issue":"1","key":"10.1016\/j.virol.2025.110558_bib65","doi-asserted-by":"crossref","DOI":"10.1038\/srep39489","article-title":"Using nearly full-genome HIV sequence data improves phylogeny reconstruction in a simulated epidemic","volume":"6","author":"Yebra","year":"2016","journal-title":"Sci. Rep."}],"container-title":["Virology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0042682225001710?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0042682225001710?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2025,11,4]],"date-time":"2025-11-04T01:58:15Z","timestamp":1762221495000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S0042682225001710"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,7]]},"references-count":61,"alternative-id":["S0042682225001710"],"URL":"https:\/\/doi.org\/10.1016\/j.virol.2025.110558","relation":{},"ISSN":["0042-6822"],"issn-type":[{"value":"0042-6822","type":"print"}],"subject":[],"published":{"date-parts":[[2025,7]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Threshold sensitivity analysis for HIV-1 transmission cluster detection using different genomic regions and subtypes","name":"articletitle","label":"Article Title"},{"value":"Virology","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.virol.2025.110558","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2025 Published by Elsevier Inc.","name":"copyright","label":"Copyright"}],"article-number":"110558"}}