{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,17]],"date-time":"2026-03-17T07:58:12Z","timestamp":1773734292260,"version":"3.50.1"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1005868","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2017,11,27]],"date-time":"2017-11-27T00:00:00Z","timestamp":1511740800000}}],"reference-count":55,"publisher":"Public Library of Science (PLoS)","issue":"11","license":[{"start":{"date-parts":[[2017,11,13]],"date-time":"2017-11-13T00:00:00Z","timestamp":1510531200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000092","name":"Ontario Genomics Institute","doi-asserted-by":"publisher","award":["OGI-131"],"award-info":[{"award-number":["OGI-131"]}],"id":[{"id":"10.13039\/501100000092","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000024","name":"Canadian Institutes of Health Research","doi-asserted-by":"publisher","award":["PJT-153391"],"award-info":[{"award-number":["PJT-153391"]}],"id":[{"id":"10.13039\/501100000024","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000024","name":"Canadian Institutes of Health Research","doi-asserted-by":"publisher","award":["BOP-149562"],"award-info":[{"award-number":["BOP-149562"]}],"id":[{"id":"10.13039\/501100000024","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000024","name":"Canadian Institutes of Health Research","doi-asserted-by":"publisher","award":["FRN-130609"],"award-info":[{"award-number":["FRN-130609"]}],"id":[{"id":"10.13039\/501100000024","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1005868","type":"journal-article","created":{"date-parts":[[2017,11,13]],"date-time":"2017-11-13T13:40:33Z","timestamp":1510580433000},"page":"e1005868","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":24,"title":["A model-based clustering method to detect infectious disease transmission outbreaks from sequence variation"],"prefix":"10.1371","volume":"13","author":[{"given":"Rosemary M.","family":"McCloskey","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3779-154X","authenticated-orcid":true,"given":"Art F. Y.","family":"Poon","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2017,11,13]]},"reference":[{"issue":"4","key":"ref1","doi-asserted-by":"crossref","first-page":"488","DOI":"10.1093\/infdis\/138.4.488","article-title":"Restriction endonuclease fingerprinting of herpes simplex virus DNA: a novel epidemiological tool applied to a nosocomial outbreak","volume":"138","author":"TG Buchman","year":"1978","journal-title":"J Infect Dis"},{"issue":"7","key":"ref2","doi-asserted-by":"crossref","first-page":"e69875","DOI":"10.1371\/journal.pone.0069875","article-title":"Finding evidence for local transmission of contagious disease in molecular epidemiological datasets","volume":"8","author":"RJ Ypma","year":"2013","journal-title":"PloS one"},{"issue":"1","key":"ref3","doi-asserted-by":"crossref","first-page":"155","DOI":"10.1186\/s13059-015-0726-x","article-title":"Real-time digital pathogen surveillance\u2014the time is now","volume":"16","author":"J Gardy","year":"2015","journal-title":"Genome biology"},{"issue":"5","key":"ref4","doi-asserted-by":"crossref","first-page":"e231","DOI":"10.1016\/S2352-3018(16)00046-1","article-title":"Near real-time monitoring of HIV transmission hotspots from routine HIV genotyping: an implementation case study","volume":"3","author":"AF Poon","year":"2016","journal-title":"The Lancet HIV"},{"issue":"3","key":"ref5","doi-asserted-by":"crossref","first-page":"e1003549","DOI":"10.1371\/journal.pcbi.1003549","article-title":"Within-host bacterial diversity hinders accurate reconstruction of transmission networks from genomic distance data","volume":"10","author":"CJ Worby","year":"2014","journal-title":"PLoS Comput Biol"},{"issue":"2","key":"ref6","doi-asserted-by":"crossref","first-page":"137","DOI":"10.1016\/S1473-3099(12)70277-3","article-title":"Whole-genome sequencing to delineate Mycobacterium tuberculosis outbreaks: a retrospective observational study","volume":"13","author":"TM Walker","year":"2013","journal-title":"Lancet Infect Dis"},{"issue":"7","key":"ref7","doi-asserted-by":"crossref","first-page":"1115","DOI":"10.1093\/infdis\/jir468","article-title":"Transmission clustering drives the onward spread of the HIV epidemic among men who have sex with men in Quebec","volume":"204","author":"BG Brenner","year":"2011","journal-title":"J Infect Dis"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"317","DOI":"10.1186\/1471-2105-14-317","article-title":"Automated analysis of phylogenetic clusters","volume":"14","author":"M Ragonnet-Cronin","year":"2013","journal-title":"BMC Bioinformatics"},{"issue":"5","key":"ref9","doi-asserted-by":"crossref","first-page":"1571","DOI":"10.1002\/hep.27310","article-title":"Phylogenetic clustering of hepatitis C virus among people who inject drugs in Vancouver, Canada","volume":"60","author":"B Jacka","year":"2014","journal-title":"Hepatology"},{"issue":"6","key":"ref10","doi-asserted-by":"crossref","first-page":"957","DOI":"10.1093\/infdis\/jiv542","article-title":"Accurate Genetic Detection of Hepatitis C Virus Transmissions in Outbreak Settings","volume":"213","author":"DS Campo","year":"2016","journal-title":"J Infect Dis"},{"issue":"6202","key":"ref11","doi-asserted-by":"crossref","first-page":"1369","DOI":"10.1126\/science.1259657","article-title":"Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak","volume":"345","author":"SK Gire","year":"2014","journal-title":"Science"},{"issue":"7650","key":"ref12","doi-asserted-by":"crossref","first-page":"309","DOI":"10.1038\/nature22040","article-title":"Virus genomes reveal factors that spread and sustained the Ebola epidemic","volume":"544","author":"G Dudas","year":"2017","journal-title":"Nature"},{"issue":"12","key":"ref13","doi-asserted-by":"crossref","first-page":"6221","DOI":"10.1128\/JVI.64.12.6221-6233.1990","article-title":"Concurrent evolution of human immunodeficiency virus type 1 in patients infected from the same source: rate of sequence change and low frequency of inactivating mutations","volume":"64","author":"P Balfe","year":"1990","journal-title":"j Virol"},{"issue":"17","key":"ref14","doi-asserted-by":"crossref","first-page":"2287","DOI":"10.1097\/00002030-200111230-00010","article-title":"Acute HIV infection: impact on the spread of HIV and transmission of drug resistance","volume":"15","author":"S Yerly","year":"2001","journal-title":"AIDS"},{"issue":"5","key":"ref15","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":"S Hu\u00e9","year":"2004","journal-title":"AIDS"},{"issue":"2","key":"ref16","doi-asserted-by":"crossref","first-page":"vew031","DOI":"10.1093\/ve\/vew031","article-title":"Impacts and shortcomings of genetic clustering methods for infectious disease outbreaks","volume":"2","author":"AF Poon","year":"2016","journal-title":"Virus Evolution"},{"issue":"1327","key":"ref17","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1098\/rstb.1995.0088","article-title":"Revealing the history of infectious disease epidemics through phylogenetic trees","volume":"349","author":"EC Holmes","year":"1995","journal-title":"Phil Trans Roy Soc Lond B"},{"issue":"1","key":"ref18","doi-asserted-by":"crossref","first-page":"347","DOI":"10.1093\/molbev\/msr217","article-title":"Estimating the basic reproductive number from viral sequence data","volume":"29","author":"T Stadler","year":"2012","journal-title":"Mol Biol Evol"},{"issue":"20","key":"ref19","doi-asserted-by":"crossref","first-page":"10864","DOI":"10.1073\/pnas.93.20.10864","article-title":"Accurate reconstruction of a known HIV-1 transmission history by phylogenetic tree analysis","volume":"93","author":"T Leitner","year":"1996","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"5","key":"ref20","doi-asserted-by":"crossref","first-page":"701","DOI":"10.1080\/10635150701607033","article-title":"Estimating a binary character\u2019s effect on speciation and extinction","volume":"56","author":"WP Maddison","year":"2007","journal-title":"Systematic biology"},{"issue":"2","key":"ref21","doi-asserted-by":"crossref","first-page":"149","DOI":"10.1016\/0166-5316(93)90035-S","article-title":"The Markov-modulated Poisson process (MMPP) cookbook","volume":"18","author":"W Fischer","year":"1993","journal-title":"Performance Evaluation"},{"issue":"4","key":"ref22","doi-asserted-by":"crossref","first-page":"431","DOI":"10.1016\/0167-9473(95)00025-9","article-title":"An EM algorithm for estimation in Markov-modulated Poisson processes","volume":"21","author":"T Ryd\u00e9n","year":"1996","journal-title":"Computational Statistics & Data Analysis"},{"issue":"6","key":"ref23","doi-asserted-by":"crossref","first-page":"368","DOI":"10.1007\/BF01734359","article-title":"Evolutionary trees from DNA sequences: a maximum likelihood approach","volume":"17","author":"J Felsenstein","year":"1981","journal-title":"Journal of Molecular Evolution"},{"issue":"6","key":"ref24","doi-asserted-by":"crossref","first-page":"890","DOI":"10.1093\/oxfordjournals.molbev.a026369","article-title":"A fast algorithm for joint reconstruction of ancestral amino acid sequences","volume":"17","author":"T Pupko","year":"2000","journal-title":"Mol Biol Evol"},{"key":"ref25","first-page":"75","article-title":"Towards a New Evolutionary Computation","author":"N Hansen","year":"2006"},{"issue":"6","key":"ref26","doi-asserted-by":"crossref","first-page":"1480","DOI":"10.1093\/molbev\/mst057","article-title":"A stochastic simulator of birth-death master equations with application to phylodynamics","volume":"30","author":"TG Vaughan","year":"2013","journal-title":"Mol Biol Evol"},{"issue":"2","key":"ref27","doi-asserted-by":"crossref","first-page":"595","DOI":"10.1534\/genetics.114.172791","article-title":"Inferring epidemiological dynamics with Bayesian coalescent inference: the merits of deterministic and stochastic models","volume":"199","author":"A Popinga","year":"2015","journal-title":"Genetics"},{"issue":"8","key":"ref28","doi-asserted-by":"crossref","first-page":"1879","DOI":"10.1093\/molbev\/msp098","article-title":"INDELible: a flexible simulator of biological sequence evolution","volume":"26","author":"W Fletcher","year":"2009","journal-title":"Mol Biol Evol"},{"issue":"3","key":"ref29","doi-asserted-by":"crossref","first-page":"e9490","DOI":"10.1371\/journal.pone.0009490","article-title":"FastTree 2\u2013approximately maximum-likelihood trees for large alignments","volume":"5","author":"MN Price","year":"2010","journal-title":"PloS one"},{"key":"ref30","doi-asserted-by":"crossref","unstructured":"Simonsen M, Mailund T, Pedersen CN. Rapid neighbour-joining. In: International Workshop on Algorithms in Bioinformatics. Springer; 2008. p. 113\u2013122.","DOI":"10.1007\/978-3-540-87361-7_10"},{"issue":"2","key":"ref31","doi-asserted-by":"crossref","first-page":"304","DOI":"10.1093\/infdis\/jit524","article-title":"The global transmission network of HIV-1","volume":"209","author":"JO Wertheim","year":"2014","journal-title":"J Infect Dis"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"321","DOI":"10.1038\/ncomms1325","article-title":"A novel methodology for large-scale phylogeny partition","volume":"2","author":"MCF Prosperi","year":"2011","journal-title":"Nat Commun"},{"issue":"6","key":"ref33","doi-asserted-by":"crossref","first-page":"926","DOI":"10.1093\/infdis\/jiu560","article-title":"The impact of clinical, demographic and risk factors on rates of HIV transmission: a population-based phylogenetic analysis in British Columbia, Canada","volume":"211","author":"AFY Poon","year":"2015","journal-title":"J Infect Dis"},{"issue":"2","key":"ref34","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1093\/bioinformatics\/btg412","article-title":"APE: analyses of phylogenetics and evolution in R language","volume":"20","author":"E Paradis","year":"2004","journal-title":"Bioinformatics"},{"issue":"4","key":"ref35","doi-asserted-by":"crossref","first-page":"592","DOI":"10.1093\/bioinformatics\/btq706","article-title":"phangorn: phylogenetic analysis in R","volume":"27","author":"KP Schliep","year":"2011","journal-title":"Bioinformatics"},{"issue":"8","key":"ref36","doi-asserted-by":"crossref","first-page":"1135","DOI":"10.1093\/cid\/cis612","article-title":"Characterizing HIV transmission networks across the United States","volume":"55","author":"JL Aldous","year":"2012","journal-title":"Clin Infect Dis"},{"issue":"11","key":"ref37","doi-asserted-by":"crossref","first-page":"1422","DOI":"10.1093\/bioinformatics\/btp163","article-title":"Biopython: freely available Python tools for computational molecular biology and bioinformatics","volume":"25","author":"PJA Cock","year":"2009","journal-title":"Bioinformatics"},{"issue":"4","key":"ref38","doi-asserted-by":"crossref","first-page":"318","DOI":"10.1089\/aid.2016.0061","article-title":"Phylogenetic evidence of HIV-1 transmission between adult and adolescent men who have sex with men","volume":"33","author":"E Wolf","year":"2017","journal-title":"AIDS research and human retroviruses"},{"issue":"2","key":"ref39","doi-asserted-by":"crossref","first-page":"215","DOI":"10.1097\/QAD.0b013e328011e691","article-title":"HIV-1 protease and reverse transcriptase mutations for drug resistance surveillance","volume":"21","author":"RW Shafer","year":"2007","journal-title":"AIDS"},{"issue":"11","key":"ref40","doi-asserted-by":"crossref","first-page":"e1000581","DOI":"10.1371\/journal.pcbi.1000581","article-title":"An evolutionary model-based algorithm for accurate phylogenetic breakpoint mapping and subtype prediction in HIV-1","volume":"5","author":"SL Kosakovsky Pond","year":"2009","journal-title":"PLoS Comput Biol"},{"issue":"4","key":"ref41","doi-asserted-by":"crossref","first-page":"772","DOI":"10.1093\/molbev\/mst010","article-title":"MAFFT multiple sequence alignment software version 7: improvements in performance and usability","volume":"30","author":"K Katoh","year":"2013","journal-title":"Mol Biol Evol"},{"issue":"6","key":"ref42","doi-asserted-by":"crossref","first-page":"e1002552","DOI":"10.1371\/journal.pcbi.1002552","article-title":"Simple epidemiological dynamics explain phylogenetic clustering of HIV from patients with recent infection","volume":"8","author":"EM Volz","year":"2012","journal-title":"PLoS Comput Biol"},{"issue":"23","key":"ref43","doi-asserted-by":"crossref","first-page":"13050","DOI":"10.1128\/JVI.00889-07","article-title":"Phylogenetic surveillance of viral genetic diversity and the evolving molecular epidemiology of human immunodeficiency virus type 1","volume":"81","author":"RJ Gifford","year":"2007","journal-title":"J Virol"},{"issue":"10","key":"ref44","doi-asserted-by":"crossref","first-page":"1488","DOI":"10.1086\/651951","article-title":"Molecular epidemiology reveals long-term changes in HIV type 1 subtype B transmission in Switzerland","volume":"201","author":"RD Kouyos","year":"2010","journal-title":"J Infect Dis"},{"issue":"3","key":"ref45","doi-asserted-by":"crossref","first-page":"e50","DOI":"10.1371\/journal.pmed.0050050","article-title":"Episodic sexual transmission of HIV revealed by molecular phylodynamics","volume":"5","author":"F Lewis","year":"2008","journal-title":"PLoS Med"},{"issue":"10","key":"ref46","doi-asserted-by":"crossref","first-page":"20160273","DOI":"10.1098\/rsbl.2016.0273","article-title":"Estimating shifts in diversification rates based on higher-level phylogenies","volume":"12","author":"T Stadler","year":"2016","journal-title":"Biology letters"},{"issue":"6","key":"ref47","doi-asserted-by":"crossref","first-page":"1084","DOI":"10.1111\/j.2041-210X.2012.00234.x","article-title":"Diversitree: comparative phylogenetic analyses of diversification in R","volume":"3","author":"RG FitzJohn","year":"2012","journal-title":"Methods in Ecology and Evolution"},{"issue":"3","key":"ref48","doi-asserted-by":"crossref","first-page":"1055","DOI":"10.1534\/genetics.113.154856","article-title":"Relating phylogenetic trees to transmission trees of infectious disease outbreaks","volume":"195","author":"RJF Ypma","year":"2013","journal-title":"Genetics"},{"issue":"12","key":"ref49","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":"V Novitsky","year":"2014","journal-title":"AIDS Res Hum Retroviruses"},{"issue":"3","key":"ref50","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":"PJ Peters","year":"2016","journal-title":"N Engl J Med"},{"key":"ref51","first-page":"095661","article-title":"Biased phylodynamic inferences from analysing clusters of viral sequences","author":"B Dearlove","year":"2016","journal-title":"bioRxiv"},{"key":"ref52","doi-asserted-by":"crossref","first-page":"e05166","DOI":"10.7554\/eLife.05166","article-title":"Large-scale whole genome sequencing of M. tuberculosis provides insights into transmission in a high prevalence area","volume":"4","author":"J Guerra-Assun\u00e7\u00e3o","year":"2015","journal-title":"Elife"},{"issue":"10","key":"ref53","doi-asserted-by":"crossref","first-page":"e47335","DOI":"10.1371\/journal.pone.0047335","article-title":"Hepatitis C virus phylogenetic clustering is associated with the social-injecting network in a cohort of people who inject drugs","volume":"7","author":"R Sacks-Davis","year":"2012","journal-title":"PloS one"},{"issue":"4","key":"ref54","doi-asserted-by":"crossref","first-page":"688","DOI":"10.1111\/1755-0998.12320","article-title":"Simulating and detecting autocorrelation of molecular evolutionary rates among lineages","volume":"15","author":"SY Ho","year":"2015","journal-title":"Molecular ecology resources"},{"issue":"3","key":"ref55","doi-asserted-by":"crossref","first-page":"352","DOI":"10.1093\/oxfordjournals.molbev.a003811","article-title":"Performance of a divergence time estimation method under a probabilistic model of rate evolution","volume":"18","author":"H Kishino","year":"2001","journal-title":"Molecular Biology and Evolution"}],"updated-by":[{"DOI":"10.1371\/journal.pcbi.1005868","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2017,11,27]],"date-time":"2017-11-27T00:00:00Z","timestamp":1511740800000}}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1005868","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,10,21]],"date-time":"2020-10-21T15:35:46Z","timestamp":1603294546000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1005868"}},"subtitle":[],"editor":[{"given":"Sergei L.","family":"Kosakovsky Pond","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2017,11,13]]},"references-count":55,"journal-issue":{"issue":"11","published-online":{"date-parts":[[2017,11,13]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1005868","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/165357","asserted-by":"object"}]},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2017,11,13]]}}}