{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,23]],"date-time":"2026-01-23T12:37:08Z","timestamp":1769171828044,"version":"3.49.0"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1006930","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2019,4,10]],"date-time":"2019-04-10T00:00:00Z","timestamp":1554854400000}}],"reference-count":68,"publisher":"Public Library of Science (PLoS)","issue":"3","license":[{"start":{"date-parts":[[2019,3,29]],"date-time":"2019-03-29T00:00:00Z","timestamp":1553817600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1006930","type":"journal-article","created":{"date-parts":[[2019,3,29]],"date-time":"2019-03-29T17:30:26Z","timestamp":1553880626000},"page":"e1006930","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":72,"title":["Bayesian inference of transmission chains using timing of symptoms, pathogen genomes and contact data"],"prefix":"10.1371","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1849-1886","authenticated-orcid":true,"given":"Finlay","family":"Campbell","sequence":"first","affiliation":[]},{"given":"Anne","family":"Cori","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1154-8093","authenticated-orcid":true,"given":"Neil","family":"Ferguson","sequence":"additional","affiliation":[]},{"given":"Thibaut","family":"Jombart","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2019,3,29]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"320","DOI":"10.1016\/S1473-3099(14)71075-8","article-title":"Chains of transmission and control of Ebola virus disease in Conakry, Guinea, in 2014: an observational study","volume":"15","author":"O Faye","year":"2015","journal-title":"Lancet Infect Dis"},{"key":"ref2","first-page":"355","article-title":"Superspreading and the effect of individual variation on disease emergence","volume":"438","author":"JO Lloyd-Smith","year":"2005","journal-title":"Nature. Nature Publishing Group"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"542","DOI":"10.1038\/35097116","article-title":"Transmission intensity and impact of control policies on the foot and mouth epidemic in Great Britain","volume":"413","author":"NM Ferguson","year":"2001","journal-title":"Nature"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"4230","DOI":"10.1128\/JCM.42.9.4230-4236.2004","article-title":"Use of the minimum spanning tree model for molecular epidemiological investigation of a nosocomial outbreak of hepatitis C virus infection","volume":"42","author":"E Spada","year":"2004","journal-title":"J Clin Microbiol"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"31","DOI":"10.1038\/nrg2626","article-title":"Sequencing technologies\u2014the next generation","volume":"11","author":"ML Metzker","year":"2010","journal-title":"Nat Rev Genet"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"e1003457","DOI":"10.1371\/journal.pcbi.1003457","article-title":"Bayesian reconstruction of disease outbreaks by combining epidemiologic and genomic data","volume":"10","author":"T Jombart","year":"2014","journal-title":"PLoS Comput Biol"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"20133251","DOI":"10.1098\/rspb.2013.3251","article-title":"A Bayesian approach for inferring the dynamics of partially observed endemic infectious diseases from space-time-genetic data","volume":"281","author":"N Mollentze","year":"2014","journal-title":"Proc Biol Sci"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"e1004633","DOI":"10.1371\/journal.pcbi.1004633","article-title":"A Systematic Bayesian Integration of Epidemiological and Genetic Data","volume":"11","author":"MSY Lau","year":"2015","journal-title":"PLoS Comput Biol"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"395","DOI":"10.1214\/15-AOAS898","article-title":"Reconstructing transmission trees for communicable diseases using densely sampled genetic data","volume":"10","author":"CJ Worby","year":"2016","journal-title":"Ann Appl Stat"},{"key":"ref10","article-title":"Genomic infectious disease epidemiology in partially sampled and ongoing outbreaks","author":"X Didelot","year":"2017","journal-title":"Mol Biol Evol"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"e1005130","DOI":"10.1371\/journal.pcbi.1005130","article-title":"SCOTTI: Efficient Reconstruction of Transmission within Outbreaks with the Structured Coalescent","volume":"12","author":"N De Maio","year":"2016","journal-title":"PLoS Comput Biol"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"e1004613","DOI":"10.1371\/journal.pcbi.1004613","article-title":"Epidemic Reconstruction in a Phylogenetics Framework: Transmission Trees as Partitions of the Node Set.","volume":"11","author":"M Hall","year":"2015","journal-title":"PLoS Comput Biol"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"e1005495","DOI":"10.1371\/journal.pcbi.1005495","article-title":"Simultaneous inference of phylogenetic and transmission trees in infectious disease outbreaks","volume":"13","author":"D Klinkenberg","year":"2017","journal-title":"PLoS Comput Biol"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"287","DOI":"10.20506\/rst.35.1.2433","article-title":"Using genomics data to reconstruct transmission trees during disease outbreaks","volume":"35","author":"MD Hall","year":"2016","journal-title":"Rev Sci Tech"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"1869","DOI":"10.1093\/molbev\/msu121","article-title":"Bayesian inference of infectious disease transmission from whole-genome sequence data","volume":"31","author":"X Didelot","year":"2014","journal-title":"Mol Biol Evol"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"121","DOI":"10.1098\/rspb.2002.2191","article-title":"The construction and analysis of epidemic trees with reference to the 2001 UK foot-and-mouth outbreak","volume":"270","author":"DT Haydon","year":"2003","journal-title":"Proc Biol Sci"},{"key":"ref17","article-title":"When are pathogen genome sequences informative of transmission events?","author":"F Campbell","year":"2018","journal-title":"PLoS Pathog"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"1122","DOI":"10.1038\/nature08182","article-title":"Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic","volume":"459","author":"GJD Smith","year":"2009","journal-title":"Nature"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"8180","DOI":"10.1073\/pnas.140102797","article-title":"Criteria for the control of drug-resistant tuberculosis","volume":"97","author":"C Dye","year":"2000","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"107","DOI":"10.1016\/S0749-3797(03)00114-4","article-title":"Halting a pneumococcal pneumonia outbreak among United States Marine Corps trainees.","volume":"25","author":"NF Crum","year":"2003","journal-title":"Am J Prev Med"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"2191","DOI":"10.1093\/jac\/dkv119","article-title":"Within-host diversity of MRSA antimicrobial resistances","volume":"70","author":"KI Stanczak-Mrozek","year":"2015","journal-title":"J Antimicrob Chemother"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"e4840","DOI":"10.1371\/journal.pone.0004840","article-title":"Increased susceptibility for superinfection with Streptococcus pneumoniae during influenza virus infection is not caused by TLR7-mediated lymphopenia","volume":"4","author":"S Stegemann","year":"2009","journal-title":"PLoS One"},{"key":"ref23","article-title":"PHYLOSCANNER: Inferring Transmission from Within- and Between-Host Pathogen Genetic Diversity","author":"C Wymant","year":"2017","journal-title":"Mol Biol Evol"},{"key":"ref24","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"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"256","DOI":"10.3201\/eid1002.030732","article-title":"Superspreading SARS events, Beijing, 2003","volume":"10","author":"Z Shen","year":"2004","journal-title":"Emerg Infect Dis"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"407","DOI":"10.1056\/NEJMoa1306742","article-title":"Hospital outbreak of Middle East respiratory syndrome coronavirus","volume":"369","author":"A Assiri","year":"2013","journal-title":"N Engl J Med"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"1481","DOI":"10.1056\/NEJMoa1411100","article-title":"Ebola Virus Disease in West Africa\u2014The First 9 Months of the Epidemic and Forward Projections","volume":"371","year":"2014","journal-title":"N Engl J Med"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"e1002170","DOI":"10.1371\/journal.pmed.1002170","article-title":"Exposure Patterns Driving Ebola Transmission in West Africa: A Retrospective Observational Study","volume":"13","author":"J Agua-Agum","year":"2016","journal-title":"PLoS Med"},{"key":"ref29","article-title":"You may have come into contact with \u2026": HIV Contact Tracing in Canada","author":"L Broeckaert","year":"2014","journal-title":"Prevention"},{"key":"ref30","first-page":"1","article-title":"Guidelines for the investigation of contacts of persons with infectious tuberculosis. Recommendations from the National Tuberculosis Controllers Association and CDC","volume":"54","year":"2005","journal-title":"MMWR Recomm Rep"},{"key":"ref31","year":"2011"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"1961","DOI":"10.1126\/science.1086478","article-title":"Transmission dynamics of the etiological agent of SARS in Hong Kong: impact of public health interventions","volume":"300","author":"S Riley","year":"2003","journal-title":"Science"},{"key":"ref33","doi-asserted-by":"crossref","DOI":"10.1098\/rspa.1927.0118","article-title":"A contribution to the mathematical theory of epidemics","author":"WO Kermack","year":"1927"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"507","DOI":"10.1016\/S1473-3099(15)70135-0","article-title":"Ebola superspreading","volume":"15","author":"CL Althaus","year":"2015","journal-title":"Lancet Infect Dis"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"1779","DOI":"10.1016\/S0140-6736(03)13414-9","article-title":"Comparative full-length genome sequence analysis of 14 SARS coronavirus isolates and common mutations associated with putative origins of infection","volume":"361","author":"YJ Ruan","year":"2003","journal-title":"Lancet"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"32","DOI":"10.1186\/1471-2334-4-32","article-title":"Mutational dynamics of the SARS coronavirus in cell culture and human populations isolated in 2003.","volume":"4","author":"VB Vega","year":"2004","journal-title":"BMC Infect Dis"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"e43","DOI":"10.1371\/journal.pmed.0020043","article-title":"SARS transmission pattern in Singapore reassessed by viral sequence variation analysis","volume":"2","author":"J Liu","year":"2005","journal-title":"PLoS Med"},{"key":"ref38","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"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"230","DOI":"10.1097\/EDE.0000000000000776","article-title":"Real-time Estimation of Epidemiologic Parameters from Contact Tracing Data During an Emerging Infectious Disease Outbreak","volume":"29","author":"L Soetens","year":"2018","journal-title":"Epidemiology"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"196","DOI":"10.1093\/aje\/kws006","article-title":"Robust reconstruction and analysis of outbreak data: influenza A(H1N1)v transmission in a school-based population","volume":"176","author":"N Hens","year":"2012","journal-title":"Am J Epidemiol"},{"key":"ref41","doi-asserted-by":"crossref","first-page":"567","DOI":"10.1093\/biostatistics\/kxs012","article-title":"Enhancing Bayesian risk prediction for epidemics using contact tracing.","volume":"13","author":"CP Jewell","year":"2012","journal-title":"Biostatistics"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"730","DOI":"10.1056\/NEJMoa1003176","article-title":"Whole-genome sequencing and social-network analysis of a tuberculosis outbreak","volume":"364","author":"JL Gardy","year":"2011","journal-title":"N Engl J Med"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"110","DOI":"10.1186\/1471-2334-13-110","article-title":"Inferring patient to patient transmission of Mycobacterium tuberculosis from whole genome sequencing data","volume":"13","author":"JM Bryant","year":"2013","journal-title":"BMC Infect Dis"},{"key":"ref44","doi-asserted-by":"crossref","DOI":"10.1098\/rstb.2016.0371","article-title":"Key data for outbreak evaluation: building on the Ebola experience","volume":"372","author":"A Cori","year":"2017","journal-title":"Philos Trans R Soc Lond B Biol Sci"},{"key":"ref45","doi-asserted-by":"crossref","first-page":"6146","DOI":"10.1073\/pnas.0307506101","article-title":"Factors that make an infectious disease outbreak controllable","volume":"101","author":"C Fraser","year":"2004","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref46","year":"2014"},{"key":"ref47","doi-asserted-by":"crossref","first-page":"2022","DOI":"10.3201\/\/eid2111.150684","article-title":"Contact Tracing Activities during the Ebola Virus Disease Epidemic in Kindia and Faranah, Guinea, 2014","volume":"21","author":"MG Dixon","year":"2015","journal-title":"Emerg Infect Dis"},{"key":"ref48","doi-asserted-by":"crossref","first-page":"1509","DOI":"10.1097\/QAD.0000000000000298","article-title":"Estimating per-act HIV transmission risk: a systematic review","volume":"28","author":"P Patel","year":"2014","journal-title":"AIDS"},{"key":"ref49","doi-asserted-by":"crossref","first-page":"456","DOI":"10.1098\/rsif.2011.0379","article-title":"Methods to infer transmission risk factors in complex outbreak data","volume":"9","author":"S Cauchemez","year":"2012","journal-title":"J R Soc Interface"},{"key":"ref50","doi-asserted-by":"crossref","first-page":"548","DOI":"10.1093\/biostatistics\/kxq068","article-title":"Contact intervals, survival analysis of epidemic data, and estimation of R(0).","volume":"12","author":"E Kenah","year":"2011","journal-title":"Biostatistics"},{"key":"ref51","doi-asserted-by":"crossref","first-page":"509","DOI":"10.1093\/aje\/kwh255","article-title":"Different epidemic curves for severe acute respiratory syndrome reveal similar impacts of control measures","volume":"160","author":"J Wallinga","year":"2004","journal-title":"Am J Epidemiol"},{"key":"ref52","doi-asserted-by":"crossref","first-page":"564","DOI":"10.1017\/ice.2015.18","article-title":"Environmental transmission of Clostridium difficile: association between hospital room size and C. difficile Infection","volume":"36","author":"J Jou","year":"2015","journal-title":"Infect Control Hosp Epidemiol"},{"key":"ref53","doi-asserted-by":"crossref","first-page":"477","DOI":"10.1038\/nrmicro1845","article-title":"Mathematical models of infectious disease transmission","volume":"6","author":"NC Grassly","year":"2008","journal-title":"Nat Rev Microbiol"},{"key":"ref54","doi-asserted-by":"crossref","first-page":"1505","DOI":"10.1093\/aje\/kwt133","article-title":"A new framework and software to estimate time-varying reproduction numbers during epidemics","volume":"178","author":"A Cori","year":"2013","journal-title":"Am J Epidemiol"},{"key":"ref55","doi-asserted-by":"crossref","first-page":"1481","DOI":"10.1056\/NEJMoa1411100","article-title":"Ebola Virus Disease in West Africa\u2014The First 9 Months of the Epidemic and Forward Projections.","volume":"371","year":"2014","journal-title":"The England New Journal of Medicine"},{"key":"ref56","doi-asserted-by":"crossref","first-page":"584","DOI":"10.1056\/NEJMc1414992","article-title":"West African Ebola Epidemic after One Year\u2014Slowing but Not Yet under Control","volume":"372","year":"2015","journal-title":"N Engl J Med"},{"key":"ref57","doi-asserted-by":"crossref","first-page":"1966","DOI":"10.1126\/science.1086616","article-title":"Transmission Dynamics and Control of Severe Acute Respiratory Syndrome","volume":"300","author":"M Lipsitch","year":"2003","journal-title":"Science"},{"key":"ref58","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1186\/1471-2458-6-207","article-title":"Factors associated with nosocomial SARS-CoV transmission among healthcare workers in Hanoi, Vietnam, 2003.","volume":"6","author":"MG Reynolds","year":"2006","journal-title":"BMC Public Health"},{"key":"ref59","first-page":"285","article-title":"Investigation of a nosocomial outbreak of severe acute respiratory syndrome (SARS) in Toronto, Canada","volume":"169","author":"M Varia","year":"2003","journal-title":"CMAJ"},{"key":"ref60","doi-asserted-by":"crossref","first-page":"1761","DOI":"10.1016\/S0140-6736(03)13410-1","article-title":"Epidemiological determinants of spread of causal agent of severe acute respiratory syndrome in Hong Kong","volume":"361","author":"CA Donnelly","year":"2003","journal-title":"Lancet"},{"key":"ref61","doi-asserted-by":"crossref","first-page":"647","DOI":"10.1128\/genomeA.01331-14","article-title":"Complete Genome Sequences of Three Ebola Virus Isolates from the 2014 Outbreak in West Africa","volume":"2","author":"T Hoenen","year":"2014","journal-title":"Genome Announc"},{"key":"ref62","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"},{"key":"ref63","article-title":"Genetic diversity and evolutionary dynamics of Ebola virus in Sierra Leone","author":"Y-G Tong","year":"2015","journal-title":"Nature"},{"key":"ref64","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1186\/1471-2148-4-21","article-title":"Moderate mutation rate in the SARS coronavirus genome and its implications","volume":"4","author":"Z Zhao","year":"2004","journal-title":"BMC Evol Biol"},{"key":"ref65","first-page":"373","article-title":"The genome comparison of SARS-CoV and other coronaviruses","volume":"25","author":"S-F Wu","year":"2003","journal-title":"Yi chuan = Hereditas\/Zhongguo yi chuan xue hui bian ji"},{"key":"ref66","first-page":"1","article-title":"Emergence of Zaire Ebola Virus Disease in Guinea\u2014Preliminary Report","author":"S Baize","year":"2014","journal-title":"N Engl J Med"},{"key":"ref67","doi-asserted-by":"crossref","first-page":"1394","DOI":"10.1126\/science.1085952","article-title":"Characterization of a novel coronavirus associated with severe acute respiratory syndrome","volume":"300","author":"PA Rota","year":"2003","journal-title":"Science"},{"key":"ref68","first-page":"306","article-title":"The mathematical theory of communication","volume":"14","author":"CE Shannon","year":"1997","journal-title":"MD Comput"}],"updated-by":[{"DOI":"10.1371\/journal.pcbi.1006930","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2019,4,10]],"date-time":"2019-04-10T00:00:00Z","timestamp":1554854400000}}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1006930","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,5,9]],"date-time":"2020-05-09T02:00:21Z","timestamp":1588989621000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1006930"}},"subtitle":[],"editor":[{"given":"Virginia E.","family":"Pitzer","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2019,3,29]]},"references-count":68,"journal-issue":{"issue":"3","published-online":{"date-parts":[[2019,3,29]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1006930","relation":{"new_version":[{"id-type":"doi","id":"10.1371\/journal.pcbi.1006930","asserted-by":"object"}]},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2019,3,29]]}}}