{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,21]],"date-time":"2026-09-21T21:32:25Z","timestamp":1790026345896,"version":"4.0.1"},"reference-count":39,"publisher":"Oxford University Press (OUP)","issue":"11","license":[{"start":{"date-parts":[[2019,1,2]],"date-time":"2019-01-02T00:00:00Z","timestamp":1546387200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000288","name":"Royal Society","doi-asserted-by":"publisher","award":["107652\/Z\/15\/Z"],"award-info":[{"award-number":["107652\/Z\/15\/Z"]}],"id":[{"id":"10.13039\/501100000288","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,5,5]]},"DOI":"10.1093\/infdis\/jiy747","type":"journal-article","created":{"date-parts":[[2018,12,28]],"date-time":"2018-12-28T15:10:18Z","timestamp":1546009818000},"page":"1722-1729","source":"Crossref","is-referenced-by-count":21,"title":["High-Resolution Evolutionary Analysis of Within-Host Hepatitis C Virus Infection"],"prefix":"10.1093","volume":"219","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8538-4995","authenticated-orcid":false,"given":"Jayna","family":"Raghwani","sequence":"first","affiliation":[{"name":"Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chieh-Hsi","family":"Wu","sequence":"additional","affiliation":[{"name":"Department of Statistics, University of Oxford, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cynthia K Y","family":"Ho","sequence":"additional","affiliation":[{"name":"Department of Medical Microbiology, Amsterdam University Medical Center, the Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Menno","family":"De Jong","sequence":"additional","affiliation":[{"name":"Department of Medical Microbiology, Amsterdam University Medical Center, the Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Richard","family":"Molenkamp","sequence":"additional","affiliation":[{"name":"Department of Medical Microbiology, Amsterdam University Medical Center, the Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Janke","family":"Schinkel","sequence":"additional","affiliation":[{"name":"Department of Medical Microbiology, Amsterdam University Medical Center, the Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Oliver G","family":"Pybus","sequence":"additional","affiliation":[{"name":"Department of Zoology, University of Oxford, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Katrina A","family":"Lythgoe","sequence":"additional","affiliation":[{"name":"Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2019,1,2]]},"reference":[{"key":"2019050502394415100_CIT0001","doi-asserted-by":"crossref","first-page":"S45","DOI":"10.1016\/j.jhep.2014.07.027","article-title":"Global epidemiology and genotype distribution of the hepatitis C virus infection","volume":"61","author":"Gower","year":"2014","journal-title":"J Hepatol"},{"key":"2019050502394415100_CIT0002","doi-asserted-by":"crossref","first-page":"1176","DOI":"10.1053\/j.gastro.2014.03.003","article-title":"New hepatitis C therapies: the toolbox, strategies, and challenges","volume":"146","author":"Pawlotsky","year":"2014","journal-title":"Gastroenterology"},{"key":"2019050502394415100_CIT0003","article-title":"Impact of IFNL4 genotype on interferon-stimulated gene expression during DAA therapy for hepatitis C","author":"Ramamurthy","journal-title":"Hepatology"},{"key":"2019050502394415100_CIT0004","article-title":"Resistance analysis of genotype 3 hepatitis C virus indicates subtypes inherently resistant to nonstructural protein 5A inhibitors","author":"Smith","year":"2018","journal-title":"Hepatology"},{"key":"2019050502394415100_CIT0005","doi-asserted-by":"crossref","first-page":"540","DOI":"10.1038\/nrg2583","article-title":"Evolutionary analysis of the dynamics of viral infectious disease","volume":"10","author":"Pybus","year":"2009","journal-title":"Nat Rev Genet"},{"key":"2019050502394415100_CIT0006","doi-asserted-by":"crossref","first-page":"404","DOI":"10.1111\/jvh.12652","article-title":"A molecular transmission network of recent hepatitis C infection in people with and without HIV: Implications for targeted treatment strategies","volume":"24","author":"Bartlett","year":"2017","journal-title":"J Viral Hepat"},{"key":"2019050502394415100_CIT0007","doi-asserted-by":"crossref","first-page":"77","DOI":"10.1016\/j.meegid.2017.12.015","article-title":"Complex patterns of hepatitis-C virus longitudinal clustering in a high-risk population","volume":"58","author":"Rose","year":"2018","journal-title":"Infect Genet Evol"},{"key":"2019050502394415100_CIT0008","doi-asserted-by":"crossref","first-page":"e1001898; discussion e1001898","DOI":"10.1371\/journal.pmed.1001898","article-title":"Dispersion of the HIV-1 epidemic in men who have sex with men in the Netherlands: a combined mathematical model and phylogenetic analysis","volume":"12","author":"Bezemer","year":"2015","journal-title":"PLoS Med"},{"key":"2019050502394415100_CIT0009","doi-asserted-by":"crossref","first-page":"6369","DOI":"10.1128\/JVI.02204-10","article-title":"Temporal variations in the hepatitis C virus intrahost population during chronic infection","volume":"85","author":"Ramachandran","year":"2011","journal-title":"J Virol"},{"key":"2019050502394415100_CIT0010","doi-asserted-by":"crossref","first-page":"e1002656","DOI":"10.1371\/journal.ppat.1002656","article-title":"A new evolutionary model for hepatitis C virus chronic infection","volume":"8","author":"Gray","year":"2012","journal-title":"Plos Pathog"},{"key":"2019050502394415100_CIT0011","doi-asserted-by":"crossref","first-page":"187","DOI":"10.1016\/j.virol.2013.09.002","article-title":"Dynamic changes in viral population structure and compartmentalization during chronic hepatitis C virus infection in children","volume":"447","author":"Gismondi","year":"2013","journal-title":"Virology"},{"key":"2019050502394415100_CIT0012","doi-asserted-by":"crossref","first-page":"e1005894","DOI":"10.1371\/journal.ppat.1005894","article-title":"Exceptional heterogeneity in viral evolutionary dynamics characterises chronic hepatitis C virus infection","volume":"12","author":"Raghwani","year":"2016","journal-title":"PLoS Pathog"},{"key":"2019050502394415100_CIT0013","doi-asserted-by":"crossref","first-page":"pii: e02262-16","DOI":"10.1128\/JVI.02262-16","article-title":"Characterization of hepatitis C virus (HCV) envelope diversification from acute to chronic infection within a sexually transmitted HCV cluster by using single-molecule, real-time sequencing","volume":"91","author":"Ho","year":"2017","journal-title":"J Virol"},{"key":"2019050502394415100_CIT0014","doi-asserted-by":"crossref","first-page":"8475","DOI":"10.1073\/pnas.0602546103","article-title":"Evolution of hepatitis C viral quasispecies and hepatic injury in perinatally infected children followed prospectively","volume":"103","author":"Farci","year":"2006","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2019050502394415100_CIT0015","doi-asserted-by":"crossref","first-page":"339","DOI":"10.1126\/science.288.5464.339","article-title":"The outcome of acute hepatitis C predicted by the evolution of the viral quasispecies","volume":"288","author":"Farci","year":"2000","journal-title":"Science"},{"key":"2019050502394415100_CIT0016","doi-asserted-by":"crossref","first-page":"14562","DOI":"10.1073\/pnas.1210592109","article-title":"Profibrogenic chemokines and viral evolution predict rapid progression of hepatitis C to cirrhosis","volume":"109","author":"Farci","year":"2012","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2019050502394415100_CIT0017","doi-asserted-by":"crossref","first-page":"2781","DOI":"10.1099\/vir.0.81084-0","article-title":"Intra-host evolutionary dynamics of hepatitis C virus E2 in treated patients","volume":"86","author":"Alfonso","year":"2005","journal-title":"J Gen Virol"},{"key":"2019050502394415100_CIT0018","doi-asserted-by":"crossref","first-page":"1969","DOI":"10.1093\/molbev\/mss075","article-title":"Bayesian phylogenetics with BEAUti and the BEAST 1.7","volume":"29","author":"Drummond","year":"2012","journal-title":"Mol Biol Evol"},{"key":"2019050502394415100_CIT0019","doi-asserted-by":"crossref","first-page":"e88","DOI":"10.1371\/journal.pbio.0040088","article-title":"Relaxed phylogenetics and dating with confidence","volume":"4","author":"Drummond","year":"2006","journal-title":"Plos Biol"},{"key":"2019050502394415100_CIT0020","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1093\/molbev\/msj021","article-title":"Choosing appropriate substitution models for the phylogenetic analysis of protein-coding sequences","volume":"23","author":"Shapiro","year":"2006","journal-title":"Mol Biol Evol"},{"key":"2019050502394415100_CIT0021","doi-asserted-by":"crossref","first-page":"713","DOI":"10.1093\/molbev\/mss265","article-title":"Improving Bayesian population dynamics inference: a coalescent-based model for multiple loci","volume":"30","author":"Gill","year":"2013","journal-title":"Mol Biol Evol"},{"key":"2019050502394415100_CIT0022","doi-asserted-by":"crossref","first-page":"28","DOI":"10.1111\/2041-210X.12628","article-title":"GGTREE: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data","volume":"8","author":"Yu","year":"2017","journal-title":"Methods Ecol Evol"},{"key":"2019050502394415100_CIT0023","doi-asserted-by":"crossref","DOI":"10.1007\/978-0-387-98141-3","volume-title":"ggplot2: elegant graphics for data analysis","author":"Wickham","year":"2009"},{"key":"2019050502394415100_CIT0024","doi-asserted-by":"crossref","first-page":"e1005421","DOI":"10.1371\/journal.pgen.1005421","article-title":"New routes to phylogeography: a bayesian structured coalescent approximation","volume":"11","author":"De Maio","year":"2015","journal-title":"Plos Genet"},{"key":"2019050502394415100_CIT0025","doi-asserted-by":"crossref","first-page":"1185","DOI":"10.1093\/molbev\/msi103","article-title":"Bayesian coalescent inference of past population dynamics from molecular sequences","volume":"22","author":"Drummond","year":"2005","journal-title":"Mol Biol Evol"},{"key":"2019050502394415100_CIT0026","doi-asserted-by":"crossref","first-page":"e1003537","DOI":"10.1371\/journal.pcbi.1003537","article-title":"BEAST 2: a software platform for bayesian evolutionary analysis","volume":"10","author":"Bouckaert","year":"2014","journal-title":"PLoS Comput Biol"},{"key":"2019050502394415100_CIT0027","doi-asserted-by":"crossref","first-page":"vew003","DOI":"10.1093\/ve\/vew003","article-title":"The effects of sampling strategy on the quality of reconstruction of viral population dynamics using Bayesian skyline family coalescent methods: a simulation study","volume":"2","author":"Hall","year":"2016","journal-title":"Virus Evol"},{"key":"2019050502394415100_CIT0028","doi-asserted-by":"crossref","first-page":"150","DOI":"10.1093\/sysbio\/syq085","article-title":"Improving marginal likelihood estimation for Bayesian phylogenetic model selection","volume":"60","author":"Xie","year":"2011","journal-title":"Syst Biol"},{"key":"2019050502394415100_CIT0029","doi-asserted-by":"crossref","first-page":"e1000660","DOI":"10.1371\/journal.pcbi.1000660","article-title":"Recombination rate and selection strength in HIV intra-patient evolution","volume":"6","author":"Neher","year":"2010","journal-title":"PLoS Comput Biol"},{"key":"2019050502394415100_CIT0030","doi-asserted-by":"crossref","first-page":"3447","DOI":"10.1128\/JVI.78.7.3447-3454.2004","article-title":"High-resolution phylogenetic analysis of hepatitis C virus adaptation and its relationship to disease progression","volume":"78","author":"Sheridan","year":"2004","journal-title":"J Virol"},{"key":"2019050502394415100_CIT0031","doi-asserted-by":"crossref","first-page":"1931","DOI":"10.1099\/vir.0.80957-0","article-title":"Evolutionary dynamics of hepatitis C virus envelope genes during chronic infection","volume":"86","author":"Brown","year":"2005","journal-title":"J Gen Virol"},{"key":"2019050502394415100_CIT0032","doi-asserted-by":"crossref","first-page":"8432","DOI":"10.1128\/JVI.00749-12","article-title":"Unexpected maintenance of hepatitis C viral diversity following liver transplantation","volume":"86","author":"Gray","year":"2012","journal-title":"J Virol"},{"key":"2019050502394415100_CIT0033","doi-asserted-by":"crossref","first-page":"131","DOI":"10.1186\/1471-2148-11-131","article-title":"The mode and tempo of hepatitis C virus evolution within and among hosts","volume":"11","author":"Gray","year":"2011","journal-title":"BMC Evol Biol"},{"key":"2019050502394415100_CIT0034","doi-asserted-by":"crossref","first-page":"12582","DOI":"10.1128\/JVI.01440-12","article-title":"Constraints on viral evolution during chronic hepatitis C virus infection arising from a common-source exposure","volume":"86","author":"Bailey","year":"2012","journal-title":"J Virol"},{"key":"2019050502394415100_CIT0035","doi-asserted-by":"crossref","first-page":"1745","DOI":"10.1126\/science.285.5434.1745","article-title":"Clonal interference and the evolution of RNA viruses","volume":"285","author":"Miralles","year":"1999","journal-title":"Science"},{"key":"2019050502394415100_CIT0036","doi-asserted-by":"crossref","first-page":"821","DOI":"10.1093\/genetics\/140.2.821","article-title":"Linkage and the limits to natural selection","volume":"140","author":"Barton","year":"1995","journal-title":"Genetics"},{"key":"2019050502394415100_CIT0037","doi-asserted-by":"crossref","first-page":"395","DOI":"10.1093\/genetics\/162.1.395","article-title":"The effect of deleterious alleles on adaptation in asexual populations","volume":"162","author":"Johnson","year":"2002","journal-title":"Genetics"},{"key":"2019050502394415100_CIT0038","doi-asserted-by":"crossref","first-page":"597","DOI":"10.1093\/genetics\/137.2.597","article-title":"A Ruby in the rubbish: beneficial mutations, deleterious mutations and the evolution of sex","volume":"137","author":"Peck JR","year":"1994","journal-title":"Genetics"},{"key":"2019050502394415100_CIT0039","doi-asserted-by":"crossref","first-page":"477","DOI":"10.1111\/j.1558-5646.1981.tb04911.x","article-title":"Fixation probabilities and fixation times in a subdivided population","volume":"35","author":"Slatkin","year":"1981","journal-title":"Evolution"}],"container-title":["The Journal of Infectious Diseases"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/jid\/article-pdf\/219\/11\/1722\/28560187\/jiy747.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,9,9]],"date-time":"2022-09-09T02:43:58Z","timestamp":1662691438000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/jid\/article\/219\/11\/1722\/5269822"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,1,2]]},"references-count":39,"journal-issue":{"issue":"11","published-online":{"date-parts":[[2019,1,2]]},"published-print":{"date-parts":[[2019,5,5]]}},"URL":"https:\/\/doi.org\/10.1093\/infdis\/jiy747","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/400283","asserted-by":"object"}]},"ISSN":["0022-1899","1537-6613"],"issn-type":[{"value":"0022-1899","type":"print"},{"value":"1537-6613","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2019,6,1]]},"published":{"date-parts":[[2019,1,2]]}}}