{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,4]],"date-time":"2026-09-04T01:01:33Z","timestamp":1788483693108,"version":"build-2803163510"},"update-to":[{"DOI":"10.1371\/journal.ppat.1007290","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2018,9,27]],"date-time":"2018-09-27T00:00:00Z","timestamp":1538006400000}}],"reference-count":49,"publisher":"Public Library of Science (PLoS)","issue":"9","license":[{"start":{"date-parts":[[2018,9,17]],"date-time":"2018-09-17T00:00:00Z","timestamp":1537142400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000024","name":"Canadian Institutes of Health Research","doi-asserted-by":"publisher","award":["MOP-133680"],"award-info":[{"award-number":["MOP-133680"]}],"id":[{"id":"10.13039\/501100000024","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000156","name":"Fonds de Recherche du Qu\u00e9bec - Sant\u00e9","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000156","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000145","name":"Alberta Innovates - Health Solutions","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000145","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["U19AI111825"],"award-info":[{"award-number":["U19AI111825"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["DP5OD012142"],"award-info":[{"award-number":["DP5OD012142"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.plospathogens.org"],"crossmark-restriction":false},"short-container-title":["PLoS Pathog"],"DOI":"10.1371\/journal.ppat.1007290","type":"journal-article","created":{"date-parts":[[2018,9,17]],"date-time":"2018-09-17T18:21:49Z","timestamp":1537208509000},"page":"e1007290","update-policy":"https:\/\/doi.org\/10.1371\/journal.ppat.corrections_policy","source":"Crossref","is-referenced-by-count":39,"title":["Longitudinal transcriptomic characterization of the immune response to acute hepatitis C virus infection in patients with spontaneous viral clearance"],"prefix":"10.1371","volume":"14","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5885-1276","authenticated-orcid":true,"given":"Brad R.","family":"Rosenberg","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4651-9302","authenticated-orcid":true,"given":"Marion","family":"Depla","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1939-3102","authenticated-orcid":true,"given":"Catherine A.","family":"Freije","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8292-9248","authenticated-orcid":true,"given":"Denis","family":"Gaucher","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sabrina","family":"Mazouz","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maude","family":"Boisvert","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1043-8826","authenticated-orcid":true,"given":"Nathalie","family":"B\u00e9dard","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Julie","family":"Bruneau","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Charles M.","family":"Rice","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8817-8238","authenticated-orcid":true,"given":"Naglaa H.","family":"Shoukry","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2018,9,17]]},"reference":[{"issue":"5","key":"ref1","doi-asserted-by":"crossref","first-page":"374","DOI":"10.1097\/COH.0000000000000179","article-title":"The hepatitis C virus epidemics in key populations (including people who inject drugs, prisoners and MSM): the use of direct-acting antivirals as treatment for prevention","volume":"10","author":"NK Martin","year":"2015","journal-title":"Curr Opin HIV AIDS"},{"issue":"9","key":"ref2","doi-asserted-by":"crossref","first-page":"553","DOI":"10.1038\/nrgastro.2013.107","article-title":"Epidemiology and natural history of HCV infection","volume":"10","author":"B Hajarizadeh","year":"2013","journal-title":"Nat Rev Gastroenterol Hepatol"},{"key":"ref3","first-page":"274","article-title":"Protective immunity against hepatitis C: many shades of gray","volume":"5","author":"MS Abdel-Hakeem","year":"2014","journal-title":"Front Immunol"},{"issue":"1","key":"ref4","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1016\/j.immuni.2013.12.010","article-title":"Immune responses to HCV and other hepatitis viruses","volume":"40","author":"SH Park","year":"2014","journal-title":"Immunity"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"100","DOI":"10.1016\/j.antiviral.2014.02.013","article-title":"The past, present and future of neutralizing antibodies for hepatitis C virus","volume":"105","author":"JK Ball","year":"2014","journal-title":"Antiviral Res"},{"issue":"1671","key":"ref6","doi-asserted-by":"crossref","DOI":"10.1098\/rstb.2014.0146","article-title":"Vaccinology in the era of high-throughput biology","volume":"370","author":"HI Nakaya","year":"2015","journal-title":"Philos Trans R Soc Lond B Biol Sci"},{"issue":"4","key":"ref7","doi-asserted-by":"crossref","first-page":"831","DOI":"10.1016\/j.immuni.2012.12.008","article-title":"Systems scale interactive exploration reveals quantitative and qualitative differences in response to influenza and pneumococcal vaccines","volume":"38","author":"G Obermoser","year":"2013","journal-title":"Immunity"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"84","DOI":"10.1186\/1741-7007-8-84","article-title":"Assessing the human immune system through blood transcriptomics","volume":"8","author":"D Chaussabel","year":"2010","journal-title":"BMC biology"},{"issue":"1","key":"ref9","doi-asserted-by":"crossref","first-page":"116","DOI":"10.1038\/ni.1688","article-title":"Systems biology approach predicts immunogenicity of the yellow fever vaccine in humans","volume":"10","author":"TD Querec","year":"2009","journal-title":"Nat Immunol"},{"issue":"13","key":"ref10","doi-asserted-by":"crossref","first-page":"3119","DOI":"10.1084\/jem.20082292","article-title":"Yellow fever vaccine induces integrated multilineage and polyfunctional immune responses","volume":"205","author":"D Gaucher","year":"2008","journal-title":"J Exp Med"},{"issue":"2","key":"ref11","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1038\/ni.2789","article-title":"Molecular signatures of antibody responses derived from a systems biology study of five human vaccines","volume":"15","author":"S Li","year":"2014","journal-title":"Nat Immunol"},{"issue":"6","key":"ref12","doi-asserted-by":"crossref","first-page":"1186","DOI":"10.1016\/j.immuni.2015.11.012","article-title":"Systems Analysis of Immunity to Influenza Vaccination across Multiple Years and in Diverse Populations Reveals Shared Molecular Signatures","volume":"43","author":"HI Nakaya","year":"2015","journal-title":"Immunity"},{"issue":"2","key":"ref13","doi-asserted-by":"crossref","first-page":"499","DOI":"10.1016\/j.cell.2014.03.031","article-title":"Global analyses of human immune variation reveal baseline predictors of postvaccination responses","volume":"157","author":"JS Tsang","year":"2014","journal-title":"Cell"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"10369","DOI":"10.1038\/ncomms10369","article-title":"Pre-vaccination inflammation and B-cell signalling predict age-related hyporesponse to hepatitis B vaccination","volume":"7","author":"S Fourati","year":"2016","journal-title":"Nature communications"},{"issue":"1","key":"ref15","doi-asserted-by":"crossref","first-page":"115","DOI":"10.1016\/j.chom.2014.06.001","article-title":"Dengue virus infection induces expansion of a CD14(+)CD16(+) monocyte population that stimulates plasmablast differentiation","volume":"16","author":"M Kwissa","year":"2014","journal-title":"Cell Host Microbe"},{"issue":"24","key":"ref16","doi-asserted-by":"crossref","first-page":"15669","DOI":"10.1073\/pnas.202608199","article-title":"Genomic analysis of the host response to hepatitis C virus infection","volume":"99","author":"AI Su","year":"2002","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"15","key":"ref17","doi-asserted-by":"crossref","first-page":"7059","DOI":"10.1128\/JVI.75.15.7059-7066.2001","article-title":"DNA microarray analysis of chimpanzee liver during acute resolving hepatitis C virus infection","volume":"75","author":"CB Bigger","year":"2001","journal-title":"J Virol"},{"issue":"4","key":"ref18","doi-asserted-by":"crossref","first-page":"648","DOI":"10.1016\/j.immuni.2017.09.006","article-title":"Early Transcriptional Divergence Marks Virus-Specific Primary Human CD8(+) T Cells in Chronic versus Acute Infection","volume":"47","author":"D Wolski","year":"2017","journal-title":"Immunity"},{"issue":"3","key":"ref19","doi-asserted-by":"crossref","first-page":"777","DOI":"10.1053\/j.gastro.2012.05.044","article-title":"Interferon-\u03b3-stimulated genes, but not USP18, are expressed in livers of patients with acute hepatitis C","volume":"143","author":"MT Dill","year":"2012","journal-title":"Gastroenterology"},{"issue":"9","key":"ref20","doi-asserted-by":"crossref","first-page":"1259","DOI":"10.1111\/j.1478-3231.2010.02283.x","article-title":"Hepatitis C: viral and host factors associated with non-response to pegylated interferon plus ribavirin","volume":"30","author":"T Asselah","year":"2010","journal-title":"Liver Int"},{"issue":"6","key":"ref21","doi-asserted-by":"crossref","first-page":"1649","DOI":"10.1093\/ije\/dys167","article-title":"Cohort profile: the International Collaboration of Incident HIV and Hepatitis C in Injecting Cohorts (InC3) Study","volume":"42","author":"J Grebely","year":"2013","journal-title":"Int J Epidemiol"},{"issue":"4","key":"ref22","doi-asserted-by":"crossref","first-page":"271","DOI":"10.1038\/nri3642","article-title":"Democratizing systems immunology with modular transcriptional repertoire analyses","volume":"14","author":"D Chaussabel","year":"2014","journal-title":"Nat Rev Immunol"},{"issue":"17","key":"ref23","doi-asserted-by":"crossref","first-page":"2176","DOI":"10.1093\/bioinformatics\/btq401","article-title":"ROAST: rotation gene set tests for complex microarray experiments","volume":"26","author":"D Wu","year":"2010","journal-title":"Bioinformatics"},{"issue":"9","key":"ref24","doi-asserted-by":"crossref","first-page":"2425","DOI":"10.1073\/pnas.1621489114","article-title":"Systems analysis of protective immune responses to RTS,S malaria vaccination in humans","volume":"114","author":"D Kazmin","year":"2017","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"21","key":"ref25","doi-asserted-by":"crossref","first-page":"11264","DOI":"10.1128\/JVI.01205-10","article-title":"Pathogenesis of hepatitis E virus and hepatitis C virus in chimpanzees: similarities and differences","volume":"84","author":"C Yu","year":"2010","journal-title":"J Virol"},{"issue":"4","key":"ref26","doi-asserted-by":"crossref","first-page":"650","DOI":"10.1093\/infdis\/jix593","article-title":"Genetic Variation at IFNL4 Influences Extrahepatic Interferon-Stimulated Gene Expression in Chronic HCV Patients","volume":"217","author":"BR Rosenberg","year":"2018","journal-title":"J Infect Dis"},{"issue":"6","key":"ref27","doi-asserted-by":"crossref","first-page":"2124","DOI":"10.1002\/hep.26263","article-title":"Plasma interferon-gamma-inducible protein-10 (IP-10) levels during acute hepatitis C virus infection","volume":"57","author":"J Grebely","year":"2013","journal-title":"Hepatology"},{"issue":"2","key":"ref28","doi-asserted-by":"crossref","first-page":"686","DOI":"10.1053\/j.gastro.2011.05.006","article-title":"Delayed induction, not impaired recruitment, of specific CD8(+) T cells causes the late onset of acute hepatitis C","volume":"141","author":"EC Shin","year":"2011","journal-title":"Gastroenterology"},{"issue":"3","key":"ref29","doi-asserted-by":"crossref","first-page":"545","DOI":"10.1016\/j.jhep.2010.12.033","article-title":"Induction of CXCR3- and CCR5-associated chemokines during acute hepatitis C virus infection","volume":"55","author":"M Zeremski","year":"2011","journal-title":"J Hepatol"},{"issue":"3","key":"ref30","doi-asserted-by":"crossref","first-page":"e9753","DOI":"10.1371\/journal.pone.0009753","article-title":"Dissecting interferon-induced transcriptional programs in human peripheral blood cells","volume":"5","author":"SJ Waddell","year":"2010","journal-title":"PLoS One"},{"issue":"1","key":"ref31","doi-asserted-by":"crossref","first-page":"78","DOI":"10.1053\/j.gastro.2011.09.039","article-title":"Serum level of IP-10 increases predictive value of IL28B polymorphisms for spontaneous clearance of acute HCV infection","volume":"142","author":"S Beinhardt","year":"2012","journal-title":"Gastroenterology"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"32","DOI":"10.1186\/s12985-016-0482-x","article-title":"Alanine aminotransferase, HCV RNA levels and pro-inflammatory and pro-fibrogenic cytokines\/chemokines during acute hepatitis C virus infection","volume":"13","author":"B Hajarizadeh","year":"2016","journal-title":"Virology journal"},{"issue":"43","key":"ref33","doi-asserted-by":"crossref","first-page":"15545","DOI":"10.1073\/pnas.0506580102","article-title":"Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles","volume":"102","author":"A Subramanian","year":"2005","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"1","key":"ref34","doi-asserted-by":"crossref","first-page":"26","DOI":"10.1053\/j.gastro.2008.11.049","article-title":"Rare birds in North America: acute hepatitis C cohorts","volume":"136","author":"AL Cox","year":"2009","journal-title":"Gastroenterology"},{"issue":"4","key":"ref35","doi-asserted-by":"crossref","DOI":"10.1126\/sciimmunol.aah6817","article-title":"Interferon-driven deletion of antiviral B cells at the onset of chronic infection","volume":"1","author":"B Fallet","year":"2016","journal-title":"Science Immunology"},{"issue":"4","key":"ref36","doi-asserted-by":"crossref","DOI":"10.1126\/sciimmunol.aah3565","article-title":"Type I interferon suppresses virus-specific B cell responses by modulating CD8+ T cell differentiation","volume":"1","author":"EA Moseman","year":"2016","journal-title":"Science Immunology"},{"issue":"4","key":"ref37","doi-asserted-by":"crossref","DOI":"10.1126\/sciimmunol.aah6789","article-title":"Inflammatory monocytes hinder antiviral B cell responses","volume":"1","author":"S Sammicheli","year":"2016","journal-title":"Science Immunology"},{"issue":"10","key":"ref38","doi-asserted-by":"crossref","first-page":"1395","DOI":"10.1084\/jem.194.10.1395","article-title":"Determinants of viral clearance and persistence during acute hepatitis C virus infection","volume":"194","author":"R Thimme","year":"2001","journal-title":"J Exp Med"},{"issue":"24","key":"ref39","doi-asserted-by":"crossref","first-page":"15661","DOI":"10.1073\/pnas.202608299","article-title":"Viral and immunological determinants of hepatitis C virus clearance, persistence, and disease","volume":"99","author":"R Thimme","year":"2002","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"4","key":"ref40","doi-asserted-by":"crossref","first-page":"R36","DOI":"10.1186\/gb-2013-14-4-r36","article-title":"TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions","volume":"14","author":"D Kim","year":"2013","journal-title":"Genome biology"},{"issue":"2","key":"ref41","doi-asserted-by":"crossref","first-page":"166","DOI":"10.1093\/bioinformatics\/btu638","article-title":"HTSeq\u2014a Python framework to work with high-throughput sequencing data","volume":"31","author":"S Anders","year":"2015","journal-title":"Bioinformatics"},{"issue":"7","key":"ref42","doi-asserted-by":"crossref","first-page":"e47","DOI":"10.1093\/nar\/gkv007","article-title":"limma powers differential expression analyses for RNA-sequencing and microarray studies","volume":"43","author":"ME Ritchie","year":"2015","journal-title":"Nucleic Acids Res"},{"issue":"3","key":"ref43","doi-asserted-by":"crossref","first-page":"R25","DOI":"10.1186\/gb-2010-11-3-r25","article-title":"A scaling normalization method for differential expression analysis of RNA-seq data","volume":"11","author":"MD Robinson","year":"2010","journal-title":"Genome biology"},{"issue":"1","key":"ref44","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1093\/bioinformatics\/btp616","article-title":"edgeR: a Bioconductor package for differential expression analysis of digital gene expression data","volume":"26","author":"MD Robinson","year":"2010","journal-title":"Bioinformatics"},{"issue":"2","key":"ref45","doi-asserted-by":"crossref","first-page":"R29","DOI":"10.1186\/gb-2014-15-2-r29","article-title":"voom: Precision weights unlock linear model analysis tools for RNA-seq read counts","volume":"15","author":"CW Law","year":"2014","journal-title":"Genome biology"},{"issue":"1","key":"ref46","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1111\/j.2517-6161.1995.tb02031.x","article-title":"Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing","volume":"57","author":"Y Benjamini","year":"1995","journal-title":"Journal of the Royal Statistical Society Series B (Methodological)"},{"issue":"17","key":"ref47","doi-asserted-by":"crossref","first-page":"e133","DOI":"10.1093\/nar\/gks461","article-title":"Camera: a competitive gene set test accounting for inter-gene correlation","volume":"40","author":"D Wu","year":"2012","journal-title":"Nucleic Acids Res"},{"issue":"8","key":"ref48","doi-asserted-by":"crossref","first-page":"786","DOI":"10.1038\/ni.2067","article-title":"Systems biology of vaccination for seasonal influenza in humans","volume":"12","author":"HI Nakaya","year":"2011","journal-title":"Nat Immunol"},{"issue":"1","key":"ref49","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1093\/nar\/30.1.207","article-title":"Gene Expression Omnibus: NCBI gene expression and hybridization array data repository","volume":"30","author":"R Edgar","year":"2002","journal-title":"Nucleic Acids Res"}],"updated-by":[{"DOI":"10.1371\/journal.ppat.1007290","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2018,9,27]],"date-time":"2018-09-27T00:00:00Z","timestamp":1538006400000}}],"container-title":["PLOS Pathogens"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.ppat.1007290","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,9,1]],"date-time":"2022-09-01T18:40:20Z","timestamp":1662057620000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.ppat.1007290"}},"subtitle":[],"editor":[{"given":"Lynn","family":"Dustin","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2018,9,17]]},"references-count":49,"journal-issue":{"issue":"9","published-online":{"date-parts":[[2018,9,17]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.ppat.1007290","relation":{"new_version":[{"id-type":"doi","id":"10.1371\/journal.ppat.1007290","asserted-by":"object"}]},"ISSN":["1553-7374"],"issn-type":[{"value":"1553-7374","type":"electronic"}],"subject":[],"published":{"date-parts":[[2018,9,17]]}}}