{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,26]],"date-time":"2026-10-26T03:26:06Z","timestamp":1792985166856,"version":"4.5.0"},"reference-count":47,"publisher":"Ovid Technologies (Wolters Kluwer Health)","issue":"3","license":[{"start":{"date-parts":[[2023,2,27]],"date-time":"2023-02-27T00:00:00Z","timestamp":1677456000000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/ http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"content-domain":{"domain":["lww.com","ovid.com"],"crossmark-restriction":true},"short-container-title":[],"abstract":"<jats:sec>\n            <jats:title>Background.<\/jats:title>\n            <jats:p>Although HBV infection is a serious health issue worldwide, the landscape of HBV genome dynamics in the host has not yet been clarified. This study aimed to determine the continuous genome sequence of each HBV clone using a single-molecule real-time sequencing platform, and clarify the dynamics of structural abnormalities during persistent HBV infection without antiviral therapy.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Patients and Methods.<\/jats:title>\n            <jats:p>Twenty-five serum specimens were collected from 10 untreated HBV-infected patients. Continuous whole-genome sequencing of each clone was performed using a PacBio Sequel sequencer; the relationship between genomic variations and clinical information was analyzed. The diversity and phylogeny of the viral clones with structural variations were also analyzed.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results.<\/jats:title>\n            <jats:p>The whole-genome sequences of 797,352 HBV clones were determined. The deletion was the most common structural abnormality and concentrated in the preS\/<jats:italic toggle=\"yes\">S<\/jats:italic> and <jats:italic toggle=\"yes\">C<\/jats:italic> regions. Hepatitis B e antibody (anti-HBe)-negative samples or samples with high alanine aminotransferase levels have significantly diverse deletions than anti-HBe-positive samples or samples with low alanine aminotransferase levels. Phylogenetic analysis demonstrated that various defective and full-length clones evolve independently and form diverse viral populations.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusions.<\/jats:title>\n            <jats:p>Single-molecule real-time long-read sequencing revealed the dynamics of genomic quasispecies during the natural course of chronic HBV infections. Defective viral clones are prone to emerge under the condition of active hepatitis, and several types of defective variants can evolve independently of the viral clones with the full-length genome.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1097\/hc9.0000000000000047","type":"journal-article","created":{"date-parts":[[2023,2,27]],"date-time":"2023-02-27T17:01:07Z","timestamp":1677517267000},"page":"e0047-e0047","update-policy":"https:\/\/doi.org\/10.1097\/lww.0000000000001000","source":"Crossref","is-referenced-by-count":8,"title":["Evolutional transition of HBV genome during the persistent infection determined by single-molecule real-time sequencing"],"prefix":"10.1097","volume":"7","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-7856-6774","authenticated-orcid":false,"given":"Soichi","family":"Arasawa","sequence":"first","affiliation":[{"name":"Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University, Kyoto, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8954-9133","authenticated-orcid":false,"given":"Haruhiko","family":"Takeda","sequence":"additional","affiliation":[{"name":"Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University, Kyoto, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5233-4120","authenticated-orcid":false,"given":"Atsushi","family":"Takai","sequence":"additional","affiliation":[{"name":"Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University, Kyoto, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7921-1104","authenticated-orcid":false,"given":"Eriko","family":"Iguchi","sequence":"additional","affiliation":[{"name":"Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University, Kyoto, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4426-1491","authenticated-orcid":false,"given":"Yuji","family":"Eso","sequence":"additional","affiliation":[{"name":"Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University, Kyoto, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8392-2526","authenticated-orcid":false,"given":"Takahiro","family":"Shimizu","sequence":"additional","affiliation":[{"name":"Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University, Kyoto, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ken","family":"Takahashi","sequence":"additional","affiliation":[{"name":"Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University, Kyoto, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5465-534X","authenticated-orcid":false,"given":"Taiki","family":"Yamashita","sequence":"additional","affiliation":[{"name":"Department of Primary Care and Emergency Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3196-3494","authenticated-orcid":false,"given":"Yoshihide","family":"Ueda","sequence":"additional","affiliation":[{"name":"Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kobe University, Kobe, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4286-2712","authenticated-orcid":false,"given":"Hiroyuki","family":"Marusawa","sequence":"additional","affiliation":[{"name":"Department of Gastroenterology and Hepatology, Osaka Red Cross Hospital, Osaka, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8509-8128","authenticated-orcid":false,"given":"Hiroshi","family":"Seno","sequence":"additional","affiliation":[{"name":"Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University, Kyoto, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"276","published-online":{"date-parts":[[2023,3]]},"reference":[{"key":"R1-20240826","doi-asserted-by":"crossref","first-page":"571","DOI":"10.1099\/jgv.0.001415","article-title":"ICTV virus taxonomy profile: hepadnaviridae","volume":"101","author":"Magnius","year":"2020","journal-title":"J Gen Virol"},{"key":"R2-20240826","doi-asserted-by":"crossref","first-page":"1972","DOI":"10.1136\/gutjnl-2015-309809","article-title":"HBV cccDNA: viral persistence reservoir and key obstacle for a cure of chronic hepatitis B","volume":"64","author":"Nassal","year":"2015","journal-title":"Gut"},{"key":"R3-20240826","doi-asserted-by":"crossref","first-page":"m2200","DOI":"10.1136\/bmj.m2200","article-title":"Hepatitis B virus persistence and reactivation","volume":"370","author":"Shi","year":"2020","journal-title":"BMJ"},{"key":"R4-20240826","doi-asserted-by":"crossref","first-page":"672","DOI":"10.1016\/j.virol.2015.02.031","article-title":"Molecular biology of hepatitis B virus infection","volume":"479-480","author":"Seeger","year":"2015","journal-title":"Virology"},{"key":"R5-20240826","doi-asserted-by":"crossref","first-page":"1617","DOI":"10.3390\/ijms23031617","article-title":"Phytomedicines to target hepatitis B virus DNA replication: current limitations and future approaches","volume":"23","author":"Sadiea","year":"2022","journal-title":"Int J Mol Sci"},{"key":"R6-20240826","doi-asserted-by":"crossref","first-page":"a021360","DOI":"10.1101\/cshperspect.a021360","article-title":"Origins and evolution of hepatitis B virus and hepatitis D virus","volume":"6","author":"Littlejohn","year":"2016","journal-title":"Cold Spring Harb Perspect Med"},{"key":"R7-20240826","doi-asserted-by":"crossref","first-page":"e1000495","DOI":"10.1371\/journal.pbio.1000495","article-title":"Genomic fossils calibrate the long-term evolution of hepadnaviruses","volume":"8","author":"Gilbert","year":"2010","journal-title":"PLoS Biol"},{"key":"R8-20240826","doi-asserted-by":"crossref","first-page":"10307","DOI":"10.1128\/JVI.00996-06","article-title":"Molecular evolution of hepatitis B virus over 25 years","volume":"80","author":"Osiowy","year":"2006","journal-title":"J Virol"},{"key":"R9-20240826","doi-asserted-by":"crossref","first-page":"1791","DOI":"10.1038\/ncomms2798","article-title":"The genome of a Mesozoic paleovirus reveals the evolution of hepatitis B viruses","volume":"4","author":"Suh","year":"2013","journal-title":"Nat Commun"},{"key":"R10-20240826","doi-asserted-by":"crossref","first-page":"8422","DOI":"10.1073\/pnas.86.21.8422","article-title":"Detection and mapping of spliced RNA from a human hepatoma cell line transfected with the hepatitis B virus genome","volume":"86","author":"Suzuki","year":"1989","journal-title":"Proc Natl Acad Sci USA"},{"key":"R11-20240826","doi-asserted-by":"crossref","first-page":"5539","DOI":"10.1128\/jvi.65.10.5539-5543.1991","article-title":"Defective hepatitis B virus particles are generated by packaging and reverse transcription of spliced viral RNAs in vivo","volume":"65","author":"Terr\u00e9","year":"1991","journal-title":"J Virol"},{"key":"R12-20240826","doi-asserted-by":"crossref","first-page":"363","DOI":"10.1006\/viro.1997.8863","article-title":"Heterogeneity and common features of defective hepatitis B virus genomes derived from spliced pregenomic RNA","volume":"238","author":"G\u00fcnther","year":"1997","journal-title":"Virology"},{"key":"R13-20240826","doi-asserted-by":"crossref","first-page":"371","DOI":"10.1006\/viro.2000.0331","article-title":"Genotype-specific synthesis and secretion of spliced hepatitis B virus genomes in hepatoma cells","volume":"271","author":"Sommer","year":"2000","journal-title":"Virology"},{"key":"R14-20240826","doi-asserted-by":"crossref","first-page":"2373","DOI":"10.1136\/gutjnl-2021-324554","article-title":"Alternative splicing of viral transcripts: the dark side of HBV","volume":"70","author":"Kremsdorf","year":"2021","journal-title":"Gut"},{"key":"R15-20240826","doi-asserted-by":"crossref","first-page":"e0212559","DOI":"10.1371\/journal.pone.0212559","article-title":"HBV preS deletion mapping using deep sequencing demonstrates a unique association with viral markers","volume":"14","author":"Suzuki","year":"2019","journal-title":"PLOS ONE"},{"key":"R16-20240826","doi-asserted-by":"crossref","first-page":"7171","DOI":"10.1128\/JVI.00243-16","article-title":"Single-molecule sequencing reveals complex genome variation of hepatitis B virus during 15 years of chronic infection following liver transplantation","volume":"90","author":"Betz-Stablein","year":"2016","journal-title":"J Virol"},{"key":"R17-20240826","doi-asserted-by":"crossref","first-page":"2651","DOI":"10.1038\/s41598-020-59397-2","article-title":"Single-molecular real-time deep sequencing reveals the dynamics of multi-drug resistant haplotypes and structural variations in the hepatitis c virus genome","volume":"10","author":"Yamashita","year":"2020","journal-title":"Sci Rep"},{"key":"R18-20240826","doi-asserted-by":"crossref","first-page":"45605","DOI":"10.1038\/srep45605","article-title":"Evolution of multi-drug resistant HCV clones from pre-existing resistant-associated variants during direct-acting antiviral therapy determined by third-generation sequencing","volume":"7","author":"Takeda","year":"2017","journal-title":"Sci Rep"},{"key":"R19-20240826","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.virusres.2008.05.007","article-title":"Hepatitis B pregenomic RNA splicing\u2014the products, the regulatory mechanisms and its biological significance","volume":"136","author":"Lee","year":"2008","journal-title":"Virus Res"},{"key":"R20-20240826","doi-asserted-by":"crossref","first-page":"30","DOI":"10.1016\/j.virol.2008.06.021","article-title":"Characterization of the contribution of spliced RNAs of hepatitis B virus to DNA synthesis in transfected cultures of Huh7 and HepG2 cells","volume":"379","author":"Abraham","year":"2008","journal-title":"Virology"},{"key":"R21-20240826","doi-asserted-by":"crossref","first-page":"18","DOI":"10.1016\/j.virusres.2013.02.004","article-title":"One single nucleotide difference alters the differential expression of spliced RNAs between HBV genotypes A and D","volume":"174","author":"Huang","year":"2013","journal-title":"Virus Res"},{"key":"R22-20240826","doi-asserted-by":"crossref","first-page":"16459","DOI":"10.1038\/srep16459","article-title":"Hepatitis B virus spliced variants are associated with an impaired response to interferon therapy","volume":"5","author":"Chen","year":"2015","journal-title":"Sci Rep"},{"key":"R23-20240826","doi-asserted-by":"crossref","first-page":"e00680","DOI":"10.1128\/AAC.00680-17","article-title":"Hepatitis B virus capsid assembly modulators, but not nucleoside analogs, inhibit the production of extracellular pregenomic RNA and spliced RNA variants","volume":"61","author":"Lam","year":"2017","journal-title":"Antimicrob Agents Chemother"},{"key":"R24-20240826","first-page":"mgen000492","article-title":"Quantitative analysis of the splice variants expressed by the major hepatitis B virus genotypes","volume":"7","author":"Lim","year":"2021","journal-title":"Microb Genom"},{"key":"R25-20240826","doi-asserted-by":"crossref","first-page":"23838","DOI":"10.1038\/s41598-021-03304-w","article-title":"More DNA and RNA of HBV SP1 splice variants are detected in genotypes B and C at low viral replication","volume":"11","author":"Luk","year":"2021","journal-title":"Sci Rep"},{"key":"R26-20240826","doi-asserted-by":"crossref","first-page":"3109","DOI":"10.1099\/jgv.0.000256","article-title":"Enhanced hepatitis B virus (HBV) pre-genomic RNA levels and higher transcription efficiency of defective HBV genomes","volume":"96","author":"Kandpal","year":"2015","journal-title":"J Gen Virol"},{"key":"R27-20240826","doi-asserted-by":"crossref","first-page":"e35052","DOI":"10.1371\/journal.pone.0035052","article-title":"Dynamics of hepatitis B virus quasispecies in association with nucleos(t)ide analogue treatment determined by ultra-deep sequencing","volume":"7","author":"Nishijima","year":"2012","journal-title":"PLoS ONE"},{"key":"R28-20240826","doi-asserted-by":"crossref","first-page":"574","DOI":"10.1128\/JVI.03000-13","article-title":"Ultradeep pyrosequencing and molecular modeling identify key structural features of hepatitis B virus RNase H, a putative target for antiviral intervention","volume":"88","author":"Hayer","year":"2014","journal-title":"J Virol"},{"key":"R29-20240826","doi-asserted-by":"crossref","first-page":"127","DOI":"10.1128\/JCM.02229-15","article-title":"Implementation of next-generation sequencing for hepatitis B Virus resistance testing and genotyping in a clinical microbiology laboratory","volume":"54","author":"Lowe","year":"2016","journal-title":"J Clin Microbiol"},{"key":"R30-20240826","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1016\/j.jcv.2018.01.011","article-title":"Substantial variation in the hepatitis B surface antigen (HBsAg) in hepatitis B virus (HBV)-positive patients from South Africa: Reliable detection of HBV by the Elecsys HBsAg II assay","volume":"101","author":"Gencay","year":"2018","journal-title":"J Clin Virol"},{"key":"R31-20240826","doi-asserted-by":"crossref","first-page":"278","DOI":"10.1111\/jvh.13025","article-title":"Primary resistance of hepatitis B virus to nucleoside and nucleotide analogues","volume":"26","author":"Chevaliez","year":"2019","journal-title":"J Viral Hepat"},{"key":"R32-20240826","doi-asserted-by":"crossref","first-page":"546","DOI":"10.1016\/j.jhep.2015.03.020","article-title":"Characterization of novel entecavir resistance mutations","volume":"63","author":"Hayashi","year":"2015","journal-title":"J Hepatol"},{"key":"R33-20240826","doi-asserted-by":"crossref","first-page":"341","DOI":"10.1016\/j.jviromet.2013.06.015","article-title":"Analysis of hepatitis B virus genotyping and drug resistance gene mutations based on massively parallel sequencing","volume":"193","author":"Han","year":"2013","journal-title":"J Virol Methods"},{"key":"R34-20240826","doi-asserted-by":"crossref","first-page":"1281","DOI":"10.1016\/j.jhep.2017.07.011","article-title":"How viral genetic variants and genotypes influence disease and treatment outcome of chronic hepatitis B. Time for an individualised approach?","volume":"67","author":"Rajoriya","year":"2017","journal-title":"J Hepatol"},{"key":"R35-20240826","doi-asserted-by":"crossref","first-page":"78","DOI":"10.1186\/s12879-019-4713-9","article-title":"Retrospective analysis of acute HBV infections occurred in 1978\u201379 and 1994\u2013 95 in North-East Italy: increasing prevalence of BCP\/pre-core mutants in sub-genotype D3","volume":"20","author":"Bruni","year":"2020","journal-title":"BMC Infect Dis"},{"key":"R36-20240826","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1186\/s12929-018-0442-4","article-title":"Applications of next-generation sequencing analysis for the detection of hepatocellular carcinoma-associated hepatitis B virus mutations","volume":"25","author":"Wu","year":"2018","journal-title":"J Biomed Sci"},{"key":"R37-20240826","doi-asserted-by":"crossref","first-page":"14816","DOI":"10.1038\/s41598-018-33051-4","article-title":"A next-generation sequencingbased platform for quantitative detection of hepatitis B virus pre-S mutants in plasma of hepatocellular carcinoma patients","volume":"8","author":"Teng","year":"2018","journal-title":"Sci Rep"},{"key":"R38-20240826","doi-asserted-by":"crossref","first-page":"46","DOI":"10.1016\/j.jcv.2017.06.001","article-title":"Clinical course and core variability in HBV infected patients without detectable anti-HBc antibodies","volume":"93","author":"Anastasiou","year":"2017","journal-title":"J Clin Virol"},{"key":"R39-20240826","doi-asserted-by":"crossref","first-page":"993","DOI":"10.1002\/hep.30279","article-title":"Clinical outcome and viral genome variability of hepatitis b virus\u2013induced acute liver failure","volume":"69","author":"Anastasiou","year":"2019","journal-title":"Hepatology"},{"key":"R40-20240826","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1016\/j.ymeth.2017.08.005","article-title":"Detecting exact breakpoints of deletions with diversity in hepatitis B viral genomic DNA from next-generation sequencing data","volume":"129","author":"Cheng","year":"2017","journal-title":"Methods"},{"key":"R41-20240826","doi-asserted-by":"crossref","first-page":"2748","DOI":"10.1099\/jgv.0.000942","article-title":"Next-generation sequencing revealed divergence in deletions of the preS region in the HBV genome between different HBV-related liver diseases","volume":"98","author":"Jia","year":"2017","journal-title":"J Gen Virol"},{"key":"R42-20240826","doi-asserted-by":"crossref","first-page":"176","DOI":"10.1002\/path.4938","article-title":"Hepatocellular carcinoma-associated single-nucleotide variants and deletions identified by the use of genome-wide high-throughput analysis of hepatitis B virus","volume":"243","author":"Liu","year":"2017","journal-title":"J Pathol"},{"key":"R43-20240826","doi-asserted-by":"crossref","first-page":"e0194366","DOI":"10.1371\/journal.pone.0194366","article-title":"Early MinION\u2122nanopore single-molecule sequencing technology enables the characterization of hepatitis B virus genetic complexity in clinical samples","volume":"13","author":"Sauvage","year":"2018","journal-title":"PLOS ONE"},{"key":"R44-20240826","doi-asserted-by":"crossref","first-page":"2201","DOI":"10.1128\/JCM.00068-15","article-title":"Characterization of full-length genomes of hepatitis B virus quasispecies in sera of patients at different phases of infection","volume":"53","author":"Yang","year":"2015","journal-title":"J Clin Microbiol"},{"key":"R45-20240826","doi-asserted-by":"crossref","first-page":"1086","DOI":"10.4254\/wjh.v7.i8.1086","article-title":"Clinical relevance of hepatitis B virus variants","volume":"7","author":"Gao","year":"2015","journal-title":"World J Hepatol"},{"key":"R46-20240826","doi-asserted-by":"crossref","first-page":"1630","DOI":"10.1186\/s40064-016-3192-3","article-title":"Characteristics of CpG Islands and their quasispecies of full-length hepatitis B virus genomes from patients at different phases of infection","volume":"5","author":"Xue","year":"2016","journal-title":"SpringerPlus"},{"key":"R47-20240826","doi-asserted-by":"crossref","first-page":"3165","DOI":"10.1128\/JCM.00602-15","article-title":"Ultradeep sequencing for detection of quasispecies variants in the major hydrophilic region of hepatitis B virus in Indonesian patients","volume":"53","author":"Yamani","year":"2015","journal-title":"J Clin Microbiol"}],"container-title":["Hepatology Communications"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.lww.com\/10.1097\/HC9.0000000000000047","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,8,26]],"date-time":"2024-08-26T15:05:26Z","timestamp":1724684726000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.lww.com\/10.1097\/HC9.0000000000000047"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,2,27]]},"references-count":47,"journal-issue":{"issue":"3","published-online":{"date-parts":[[2023]]}},"URL":"https:\/\/doi.org\/10.1097\/hc9.0000000000000047","relation":{},"ISSN":["2471-254X"],"issn-type":[{"value":"2471-254X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,2,27]]},"assertion":[{"value":"2022-11-30","name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2022-12-20","name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}}]}}