{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,4]],"date-time":"2026-06-04T14:49:11Z","timestamp":1780584551101,"version":"3.54.1"},"reference-count":37,"publisher":"MDPI AG","issue":"5","license":[{"start":{"date-parts":[[2025,5,8]],"date-time":"2025-05-08T00:00:00Z","timestamp":1746662400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Novo Nordisk Foundation","award":["NNF19OC0054518"],"award-info":[{"award-number":["NNF19OC0054518"]}]},{"name":"Novo Nordisk Foundation","award":["NNF19OC0055462"],"award-info":[{"award-number":["NNF19OC0055462"]}]},{"name":"Novo Nordisk Foundation","award":["2022-0265"],"award-info":[{"award-number":["2022-0265"]}]},{"name":"Novo Nordisk Foundation","award":["R325-A19151"],"award-info":[{"award-number":["R325-A19151"]}]},{"name":"Novo Nordisk Foundation","award":["DNRF170"],"award-info":[{"award-number":["DNRF170"]}]},{"name":"Sygeforsikringen \u201cDanmark\u201d","award":["NNF19OC0054518"],"award-info":[{"award-number":["NNF19OC0054518"]}]},{"name":"Sygeforsikringen \u201cDanmark\u201d","award":["NNF19OC0055462"],"award-info":[{"award-number":["NNF19OC0055462"]}]},{"name":"Sygeforsikringen \u201cDanmark\u201d","award":["2022-0265"],"award-info":[{"award-number":["2022-0265"]}]},{"name":"Sygeforsikringen \u201cDanmark\u201d","award":["R325-A19151"],"award-info":[{"award-number":["R325-A19151"]}]},{"name":"Sygeforsikringen \u201cDanmark\u201d","award":["DNRF170"],"award-info":[{"award-number":["DNRF170"]}]},{"name":"Danish Cancer Society","award":["NNF19OC0054518"],"award-info":[{"award-number":["NNF19OC0054518"]}]},{"name":"Danish Cancer Society","award":["NNF19OC0055462"],"award-info":[{"award-number":["NNF19OC0055462"]}]},{"name":"Danish Cancer Society","award":["2022-0265"],"award-info":[{"award-number":["2022-0265"]}]},{"name":"Danish Cancer Society","award":["R325-A19151"],"award-info":[{"award-number":["R325-A19151"]}]},{"name":"Danish Cancer Society","award":["DNRF170"],"award-info":[{"award-number":["DNRF170"]}]},{"name":"Novo Nordisk Foundation BRIDGE research fellowship","award":["NNF19OC0054518"],"award-info":[{"award-number":["NNF19OC0054518"]}]},{"name":"Novo Nordisk Foundation BRIDGE research fellowship","award":["NNF19OC0055462"],"award-info":[{"award-number":["NNF19OC0055462"]}]},{"name":"Novo Nordisk Foundation BRIDGE research fellowship","award":["2022-0265"],"award-info":[{"award-number":["2022-0265"]}]},{"name":"Novo Nordisk Foundation BRIDGE research fellowship","award":["R325-A19151"],"award-info":[{"award-number":["R325-A19151"]}]},{"name":"Novo Nordisk Foundation BRIDGE research fellowship","award":["DNRF170"],"award-info":[{"award-number":["DNRF170"]}]},{"name":"Danish National Research Foundation","award":["NNF19OC0054518"],"award-info":[{"award-number":["NNF19OC0054518"]}]},{"name":"Danish National Research Foundation","award":["NNF19OC0055462"],"award-info":[{"award-number":["NNF19OC0055462"]}]},{"name":"Danish National Research Foundation","award":["2022-0265"],"award-info":[{"award-number":["2022-0265"]}]},{"name":"Danish National Research Foundation","award":["R325-A19151"],"award-info":[{"award-number":["R325-A19151"]}]},{"name":"Danish National Research Foundation","award":["DNRF170"],"award-info":[{"award-number":["DNRF170"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>The impact of hepatitis B virus (HBV) diversity and evolution on disease progression is not well-understood. This study aims to compare intra-individual viral evolution in two groups of chronic hepatitis B (CHB) patients, using antiviral treatment initiation as a measure of lack of immunological control. From the Danish Database for Hepatitis B and C (DANHEP), 25 CHB patients were included; 14 with antiviral treatment initiation (TI group), and 11 without (NTI group). For each patient, three serial plasma samples taken before potential treatment initiation were selected. HBV DNA was amplified by PCR and analyzed by next-generation sequencing. HBV DNA and alanine transaminase were elevated in the TI group throughout the study period. Significantly higher substitution rates in the NTI group versus the TI group were found both within the viral population and at consensus level. Putative predicted CD8+ T cell epitopes contained significantly more substitutions in the NTI group. Genome-wide association analysis revealed several amino acid residues in the HBV genome associated with treatment initiation. This study shows that HBV has a higher rate of substitutions in CHB patients not requiring treatment. This could be linked to host immune pressure leading to disease control.<\/jats:p>","DOI":"10.3390\/v17050684","type":"journal-article","created":{"date-parts":[[2025,5,8]],"date-time":"2025-05-08T04:06:21Z","timestamp":1746677181000},"page":"684","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Higher Rates of Viral Evolution in Chronic Hepatitis B Patients Linked to Predicted T Cell Epitopes"],"prefix":"10.3390","volume":"17","author":[{"given":"Magnus Illum","family":"Dalegaard","sequence":"first","affiliation":[{"name":"Department of Infectious Diseases, Copenhagen University Hospital, 2650 Hvidovre, Denmark"},{"name":"Copenhagen Hepatitis C Program (COHEP), Department of Infectious Diseases, Copenhagen University Hospital, 2650 Hvidovre, Denmark"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anni","family":"Winckelmann","sequence":"additional","affiliation":[{"name":"Department of Infectious Diseases, Copenhagen University Hospital, 2650 Hvidovre, Denmark"},{"name":"Copenhagen Hepatitis C Program (COHEP), Department of Infectious Diseases, Copenhagen University Hospital, 2650 Hvidovre, Denmark"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ulrik","family":"Fahn\u00f8e","sequence":"additional","affiliation":[{"name":"Department of Infectious Diseases, Copenhagen University Hospital, 2650 Hvidovre, Denmark"},{"name":"Copenhagen Hepatitis C Program (COHEP), Department of Infectious Diseases, Copenhagen University Hospital, 2650 Hvidovre, Denmark"},{"name":"Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alexander P.","family":"Underwood","sequence":"additional","affiliation":[{"name":"Department of Infectious Diseases, Copenhagen University Hospital, 2650 Hvidovre, Denmark"},{"name":"Copenhagen Hepatitis C Program (COHEP), Department of Infectious Diseases, Copenhagen University Hospital, 2650 Hvidovre, Denmark"},{"name":"Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9650-8965","authenticated-orcid":false,"given":"Anders Gorm","family":"Pedersen","sequence":"additional","affiliation":[{"name":"Department of Health Technology, Section for Bioinformatics, Technical University of Denmark, 2800 Kongens Lyngby, Denmark"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9604-4582","authenticated-orcid":false,"given":"Signe","family":"Bollerup","sequence":"additional","affiliation":[{"name":"Department of Infectious Diseases, Copenhagen University Hospital, 2650 Hvidovre, Denmark"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7815-4806","authenticated-orcid":false,"given":"Jens","family":"Bukh","sequence":"additional","affiliation":[{"name":"Department of Infectious Diseases, Copenhagen University Hospital, 2650 Hvidovre, Denmark"},{"name":"Copenhagen Hepatitis C Program (COHEP), Department of Infectious Diseases, Copenhagen University Hospital, 2650 Hvidovre, Denmark"},{"name":"Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3133-2724","authenticated-orcid":false,"given":"Nina","family":"Weis","sequence":"additional","affiliation":[{"name":"Department of Infectious Diseases, Copenhagen University Hospital, 2650 Hvidovre, Denmark"},{"name":"Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2300 Copenhagen, Denmark"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2025,5,8]]},"reference":[{"key":"ref_1","unstructured":"(2017). World Health Organization Global Hepatitis Report, World Health Organization."},{"key":"ref_2","unstructured":"WHO (2024, May 03). Hepatitis B. Available online: https:\/\/www.who.int\/news-room\/fact-sheets\/detail\/hepatitis-b."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"107","DOI":"10.1177\/1756283X09354562","article-title":"Efficacy and Safety of Tenofovir Disoproxil Fumarate in Patients with Chronic Hepatitis B","volume":"3","author":"Heathcote","year":"2010","journal-title":"Therap Adv. Gastroenterol."},{"key":"ref_4","first-page":"201","article-title":"Entecavir: A New Nucleoside Analogue for the Treatment of Chronic Hepatitis B","volume":"43","author":"Rivkin","year":"2007","journal-title":"Drugs Today"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"2313","DOI":"10.1016\/S0140-6736(18)31865-8","article-title":"Chronic Hepatitis B Virus Infection","volume":"392","author":"Seto","year":"2018","journal-title":"Lancet"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"370","DOI":"10.1016\/j.jhep.2017.03.021","article-title":"EASL 2017 Clinical Practice Guidelines on the Management of Hepatitis B Virus Infection","volume":"67","author":"Lampertico","year":"2017","journal-title":"J. Hepatol."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"760","DOI":"10.3109\/00365521.2011.565068","article-title":"Low Liver Stiffness among Cirrhotic Patients with Hepatitis B after Prolonged Treatment with Nucleoside Analogs","volume":"46","author":"Andersen","year":"2011","journal-title":"Scand. J. Gastroenterol."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"249","DOI":"10.1016\/j.bpg.2017.04.010","article-title":"Natural History of Acute and Chronic Hepatitis B: The Role of HBV Genotypes and Mutants","volume":"31","author":"Lin","year":"2017","journal-title":"Best. Pract. Res. Clin. Gastroenterol."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"S13","DOI":"10.1002\/hep.22881","article-title":"Hepatitis B: The Virus and Disease","volume":"49","author":"Liang","year":"2009","journal-title":"Hepatology"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"S71","DOI":"10.1016\/j.jhep.2016.01.026","article-title":"Adaptive Immunity in HBV Infection","volume":"64","author":"Bertoletti","year":"2016","journal-title":"J. Hepatol."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"881","DOI":"10.3748\/wjg.v28.i9.881","article-title":"Innate and Adaptive Immune Escape Mechanisms of Hepatitis B Virus","volume":"28","author":"Zhao","year":"2022","journal-title":"World J. Gastroenterol."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"126","DOI":"10.3748\/wjg.v22.i1.126","article-title":"Genetic Variation of Hepatitis B Virus and Its Significance for Pathogenesis","volume":"22","author":"Zhang","year":"2016","journal-title":"World J. Gastroenterol."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"105159","DOI":"10.1016\/j.jcv.2022.105159","article-title":"Novel Hepatitis B Virus Reverse Transcriptase Mutations in Patients with Sustained Viremia despite Long-Term Tenofovir Treatment","volume":"150\u2013151","author":"Winckelmann","year":"2022","journal-title":"J. Clin. Virol."},{"key":"ref_14","unstructured":"(2022, May 03). Github, SNPgenie. Available online: Https:\/\/Github.Com\/Chasewnelson\/Snpgenie."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"3709","DOI":"10.1093\/bioinformatics\/btv449","article-title":"SNPGenie: Estimating Evolutionary Parameters to Detect Natural Selection Using Pooled next-Generation Sequencing Data","volume":"31","author":"Nelson","year":"2015","journal-title":"Bioinformatics"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"305","DOI":"10.1111\/j.1399-0039.2012.01941.x","article-title":"Super High Resolution for Single Molecule-Sequence-Based Typing of Classical HLA Loci at the 8-Digit Level Using next Generation Sequencers","volume":"80","author":"Shiina","year":"2012","journal-title":"Tissue Antigens"},{"key":"ref_17","doi-asserted-by":"crossref","unstructured":"Underwood, A.P., S\u00f8lund, C., Jacobsen, K., Binderup, A., Fernandez-Antunez, C., Mikkelsen, L.S., Inekci, D., Villadsen, S.L., Castruita, J.A.S., and Pinholt, M. (2024). Neutralizing Antibody and CD8+ T Cell Responses Following BA.4\/5 Bivalent COVID-19 Booster Vaccination in Adults with and without Prior Exposure to SARS-CoV-2. Front. Immunol., 15.","DOI":"10.3389\/fimmu.2024.1353353"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"907","DOI":"10.1038\/s41587-019-0201-4","article-title":"Graph-Based Genome Alignment and Genotyping with HISAT2 and HISAT-Genotype","volume":"37","author":"Kim","year":"2019","journal-title":"Nat. Biotechnol."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"e29115","DOI":"10.1371\/journal.pone.0029115","article-title":"Bayesian Variable Selection in Searching for Additive and Dominant Effects in Genome-Wide Data","volume":"7","author":"Peltola","year":"2012","journal-title":"PLoS ONE"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"302","DOI":"10.1111\/jvh.13430","article-title":"Global Evolutionary Analysis of Chronic Hepatitis C Patients Revealed Significant Effect of Baseline Viral Resistance, Including Novel Non-Target Sites, for DAA-Based Treatment and Retreatment Outcome","volume":"28","author":"Pedersen","year":"2021","journal-title":"J. Viral Hepat."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"e110012","DOI":"10.1371\/journal.pone.0110012","article-title":"Novel Point and Combo-Mutations in the Genome of Hepatitis B Virus-Genotype D: Characterization and Impact on Liver Disease Progression to Hepatocellular Carcinoma","volume":"9","author":"Datta","year":"2014","journal-title":"PLoS ONE"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"3454","DOI":"10.1128\/JVI.02164-09","article-title":"Distinct Hepatitis B Virus Dynamics in the Immunotolerant and Early Immunoclearance Phases","volume":"84","author":"Wang","year":"2010","journal-title":"J. Virol."},{"key":"ref_23","doi-asserted-by":"crossref","unstructured":"Valenzuela, P., Quiroga, M., Zaldivar, J., Gray, P., and Rutter, W.J. (1980). The Nucleotide Sequence of the Hepatitis B Viral Genome and the Identification of the Major Viral Genes. Animal Virus Genetics, Academic Press.","DOI":"10.1016\/B978-0-12-255850-4.50010-X"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"270","DOI":"10.1016\/j.jcv.2010.05.010","article-title":"Acute Hepatitis B Infection Associated with Drug-Resistant Hepatitis B Virus","volume":"48","author":"Xu","year":"2010","journal-title":"J. Clin. Virol."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"1484","DOI":"10.3109\/00365521.2011.619273","article-title":"Danhep group HBeAg and Not Genotypes Predicts Viral Load in Patients with Hepatitis B in Denmark: A Nationwide Cohort Study","volume":"46","author":"Krarup","year":"2011","journal-title":"Scand. J. Gastroenterol."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"335","DOI":"10.1016\/j.chom.2020.05.010","article-title":"A Combination of Human Broadly Neutralizing Antibodies against Hepatitis B Virus HBsAg with Distinct Epitopes Suppresses Escape Mutations","volume":"28","author":"Wang","year":"2020","journal-title":"Cell Host Microbe"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"665","DOI":"10.1038\/s41577-019-0221-9","article-title":"Defining \u201cT Cell Exhaustion\u201d","volume":"19","author":"Blank","year":"2019","journal-title":"Nat. Rev. Immunol."},{"key":"ref_28","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":"ref_29","doi-asserted-by":"crossref","first-page":"105184","DOI":"10.1016\/j.meegid.2021.105184","article-title":"Analysis of Entire Hepatitis B Virus Genomes Reveals Reversion of Mutations to Wild Type in Natural Infection, a 15 Year Follow-up Study","volume":"97","author":"Chen","year":"2022","journal-title":"Infect. Genet. Evol."},{"key":"ref_30","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":"ref_31","doi-asserted-by":"crossref","first-page":"336","DOI":"10.1016\/j.tim.2017.03.003","article-title":"Short-Sighted Virus Evolution and a Germline Hypothesis for Chronic Viral Infections","volume":"25","author":"Lythgoe","year":"2017","journal-title":"Trends Microbiol."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"83","DOI":"10.3390\/v3020083","article-title":"Genomic Analysis of Hepatitis B Virus Reveals Antigen State and Genotype as Sources of Evolutionary Rate Variation","volume":"3","author":"Harrison","year":"2011","journal-title":"Viruses"},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"517","DOI":"10.1016\/0161-5890(91)90166-H","article-title":"Inhibitory Activity of Monoclonal Antibody F35.25 on the Interaction between Hepatocytes (HepG2 Cells) and PreS1-Specific Ligands","volume":"28","author":"Petit","year":"1991","journal-title":"Mol. Immunol."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"3544","DOI":"10.4049\/jimmunol.144.9.3544","article-title":"Importance of Subtype in the Immune Response to the Pre-S(2) Region of the Hepatitis B Surface Antigen. II. Synthetic Pre-S(2) Immunogen","volume":"144","author":"Milich","year":"1990","journal-title":"J. Immunol."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1128\/JVI.01785-16","article-title":"Mapping of Functional Subdomains in the Terminal Protein Domain of Hepatitis B Virus Polymerase","volume":"91","author":"Clark","year":"2017","journal-title":"J. Virol."},{"key":"ref_36","doi-asserted-by":"crossref","unstructured":"Buhlig, T.S., Bowersox, A.F., Braun, D.L., Owsley, D.N., James, K.D., Aranda, A.J., Kendrick, C.D., Skalka, N.A., and Clark, D.N. (2020). Molecular, Evolutionary, and Structural Analysis of the Terminal Protein Domain of Hepatitis B Virus Polymerase, a Potential Drug Target. Viruses, 12.","DOI":"10.3390\/v12050570"},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"929","DOI":"10.1016\/0092-8674(93)90472-3","article-title":"Prominent Role of Secondary Anchor Residues in Peptide Binding to HLA-A2.1 Molecules","volume":"74","author":"Ruppert","year":"1993","journal-title":"Cell"}],"container-title":["Viruses"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1999-4915\/17\/5\/684\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,9]],"date-time":"2025-10-09T17:29:01Z","timestamp":1760030941000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1999-4915\/17\/5\/684"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,5,8]]},"references-count":37,"journal-issue":{"issue":"5","published-online":{"date-parts":[[2025,5]]}},"alternative-id":["v17050684"],"URL":"https:\/\/doi.org\/10.3390\/v17050684","relation":{},"ISSN":["1999-4915"],"issn-type":[{"value":"1999-4915","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,5,8]]}}}