World Health Organisation. Global hepatitis report 2024: action for access in low- and middle-income countries. (2024).
Revill, P. A. et al. The evolution and clinical impact of hepatitis B virus genome diversity. Nat. Rev. Gastroenterol. Hepatol. 17, 618–634 (2020).
McNaughton, A. L. et al. Insights from deep sequencing of the HBV genome-unique, tiny, and misunderstood. Gastroenterology 156, 384–399 (2019).
Zhang, M. et al. Infection courses, virological features and IFN-alpha responses of HBV genotypes in cell culture and animal models. J. Hepatol. 75, 1335–1345 (2021).
European Association for the Study of the Liver. Electronic address, e.e.e. & European Association for the Study of the, L EASL Clinical Practice Guidelines on the management of hepatitis B virus infection. J. Hepatol. 83, 502–583 (2025).
Yan, H. et al. Sodium taurocholate cotransporting polypeptide is a functional receptor for human hepatitis B and D virus. Elife 1, e00049 (2012).
Ni, Y. et al. Hepatitis B and D viruses exploit sodium taurocholate co-transporting polypeptide for species-specific entry into hepatocytes. Gastroenterology 146, 1070–1083 (2014).
Turton, K. L., Meier-Stephenson, V., Badmalia, M. D., Coffin, C. S. & Patel, T. R. Host transcription factors in hepatitis B virus RNA synthesis. Viruses 12, 160 (2020).
Hong, X., Kim, E. S. & Guo, H. Epigenetic regulation of hepatitis B virus covalently closed circular DNA: implications for epigenetic therapy against chronic hepatitis B. Hepatology 66, 2066–2077 (2017).
Junker-Niepmann, M., Bartenschlager, R. & Schaller, H. A short cis-acting sequence is required for hepatitis B virus pregenome encapsidation and sufficient for packaging of foreign RNA. EMBO J. 9, 3389–3396 (1990).
Yu, Y. et al. An RNA-based system to study hepatitis B virus replication and evaluate antivirals. Sci. Adv. 9, eadg6265 (2023).
Seeger, C. & Mason, W. S. Hepatitis B virus biology. Microbiol. Mol. Biol. Rev. 64, 51–68 (2000).
Tu, T., Zhang, H. & Urban, S. Hepatitis B virus DNA integration: in vitro models for investigating viral pathogenesis and persistence. Viruses 13, 180 (2021).
Zoulim, F., Chen, P. J., Dandri, M., Kennedy, P. & Seeger, C. Hepatitis B virus DNA integration: implications for diagnostics, therapy, and outcome. J. Hepatol. 81, 1087–1099 (2024).
Tu, T., Budzinska, M. A., Shackel, N. A. & Urban, S. HBV DNA Integration: molecular Mechanisms and Clinical Implications. Viruses 9, 75 (2017).
Decorsiere, A. et al. Hepatitis B virus X protein identifies the Smc5/6 complex as a host restriction factor. Nature 531, 386–389 (2016).
D’Arienzo, V. et al. A PCR assay to quantify patterns of HBV transcription. J. Gen. Virol. 102, 001373 (2021).
Stadelmayer, B. et al. Full-length 5’RACE identifies all major HBV transcripts in HBV-infected hepatocytes and patient serum. J. Hepatol. 73, 40–51 (2020).
Altinel, K. et al. Single-nucleotide resolution mapping of hepatitis B virus promoters in infected human livers and hepatocellular carcinoma. J. Virol. 90, 10811–10822 (2016).
Kim, S. C. et al. Efficacy of antiviral therapy and host-virus interactions visualised using serial liver sampling with fine-needle aspirates. JHEP Rep. 5, 100817 (2023).
Harris, J. M. et al. Oxygen-dependent histone lysine demethylase 4 restricts hepatitis B virus replication. J. Biol. Chem. 300, 105724 (2024).
Testoni, B. et al. Evaluation of the HBV liver reservoir with fine needle aspirates. JHEP Rep. 5, 100841 (2023).
Lumley, S. F. et al. Pan-genotypic probe-based enrichment to improve efficiency of Hepatitis B virus sequencing. bioRxiv, 2023.2002.2020.529276 (2023).
Ng, E. et al. An enrichment protocol and analysis pipeline for long read sequencing of the hepatitis B virus transcriptome. J. Gen. Virol. 104, 001856 (2023).
Meier, M. A. et al. Ubiquitous expression of HBsAg from integrated HBV DNA in patients with low viral load. J. Hepatol. 75, 840–847 (2021).
Suslov, A. et al. Transition to HBeAg-negative chronic hepatitis B virus infection is associated with reduced cccDNA transcriptional activity. J. Hepatol. 74, 794–800 (2021).
Magri, A. et al. Inflammatory gene expression associates with hepatitis B virus cccDNA- but not integrant-derived transcripts in HBeAg negative disease. Viruses 14, 1070 (2022).
Rossi, M. et al. Phenotypic CD8 T cell profiling in chronic hepatitis B to predict HBV-specific CD8 T cell susceptibility to functional restoration in vitro. Gut 72, 2123–2137 (2023).
Le Bert, N. et al. Effects of hepatitis B surface antigen on virus-specific and global T cells in patients with chronic hepatitis B virus infection. Gastroenterology 159, 652–664 (2020).
Wisskirchen, K. et al. Isolation and functional characterization of hepatitis B virus-specific T-cell receptors as new tools for experimental and clinical use. PLoS One 12, e0182936 (2017).
Cornberg, M., Lok, A. S., Terrault, N. A., Zoulim, F. & Faculty, E.-A.H.T.E.C Guidance for design and endpoints of clinical trials in chronic hepatitis B – Report from the 2019 EASL-AASLD HBV Treatment Endpoints Conference(double dagger). J. Hepatol. 72, 539–557 (2020).
Lok, A. S. F. Toward a Functional Cure for Hepatitis B. Gut Liver 18, 593–601 (2024).
Block, T. M. et al. New potent HBV replication inhibitors for the management of chronic hepatitis B are needed. Nat. Rev. Gastroenterol. Hepatol. 22, 150–151 (2025).
Ghany, M. G., Buti, M., Lampertico, P., Lee, H. M. & Faculty, A.-E.H.-H.T.E.C Guidance on treatment endpoints and study design for clinical trials aiming to achieve cure in chronic hepatitis B and D: report from the 2022 AASLD-EASL HBV-HDV treatment endpoints conference. Hepatology 78, 1654–1673 (2023).
Lim, C. S. et al. Quantitative analysis of the splice variants expressed by the major hepatitis B virus genotypes. Micro. Genom. 7, mgen000492 (2021).
Tu, T., Budzinska, M. A., Vondran, F. W. R., Shackel, N. A. & Urban, S. Hepatitis B virus DNA integration occurs early in the viral life cycle in an in vitro infection model via sodium taurocholate cotransporting polypeptide-dependent uptake of enveloped virus particles. J. Virol. 92, 11 (2018).
Ren, X. et al. Hepatitis B virus genotype and basal core promoter/precore mutations are associated with hepatitis B-related acute-on-chronic liver failure without pre-existing liver cirrhosis. J. Viral Hepat. 17, 887–895 (2010).
Derti, A. et al. A quantitative atlas of polyadenylation in five mammals. Genome Res. 22, 1173–1183 (2012).
Anderson, M. et al. Circulating pregenomic hepatitis B virus RNA is primarily full-length in chronic hepatitis b patients undergoing nucleos(t)ide analogue therapy. Clin. Infect. Dis. 72, 2029–2031 (2021).
Testoni, B. et al. Quantification of circulating HBV RNA expressed from intrahepatic cccDNA in untreated and NUC treated patients with chronic hepatitis B. Gut 73, 659–667 (2024).
Wooddell, C. I. et al. RNAi-based treatment of chronically infected patients and chimpanzees reveals that integrated hepatitis B virus DNA is a source of HBsAg. Sci. Transl. Med 9, eaan0241 (2017).
van Buuren, N. et al. Targeted long-read sequencing reveals clonally expanded HBV-associated chromosomal translocations in patients with chronic hepatitis B. JHEP Rep. 4, 100449 (2022).
Chheda, U. et al. Factors affecting stability of RNA – temperature, length, concentration, pH, and buffering species. J. Pharm. Sci. 113, 377–385 (2024).
Chapus, F. et al. Helicases DDX5 and DDX17 promote heterogeneity in HBV transcription termination in infected human hepatocytes. J. Hepatol. 81, 609–620 (2024).
Yuen, M. F. et al. Safety, tolerability and antiviral activity of the antisense oligonucleotide bepirovirsen in patients with chronic hepatitis B: a phase 2 randomized controlled trial. Nat. Med. 27, 1725–1734 (2021).
Kramvis, A. & Kew, M. C. Relationship of genotypes of hepatitis B virus to mutations, disease progression and response to antiviral therapy. J. Viral Hepat. 12, 456–464 (2005).
Washizaki, A. et al. Neutralization of hepatitis B virus with vaccine-escape mutations by hepatitis B vaccine with large-HBs antigen. Nat. Commun. 13, 5207 (2022).
Gout, J. F., Thomas, W. K., Smith, Z., Okamoto, K. & Lynch, M. Large-scale detection of in vivo transcription errors. Proc. Natl. Acad. Sci. USA 110, 18584–18589 (2013).
Avellon, A. & Echevarria, J. M. Frequency of hepatitis B virus ‘a’ determinant variants in unselected Spanish chronic carriers. J. Med Virol. 78, 24–36 (2006).
Norder, H., Courouce, A. M. & Magnius, L. O. Molecular basis of hepatitis B virus serotype variations within the four major subtypes. J. Gen. Virol. 73, 3141–3145 (1992).
Scholtes, C. et al. Performance of the cobas(R) HBV RNA automated investigational assay for the detection and quantification of circulating HBV RNA in chronic HBV patients. J. Clin. Virol. 150-151, 105150 (2022).
Butler, E. K. et al. Hepatitis B virus serum DNA and RNA levels in nucleos(t)ide analog-treated or untreated patients during chronic and acute infection. Hepatology 68, 2106–2117 (2018).
Degasperi, E. et al. Differential HBV RNA and HBcrAg patterns in untreated patients with chronic hepatitis delta. J. Hepatol. 82, 1004–1011 (2024).
Tombacz, D. et al. Long-read assays shed new light on the transcriptome complexity of a viral pathogen. Sci. Rep. 10, 13822 (2020).
Balazs, Z. et al. long-read sequencing of human cytomegalovirus transcriptome reveals RNA isoforms carrying distinct coding potentials. Sci. Rep. 7, 15989 (2017).
Gu, Z. et al. Hepatitis B virus enhancer 1 activates preS1 and preS2 promoters of integrated HBV DNA impairing HBsAg secretion. JHEP Rep. 6, 101144 (2024).
Qian, Z. et al. HBV integrations reshaping genomic structures promote hepatocellular carcinoma. Gut 73, 1169–1182 (2024).
Tu, T. & Jilbert, A. R. Detection of hepatocyte clones containing integrated hepatitis B virus DNA using inverse nested PCR. Methods Mol. Biol. 1540, 97–118 (2017).
Li, C. L. et al. HBV DNA integration into telomerase or MLL4 genes and TERT promoter point mutation as three independent signatures in subgrouping HBV-related HCC with distinct features. Liver Cancer 13, 41–55 (2024).
Seydel, C. Beyond cell atlases: spatial biology reveals mechanisms behind disease. Nat. Biotechnol. 43, 841–844 (2025).
Li, D., Hamadalnil, Y. & Tu, T. Hepatitis B viral protein HBx: roles in viral replication and hepatocarcinogenesis. Viruses 16, 1361 (2024).
Hernandez, S. et al. Canonical and divergent N-terminal HBx isoform proteins unveiled: characteristics and roles during HBV replication. Biomedicines 9, 1701 (2021).
Iden, M. et al. Multi-omics mapping of human papillomavirus integration sites illuminates novel cervical cancer target genes. Br. J. Cancer 125, 1408–1419 (2021).
Wang, Z. et al. Long-read sequencing reveals the structural complexity of genomic integration of HPV DNA in cervical cancer cell lines. BMC Genom.25, 198 (2024).
Santiago, J. C. et al. Variation within major internal repeats of KSHV in vivo. Virus Evol. 9, vead034 (2023).
Fulop, A. et al. Integrative profiling of Epstein-Barr virus transcriptome using a multiplatform approach. Virol. J. 19, 7 (2022).
Wright, C. J., Smith, C. W. J. & Jiggins, C. D. Alternative splicing as a source of phenotypic diversity. Nat. Rev. Genet 23, 697–710 (2022).
McCoullough, L. C. et al. The in vitro replication phenotype of hepatitis B virus (HBV) splice variants Sp3 and Sp9 and their impact on wild-type HBV replication. J. Virol. 98, e0153823 (2024).
Velkov, S., Ott, J. J., Protzer, U. & Michler, T. The global hepatitis B virus genotype distribution approximated from available genotyping data. Genes (Basel) 9, 495 (2018).
Hou, J. et al. Prevalence of naturally occurring surface gene variants of hepatitis B virus in nonimmunized surface antigen-negative Chinese carriers. Hepatology 34, 1027–1034 (2001).
Wettengel, J. M. et al. Rapid and robust continuous purification of high-titer hepatitis B virus for in vitro and in vivo applications. Viruses 13, 1503 (2021).
Belloni, L. et al. Nuclear HBx binds the HBV minichromosome and modifies the epigenetic regulation of cccDNA function. Proc. Natl. Acad. Sci. USA 106, 19975–19979 (2009).
Dobrica, M. O. et al. CTCF regulates hepatitis B virus cccDNA chromatin topology. J Gen Virol 105, 001939 (2024).
Tsukuda, S. et al. The N6-methyladenosine demethylase ALKBH5 regulates the hypoxic HBV transcriptome. PLoS Pathog. 20, e1011917 (2024).
Li, H. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics 34, 3094–3100 (2018).
Lawrence, M. et al. Software for computing and annotating genomic ranges. PLoS Comput Biol. 9, e1003118 (2013).
Garrido-Martin, D., Palumbo, E., Guigo, R. & Breschi, A. ggsashimi: Sashimi plot revised for browser- and annotation-independent splicing visualization. PLoS Comput. Biol. 14, e1006360 (2018).
Minh, B. Q. et al. IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Mol. Biol. Evol. 37, 1530–1534 (2020).
Kalyaanamoorthy, S., Minh, B. Q., Wong, T. K. F., von Haeseler, A. & Jermiin, L. S. ModelFinder: fast model selection for accurate phylogenetic estimates. Nat. Methods 14, 587–589 (2017).