{"entity": "publication", "iuid": "53ce330a7939418eb8624fbcf3896e2a", "timestamp": "2026-10-19T15:54:27.284Z", "links": {"self": {"href": "https://publications.scilifelab.se/publication/53ce330a7939418eb8624fbcf3896e2a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/53ce330a7939418eb8624fbcf3896e2a"}}, "title": "Novel Long-Read Sequencing Method for Characterisation of Hepatitis B Transcripts Show High Expression of Chimeric HBV/Human RNA.", "authors": [{"family": "Stenb\u00e4ck", "given": "Joakim Bedner", "initials": "JB"}, {"family": "Ringlander", "given": "Johan", "initials": "J", "orcid": "0000-0002-8483-6504", "researcher": {"href": "https://publications.scilifelab.se/researcher/4f8d5a11484b4dd89b54bb9d8ced50a7.json"}}, {"family": "Andersson", "given": "Maria", "initials": "M", "orcid": "0000-0003-0005-7114", "researcher": {"href": "https://publications.scilifelab.se/researcher/3ca937170d604667b0a616b394913e65.json"}}, {"family": "Thomsen", "given": "Jakob Holm Dalsgaard", "initials": "JHD", "orcid": "0009-0005-7565-9592", "researcher": {"href": "https://publications.scilifelab.se/researcher/6e05ede60153468faefc20d79c99560a.json"}}, {"family": "Abrahamsson", "given": "Sanna", "initials": "S"}, {"family": "Rydell", "given": "Gustaf E", "initials": "GE", "orcid": "0000-0001-8093-2251", "researcher": {"href": "https://publications.scilifelab.se/researcher/b9337361b99e4a1bb8a6b29901dc9199.json"}}, {"family": "Lindh", "given": "Magnus", "initials": "M"}], "type": "journal article", "published": "2026-03-00", "journal": {"title": "Liver Int.", "issn": "1478-3231", "volume": "46", "issue": "3", "pages": "e70521", "issn-l": "1478-3223"}, "abstract": "Hepatitis B virus (HBV) genomes integrated into human DNA significantly contribute to surface antigen (HBsAg) production and may drive hepatocellular carcinoma (HCC). Long-read sequencing methods like Nanopore offer advantages over short-read next-generation sequencing (NGS) by providing continuous reads of whole transcripts, but their application to HBV integration analysis remains limited.\n\nTo develop and apply a method combining semi-nested PCR with Nanopore sequencing to analyse HBV transcripts, including canonical RNA, HBV-human fusion transcripts, and spliced forms in patients with HBV- or hepatitis D virus (HDV)-induced liver disease.\n\nNine liver-transplanted patients with HBV- or HDV-related cirrhosis or HCC were studied. Semi-nested PCR was used to amplify all HBV transcripts, followed by Nanopore sequencing. The approach allowed differentiation between canonical (cccDNA-derived) and fusion transcripts. Reads containing the 3' redundancy beyond nucleotide 1826, exclusive to cccDNA-derived RNA, were quantified to determine the source of HBV RNA.\n\nUnique and total HBV-human fusion RNA reads correlated with serum levels of HBV DNA and HBsAg. Integration-derived RNA accounted for a median of 97% (range: 16%-100%) of HBV RNA. PreS1 RNA levels were much lower than preS2 but sufficient for HDV particle production in an HDV patient without cccDNA-derived transcripts.\n\nThis method enables a simplified and comprehensive analysis of HBV transcripts. The results highlight the predominance of integration-derived RNA and support the presence of cccDNA-independent hepatitis D virus production. Nanopore sequencing offers valuable insights into HBV and HDV biology, supporting its role in understanding viral pathogenesis and therapeutic targeting.", "doi": "10.1111/liv.70521", "pmid": "41684309", "labels": {"Clinical Genomics Gothenburg": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12902805"}, {"db": "BioProject", "key": "PRJNA1085039"}], "notes": [], "created": "2026-10-16T15:06:44.122Z", "modified": "2026-10-16T15:06:44.193Z"}