Hepatitis B virus serum RNA transcript isoform composition and proportion in chronic hepatitis B patients by nanopore long-read sequencing

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• dc.contributor.author Vachon, Alicia
• dc.contributor.author Seo, Grace E.
• dc.contributor.author Patel, Nishi H.
• dc.contributor.author Coffin, Carla S.
• dc.contributor.author Marinier, Eric
• dc.contributor.author Eyras Jiménez, Eduardo
• dc.contributor.author Osiowy, Carla
• dc.date.accessioned 2024-05-13T05:36:27Z
• dc.date.available 2024-05-13T05:36:27Z
• dc.date.issued 2023
• dc.description.abstract Introduction: Serum hepatitis B virus (HBV) RNA is a promising new biomarker to manage and predict clinical outcomes of chronic hepatitis B (CHB) infection. However, the HBV serum transcriptome within encapsidated particles, which is the biomarker analyte measured in serum, remains poorly characterized. This study aimed to evaluate serum HBV RNA transcript composition and proportionality by PCR-cDNA nanopore sequencing of samples from CHB patients having varied HBV genotype (gt, A to F) and HBeAg status. Methods: Longitudinal specimens from 3 individuals during and following pregnancy (approximately 7 months between time points) were also investigated. HBV RNA extracted from 16 serum samples obtained from 13 patients (73.3% female, 84.6% Asian) was sequenced and serum HBV RNA isoform detection and quantification were performed using three bioinformatic workflows; FLAIR, RATTLE, and a GraphMap-based workflow within the Galaxy application. A spike-in RNA variant (SIRV) control mix was used to assess run quality and coverage. The proportionality of transcript isoforms was based on total HBV reads determined by each workflow. Results: All chosen isoform detection workflows showed high agreement in transcript proportionality and composition for most samples. HBV pregenomic RNA (pgRNA) was the most frequently observed transcript isoform (93.8% of patient samples), while other detected transcripts included pgRNA spliced variants, 3' truncated variants and HBx mRNA, depending on the isoform detection method. Spliced variants of pgRNA were primarily observed in HBV gtB, C, E, or F-infected patients, with the Sp1 spliced variant detected most frequently. Twelve other pgRNA spliced variant transcripts were identified, including 3 previously unidentified transcripts, although spliced isoform identification was very dependent on the workflow used to analyze sequence data. Longitudinal sampling among pregnant and post-partum antiviral-treated individuals showed increasing proportions of 3' truncated pgRNA variants over time. Conclusions: This study demonstrated long-read sequencing as a promising tool for the characterization of the serum HBV transcriptome. However, further studies are needed to better understand how serum HBV RNA isoform type and proportion are linked to CHB disease progression and antiviral treatment response.
• dc.format.mimetype application/pdf
• dc.identifier.citation Vachon A, Seo GE, Patel NH, Coffin CS, Marinier E, Eyras E, et al. Hepatitis B virus serum RNA transcript isoform composition and proportion in chronic hepatitis B patients by nanopore long-read sequencing. Front Microbiol. 2023 Aug 14;14:1233178. DOI: 10.3389/fmicb.2023.1233178
• dc.identifier.doi http://dx.doi.org/10.3389/fmicb.2023.1233178
• dc.identifier.issn 1664-302X
• dc.identifier.uri http://hdl.handle.net/10230/60109
• dc.language.iso eng
• dc.publisher Frontiers
• dc.relation.ispartof Front Microbiol. 2023 Aug 14;14:1233178
• dc.rights © 2023 Vachon, Seo, Patel, Coffin, Marinier, Eyras and Osiowy. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. http://creativecommons.org/licenses/by/4.0/
• dc.rights.accessRights info:eu-repo/semantics/openAccess
• dc.rights.uri http://creativecommons.org/licenses/by/4.0/
• dc.subject.keyword Hepatitis B virus
• dc.subject.keyword Long-read sequencing
• dc.subject.keyword Nanopore
• dc.subject.keyword pgRNA
• dc.subject.keyword Serum HBV RNA
• dc.subject.keyword Spliced RNA
• dc.subject.keyword Transcript
• dc.title Hepatitis B virus serum RNA transcript isoform composition and proportion in chronic hepatitis B patients by nanopore long-read sequencing
• dc.type info:eu-repo/semantics/article
• dc.type.version info:eu-repo/semantics/publishedVersion