Improved hepatitis delta virus genome characterization by single molecule full‐length genome sequencing combined with VIRiONT pipeline

Hepatitis B virus (HBV) and hepatitis D virus (HDV) coinfection confers a greater risk for accelerated liver disease progression. Full‐length characterization of HDV genome is necessary to understand pathogenesis and treatment response. However, owing to its high variability and tight structure, seq...

Full description

Saved in:
Bibliographic Details
Published in:Journal of medical virology 2023-03, Vol.95 (3), p.e28634-n/a
Main Authors: Charre, Caroline, Regue, Hadrien, Dény, Paul, Josset, Laurence, Chemin, Isabelle, Zoulim, Fabien, Scholtes, Caroline
Format: Article
Language:English
Subjects:
Amplification
Coinfection
Gene sequencing
Genomes
Genotype
Genotypes
genotyping
HDV editing
Health risks
Health services
Hepatitis
Hepatitis B
Hepatitis B virus - genetics
Hepatitis D
Hepatitis delta virus
hepatitis delta virus (HDV)
Hepatitis Delta Virus - genetics
Humans
Life cycles
Life Sciences
Liver diseases
local pipeline
long‐read sequencing
Microbiology and Parasitology
Nucleotide sequence
Pathogenesis
Sequence analysis
Virology
Viruses
whole‐genome sequencing
Workflow
Citations: Items that this one cites
Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary:Hepatitis B virus (HBV) and hepatitis D virus (HDV) coinfection confers a greater risk for accelerated liver disease progression. Full‐length characterization of HDV genome is necessary to understand pathogenesis and treatment response. However, owing to its high variability and tight structure, sequencing approaches remain challenging. Herein, we present a workflow to amplify, sequence, and analyze the whole HDV genome in a single fragment. Sequencing was based on the Oxford Nanopore Technologies long‐read sequencing followed by a turnkey analysis pipeline (VIRiONT, VIRal in‐house ONT sequencing analysis pipeline) that we developed and make available online for free. For the first time, HDV genome was successfully amplified and full‐length sequenced in a single fragment, allowing accurate subtyping from 30 clinical samples. High variability of edition, a crucial step in viral life cycle, was found among samples (from 0% to 59%). Additionally, a new subtype of HDV genotype 1 was identified. We provide a complete workflow for assessment of HDV genome at full‐length quasispecies resolution overcoming genome assembly issues and helping to identify modifications throughout the whole genome. This will help a better understanding of the impact of genotype/subtype, viral dynamics, and structural variants on HDV pathogenesis and treatment response.
ISSN:0146-6615
1096-9071
DOI:10.1002/jmv.28634