Study of the complete amplified and single-fragment sequenced genomes of circulating hepatitis B and Delta viruses in infected patients : development and applications ; Étude des génomes complets, amplifiés et séquencés en un seul fragment, des virus de l’hépatite B et Delta circulants chez les patients infectés : mise au point et applications

More than 250 million people are chronically infected by Hepatitis B virus (HBV) worldwide. Chronic HBV carriers have an increased risk of developing severe liver disease, including cirrhosis and hepatocellular carcinoma, the second most deadly cancer in the world. Co-infection with hepatitis Delta virus (HDV) is an aggravating factor. At least 12 million people according to the latest WHO estimates are coinfected by HBV and HDV. HDV is not sensitive to nucleotide analogues used for HBV treatment and the response rate to IFNα is less than 25%. New therapeutic strategies at the interface between these two viruses and the host, without directly targeting HDV, have been developed. The entry inhibitor myrcludex received its marketing authorization in France September 2020. In this context, the genetic characterization of the complete genome of these two viruses is essential to better understand the pathophysiology and response to treatments.The objectives of this thesis work were: • the development of a targeted sequencing technique, for both HBV and HDV, allowing the characterization of the entire circulating genomes, without fragmentation, leading to the possibility of identifying large deletions and linking several distant genetic events on the same variant; • the creation of a bioinformatic pipeline that can be used locally (a prerequisite for patient data confidentiality) and that is easy to implement by any laboratories; • the characterization of circulating HBV and HDV variants that is necessary for the exploration of the pathogenicity and the development of new treatments. The experimental approach is based on the exploitation of an evolving sequencing method based on nanopore technology (ONT, Oxford Nanopore Technologies), known for its ability to read very large fragments without the fragmentation step that is required by other second-generation sequencing techniques such as Illumina or Ion Torrent. The ONT sequencing of the complete HBV and HDV genomes was obtained after their complete amplification in a ...