Advanced sequencing approaches detected insertions of viral and human origin in the viral genome of chronic hepatitis E virus patients

• Published in: Scientific reports 2022-02, Vol.12 (1), p.1720-1720, Article 1720
• Main Authors: Papp, C.-Patrick, Biedermann, Paula, Harms, Dominik, Wang, Bo, Kebelmann, Marianne, Choi, Mira, Helmuth, Johannes, Corman, Victor M., Thürmer, Andrea, Altmann, Britta, Klink, Patrycja, Hofmann, Jörg, Bock, C.-Thomas
• Format: Article
• Language: English
• Subjects: 631/326/596/2148; 631/326/596/2554; 692/699/255/234/2513; Antiviral agents; DNA, Viral - genetics; Genome, Viral; Genomes; Genotypes; Hepatitis; Hepatitis E - diagnosis; Hepatitis E - genetics; Hepatitis E - virology; Hepatitis E virus - genetics; Hepatitis, Chronic - diagnosis; Hepatitis, Chronic - genetics; Hepatitis, Chronic - virology; High-Throughput Nucleotide Sequencing; Humanities and Social Sciences; Humans; multidisciplinary; Mutagenesis, Insertional; Polymerase Chain Reaction; Polymorphism, Single Nucleotide; RNA-Directed DNA Polymerase - genetics; Science; Science (multidisciplinary); Sequence Analysis, DNA; Whole Genome Sequencing
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-022-05706-w

The awareness of hepatitis E virus (HEV) increased significantly in the last decade due to its unexpectedly high prevalence in high-income countries. There, infections with HEV-genotype 3 (HEV-3) are predominant which can progress to chronicity in immunocompromised individuals. Persistent infection and antiviral therapy can select HEV-3 variants; however, the spectrum and occurrence of HEV-3 variants is underreported. To gain in-depth insights into the viral population and to perform detailed characterization of viral genomes, we used a new approach combining long-range PCR with next-generation and third-generation sequencing which allowed near full-length sequencing of HEV-3 genomes. Furthermore, we developed a targeted ultra-deep sequencing approach to assess the dynamics of clinically relevant mutations in the RdRp-region and to detect insertions in the HVR-domain in the HEV genomes. Using this new approach, we not only identified several insertions of human (AHNAK, RPL18) and viral origin (RdRp-derived) in the HVR-region isolated from an exemplary sample but detected a variant containing two different insertions simultaneously (AHNAK- and RdRp-derived). This finding is the first HEV-variant recognized as such showing various insertions in the HVR-domain. Thus, this molecular approach will add incrementally to our current knowledge of the HEV-genome organization and pathogenesis in chronic hepatitis E.