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1.
Liver Int ; 43(4): 794-804, 2023 04.
Article in English | MEDLINE | ID: mdl-36617681

ABSTRACT

BACKGROUND AND AIMS: Hepatitis E virus is a major cause of acute hepatitis worldwide and can progress to chronicity in immunocompromised individuals. Various virus-host recombination events have been reported in the hypervariable region of the hepatitis E virus genome, but the patterns of assembly and selection remain unclear. METHODS: To gain further insight into viral evolution, we assessed the presence of low abundance variants in 16 samples from individuals with acute or chronic infection using a targeted next-generation sequencing approach. RESULTS: In seven samples, different variants with insertions and/or deletions were identified. Among them, eight insertions originating either from human genes or from the hepatitis E virus genome. Five different deletions could be identified. The amino acid composition of sequences with insertions showed a higher frequency of lysine and a lower abundance of proline, and additionally acetylation and ubiquitination sites were more frequent than in hepatitis E virus wild-type sequences. CONCLUSIONS: These findings suggest that the nucleotide composition of insertions and sites for post-translational modification may contribute to recombination events. Although the impact of low-level hepatitis E virus variants is uncertain, our results highlight the importance of a highly sensitive next-generation sequencing approach to capture the full diversity of hypervariable region.


Subject(s)
Hepatitis E virus , Humans , Hepatitis E virus/genetics , Persistent Infection , Genome, Viral/genetics
2.
Sci Rep ; 12(1): 1720, 2022 02 02.
Article in English | MEDLINE | ID: mdl-35110582

ABSTRACT

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.


Subject(s)
DNA, Viral/genetics , Genome, Viral , Hepatitis E virus/genetics , Hepatitis E/virology , Hepatitis, Chronic/virology , Mutagenesis, Insertional , Sequence Analysis, DNA , Hepatitis E/diagnosis , Hepatitis E/genetics , Hepatitis, Chronic/diagnosis , Hepatitis, Chronic/genetics , High-Throughput Nucleotide Sequencing , Humans , Polymerase Chain Reaction , Polymorphism, Single Nucleotide , RNA-Directed DNA Polymerase/genetics , Whole Genome Sequencing
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