Impact of hepatitis E virus host- and virus-derived insertions on the antiviral response in primary human hepatocytes

Despite the global burden of hepatitis E virus (HEV) infection, host-virus interactions underlying HEV pathogenesis and progression to chronicity remain incompletely understood. This study aimed to characterize the host transcriptomic response to infection with HEV variants harboring different host- and virus-derived insertions in the hypervariable region (HVR), with a focus on innate immune activation. We performed bulk RNA sequencing on PHHs from three donors infected with in vivo-identified HEV-3 variants harboring different HVR insertions (RPS17, HVR duplication, SERPINA1, TRIM22). To compare their replication fitness, we quantified progeny virus titers and viral RNA reads in the cellular transcriptome. Host transcriptomic responses were analyzed in detail at multiple time points to assess virus-induced differential gene expression. To further characterize the response to HEV infection with different HVR insertion variants, we performed gene ontology analysis and identified individual HEV-induced genes. Progeny virus titers at 72 hours post infection (h p.i.) were comparable across all PHH donors and HVR insertion variants. Two donors mounted robust host responses to HEV infection, characterized by widespread gene deregulation and interferon stimulated gene (ISG) upregulation at 72 h p.i. The HVR duplication insertion variant consistently triggered a weaker host response compared to RPS17, SERPINA1 and TRIM22 variants, with significantly fewer differentially expressed genes and reduced ISG induction. Gene ontology term analysis revealed enrichment of antiviral pathways upon infection with the different insertion variants, which was less pronounced for the HVR duplication variant. These findings reveal that HEV HVR rearrangement variants elicit distinct host response patterns. Importantly, our results suggest a positive correlation of viral replication and host response induction. This indicates that the HVR may play a crucial role in shaping host-virus interactions.