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

Methods

We performed bulk RNA sequencing on PHHs from three donors infected with HEV-3 variants harboring different HVR insertions (RPS17, HVR duplication, SERPINA1, TRIM22), which have been previously identified in vivo in a chronic HEV patient. To compare the replication fitness of the different insertion variants, we quantified progeny virus titers and viral RNA reads in the cellular transcriptome. Host transcriptomic responses were analyzed in detail at multiple time points post infection to assess virus-induced differential gene expression.

To further characterize the response to HEV infection with different HVR insertion variants, we performed gene ontology term enrichment analysis and identified individual HEV-induced genes. Results Progeny virus titers at 72 hours post infection (h p.i.) were comparable across all PHH donors and HVR insertion variants. Donors 1 and 2 mounted robust host responses to HEV infection, characterized by widespread gene deregulation and interferon stimulated gene (ISG) upregulation at 72 h p.i.

In contrast, donor 3 exhibited minimal virus-induced transcriptional changes. Across all variants, the HVR duplication insertion variant consistently triggered a weaker host response compared to RPS17, SERPINA1 and TRIM22 insertion 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.

Conclusions These findings reveal that HEV HVR rearrangement variants elicit distinct host response patterns, with the HVR duplication variant showing notably diminished innate immune activation compared to host-derived insertions. 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 and emphasizes the importance of comprehensive HVR characterization in understanding HEV pathogenesis.

Impact and implications This study provides novel insights into HEV-host interactions, characterizing donor-specific and variant-dependent differences in antiviral responses. Our findings highlight the importance of understanding the role of the HVR in chronic [URG3.1][SS3.2]HEV infection, a major clinical challenge particularly in immunocompromised patients where persistent viremia can lead to progressive liver damage.

The observed variations in innate immune activation patterns across different donors and viral variants suggest a critical role of innate immunity in shaping HEV pathogenesis and potentially determining infection outcomes.