Unraveling Hepatitis E Virus Adaptation

Hepatitis E virus (HEV) is an RNA virus known for causing acute viral hepatitis in humans. This study in Nature Communications highlights genetic variability in its hypervariable region (HVR), suggesting the virus can undergo substantial genomic rearrangements. It identifies specific sequence patterns within and outside the HVR that enhance HEV replication. This approach may pave the way for more effective, personalized treatments.

Researcher Daniel Todt PhD, group leader at the Department for Molecular and Medical Virology at Ruhr University Bochum explains the finding underlining the importance of functional nuclear localization sequence (NLS) in promoting replication advantage, the exact mode of action within infected cells currently investigated in their lab,

“We found that insertions in the HVR increased viral replication about 20-fold in cell culture. One common pattern in all the inserted gene snippets was a predicted NLS. In our HEV lab strain, the NLS includes four lysine residues and one arginine residue. When incrementally replacing these residues with alanine, we observed a loss of the replication increases down to levels of a strain without any insertion in the HVR.”

The study indicates that while these insertions did not affect sensitivity to ribavirin in subgenomic replicon assays, they notably enhanced viral replication. Through alanine scanning mutagenesis, researchers demonstrated that these lysine residues are critical for increasing replication rates. Fluorescence dye-coupled constructs showed that altering lysine residues affected how the virus is localized within cells.

Todt’s lab focuses on RNA virus genomics and developing new therapeutic strategies for HEV, and their method enables them to assess the ratio of insertions in the virus population.

“We isolated the RNA of the virus populations from patient plasma specimens and amplified parts of the viral genome, including the HVR via PCR. The fragments were engineered into a plasmid and transformed into bacteria. Positive bacterial clones were selected and enriched fragments including viral genomic rearrangements, were sequenced via Sanger sequencing of 187 clones,” Todt explains.

This study examined genetic insertions in serum samples from a patient who experienced treatment failure with ribavirin. Researchers analyzed these insertions to evaluate their impact on viral replication and ribavirin sensitivity.

“Currently, there are a few determinants described, ranging from single nucleotide variants to insertions in the HVR of up to 180 nucleotides. They all influence viral replication and can act synergistically. Viral replication in general and HEV replication specifically is a complex, multifactorial process, that we do not completely understand. Nevertheless, the increase in replication seems to correlate directly with treatment failure in vivo.”

To improve patient outcomes, Todt recommends, “we suggest sequencing of viral populations in chronically infected patients before, or at least once during ribavirin therapy, to early identify patients at risk for treatment failure.”

These findings highlight the complexity of HEV adaptation mechanisms, involving interactions between viral and host genetic sequences during infection. Understanding these mechanisms is essential for developing targeted therapeutic strategies against HEV and other RNA viruses with similar adaptive capabilities for future research.

“Next to identifying determinants for treatment failure as diagnostic markers, our lab’s mission also is to provide anti-HEV compounds as an alternative option to ribavirin. We envision a setup compared to HIV management in clinics, where therapy is adapted to the viral sequence in a personalized medicine approach,” Todt concludes.

Reference

Wißing, M.H., Meister, T.L., Nocke, M.K. et al. Genetic determinants of host- and virus-derived insertions for hepatitis E virus replication. Nat Commun 15, 4855 (2024). Published June 6, 2024. Accessed July 12, 2024. https://doi.org/10.1038/s41467-024-49219-8