Intra-host viral population dynamics during acute hepatitis E virus infection

Mbio, Page e0115126

The hepatitis E virus (HEV) is the most common cause of acute viral hepatitis worldwide. RNA viruses like HEV can establish viral populations with high intra-host variability, enabling them to rapidly adapt to changing immune responses, as observed in chronic infections. This study aimed to investigate how intra-host evolution shapes HEV populations during acute asymptomatic infection. Using a highly sensitive HEV amplicon sequencing approach, we characterized intra-host viral diversity and mutational signatures present in serum samples from a cohort of over 80 asymptomatic blood donors infected with acute HEV-3. The overall diversity within the host was constrained; however, several recurrent substitutions were identified, and four mutations in the polymerase region were found to be enriched among the donors. Despite being markedly replication-deficient in vitro, their replication defects could be rescued in an RNA-dependent RNA polymerase trans-complementation assay. Longitudinal sampling in a subset of donors revealed temporal shifts in variant frequencies, indicating ongoing early selection dynamics. In contrast to chronic HEV infection in immunosuppressed patients, acute-phase populations exhibited a significantly lower number of single-nucleotide variants (SNVs) and an absence of high-frequency variants. The presence of premature stop codons and other defective genomes was primarily detected during the acute phase of infection. This finding further supports the hypothesis that the early evolutionary landscape is highly dynamic, but constrained. Although HEV diversity is markedly restricted during acute infection, early evolutionary changes indicate that selective forces act even within the short window of acute, self-limiting, and asymptomatic disease. These findings offer mechanistic insights into early intra-host evolution, highlight conditions under which deleterious variants can transiently persist, and lay the groundwork for linking genotypic features to clinical outcomes and treatment responsiveness.IMPORTANCEThe hepatitis E virus is the leading cause of acute viral hepatitis globally. While studies of chronic infections have shown that HEV can evolve and adapt in ways that influence antiviral treatment responses, little is known about how the virus changes during the early, acute phase of infection. By analyzing viral populations in asymptomatic blood donors, this study demonstrates that HEV undergoes dynamic evolutionary changes even during short, self-limiting infections. Although overall viral diversity remains restricted, selective pressures still drive the emergence of new variants, including some with impaired replication capacity. These findings provide important mechanistic insight into early intra-host viral evolution and the conditions that allow defective variants to transiently persist. This work establishes a foundation for future studies linking viral genetic variation to disease progression, clinical outcomes, and treatment responsiveness.

DOI: 10.1128/mbio.01151-26