Intra-host IRES heterogeneity shapes hepatitis C virus translation through epistatic and population-level effects

Hepatitis C virus (HCV) resides within each patient as a diverse collection of closely related genetic sequences. Traditionally, researchers have inferred the functional properties of HCV's RNA from a single, dominant genome. However, the impact of non-coding intra-host variability, particularly within the internal ribosome entry site (IRES), on viral translation remains unclear.

In this study, researchers analyzed the complete IRES sequences from chronically infected patients using a variety of methods, including molecular cloning, bicistronic reporters, full-length replication-deficient viral RNAs, and reconstructed intra-host populations. They discovered that natural IRES mutations can have context-dependent effects on viral translation, and certain combinations of mutations produce phenotypes that are not predictable from single mutations, indicating intragenic epistasis.

Furthermore, some variants exhibited different behavior in bicistronic reporters and full-length viral RNAs, suggesting that both genomic and cellular contexts influence IRES function. Reconstructed genotype 1a populations largely mirrored the activity of their dominant haplotypes, while reconstructed genotype 3a populations translated considerably more efficiently than their corresponding dominant sequences, demonstrating that low-frequency variants can collectively modulate translation at the population level.

This research highlights that the translational phenotype of HCV cannot always be accurately predicted from the dominant sequence alone, and emphasizes the importance of considering epistasis, genomic context, and intra-host population composition as interacting factors that determine viral RNA translation.