HCV RNA genomes
have evolved under selective pressures exerted by innate immune
sensors that recognize long double-stranded RNA helices (23).
Based on SHAPE-informed secondary structure models, we
generated global profiles of lengths of RNA helices in the three
HCV genomes (Fig. 5A, Upper). Because many helices in the
minimum free-energy structures have high Shannon entropies
(Figs. S1–S3), these profiles represent an upper limit on the