Spontaneous mutations are the ultimate source of genetic variation and have a prominent role in evolution. RNA viruses such as hepatitis C virus (HCV) have extremely high mutation rates, but these rates have been inferred from a minute fraction of genome sites, limiting our view of how RNA viruses create diversity. Here, by applying high-fidelity ultradeep sequencing to a modified replicon system, we scored >15,000 spontaneous mutations, encompassing more than 90% of the HCV genome. This revealed >1,000-fold differences in mutability across genome sites, with extreme variations even between adjacent nucleotides. We identify base composition, the presence of high- and low-mutation clusters and transition/transversion biases as the main factors driving this heterogeneity. Furthermore, we find that mutability correlates with the ability of HCV to diversify in patients. These data provide a site-wise baseline for interrogating natural selection, genetic load and evolvability in HCV, as well as for evaluating drug resistance and immune evasion risks.

The susceptibility of Trichoplusia ni larvae to several BaciUlus thuringiensis insecticidal crystal proteins (ICPs) was tested. Neonatal larvae proved to be susceptible to solubilized trypsin-treated CryIA(a), CryIA(b), and CryLA(c) (50%Yo lethal concentrations [LCsos], 570, 480, and 320 ng/cm2, respectively) but showed little susceptibility to CryIB and CryID (LC50s, 5,640 and 2,530 ng/cm2, respectively). The toxicity of ICPs was correlated to binding to the epithelial brush border of the midgut, as revealed by immunocytochemical staining with monoclonal antibodies. In vitro binding experiments with iodinated ICPs and brush border membrane vesicles indicated that CryIA(b) and CryLA(c) share the same high-affinity binding site, whereas CryLA(a) binds to a different one. The affinities of CryLA(b) and CryIA(c) for the binding site were similar (Kd = 3.6 and 4.7 nM, respectively), and the mean binding-site concentration was 0.71 pmol/mg of vesicle protein. Selection of a population with increasing concentrations of CryIA(b) produced 31-fold resistance in seven generations. The realized heritability (h2) was 0.19. The increase of homozygosity (for resistance factors) as selection proceeded was reflected in the increase in the slopes of the dose-mortality curves. Resistance was specific for CryIA(b) and did not extend to CryIA(a) or even to CryIA(c). This result was not predicted by the binding-site model, in which CryIA(b) and CryLA(c) bind to the same high-affinity binding site. This result may suggest a more complicated relationship between in vitro binding of ICPs to specific sites in the epithelial membrane of the midgut and the in vivo toxic effect.