A major challenge in solving the QSR problem is that the quasispecies sequences are only slightly different from each other. The amount and distribution along the genome of differences between quasispecies varies significantly between virus species, as different species have different mutation rates and genomic architectures. In particular, due to the lower mutation rate and longer conserved regions, HCV quasispecies are harder to reconstruct than quasispecies of HBV and HIV. Additionally, the QSR problem is made difficult by the limited read length and relatively high error rate of high throughput sequencing data generated by current technologies.