They weren't trying to find a part of the genome that couldn't mutate - they were just trying to determine what the target of their two drugs was. The fact that both drugs produced changes in parts of NS5A and these changes conferred resistance to the drugs confirmed that NS5A was indeed the target.
Their actual drug candidate seems potent enough to cope with any single point substitutions - you do get resistance in the sense of needing a higher dose, but still within the therapeutic range. (And the resistant species appear to be less fit to boot).
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