Rational Design and Adaptive Management of Combination Therapies for Hepatitis C Virus Infection

Recent discoveries of direct acting antivirals against Hepatitis C virus (HCV) have raised hopes of effective treatment via combination therapies. Yet rapid evolution and high diversity of HCV populations, combined with the reality of suboptimal treatment adherence, make drug resistance a clinical and public health concern. We develop a general model incorporating viral dynamics and pharmacokinetics/ pharmacodynamics to assess how suboptimal adherence affects resistance development and clinical outcomes. We derive design principles and adaptive treatment strategies, identifying a high-risk period when missing doses is particularly risky for de novo resistance, and quantifying the number of additional doses needed to compensate when doses are missed. Using data from large-scale resistance assays, we demonstrate that the risk of resistance can be reduced substantially by applying these principles to a combination therapy of daclatasvir and asunaprevir. By providing a mechanistic framework to link patient characteristics to the risk of resistance, these findings show the potential of rational treatment design.Author Summary: Hepatitis C virus (HCV) affects approximately 170 million people world-wide and chronic infections can lead to cirrhosis and liver cancer. New combination therapies of direct acting antivirals have achieved remarkably high cure rates in clinical trials. However, high mutation rates and high diversity of HCV populations, combined with the reality of suboptimal treatment adherence, make drug resistance a clinical and public health concern. By constructing a mechanistic framework to assess the risk of drug resistance, we provide guidelines for rational design and adaptive management of these promising new therapies. In particular, we identify a high-risk period when missing doses is particularly risky, and quantify the number of extra doses needed to compensate when doses are missed. This framework is a step towards developing a tool for clinicians to design combination therapies and adaptively manage treatment regimens to achieve favorable clinical outcomes.