Summary:

Infection by hepatitis C virus (HCV) leads to one of two outcomes, which varies amongst patients. Either the infection resolves itself within a matter of weeks, or it can persist over several years. It is difficult to ascertain to what extent this outcome is determined by the virus genotype itself using transmission networks, as these tend to be poorly known. Recently, phylogenetic methods have been created to estimate the proportion of set-point viral load that is inherited from one HIV-infected patient to the next. Studies found that up to half the variance in this trait is determined by the virus genotype. Here, we aim to investigate whether we can detect a similar signal in HCV infections. We first simulate inheritance of a binary trait outcome along a given phylogenetic tree to predict how traits gather in groups, and explain how these simulations are used to ascertain the virus effect on the infection outcome. Finally, we apply our method to HCV cohort data from Australia to try and detect an effect of virus genotype on whether hosts will clear the virus rapidly or develop a chronic infection. We also investigate whether key host SNPs, which are known to affect HCV infection outcome, affect this measure of inheritance.