Data from: Evidence that hepatitis C virus genome partly controls infection outcome

Infection by hepatitis C virus (HCV) leads to one of two outcomes; either
the infection resolves within approximately 6 months or the virus can
persist indefinitely. Host genetics are known to affect the likelihood of
clearance or persistence. By contrast, the importance of the virus
genotype in determining infection outcome is unknown, as quantifying this
effect traditionally requires well-characterized transmission networks,
which are rare. Extending phylogenetic approaches previously developed to
estimate the virus control over set-point viral load in HIV-1 infections,
we simulate inheritance of a binary trait along a phylogenetic tree, use
this data to quantify how infection outcomes cluster and ascertain the
effect of virus genotype on these. We apply our method to the Hepatitis C
Incidence and Transmission Study in prisons (HITS-p) data set from
Australia, as this cohort prospectively identified incident cases
including viraemic subjects who ultimately clear the virus, thus providing
us with a unique collection of sequences from clearing infections. We
detect significant correlations between infection outcome and virus
distance in the phylogeny for viruses of Genotype 1, with estimates lying
at around 67%. No statistically significant estimates were obtained for
viruses of Genotype 3a.