Abstract
Opioid substitution and syringes exchange programs have drastically reduced hepatitis C virus (HCV) spread in France but HCV sexual transmission in men having sex with men (MSM) has recently arisen as a significant public health concern. The fact that the virus is transmitting in a heterogeneous population, with ‘new’ and ‘classical’ hosts, makes prevalence and incidence rates poorly informative. However, additional insights can be gained by analyzing virus phylogenies inferred from dated genetic sequence data. Here, using a phylodynamics approach based on Approximate Bayesian Computation, we estimate key epidemiological parameters of an ongoing HCV epidemic in MSM in Lyon (France). We show that this new epidemics is largely independent from the ‘classical’ HCV epidemics and that its doubling time is one order of magnitude lower (55.6 days versus 511 days). These results have practical implications for HCV control and illustrate the additional information provided by virus genomics in public health.