Lineages through time plots obtained for the NS3 and NS5b sequences using a death/birth model both showed deviation above a line plotted between the initial and final points in the plot, indicating that diversification has not been constant and has decreased over time (Fig. 4). This inference is confirmed by the gamma statistic which was −15 and −14 for NS3 and NS5b, respectively, (P < 0.0001, one-tailed, for both NS3 and NS5b). The best fit model with continuous-time and varying speciation/extinction rates from the laser package was obtained with the fitEXVAR function, which indicated that the rate of speciation for new HCV 3a variants has remained constant over time but the rate of extinction was increasing over time.