Table 1.
Abbreviations and terms used throughout the manuscript.
Figure 1.
Plots through time of NeT (estimated from genetic data using the Bayesian skyline plot) versus N (estimated from surveillance data using back calculation).
The plot of N is drawn by means of locally weighted smoothing on the scatter plot (lowess) of the estimated N. We have truncated the plots after 1990 as we wish to characterise HCV transmission prior the virus' discovery in 1989. The vertical axes of the plots through time of NeT N for each HCV subtype (B) have been scaled between maximum and minimum values.
Table 2.
Estimates of transmission parameters for each HCV subtype.
Figure 2.
Scatter plot of the proportion of IDUs against the phylodynamic transmission potential ( = N/NeT) for each subtype.
Figure 3.
Contour plots showing how generation time (T), basic reproductive number (R0) and the proportion of transmitters in the population (u) co-vary.
Gray bands highlight different values of u. The area between the white dashed lines represents R0 values estimated by sensitivity analysis of mortality and recovery rate (Table S3). The area between the yellow dashed lines represents the 95% confidence limits of R0 values estimated assuming 40 years of infectivity and 70 years of life expectancy. The black dots show the maximum T value for each subtype, which is defined by empirical values for u and the median values of R0 (see text).
Table 3.
Sensitivity analysis of the transmission parameters (var(Z), u, R0,a) accounting for different generation times (T) using the two-group (transmitter, non-transmitter) model of secondary infections (Eq.1).
Figure 4.
Estimated distributions of the number of secondary infections per primary infection for each HCV subtype.
Figure 5.
Cumulative proportion of onward infection versus the infected population ranked by the number of secondary infections they create.
20% of onward infections is indicated with a grey horizontal line. The proportion of the population that generates 80% of onward infections is shown by a vertical dashed line. HCV subtype 1a is close to the 80-20 rule (i.e. 80% of the infections are caused by the most infectious 18%).