Estimates of transmission parameters for each HCV subtype.

1<p>The phylodynamic transmission parameter PTP = <i>N</i>/(<i>NeT</i>) has been estimated as the coefficient of the linear regression of <i>N</i> versus <i>NeT</i> without constant term. For the confidence intervals the autocorrelation structure of each variable has been taken into account according to the Newey-West correction.</p>2<p>Generation time estimated as Var(<i>Z</i>)/PTP (maximum estimate assuming that the minimum proportion of transmitters equals the proportion of IDUs in each subtype).</p>3<p>Proportion of transmitters, practically equal to the proportion of IDUs within each subtype.</p>4<p>Upper 1% of the distribution of secondary infections including transmitters and non-transmitters.</p

Cumulative proportion of onward infection versus the infected population ranked by the number of secondary infections they create.

<p>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%).</p

Contour plots showing how generation time (<i>T</i>), basic reproductive number (<i>R</i>₀) and the proportion of transmitters in the population (<i>u</i>) co-vary.

<p>Gray bands highlight different values of <i>u</i>. The area between the white dashed lines represents <i>R</i>₀ values estimated by sensitivity analysis of mortality and recovery rate (<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002876#pcbi.1002876.s007" target="_blank">Table S3</a>). The area between the yellow dashed lines represents the 95% confidence limits of <i>R</i>₀ values estimated assuming 40 years of infectivity and 70 years of life expectancy. The black dots show the maximum <i>T</i> value for each subtype, which is defined by empirical values for <i>u</i> and the median values of <i>R</i>₀ (see text).</p

Scatter plot of the proportion of IDUs against the phylodynamic transmission potential ( = <i>N</i>/<i>NeT</i>) for each subtype.

<p>Scatter plot of the proportion of IDUs against the phylodynamic transmission potential ( = <i>N</i>/<i>NeT</i>) for each subtype.</p

Abbreviations and terms used throughout the manuscript.

<p>Abbreviations and terms used throughout the manuscript.</p

Sensitivity analysis of the transmission parameters (var(<i>Z</i>), <i>u</i>, <i>R</i>_0,a) accounting for different generation times (<i>T</i>) using the two-group (transmitter, non-transmitter) model of secondary infections (Eq.1).

<p>The proportion of the transmitters (<i>u</i>) contrasted to the proportion of IDU, provides us information about epidemiologically probable generation times (<i>T</i>) i.e. we do not expect that the proportion of transmitters would be less than the proportion of IDU in the same population.</p