Epidemiological and genomic parameters for ten major outbreak causing pathogens.

<p>Epidemiological and genomic parameters for ten major outbreak causing pathogens.</p

Impact of transmission divergence on outbreak reconstruction.

<p>Transmission divergence is defined as the number of mutations separating pathogen WGS sampled from transmission pairs. <b>A) Change in accuracy of outbreak reconstruction.</b> Accuracy of outbreak reconstruction is defined as the proportion of correctly assigned ancestries in the consensus transmission tree, itself defined as the tree with the most frequent posterior infector for each infectee. Coloured points represent individual simulated outbreaks. The solid black line represents the fitted relationship of the form <i>i</i>—<i>i</i>*exp(-<i>a</i>*<i>K</i>), where <i>K</i> is the transmission divergence and <i>a</i> and <i>i</i> the fitting variables. Dotted black lines represent the corresponding 95% prediction interval. <b>B) Change in posterior entropy.</b> Posterior entropy is related to the number of plausible posterior infectors for a given case. Lower average entropy indicates greater statistical confidence in the proposed transmission tree. The solid black line represents the fitted relationship of the form <i>i</i>*exp(-<i>a</i>*<i>K</i>)—<i>i</i>, where <i>K</i> is the transmission divergence and <i>a</i> and <i>i</i> the fitting variables.</p

Impact of the proportion of unique sequences on outbreak reconstruction.

<p><b>A) Change in accuracy of outbreak reconstruction.</b> Accuracy of outbreak reconstruction is defined as the proportion of correctly assigned ancestries in the consensus transmission tree, itself defined as the tree with the most frequent posterior infector for each infectee. Coloured points represent individual simulated outbreaks. The solid black line represents the fitted linear model, the dotted black lines the 95% prediction interval. <b>B) Change in posterior entropy.</b> Posterior entropy is related to the number of plausible posterior infectors for a given case. Lower average entropy indicates greater statistical confidence in the proposed transmission tree. The solid black line represents the fitted linear model, the dotted black lines the 95% prediction interval.</p

epicontacts

<p>A collection of tools for representing epidemiological contact data, composed of case line lists and contacts between cases. Also contains procedures for data handling, interactive graphics, and statistics.</p

Inference of individual effective reproduction numbers.

<p>This violinplot shows the estimates of individual effective reproduction numbers (<i>R</i>) for simulated outbreaks with the ‘Base’ setting (see <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003457#pcbi-1003457-t001" target="_blank">Table 1</a>), based on 50 simulated epidemics, with (left) or without (right) using genetic information in the model. Each dot represents an infected individual. The dashed line indicates identity.</p

Quality of the transmission tree reconstruction in simulated datasets.

<p>This violinplot represents the proportion of correctly inferred transmissions in the consensus ancestries, obtained by retaining the most frequent infectors in the posterior trees for each case. Each colored ‘violin’ represents the density of points for a given simulation setting, indicated on the x-axis (see <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003457#pcbi-1003457-t001" target="_blank">Table 1</a> for details).</p

Detection of group-level heterogeneity in infectivity.

<p>This violinplot shows actual and estimated values of effective reproduction numbers (<i>R</i>) at an individual level, for outbreaks simulated with two groups of hosts having contrasted infectivity (‘Low’ and ‘high’). The top panel corresponds to simulations with equally-sized groups (‘Low/high settings’), while the bottom panel corresponds to simulations with super-spreaders.</p

Consensus transmission tree reconstruction of the SARS outbreak.

<p>This figure indicates the most supported transmission tree reconstructed by <i>outbreaker</i>. Cases are represented by spheres colored according to their collection dates. Edges are colored according to the corresponding numbers of mutations, with lighter shades of grey for larger numbers. Edge annotations indicate numbers of mutations and frequencies of the ancestries in the posterior samples.</p

Parameters of the simulated outbreaks.

<p>Parameters of the simulated outbreaks.</p

Detection of imported cases.

<p>This figure shows the specificity and sensitivity of the procedure for detecting imported cases based on the identification of genetic outliers. Colored rectangles represent the percentage of simulations within a given specificity/sensitivity range. All simulation settings were pooled for this analysis.</p