Epidemic curve.

<p>Daily number of referred/visiting patients at KGH (confirmed cases only) from the of April to the of January , <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0003398#pntd.0003398-Shaffer1" target="_blank">[1]</a>.</p

Value of the parameters used in the numerics.

<p>See List of Symbols and Glossary in the Supporting Information, <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0004957#pntd.0004957.s001" target="_blank">S1 Text</a>, for further details.</p

Estimating the relative contributions of zoonotic spillover and human-to-human transmission.

<p>Comparison with ABM III.(<b>a</b>) Cumulative number of infections for zoonotic spillover with human-to-human transmission and depletion of susceptibles (‘Poisson with Feedback’ model) generated by the ABM (10 independent runs). The green and red points represent cumulative infections arising from zoonotic and human-to-human transmission respectively. The continuous blue and black line represent the analytical solutions and the isolated contributions of zoonotic, , and human-to-human transmission, , recalculated with parameters (median values of <i>ζ</i> and <i>κ</i>, right panel) estimated from the MCMC. (<b>b</b>) Traceplot of the time series and histogram of the two parameters: <i>ζ</i> (median 0.008338, mean 0.008364, SE 0.0006919, bandwidth 0.0001162) and <i>κ</i> (median 0.055118, mean 0.055134, SE 0.0033703, bandwidth 0.0005541) number of iterations 10000, burning time 1000, thinning interval 1. The small discrepancy between the parameters and the ones imposed in the ABM (respectively 0.05 and 0.01) is expected as the ABM simulates Bernoulli trials rather than Poisson processes. Full agreement is expected when the number of trials approaches infinity.</p

Comparison with ABM I.

<p>(<b>a</b>) Cumulative number of zoonotic infections generated by the ABM (10 independent runs, grey points) for the case when the rate of infection is not affected by the number of humans already infected (no human-to-human transmission) or by depletion of susceptibles (’Simple Poisson’ model). According to <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0004957#pntd.0004957.e001" target="_blank">model (1)</a> the mean cumulative number of zoonotic infections grows linearly with <i>λ</i> (green line). (<b>b</b>) Quantile-Quantile plot of the distribution of infections, generated by the ABM compared with the theoretical Poisson distribution. (<b>c</b>) As in panel a, but the rate of infection is also subjected to random variation (‘Poisson-Gamma-Mixture’ model); the green line represents the mean cumulative number of zoonotic infections as in panel a. (<b>d</b>) Quantile-Quantile plot of the distribution of infections generated by the ABM compared with the theoretical negative binomial distribution.</p

Application to LF.

<p>(<b>a</b>) Predicted cumulative number of zoonotic and human-to-human infections (governed by ‘Poisson with Feedback’ model, <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0004957#pntd.0004957.e037" target="_blank">Eq (12)</a>) for constant zoonotic exposure and (<b>b</b>) As in (a), but exposure to zoonotic LASV is governed by an piecewise linear trend in exposure to zoonotic LASV (<i>i.e.</i> the piecewise zoonotic exposure <i>ζ</i> is linearly increasing up to March 2011 followed by a decrease up to January 2012). The parameters are optimized with the data from KGH (red line) by employing MCMC (number of iterations 50000, burning time 1000, thinning interval 1). The grey dots represent 100 independent stochastic realisations; 5 five random examples of which are visualized in blue lines. The black line represents the cumulative number of occurrences averaged over the 100 multiple stochastic realisations.</p

Nosocomial outbreaks.

<p>A: Diagrammatic representation of LF cases admitted at Jos Hospital, Nigeria (total duration of the outbreak days), showing period of illness and interrelation among patients <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0003398#pntd.0003398-Carey1" target="_blank">[2]</a>. The horizontal bars represent each patient. The x-axis is the time expressed in days from the start of the outbreak, when TS developed the illness (thus time in the calculation corresponds to December 1969). The grey portion of the bars are the period between the onset of the symptoms and admission to hospital; the black portion of the bars are the period between admission to hospital and discharge/death of the patients; the red thin lines are the period of exposure to the index case TS. The green bar represent the time when the patient was at the ward for unrelated illness. Note, the same diagram in <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0003398#pntd.0003398-Carey1" target="_blank">[2]</a> present an extra case, JT, which is not included here. This case refers to Dr. Jeanette M. Troup one of the first scientists working on Lassa Fever Virus, who contracted the disease from an autopsy accident incurred during examination of one of the fatal cases. B: Diagrammatic representation of LF cases admitted at Zorzor Hospital (total duration of the outbreak days), Liberia, showing period of illness and interrelation among patients <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0003398#pntd.0003398-Monath1" target="_blank">[3]</a>. C: As in <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0003398#pntd-0003398-g001" target="_blank">Fig. 1.A</a>, but the periods of illness (symptoms plus time at hospital) are randomly permuted. The contact network is kept the same. D: An example of how the time was calculated. In this particular case if and otherwise, where is the time when case is no longer exposed to case .</p

Impact of super-spreaders II.

<p>A: proportion of cases when the individual effective reproduction number is greater than one. (<i>i.e.</i> the ratio of the cardinalities of and , where is set of all simulated and the subset of cases when is greater than one). B: the expected, relative number of cases generated by this proportion. (<i>i.e.</i> the fraction of the areas of )</p

Individual effective reproduction number and generation time.

<p>Box-plot for the individual for the nosocomial outbreak described in <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0003398#pntd.0003398-Carey1" target="_blank">[2]</a> based on the permutations of the duration of illness. It shows the first and third percentiles, the minimum and maximum values, the median, and outliers (red dots). The dashed line represents the case when the effective reproduction number is equal to . A: nosocomial outbreak in Jos <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0003398#pntd.0003398-Carey1" target="_blank">[2]</a>. B: nosocomial outbreak in Zorzor <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0003398#pntd.0003398-Monath1" target="_blank">[3]</a>. C: Distribution of generation time for the two nosocomial outbreaks. The statistics are based on the permutations of the duration of illness. D: Distribution of generation time for extra-nosocomial cases. The statistics are based on the permutations of the duration of illness.</p

Contribution of human-to-human transmission.

<p>Mean value of the total effective reproduction number, and its daily mean, , for the KGH epidemic curve <i>vs</i> the proportion of cases due to human-to-human transmission (blue line). The shaded grey area covers the range between the and percentiles in and/or ; the dashed red line represents the mean, nosocomial, effective reproduction number. A and B: and based on the full networks (in Jos and in Zorzor) of nosocomial cases; days. C and D: and based on the extra-nosocomial cases in Jos; days.</p

Impact of super-spreaders I.

<p>A: Distribution of all individual for both nosocomial outbreaks, based on the permutations of the duration of illness. Mean value of the joint data: , median: , maximum: , proportion of cases when : , proportion of cases when : . B: Distribution of the effective reproduction number for cases of hospitalized patients in KGH for different values of the contribution of human-to-human transmission, , the corresponding data for the extra-nosocomial ( permutation based on , , , , cases in Jos) and all nosocomial outbreaks (based on all Jos and Zorzor cases) are also shown. C: Distribution of the total effective reproduction number, <i>i.e.</i> the average number of cases during the entire duration of the epidemic for different values the contribution of human-to-human transmission, .</p