Cluster structure and age of infection.

<p>(<b>A</b>) Factors influencing the observed viral landscape in a cluster including (i) viral transmission, (ii) the viral eclipse phase, and (iii) intracellular viral replication. (<b>B, C</b>) Relationship between the maximal cluster extension and the age of the assumed founder cell of the cluster (<b>B</b>) and the time until this cluster extension was possibly reached, (<b>C</b>), i.e., the difference between the age of the assumed founder cell and cells that were more recently added to the cluster. Estimates were obtained using the model on intracellular HCV replication discussed in the text. The mean and the 2.5% and 97.5% percentiles of 10,000 bootstrap replicates for each individual cluster are shown. (<b>D</b>) Comparison of the average fractional decrease in intracellular HCV RNA, , between the founder cell and the surrounding cells of a cluster comprising 9 cells. Expansion of individual foci was simulated in a 2D-grid with different assumptions for the average duration of the eclipse phase , and the probability for viral transmission, . We simulated 1000 individual foci and selected all foci showing clusters comprising 9 cells with radial spread. The average fractional decrease is calculated relative to the amount of viral RNA within the founder cell of the cluster. The mean and 95%-percentiles are shown. For a detailed description of the simulation environment see <i>Supporting Information</i> (<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003934#pcbi.1003934.s007" target="_blank">Text S3</a>).