Enhanced bias in progeny accumulation between variants in <i>cis</i>-acting genes or elements simulated by the model.

<p>(A) Simulation of the accumulation of the wild type (WT; magenta) and a variant with 50% efficiency of genomic RNA synthesis (green), which were co-inoculated into cells at a 1:1 ratio. Each pie chart shows the amount of genomic RNAs that accumulated in each cell. The accumulation ratios of the variant to WT are indicated below the pie charts, and underlining indicates coinfections. The area size of the pie charts represents the total amount of genomic RNAs. (B) An example of a simulated change in genomic RNA accumulation and replication complex (RC) site occupancy over time in a cell coinfected with the WT (magenta) and a variant with 50% genomic RNA synthesis efficiency (green). (C) History of changes in the ratio of the variant to total genomes in cells 1–10 of panel A. The dashed line indicates <i>t</i> = 8,400, which corresponds to experimental ∼4 hpi. The efficiency of genome RNA synthesis of the variant is 50% of that for the co-inoculated WT RNA; therefore, a variant to total ratio of <33.3% [i.e., 50%/(50% + 100%)] indicates the occurrence of enhanced bias in progeny accumulation (EBPA). The dotted line indicates 33.3% accumulation of the variant. (D) The accumulations of WT (magenta) and co-inoculated variants with different genomic RNA synthesis efficiencies (green) in 1,000 cells were simulated. The relative accumulation of the variants is also shown in a table below the bar graph. Means ± SEs calculated using bootstrap analysis of 1,000 simulated cellular infections are shown. R scripts <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002094#pbio.1002094.s035" target="_blank">S9 Text</a> and <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002094#pbio.1002094.s036" target="_blank">S10 Text</a> were used to generate panels A–B and C, respectively. <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002094#pbio.1002094.s035" target="_blank">S9 Text</a> was also used to generate <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002094#pbio.1002094.s008" target="_blank">S2 Movie</a>. To generate panel D, R scripts <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002094#pbio.1002094.s037" target="_blank">S11 Text</a> and <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002094#pbio.1002094.s038" target="_blank">S12 Text</a> were used, and the data obtained by the authors are shown in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002094#pbio.1002094.s004" target="_blank">S4 Data</a>.