Figure 4. The effect of recombination on chosen parameters of the model.

Orange and blue bars correspond to runs with and without recombination, respectively. Panel A shows the viral diversity as a number of strains in the population (results for other measures of diversity were qualitatively similar). It can be seen that recombination has a significant impact on diversity regardless of the stage of infection. Panel B shows the mean number of escapes measured by the mean HD at the escape loci. The panel shows that recombination accelerates the evolution of immune escape in the virus in the early phase of infection because it accelerates the acquisition of the escape mutations when they are beneficial. Note that the strain with mutations at all loci (HD = 30) has arisen only in the runs with recombination (one blue bar missing in panel B). The parameters are identical as in Fig. 3 and the plot also shows an average of 10000 simulation runs.