Figure 4

(A) Schematic of a transmission network of HIV-1 through the human population. An escape variant of a particular CTL epitope can rapidly become the consensus sequence if reversion of the escape happens little or not at all. Of the 50 hosts (circles), only 5 hosts (filled circles) carry an MHC allele that can bind the epitope. The black circles represent hosts that are infected by the escape variant of the virus, but lack the relevant MHC allele. Grey lines represent transmission of the wildtype virus, whereas black lines represent transmission of the escape variant. (B) Schematic of the accumulation of escapes in the variable protein regions. When escape mutations occur more often, or reversion happen more slowly in variable protein regions (gray shaded areas), and the number of accumulated escape mutations is large enough, a clustering of CTL epitopes (plotted as arrow-delimited lines) is to be expected. One underlying assumption is that the variable and conserved protein regions are larger than a few amino acids in size [12].