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Reconstructing the Dynamics of HIV Evolution within Hosts from Serial Deep Sequence Data

Figure 1

Simulated trajectories of genotype frequencies (solid and dashed lines) and population-level coreceptor usage phenotype (shaded regions) under the fitness valley and gradual models of HIV coreceptor usage evolution.

Simulations were generated under a five-allele Moran model with mortality selection [42], effective population size , forward mutation rate of per replication, and fitness vectors of (1, 1.025, 1.05, 1.075, 1.1) and (1, 0.999, 0.999, 0.999, 1.1) corresponding to gradual and valley landscapes, respectively. Note that the relatively rapid and complete fixation of the fifth variant is partly due to the model assumption of no back mutation, and is not consistent with the observation that CXCR4-using variants tend to remain a minority species in HIV infections.

Figure 1