Inferring frequency dependent selection from the molecular evolution of a rapidly evolving virus: A theoretical investigation

Hypotheses have been put forward suggesting that immune selection generates much of the intra-patient genetic diversity of rapidly evolving viruses. A Monte Carlo simulation is presented which models sequence evolution in an HIV-like virus under selection from the immune system. Measurements of evolutionary change are then made from the resulting sequences, generating predicted outcomes for each scenario. Frequency dependent immune selection is shown by two statistical measurements to have a significant effect on viral sequence evolution. The use of drawing inferences about underlying evolutionary processes from samples of viral diversity in infected individuals is discussed