Standing genetic variation and the evolution of drug resistance in HIV. PLoS Comput Biol 8(6), e1002527

Supplementary text S1 for Pennings, P.S., Standing genetic variation and the evolution of drug resistance in HIV, PLoS Comp Biol, 2012 Model. The model describes population dynamics and population genetics of a panmictic virus population in a single patient. Only virus in infected cells is considered and the dy-namics of free virus and uninfected cells are ignored. The total number of cells that can be infected is limited to K, the carrying capacity. Because the life cycle of the virus is simplified to just one step in which infected cells “give birth ” to infected cells, all drugs have the same effect: they reduce the number of cells that can be infected by the virus in an infected cell. We will refer to the infected cells by the virus they are infected with. When patients fail therapy, this is often due to virus that is resistant against just one drug even if the patient was treated with three drugs (as described in the Introduction). We therefore assume in our model that there are just two types of viruses: wildtype virus that is susceptible to all drugs and resistant virus that is resistant against one of the drugs in the regimen of the patient. We assume that prior to establishment of single drug-resistant virus (hereafter: resistant virus), there is no virus present that is resistant against more than on