A formal description of the population genetics model to study the spread of drug resistant malaria

Simulations were run varying drug usage (i.e., proportion of infections treated) and fitness penalty between 0.0 and 1.0 in increments of 0.02 for both parameters. The models were run with constant MOIs of 1 (100 % selfing), 2, 3 and 4. The application to perform these simulations is made available in http://popgen.eu/soft/ogaraK. In order to facilitate understanding of the resistance profile of each clone we will use, whenever pertinent, a binary representation per locus where 0 represents a locus that is sensitive and 1 when a locus might confer resistance. As an example, in a case where we model two drugs and 1 resistance locus per drug, the totally sensitive clone can be represented by c0,0; clone c0,1 is sensitive to drug 1 and resistant to drug 2. For clarity and unless otherwise stated, all textual examples presented below will assume 2 drugs with 1 locus per drug. The following symbols are also employed: