An integrative statistical model for inferring strain admixture within clinical Plasmodium falciparum isolates

Abstract: Since the arrival of genetic typing methods in the late 1960's, researchers have puzzled at the clinical consequence of observed strain mixtures within clinical isolates of Plasmodium falciparum. We present a new statistical model that infers the number of strains present and the amount of admixture with the local population (panmixia) using whole-genome sequence data. The model provides a rigorous statistical approach to inferring these quantities as well as the proportions of the strains within each sample. Applied to 168 samples of whole-genome sequence data from northern Ghana, the model provides significantly improvement fit over models implementing simpler approaches to mixture for a large majority (129/168) of samples. We discuss the possible uses of this model as a window into within-host selection for clinical and epidemiological studies and outline possible means for experimental validation.