High-resolution micro-epidemiology of parasite spatial and temporal dynamics in a high malaria transmission setting in Kenya

Novel interventions that leverage the heterogeneity of parasite transmission are needed to push malaria further towards elimination. To better understand spatial and temporal dynamics of transmission, we applied amplicon NGS of two polymorphic gene regions (csp and ama1) to a cohort identified via reactive case detection in a high-transmission setting in western Kenya. From 4/2013-6/2014, we enrolled 442 symptomatic children with malaria, 442 matched controls, and all household members of both groups. We evaluated genetic similarity between infected individuals using three novel indices: sharing of parasite haplotypes on binary and proportional scales and the L1 norm. Symptomatic children more commonly shared haplotypes with their own household members. Furthermore, we identified robust temporal structuring of parasite genetic similarity that we exploited to identify the molecular signature of an outbreak. These findings of both micro- and macro-scale organization of parasite populations might be harnessed to inform next-generation malaria control measures.