Temporal and spatial analysis of Plasmodium falciparum genomics reveals patterns of connectivity in a low-transmission district in Southern Province, Zambia

Understanding temporal and spatial dynamics of ongoing malaria transmission will be critical to inform effective interventions and elimination strategies in low transmission regions approaching elimination. Parasite genomics are being used as a tool to monitor epidemiologic trends, including assessing residual transmission across seasons or importation of malaria into these regions. Southern Province, Zambia is a low-transmission setting with seasonal malaria. We genotyped 441 Plasmodium falciparum samples using molecular inversion probes at 1,832 positions across the genome, using dried blood spots collected from 2012-2018 from 8 health centers in the catchment area of Macha Hospital in Choma District. We show that highly related parasites persist across multiple seasons, suggesting that the persistence of malaria is at least in part fueled by parasites "seeding" across the dry season. In addition, we identify clusters of clonal parasites that are dissimilar to the general population, suggesting that introduction of parasites from elsewhere may contribute to the continued malaria burden. We identified signals of population size fluctuation over the course of individual transmission seasons, suggesting a ramp-up of malaria transmission from a seasons beginning. Despite the small spatial scale of the study (2,000 sq km), we identified an inverse relationship between genetic relatedness of parasite pairs and distance between health centers, as well as increased relatedness between specific health centers. These results, leveraging both genomic and epidemiological data, provide a comprehensive picture of fluctuations in parasite populations in this pre-elimination setting of southern Zambia.