Single Cell Genomic Dissection of Complex African Malaria Infections Suggest Strong Barriers to Reinfection

Malaria patients can carry one or more clonal lineage of the parasite, Plasmodium falciparum. Well-defined, complete haplotypes at single-cell resolution are ideal for describing within-host population structure and unambiguously determining parasite diversity, transmission dynamics and recent ancestry but have not been analyzed on a large scale. We generated 485 near-complete single-cell genome sequences isolated from fifteen P. falciparum patients from Chikhwawa, Malawi, an area of intense malaria transmission. Matched single-cell and bulk genomic analyses revealed patients harbored up to seventeen unique lineages. Current statistical approaches were unable to accurately reconstruct infection composition from bulk sequence data. Analysis of parasite relatedness within patients suggests superinfection by repeated mosquito bites is rarer than co-transmission of parasites from a single mosquito. Our single-cell analysis indicates strong barriers to establishment of secondary infections, providing new insights into the biology and transmission of malaria.