The origins and relatedness structure of mixed infections vary with local prevalence of P. falciparum malaria

• DOI: 10.7554/elife.40845
• Publication Date: 2019-07-12T12:00:54Z
• Authors: Sha Joe Zhu; Jason A Hendry; Jacob Almagro-Garcia; Richard D Pearson; Roberto Amato; Alistair Miles; Daniel J Weiss; Tim CD Lucas; Michele Nguyen; Peter W Gething; Dominic Kwiatkowski; Gil McVean
• Keywords: relatedness; 0301 basic medicine; Asia; Genotype; QH301-705.5; Science; Plasmodium falciparum; malaria; 03 medical and health sciences; Prevalence; Humans; Biology (General); Malaria, Falciparum; genome; 0303 health sciences; Whole Genome Sequencing; Coinfection; Q; R; 3. Good health; Epidemiology and Global Health; Africa; Medicine; epidemiology

Individual malaria infections can carry multiple strains of Plasmodium falciparum with varying levels relatedness. Yet, how local epidemiology affects the properties such mixed remains unclear. Here, we develop an enhanced method for strain deconvolution from genome sequencing data, which estimates number strains, their proportions, identity-by-descent (IBD) profiles and individual haplotypes. Applying it to Pf3k data set, find that rate infection varies 29% 63% across countries 51% involve more than two strains. Furthermore, estimate 47% symptomatic dual contain sibling likely have been co-transmitted a single mosquito, evidence propagated over successive cycles. Finally, leveraging Malaria Atlas Project, prevalence correlates within Africa, but not Asia, both level IBD.