Contrasting genomic epidemiology between sympatricPlasmodium falciparumandPlasmodium vivaxpopulations

Abstract

The malaria parasitesPlasmodium falciparumandPlasmodium vivaxdiffer in key biological processes and associated clinical effects, but consequences on population-level transmission dynamics are difficult to predict. This co-endemic malaria study from Guyana details important epidemiological contrasts between the species by coupling population genomics (1,396 spatiotemporally-matched parasite genomes) with sociodemographic analysis (nationwide patient census). We describe howP. falciparumforms large, interrelated subpopulations that sporadically expand but generally exhibit restrained dispersal, whereby spatial distance and patient travel statistics predict parasite identity-by-descent (IBD). Case bias towards working-age adults is also strongly pronounced.P. vivaxexhibits 46% higher average diversity (π) and 6.5x lower average IBD. It occupies a wider geographic range, without evidence for outbreak-like expansions, only microgeographic patterns of isolation-by-distance, and weaker case bias towards adults. Possible latency-relapse effects also manifest in various analyses. For example, 11.0% of patients diagnosed withP. vivaxin Greater Georgetown report no recent travel to endemic zones, andP. vivaxclones recur in 11/46 patients incidentally sampled twice during the study. Polyclonality rate is also 2.1x higher than inP. falciparum, does not trend positively with estimated incidence, and correlates uniquely to selected demographics. We discuss possible underlying mechanisms and implications for malaria control.