Temporal and spatial dynamics ofPlasmodium falciparumclonal lineages in Guyana

Abstract

AbstractPlasmodiumparasites, the causal agents of malaria, are eukaryotic organisms that obligately undergo sexual recombination within mosquitoes. However, in low transmission settings where most mosquitoes become infected with only a single parasite clone, parasites recombine with themselves, and the clonal lineage is propagated rather than broken up by outcrossing. We investigated whether stochastic/neutral factors drive the persistence and abundance ofPlasmodium falciparumclonal lineages in Guyana, a country with relatively low malaria transmission, but the only setting in the Americas in which an important artemisinin resistance mutation (pfk13C580Y) has been observed. To investigate whether this clonality was potentially associated with the persistence and spatial spread of the mutation, we performed whole genome sequencing on 1,727Plasmodium falciparumsamples collected from infected patients across a five-year period (2016- 2021). We characterized the relatedness between each pair of monoclonal infections (n=1,409) through estimation of identity by descent (IBD) and also typed each sample for known or candidate drug resistance mutations. A total of 160 clones (mean IBD ≥ 0.90) were circulating in Guyana during the study period, comprising 13 highly related clusters (mean IBD ≥ 0.40). In the five-year study period, we observed a decrease in frequency of a mutation associated with artemisinin partner drug (piperaquine) resistance (pfcrtC350R) and limited co-occurence ofpfcrtC350R with duplications ofplasmepsin 2/3, an epistatic interaction associated with piperaquine resistance. We additionally report polymorphisms exhibiting evidence of selection for drug resistance or other phenotypes and reported a novelpfk13mutation (G718S) as well as 61 nonsynonymous substitutions that increased markedly in frequency. However,P. falciparumclonal dynamics in Guyana appear to be largely driven by stochastic factors, in contrast to other geographic regions. The use of multiple artemisinin combination therapies in Guyana may have contributed to the disappearance of thepfk13C580Y mutation.Author SummaryMalaria is caused by eukaryoticPlasmodiumparasites, which undergo sexual recombination within mosquitoes. In settings with low transmission, such as Guyana, these parasites often recombine with themselves, leading to the propagation of identical clones. We explored the population genomics ofPlasmodium falciparummalaria parasites in Guyana over five years to characterize clonal transmission dynamics and understand whether they were influenced by local drug resistance mutations under strong selection, includingpfk13C580Y, which confers resistance to artemisinin, andpfcrtC350R, which confers resistance to piperaquine. Using whole genome sequencing on 1,463 samples, we identified 160 clones, in which all parasites share at least 90% of their genomes through recent common ancestry. We observed a decrease in frequency of thepfcrtC350R mutation, as well as the disappearance ofpfk13C580Y. Our findings contrast with the deterministic rise of drug resistance mutations observed in other geographic regions, sometimes associated with clonality. The simultaneous use of at least two different artemisinin combination therapies may have prevented the spread of an artemisinin-resistant clone in Guyana, suggesting a strategy for resistance management in other geographic regions.