Evolution of Partial Resistance to Artemisinins in Malaria Parasites in Uganda

Abstract

Background: Partial resistance of Plasmodium falciparum to the artemisinin component of artemisinin-based combination therapies, the most important malaria drugs, emerged in Southeast Asia and now threatens East Africa. Partial resistance, which manifests as delayed clearance after therapy, is mediated principally by mutations in the kelch protein K13 (PfK13). Limited longitudinal data are available on the emergence and spread of artemisinin resistance in Africa.

Methods: We performed annual surveillance among patients who presented with uncomplicated malaria at 10 to 16 sites across Uganda from 2016 through 2022. We sequenced the gene encoding kelch 13 (pfk13) and analyzed relatedness using molecular methods. We assessed malaria metrics longitudinally in eight Ugandan districts from 2014 through 2021.

Results: By 2021-2022, the prevalence of parasites with validated or candidate resistance markers reached more than 20% in 11 of the 16 districts where surveillance was conducted. The PfK13 469Y and 675V mutations were seen in far northern Uganda in 2016-2017 and increased and spread thereafter, reaching a combined prevalence of 10 to 54% across much of northern Uganda, with spread to other regions. The 469F mutation reached a prevalence of 38 to 40% in one district in southwestern Uganda in 2021-2022. The 561H mutation, previously described in Rwanda, was first seen in southwestern Uganda in 2021, reaching a prevalence of 23% by 2022. The 441L mutation reached a prevalence of 12 to 23% in three districts in western Uganda in 2022. Genetic analysis indicated local emergence of mutant parasites independent of those in Southeast Asia. The emergence of resistance was observed predominantly in areas where effective malaria control had been discontinued or transmission was unstable.

Conclusions: Data from Uganda showed the emergence of partial resistance to artemisinins in multiple geographic locations, with increasing prevalence and regional spread over time. (Funded by the National Institutes of Health.).

Figure 1.. Map of Uganda and Study Districts.

IRS denotes indoor residual spraying of insecticides.

Figure 2.. Prevalence of Indicated PfK13 Mutations in Studied Ugandan Districts.

In Panel B, a horizontal dash along the x axis indicates no prevalence, and no dash means no samples were obtained in that year.

Figure 3.. Phylogenetic Relatedness of Parasites from Uganda.

Dendrograms show the relatedness of parasites from Uganda with the indicated PfK13 mutations, wild-type parasites, and parasites containing other PfK13 mutations (other) according to the characterization of seven microsatellite loci flanking PfK13 (Panel A) and the relatedness of mutant isolates from Uganda and Southeast Asia according to polymorphic loci distributed across the genome (Panel B).

Figure 4.. Relationship between Malaria Metrics and Prevalence of PfK13 Mutations.

Malaria incidence and mutation prevalence are shown for sites that received indoor residual spraying of insecticides. The metrics shown were assessed monthly and are displayed with locally weighted scatterplot smoothing. Arrows indicate times of insecticide application; the darkest arrows indicate an apparently ineffective insecticide (clothiandin–deltamethrin). Histogram bars indicate the prevalence of PfK13 mutations. A horizontal dash along the x axis indicates sample collection occurred but no mutations were detected. Other metrics of malaria (test positivity and median age of presentation with malaria) are shown in Figures S1, S2, and S3.