A genetic variant that was absent from malaria samples collected in Uganda two decades ago has now become common in parts of the country. Researchers say the change is linked to reduced susceptibility to several important antimalarial drugs.
The variant occurs in Plasmodium falciparum, the parasite responsible for the most severe form of human malaria. In laboratory testing, parasites carrying it were less susceptible to lumefantrine, mefloquine and dihydroartemisinin, an active metabolite of the antimalarial drug artemether.
The study, published August 17 in Nature Medicine, does not show that these medicines have stopped working in patients. Instead, it reveals a genetic change that has become increasingly common and appears to affect the parasite's response to treatment.
That distinction is important. The finding is not evidence of widespread treatment failure, but it gives researchers another clue to follow as malaria parasites continue to evolve.
A Genetic Change Emerged After Treatment Changed
To determine how the variant evolved, researchers examined genetic data from malaria parasites collected in Uganda over several years.
Their strongest signal appeared around px1, a gene that produces a protein involved in the parasite's biology. Within this region, they identified three mutations and two deletions that co-occurred in a specific genetic combination, which they named the PIN haplotype.
The timing was striking.
Uganda introduced artemether-lumefantrine as its first-line treatment for uncomplicated malaria in 2006. The PIN haplotype was not detected in samples collected in 2004, but it appeared in samples from 2008 onwards.
It subsequently became much more common.
By 2024, researchers found the PIN haplotype in 84% of sampled parasites in northern Uganda and in 55% in eastern Uganda.
The timing suggests that the parasite population has experienced strong evolutionary pressure, although the study cannot establish that the introduction of artemether-lumefantrine directly caused the emergence of the variant.
The Parasites Were Less Sensitive to Several Drugs
Once researchers saw how quickly the genetic pattern had spread, they wanted to know whether it was affecting the parasite's response to treatment.
They compared parasites carrying the PIN haplotype with those carrying the usual (wild-type) version of px1.
Among 465 parasite samples, those carrying the PIN haplotype showed reduced ex vivo susceptibility to lumefantrine, mefloquine and dihydroartemisinin. In this context, ex vivo means the parasites were tested outside the human body.
The association remained after the researchers accounted for other parasite characteristics known to influence drug response, including mutations in K13 and MDR1.
Dihydroartemisinin is particularly relevant because it is the active metabolite produced when the body processes artemether. Artemether and lumefantrine are combined in a major treatment used for uncomplicated P. falciparum malaria.
The results suggested that the PX1-related changes could be contributing to how parasites respond to these medicines.
Researchers Tested the Gene
The team then moved beyond observing naturally occurring parasite variants and tested px1 directly.
They disrupted the gene in P. falciparum parasites grown in the laboratory. The modified parasites became more susceptible to lumefantrine, mefloquine and dihydroartemisinin.
That result strengthened the evidence that PX1 has a role in the parasite's response to these drugs.
It does not, however, explain exactly how the mutations within the PIN haplotype produce that effect. The researchers say more work is needed to understand the biological mechanism.
That question becomes particularly important because Uganda is already facing another form of malaria drug resistance.
Uganda Already Has Artemisinin Resistance
Scientists have been tracking partial resistance to artemisinin in Uganda, which has been linked to mutations in the parasite's K13 gene.
Two mutations, C469Y and A675V, have become particularly important in Uganda.
The researchers found that the PIN haplotype predated the detection of these K13 mutations in their Ugandan samples.
PIN was first observed in 2008, while the K13 mutations were first reported in northern Uganda in 2016.
This led the researchers to consider whether parasites carrying PIN might have provided a genetic background that facilitated the emergence of later resistance-associated changes.
That remains a possibility rather than a proven explanation. The study does not establish that PIN caused K13 mutations or directly enabled their development.
What the researchers do know is that the parasite has acquired different genetic changes that can influence its response to antimalarial medicines.
What Does This Mean for Patients?
The study's findings need to be interpreted carefully.
Reduced susceptibility measured in laboratory experiments does not automatically mean treatment failure in patients. The researchers did not demonstrate that people infected with PIN-carrying parasites are more likely to remain infected after receiving standard malaria treatment.
The authors also note that the clinical consequences of declining susceptibility to artemisinin-based therapies and lumefantrine in Uganda remain uncertain.
That makes the PIN haplotype a surveillance concern rather than evidence that current malaria treatments should be abandoned.
The next step is to determine whether the laboratory findings correspond to changes in how patients respond to treatment.
Is the Variant Spreading Beyond Uganda?
Researchers also examined parasite genomes from other parts of Africa to determine whether the PIN haplotype had appeared elsewhere.
In a global dataset, they found the haplotype in only five of 3,570 samples examined for its distribution. Those samples came from the Democratic Republic of the Congo and Kenya.
That does not provide evidence that PIN has become widespread outside Uganda. The variant was uncommon in those historical samples, and more recent surveillance will be needed to determine its current distribution.
Still, tracking its movement matters. Malaria parasites can cross borders with human populations, potentially introducing genetic traits into new parasite populations.
What Researchers Need to Find Out Next
Several questions remain unanswered.
Scientists need to establish how the PX1 changes alter the parasite's biology and whether the effect becomes more pronounced when they occur alongside other resistance-associated mutations.
They also need to determine whether the reduced drug susceptibility seen in laboratory testing translates into poorer treatment outcomes.
And because the PIN haplotype has risen so quickly in northern and eastern Uganda, researchers will want to know whether a similar increase is occurring elsewhere.
Those answers could determine how significant the discovery becomes for malaria control.
For now, the PIN haplotype is best understood as an early warning from a parasite population that is changing under pressure. The discovery gives scientists another genetic marker to track while they work to keep effective malaria treatments ahead of the parasite's evolution.
