Malaria’s next threat: How incomplete doses are breeding drug resistance in Africa
By Willow Health, September 17, 2026‘When patients fail to complete their recommended doses, only the weaker parasites die, leaving the stronger parasites to survive on low drug levels and grow hardier, – Dr Sammy Mahugu, Head of Case Management, National Malaria Control Programme (NMCP).
Malaria parasites in East Africa are developing resistance to artemisinin, the drug at the heart of modern malaria treatment. This is raising fears that decades of progress against the disease could be reversed.
The resistance has now been confirmed in several countries, including Kenya, through two separate scientific studies. Health experts warn that if it continues to spread unchecked, it could weaken the very medicines used to treat and control malaria across the continent.
A study published in The Lancet on August 13, 2026 confirmed emerging Artemisinin Partial Resistance (ART-R) in Rwanda, Uganda, Ethiopia and Eritrea. A separate Kenyan study, carried out across 28 health facilities in Homa Bay and Migori counties between September 2020 and 2022, and extended to 2024 in one site, found that the malaria parasite Plasmodium falciparum was developing partial resistance to artemisinin.
ART-R means the parasite takes longer to clear from the body after treatment with an Artemisinin-Based Combination Therapy (ACT), or returns soon after treatment. Partial resistance also means a patient can become severely ill from malaria soon after being given ACTs.
Artemisinin has remained vital in treating uncomplicated malaria cases for over two decades. The parasite’s growing resistance to it signals a setback in the fight against the disease, since it is a key ingredient in ACTs, the first-line treatment for uncomplicated malaria.
Some malaria parasites were found to have a genetic change linked to slower response to treatment
Kenya’s Multiple First-Line Therapies (MFTs) for malaria, all artemisinin-based, are Artemether-Lumefantrine (AL), Dihydroartemisinin-Piperaquine (DHA-PIP), Artesunate-Amodiaquine (AS-AQ) and Artesunate-Pyronaridine (AS-PYD).
The Lancet study, titled Mapping the Prevalence of Molecular Markers of Plasmodium Falciparum Artemisinin Partial Resistance in Africa, found that resistance had emerged significantly in Rwanda. The highest predicted prevalence of k13 mutations in 2024 was recorded in Rwanda’s Northern Province, at 62.2 per cent. K13 mutations are changes in a specific gene, called kelch13, found in the malaria parasite (Plasmodium falciparum).
The Kenyan study, published in the Scientific Reports Journal in April 2026, confirmed that Plasmodium falciparum carried resistance markers for artemisinin. Titled Spatiotemporal Antimalarial Drug Resistance Saturation and Emerging Artemisinin Tolerance in Western Kenya, some of its findings were validated by the World Health Organization (WHO).
Researchers found that 0.5 per cent of the parasite samples carried a specific genetic marker called k13 A675V (a mutation linked to slower parasite clearance after treatment), which is linked to resistance and has been confirmed by WHO. In other words, some malaria parasites were found to have a genetic change linked to a slower response to treatment, a sign that the parasite may be developing resistance to malaria drugs.
A larger share, 7.8 per cent, carried another marker, A578S (a similar mutation suspected of reducing the drug’s effectiveness), which is also believed to signal resistance, though the WHO has not yet confirmed this one. Both studies agreed that if this resistance is allowed to spread unchecked across Africa, it could undo much of the progress made in fighting malaria.
Weak lab testing and slow diagnosis mean many Kenyans are given malaria drugs they don’t need
Dr Sammy Mahugu, Head of Case Management at the National Malaria Control Programme (NMCP), acknowledged the spread of resistance in Kenya. He cited the widespread and prolonged use of a single ACT regimen, AL, as a risk. “Continued pressure on one drug combination could hasten the development and spread of resistance,” he said.
Malaria stakeholders also pointed to gaps in lab diagnosis and case management as risk factors. Regina Kandie, NMCP’s Diagnostic Head, said poor microscopy skills and delayed detection had led to patients being prescribed antimalarials unnecessarily, increasing the risk of drug-resistant parasites.
Dr Mahugu explained that when patients do not complete their recommended doses, only the weaker parasites die. The stronger parasites survive on low drug levels and grow hardier. “I acknowledge that there was a time I stopped taking malaria drugs when the fever, headache and fatigue disappeared. I’m just learning that this makes the disease more severe the next time it occurs,” said Masolo Mabonga, a resident of Bungoma.
He said the number of tablets and their side effects had pushed him to abandon treatment once symptoms eased, without realising he was helping the parasites become harder to treat.
“Mostly they say that when you don’t complete the dose you’ll not fully heal, but when symptoms are gone one feels healed. There needs [to be] more public education explaining the drug resistance risk posed by incomplete doses,” he added.
The World Malaria Report 2025, which captured developments through 2024, also spotlighted the growing threat of antimalarial drug resistance.
Increasing cases, deaths, drug resistance, impact of funding cuts could reverse progress made in last 20 years
“Partial resistance to Artemisinin derivatives, which are the backbone of malaria treatments after failures [of] Chloroquine and Sulfadoxine-Pyrimethamine, has been confirmed in at least eight countries in Africa,” the report stated.
Despite the availability of first-line antimalarials, Africa recorded an estimated 282 million malaria cases and over 600,000 deaths in 2024. This is nine million more cases than the 273 million reported in 2023. Africa accounted for 94 per cent of all global cases and 95 per cent of global malaria deaths that year. According to the report, 75 per cent of malaria deaths in Africa were among children under five.
“The increasing cases and deaths, the growing threat of drug resistance and impact of funding cuts are threatening to reverse the progress made in the past two decades,” said Dr Tedros Ghebreyesus, the WHO Director-General.
During the release of the report, stakeholders behind Protect The Cure, a public health initiative tackling antimalarial resistance, described artemisinin as a once-miracle drug for malaria. They expressed concern that the drug, which had saved millions of lives, was losing its power, and called for urgent malaria policy reforms.
Professor Maciej Boni of Temple University, Philadelphia, said it was worrying that Artemether-Lumefantrine’s efficacy had also dropped below 90 per cent, the minimum recommended threshold.
The parasites are mutating and reducing efficacy of current antimalarial combinations
“It’s still difficult to know if the artemisinin-resistant parasites are responsible for this drop in the drug’s efficacy,” he said.
Dr André Tchouatieu of Medicines for Malaria Venture (MMV) said the first resistance to an antimalarial was reported in Cambodia in 2001, with the first case in Africa recorded in 2013. Sulfadoxine-Pyrimethamine, Lumefantrine and Chloroquine have all recorded resistance. “We are exploring new drugs to reduce artemisinin resistance because the parasites are mutating and reducing the efficacy of current antimalarial combinations,” he said.
MMV has already introduced new first-line treatments. These include Triple Artemether-Lumefantrine-Amodiaquine (ALAQ), made by adding a single low dose of primaquine to ACT, and Ganaplacide-Lumefantrine, a three-day regimen and the first non-artemisinin malaria drug discovery since ACTs were developed in 1999.
“The new developments will ease pressure from artemisinin. I urge countries to ease registration of new drugs and engage communities in readiness to embrace forthcoming first-line antimalarials,” Tchouatieu urged.
In April 2026, the Ministry of Health announced it would adopt Multiple First-Line Therapies to counter drug resistance. Through the NMCP, the ministry developed Kenya’s Multiple First-Line Therapies (MFT) Implementation Plan (2026-2030) to guide the rollout of the new treatment guidelines recommended by the WHO and malaria experts.
Diversifying drug pressure across parasites reduces selective advantage of any single resistance gene
Public Health Principal Secretary Mary Muthoni said the rollout would include stronger surveillance and sustained research to support evidence-based malaria control. “Our commitment to science-based health policies is evident in diversifying malaria treatment and management options to improve health outcomes,” she told the press on World Malaria Day, April 24.
The idea behind MFTs is simple: using different drugs on parasites, instead of relying on one, makes it harder for any single resistance gene to gain the upper hand. This slows down how quickly resistance can develop against any one ACT combination.
Dr Arnaud Le Menach, lead author of the World Malaria Report, called for strengthened political commitment in the fight against malaria. “Parliamentarians and civil society must ensure the WHO guidelines on malaria treatment are actualised in their countries through policies and funding,” he said.
Dr Charles Adenkule, CEO of the Roll Back Malaria Partnership, urged African populations to complete their malaria doses to avoid helping the parasites mutate and develop resistance to first-line treatments.
Experts also reiterated the importance of accurate diagnosis. They discouraged giving antimalarials too early to anyone showing up at health facilities with fever, warning that unnecessary prescriptions would only fuel drug resistance.