Kenya plans to rotate frontline malaria drugs amid resistance fears

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The Ministry of Health (MOH) of Kenya has finalised plans to rotate first-line malaria treatments, as growing evidence shows that the country’s most widely used treatment falls short of the World Health Organization's (WHO) cure threshold.

By rotating four artemisinin-based combination therapies (ACTs) every two to three years, the Ksh 1.98 billion (about $US 15.4 million) strategy wants to slow the spread of drug-resistant malaria parasites before widespread treatment failures emerge. The MOH introduced the plan for the first time on 25 April. The ministry will begin rolling out malaria treatment using these new combinations in four counties from October, according to a script from a virtual meeting between the MOH and partners that Defrontera obtained. (The government did not disclose the four counties.) 

The ambitious effort puts Kenya among African countries confronting the rising threat of antimalarial drug resistance. For decades, ACTs have been the backbone of malaria control in Africa, which carries roughly 95% of the world’s malaria cases and deaths. While the drugs have helped bring down deaths from the disease, the decline in their effectiveness poses a major threat to malaria control on the continent. 

One drug at the centre of resistance fears is artemether-lumefantrine (AL), sold widely under the brand name Coartem. AL is Kenya’s first-line treatment for uncomplicated malaria. Studies conducted by the ministry in western Kenya to test the medicine’s effectiveness showed that AL’s cure rate has steadily declined over the past several years. According to planning documents that Defrontera reviewed, studies in Busia and Siaya counties in 2017 showed that about 89% of patients treated with AL recovered fully, compared with 93% for the second-line therapy dihydroartemisinin-piperaquine (DHA-PPQ). Under WHO’s guidance, first-line malaria therapies should achieve cure rates above 90%; below that threshold, the global health agency recommends countries consider changing treatment policy. Other studies in 2021 and 2022 found even lower cure rates for AL Siaya (57%), Busia (77%) and Bungoma (79%) counties. All three counties are in Kenya's malaria belt. 

Researchers caution that the findings do not yet mean ACTs are failing, however. Instead, public health officials say the data point to “partial resistance,” in which the medicines take longer to clear malaria parasites from the bloodstream.

“Usually when it works really well by day two, actually, in some patients, you do not see parasites,” said Isabella Oyier, a professor of molecular epidemiology who attended the ministry meeting. “But if we lose the artemisinin component and we then have these large parasite burdens within the bloodstream still in patients on day two or day three, then the partner drugs have a lot of work to do.” 

ACTs work as a two-part treatment. When taken, the fast-acting artemisinin rapidly reduces the parasite burden in the bloodstream, while the partner drug eliminates remaining parasites. Scientists worry that if artemisinin becomes less effective, the partner medicines could come under increasing pressure, further accelerating resistance. Kenya’s plan is to rotate between multiple ACTs rather than rely heavily on a single therapy for years at a time. The new treatment guidelines include AL, artesunate-amodiaquine (ASAQ), DHA-PPQ, and artesunate-pyronaridine (ASPY). Health officials said they hope rotating drugs will reduce the selective pressure that allows resistant parasites to survive and spread. 

“When the drug is exposed to a parasite for a long time, the parasites develop resistance,” said Edwin Onyango, who leads malaria surveillance under Kenya’s National Malaria Control Programme, during the virtual meeting. 

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But the strategy comes with logistical and financial challenges. Kenya faces an annual malaria funding gap of more than Ksh 18 billion (around $US 139 million), even before recent cuts in U.S. global health funding. The new plan’s costs include procuring the medicines, training healthcare workers, monitoring the drugs’ effectiveness, and running public awareness campaigns.

In the meeting, Kibor Keitany, head of the National Malaria Control Programme (NMCP), said the government was exploring ways to transition from heavy donor dependence, including integrating malaria treatment into national health insurance benefit packages. He notes that drug resistance carries particular urgency because malaria has repeatedly evolved around once-powerful medicines. For example, Kenya abandoned chloroquine in 1999 after widespread resistance rendered it ineffective, replacing it with sulfadoxine-pyrimethamine, popularly known as Fansidar, before eventually shifting to ACTs in the mid-2000s.

Simon Kariuki, chief research officer at the Kenya Medical Research Institute (KEMRI), backs Kenya’s new approach. “We cannot go back there,” he said, “We need to preserve the six different ACT combinations that we have at the moment.”

In high-burden malaria counties, clinicians say the rising threat of antimalarial drug resistance is visible. In January this year, at Kaluo Health Centre in Siaya County, clinician Anne Odinga treated a 4-year-old boy named Jeremy, whose blood tests still showed malaria parasites a week after completing artemisinin treatment. Having malaria parasites in the blood after treatment does not by itself confirm drug resistance, but cases like Jeremy’s are becoming increasingly concerning for frontline health workers in Kenya.

While scientists and public health experts seek new classes of malaria drugs and better ways to fight the disease, researchers say ACTs remain broadly effective across Kenya. But the government must focus on preserving the therapies that still work. It is the only way to combat the deadly disease in Kenya.

Malaria is a special focus for Defrontera, with its series, The Deadliest Bite.