Kenya to introduce new malaria medicine as 20-year treatment faces resistance

Kenya is preparing to diversify its malaria treatment options after research uncovered genetic changes in malaria parasites that could weaken the effectiveness of the drug used to treat the disease for the past two decades.

The Ministry of Health will introduce artesunate-pyronaridine (ASPY) in four counties from January 2027, marking a major shift in the country's approach to preventing drug resistance.

The first consignment of the new medicine is expected in November, with Baringo, Kakamega, Siaya and Busia selected for the initial rollout. The treatment will be administered alongside artemether-lumefantrine (AL), which has remained Kenya's main malaria medicine for the last 20 years.

Dr Regina Kandie, Head of Diagnostics and Case Management at the National Malaria Control Programme, said the government was expanding the available treatment options to protect patients and maintain the effectiveness of existing medicines.

"The Ministry of Health is introducing a new molecule ASPY that will be used across the country," she said.

The medicine will be supplied through the Kenya-United States government partnership on health, an arrangement expected to support its availability at affordable prices in public hospitals.

The decision comes after a six-year investigation by the Kenya Medical Research Institute (KEMRI) detected signs of partial resistance to artemisinin, the key component of AL, in samples collected from seven counties.

The findings, published in the Malaria Journal this week, have raised concerns about the possibility of malaria parasites becoming less responsive to the treatment currently relied upon by millions of patients.

Researchers analysed 679 parasite samples obtained from people who had malaria symptoms between 2018 and 2024. The specimens were collected from patients visiting public and private hospitals in Busia, Kericho, Kisumu, Kisii, Nakuru, Baringo and Laikipia.

The seven counties represent four of Kenya's five malaria transmission zones, allowing researchers to examine the genetic changes across areas with different levels of malaria transmission.

The investigation identified 24 mutations, four of which are recognised by the World Health Organization (WHO) as validated indicators of partial resistance to artemisinin.

A675V was the most frequently detected mutation, appearing in 20 samples. C469Y was identified in three samples, while R561H and P553L were each found once.

Researchers said the genetic pattern suggested that the mutations were developing within Kenya rather than being introduced from Asia, where similar resistance concerns have previously been reported.

One of the notable findings was the concentration of the A675V mutation in Baringo, which accounted for more than half of all samples carrying the genetic change. The researchers described the discovery as new.

Baringo's malaria transmission pattern makes the finding particularly important. Unlike counties such as Kisumu and Busia, where malaria infections are more common, Baringo falls within a semi-arid zone where transmission is seasonal.

Residents in areas with lower transmission rates may have less natural immunity against malaria because they are not exposed to the infection as frequently as populations in high-transmission regions.

Dr Patrick Boruett, Director of Preventive Health in Baringo, confirmed that the county would participate in the initial introduction of the new treatment strategy.

"Baringo is one of the counties rolling out the multiple first-line therapies and this will help in ensuring we preserve the anti-malaria drugs that we have," he said.

Busia, another county selected for the first phase, has also recorded signs of resistance, with health workers reporting difficulties when patients fail to respond to treatment as expected.

Fred Imeda, a clinical malaria mentor in the county, said resistance could complicate the management of patients, particularly when the prescribed medicine does not produce the expected improvement.

"Drug resistance usually gives us a challenge with the patients during treatment. You get a patient, you initiate treatment but you find the patient is not improving within the prescribed timelines."

Dr Kandie said introducing a different medicine would help prevent malaria parasites from adapting to the treatments that have been used for many years.

"The introduction of the new molecule is to confuse the parasite so that the patient can respond to treatment once they have been tested and it has been confirmed that they have malaria," she said.

Despite the introduction of ASPY, the government will retain AL for particular groups of patients who may not be suitable for the new treatment.

Pregnant women and children under five kilogrammes will continue receiving AL because health authorities have not established sufficient information about the possible side effects of ASPY among these groups.

Dr Kandie also noted that some patients may experience hypersensitivity reactions to the new medicine, making it necessary to maintain the existing treatment for them.

"We are still not certain about the side effects of ASPY on pregnant mothers and children and there are patients who have hypersensitivity reactions to ASPY so these cases will maintain treatment using AL" she said.

The Ministry of Health will implement the changes under the Multiple First-Line Therapies Implementation Plan covering the 2026 to 2030 period.

The programme will introduce a drug rotation system, under which different malaria treatments will be alternated after every two years to reduce the pressure placed on a single medicine and limit the development of resistance.

Baringo, Kakamega, Siaya and Busia will form the first group of counties to adopt the approach from January 2027, before the programme is extended to the remaining parts of the country.

Preparations are already underway, with health officers in Baringo trained to serve as trainers. They will be responsible for equipping other health workers across the county's medical facilities with the knowledge required to administer the new treatment.

Community health promoters will also be involved, particularly in areas where malaria infections are common. Their role will include educating residents about the new medicines and encouraging proper use to avoid practices that could contribute to drug resistance.

Dr Ndinda Kusu, project lead and senior malaria advisor at Jhpiego, said public awareness would be an important part of the programme to ensure communities understand the changes and use the medicines responsibly.

Dr Kandie said introducing a different treatment after two decades of relying on AL would require cooperation among all stakeholders to ensure health facilities and communities are prepared for the transition.

Kenya's move comes amid growing concerns over the spread of partial artemisinin resistance across Africa, with the WHO confirming the problem in Eritrea, Rwanda, Uganda and Tanzania.

The agency has also identified Ethiopia, Namibia, Sudan and Zambia as countries where resistance is suspected.

According to the WHO, the resistant parasites found in African countries appear to have developed independently rather than spreading from Southeast Asia.

The World Malaria Report 2025 warns that partial resistance has either been confirmed or suspected in several African countries, raising concerns about the long-term effectiveness of existing malaria treatments.

The report also highlights other challenges facing malaria control programmes, including genetic changes in parasites that are making some rapid diagnostic tests less reliable and increasing resistance to insecticides used to control mosquitoes.

Dr Kusu said countries needed to act before resistance became widespread, warning that the consequences could be difficult to manage because alternative treatments were limited and expensive.

She said preventing resistance was more effective than waiting until it had become established and begun circulating widely among populations.

"When you look at resistance whether it is anti-malarial, anti-fungal or antibiotics, it is better to prevent than to think of getting the resistance circulating. We do not have many options in terms of treatment, and when the options are there, they are very costly. We have to prevent anti-malarial drug resistance," she said.