Kenyan scientists strengthen molecular surveillance to track emerging malaria drug resistance

Kenyan researchers are scaling up a nationwide molecular surveillance system to detect early genetic changes in malaria parasites that could reduce effectiveness of current treatments.

This follows the identification of resistance-linked mutations in parts of western Kenya.

The initiative is led by scientists at the KEMRI-Wellcome Trust Research Programme in collaboration with the Ministry of Health and the National Malaria Control Programme (NMCP).

Researchers have identified four anti-malarial resistance mutations circulating across eight counties in western Kenya, mainly in communities around Lake Victoria, one of the country’s highest malaria transmission zones.

The work is anchored in a malaria molecular epidemiology programme designed to generate real-time genetic data to inform national malaria surveillance and policy decisions.

 The approach integrates molecular analysis into routine malaria diagnosis through a network of sentinel health facilities linked to the National Malaria Reference Laboratory.

Prof Isabella Oyier, Head of the Biosciences Department at the KEMRI-Wellcome Trust Research Programme, said the system enables scientists to track parasite genetic changes as they emerge, rather than waiting for widespread treatment failure.

One mutation identified through the surveillance network — known as the 675 variant of concern — has drawn particular attention. The same mutation has previously been reported in Uganda, where studies linked it to delayed parasite clearance after treatment with artemisinin-based drugs.

“When parasites are not cleared by day three of treatment, that raises concerns about reduced drug susceptibility,” said Prof Oyier.

Kenya currently relies on artemisinin-based combination therapies (ACTs), including Coartem, as the first-line treatment for uncomplicated malaria. These medicines have contributed significantly to the reduction in malaria deaths across Africa over the past two decades.

However, Prof Oyier emphasised that the newly detected mutations do not indicate confirmed treatment failure. Instead, they serve as an early warning signal requiring closer monitoring.

To strengthen this system, scientists are embedding molecular surveillance into routine malaria testing across sentinel facilities in eight endemic counties. Patient samples collected during routine care are analysed using advanced laboratory techniques, including next-generation sequencing, to identify genetic markers linked to anti-malarial drug resistance.

Data generated by the system are regularly shared with the NMCP, enabling health authorities to monitor the frequency and spread of resistance-linked mutations over time.

“Genomic surveillance tells us the mutations are present,” Oyier said. “Therapeutic efficacy trials tell us whether those mutations are actually affecting patient outcomes.”

The World Health Organization recommends that malaria-endemic countries conduct therapeutic efficacy trials at least every two years. These trials assess whether first- and second-line treatments remain effective under real-world conditions by monitoring how quickly parasites are cleared after treatment.

A key benchmark is whether parasites are eliminated within three days, a standard measure of artemisinin effectiveness.

Beyond drug resistance, Kenyan scientists are also monitoring mutations linked to diagnostic resistance. These include deletions affecting histidine-rich protein 2 (HRP2), which could compromise some rapid diagnostic tests. Such diagnostic resistance has already been documented in parts of the Horn of Africa.

Researchers say that, for now, Kenya’s rapid diagnostic tests and microscopy-based diagnosis remain effective. The resistance signals detected so far relate primarily to parasite response to drugs rather than diagnostic failure.

Malaria parasites naturally mutate as they replicate. Most genetic changes have no clinical impact. However, when a mutation provides a survival advantage — such as resistance to treatment — it can spread through natural selection and become more common over time.

Western Kenya’s persistently high transmission makes it a critical region for early detection. Scientists are also studying the complexity of infection, which measures how many genetically distinct parasites infect a single patient, alongside whole-genome analyses to better understand the structure of Kenya’s parasite population.

Health authorities say early identification of resistance is essential to protect existing treatments and avoid costly changes to national malaria drug policy.

Oversight of medicine quality remains the responsibility of the Pharmacy and Poisons Board, which tests anti-malarial drugs entering the Kenyan market. Therapeutic efficacy trials, meanwhile, assess how these medicines perform in patients.

For now, Kenya’s first-line malaria treatments remain effective, Prof Oyier said, but she stressed the need for sustained molecular monitoring.

“Malaria parasites are constantly evolving,” she said. “The goal is to detect resistance early and respond before treatment failure becomes widespread.”

Malaria remains one of Kenya’s leading causes of illness, particularly among children in high-transmission regions. Health officials believe a robust molecular surveillance platform could serve as a long-term early warning system, guiding targeted interventions and evidence-based treatment decisions as parasite genetics continue to evolve.