Kenyan children are dying in a malaria diagnostic blind spot

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As she stepped out of the house to do her laundry, Millicent Achieng left her seven-year-old boy playing with his friends in Nyalenda Estate in Kisumu County. When she returned to the house, the boy was convulsing violently. Over a period of five months and three referral hospitals, doctors confirmed her fears that malaria had caused her son’s convulsions. The doctors also delivered a permanent and heartbreaking diagnosis about her son.

“They told me my son would hear, but he would not speak again, and when I brought him home, I noticed that he could not walk either,” said Millicent.

All this while, her son had meningitis—a disease caused by viruses and bacteria that leads to the swelling of the meninges, the protective linings that cover the brain—which the clinicians had not had the curiosity to check as they were treating malaria.

Millicent’s case reflects a deeper problem in Kenya’s health system. In high malaria-burden regions in western Kenya, clinicians often diagnose and treat malaria first, sometimes at the expense of identifying other, potentially fatal conditions such as meningitis, pneumonia, and others.

Researchers from the Centre for Global Health Research, a Kenya Medical Research Institute (KEMRI) station in Kisumu, say Millicent’s son is not an isolated case in the counties in the former Western and Nyanza provinces. Many children walk into health facilities with malaria; some die and have the cause of death recorded as malaria, when the actual cause is another disease.

When the researchers conducted post-mortems on nearly 700 children who died between 2018 and 2024, they found that while some children tested positive for malaria, what killed them were other conditions, including malnutrition (28%), blood infection (sepsis–18%), HIV (8%), and pneumonia (6%).

The Child Health and Mortality Prevention Surveillance (CHAMPS), a twenty-year network operating across 22 sites in nine countries, provided this data. Using minimally invasive tissue sampling—considered more accurate than routine clinical diagnosis—CHAMPS investigates the biological causes of death in children in Kisumu and Siaya counties. The findings suggest that malaria is often present in children who arrive at hospitals in this region, but it is not always the primary cause of death.

Dr Hellen Muttai, CHAMPS Kenya’s site director, said that studying records from the health facilities where the children sought care also revealed that, in some cases, the children had malaria but were never treated for it.

Dr Muttai explained: “After the child has died and you do the test, that is when you find they had malaria. But a lot of times, they were being treated for something else, and for good reasons. Maybe they came with pneumonia, or they came with malnutrition, or a lot of times they would even come with HIV or other infections, and that is what they are treated for.”

The fact that children in the former Nyanza and Western regions may have malaria and not be treated for it concerns public health specialists because of the number of children at risk. The lake region’s warm and moist climate is a perfect breeding ground for malaria-carrying mosquitoes. Mosquitoes bite people and transmit malaria all year round. The Ministry of Health reports as many as eight malaria cases per 10 people each year in these counties. Malaria killed 10,811 people in Kenya in 2023—part of the 569,000 deaths across Africa—and most deaths occurred in the lake region.

Due to these high numbers of infections, the volume of cases physicians see has conditioned them to prioritise malaria.

But the larger concern, experts say, is diagnostic uncertainty. In settings where malaria is common, the parasite can coexist with, and clinically mask, other diseases, making it difficult to determine what is actually killing patients.

Lilyana Dayo, Kisumu County Malaria Coordinator, says physicians often cannot tell the difference between the signs and symptoms of malaria and other diseases, as most children present with fever and headache.

“Sometimes some of the clinicians are carried away and fail, at the first instance, to look beyond malaria to conditions such as meningitis or sepsis, which present like malaria,” Dayo told Defrontera.

Additionally, research has shown that malaria itself may alter how the body responds to other infections. Malaria parasites, particularly Plasmodium falciparum, which is responsible for more than 90% of infections in Western and Nyanza, can induce a general state of immune defect. This affects the ability of the child’s body to fight both the malaria parasite and other unrelated infections.

Children who live in areas with year-round transmission have repeated exposure to malaria that leads to what researchers call “tolerance”, where the body limits inflammation to protect itself from severe disease. While this is beneficial for surviving malaria, it can also reduce the immune response to other infections, such as pneumonia. In this state, Dr Muttai said, children die because the body cannot fight both diseases while other hidden conditions continue the onslaught, creating a “complicated clinical picture”.

“Malaria, for example, will come with complications like anaemia, can come with complications affecting the kidneys, affecting the brain in cerebral malaria. Then when you have a different infection in the lungs, then you have pneumonia,” Dr Muttai explained.

The conditions worsen because of delays in care. One of the findings from CHAMPS is that more than half (57%) of the children died at home as parents downplayed care or tried herbal medicine. In Millicent’s case, the delay in care was due to a lack of money. She could not afford the cost of diagnosis, even for malaria itself—a delay that lasted more than four days.

A keen clinical eye is particularly important in Kenya, where diagnostic equipment, according to Kisumu County Health Minister Dr Gregory Ganda, is limited. When it is available, it is expensive and often out of reach. Less than half of public facilities have microscopy, the gold standard for malaria diagnosis, and access is even lower in primary-level facilities. Rapid diagnostic tests are more widely used but do not always capture co-existing conditions.

In many settings, clinicians rely on symptoms or rapid judgement rather than confirmed diagnosis—a practice Dr Ganda describes as “medicine by chance”.

“You can be having a boil, and it is missed, and you are being treated for malaria—that happens a lot. So, we expect that because of our diagnostic capabilities, especially in the lower-level facilities, they are not high,” Dr Ganda said.

Ms Dayo and other public health officials say that until the government improves diagnostic capacity, national and county health departments will continue to train clinicians to better identify infections that may be hidden behind malaria. With this enhanced capacity, clinicians would begin a treat-as-you-investigate process for children, especially if they suspect life-threatening conditions like meningitis.

Dr Muttai said: “If you highly suspect meningitis, it is important to start treatment immediately because you cannot wait and say, ‘let me do a lumbar puncture’, which may take 24 to 48 hours, and you cannot wait for those results. So usually, you start treatment immediately. Once you get the results, then you can modify.”

In the lake region, where malaria is a dominant concern, clinicians need both sharper clinical judgement and better diagnostic equipment—not only to treat malaria, but to recognise when it is not the disease that is killing the patient.