Cases of a mosquito borne virus that can cause crippling disability are rising worldwide. Scientists are trying to understand how many people are affected in Kenya and Tanzania.
The illness often begins like many others in East Africa. A fever. Headaches. Aching joints. For some patients, the pain fades within days. For others, it tightens its grip for months or years, bending bodies, disrupting work and, in the most severe cases, damaging the brain.
This is Chikungunya, a mosquito borne virus that for decades has lingered in the shadow of better known diseases. Now it is resurging, in East Africa and far beyond, forcing scientists to confront how little is still known about its true impact.
Nearly ten years ago, that uncertainty confronted doctors in Kenya’s coastal county of Kilifi. Newborns were being admitted to hospital with alarming neurological symptoms. Prof George Warimwe, a scientific investigator working in the area, initially suspected Zika virus, which in 2016 was spreading rapidly across parts of Latin America and had been linked to birth defects.
Tests ruled it out.
Warimwe and his team turned their attention to other mosquito borne infections known to circulate locally. One quickly stood out.
“We set up diagnostic tests against a range of mosquito-borne viruses and started screening stored samples from patients admitted with neurological illness. Chikungunya virus is known to cause neurological disease, so naturally this was among the first pathogens to check for”, Warimwe recalls.
First identified in Tanzania in 1952, Chikungunya takes its name from the Makonde language, meaning “to become contorted”. The description reflects the intense joint pain that defines the disease. Patients typically experience fever and severe aches that can last for months or even years, sometimes making it impossible to work or walk. In children, the virus can also cause impaired consciousness and long term cognitive problems.
Warimwe’s suspicion proved correct. Around one in ten children admitted to Kilifi’s referral hospital with neurological illness were infected with Chikungunya. Some were only weeks old, suggesting they had been infected before birth.
The findings revealed a largely unrecognised crisis. While much of the world focused on Zika, Chikungunya was quietly leaving its mark on Kenyan families.
A virus resurfaces
Nearly a decade on, Kenya has expanded its surveillance of Chikungunya, investing in better testing, disease monitoring and mosquito tracking. As a result, the country has reported more than 600 cases so far this year.
The increase mirrors a wider global surge. Since January, almost half a million infections have been recorded worldwide, with major outbreaks in Brazil and India, and new flare ups across the Indian Ocean islands. Locally acquired cases have also been detected for the first time in places such as China, New York and Paris. Several European countries have reported hundreds of travel related infections.
In Kenya, most cases this year have been reported in Mombasa, close to Kilifi. But experts believe the official figures significantly underestimate the true scale of the outbreak.
Chikungunya often resembles other common illnesses such as malaria or dengue, leading to frequent misdiagnosis. Doctors are still learning the full range of symptoms, which do not always match textbook descriptions. Limited access to reliable diagnostics further complicates detection.
Measuring the hidden burden
This week, a new disease detection programme led by Warimwe and funded by the Coalition for Epidemic Preparedness Innovations, or CEPI, has been launched to address these gaps.
The project trains medical staff at ten hospitals and clinics across Kenya and Tanzania to screen every patient who presents with fever or neurological symptoms that could indicate Chikungunya infection. The sites include busy urban centres and remote rural communities.
“Participation in the study is entirely voluntary, but the study has potential to yield significant public health benefits” says Warimwe.
The programme aims to identify cases early, improve care for patients and map how the virus spreads through communities.
The study is known as Accelerating CHIkungunya burden Estimation to inform Vaccine Evaluation, or ACHIEVE. It is supported by up to $10.3 million from CEPI and will run over two years. Researchers will assess the overall burden of disease and focus closely on infections in pregnant women, examining how the virus may pass from mother to child.
For CEPI, which supports vaccine development against emerging infectious diseases, the findings are critical. Understanding who is most affected and where will help shape future vaccine trials and guide decisions on how doses should be distributed.
“These insights could for example help determine whether children and their mothers should be prioritised – or inform us as to whether we need to also concentrate on other vulnerable groups at risk for this debilitating disease” explains Gabrielle Breugelmans, Director of Epidemiology and Data Science at CEPI. “It’s all about matching protection to the people and places that need it most.”
Beyond infection counts, the study will analyse which strains of Chikungunya virus are circulating in East Africa, measure immune responses across age groups and assess the economic impact on households and health systems.
Climate concerns
ACHIEVE will track patients with fever or neurological illness alongside pregnant women at delivery, allowing scientists to observe how the virus behaves across seasons.
Climate change is expected to play a significant role. Warmer temperatures and heavier rainfall expand the habitats where mosquitoes thrive.
“Warmer, wetter climates create the perfect conditions for infected mosquitoes to expand the areas where they live and breed” warns Breugelmans. “The Chikungunya hotspots of today will not be the same hotspots of tomorrow, so we can’t take our eyes off this moving viral target.”
For Warimwe, the goal is straightforward. Data, he says, can translate into relief.
“Our past work showed chikungunya is especially common in young children,” he says. “Now, ACHIEVE will assess how widespread the disease is in East Africa and provide the knowledge needed to direct lifesaving countermeasures where they’re needed most”.
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