The narrow wooden benches in the student health clinic at Dire Dawa University in Ethiopia’s second-largest city began to fill up in March last year: feverish students slumped against their friends, cradling aching heads in their hands.
Helen Asaminew, the presiding nurse, was baffled. The students had the hallmark symptoms of malaria. But people didn’t get malaria in cities, and the students hadn’t traveled anywhere. It was the dry season. There was no malaria for hundreds of miles.
Yet when Ms. Asaminew had their blood tested, the telltale ring-shaped parasite signaling malaria turned up in most of the samples. By April, one out of every two students living in the male dormitories had the disease, 1,300 cases in all.
The crowded clinic was the starting point of a medical mystery that forewarns an alarming new public health crisis in Africa.
At its center is Anopheles stephensi, a malaria-carrying species of mosquito that arrived in the port city of the tiny East African nation of Djibouti a decade ago and was largely ignored by public health officials. It is resistant to all insecticides and has adapted to thrive in urban environments and survive in dry seasons. It is now breeding in locations across the center of the continent, and entomologists say further spread is inevitable.
Africa has expertise and strategies to fight malaria as a rural disease but now faces the threat of urban outbreaks, putting vastly more people at risk and threatening to wipe away recent progress against malaria, which still kills 620,000 people each year, mostly in Africa. Although some mosquito experts say it is too soon to be certain of the magnitude of the threat, the potential for outbreaks in cities, they fear, may set up a competition between urban and rural areas for scare resources to fight the disease.
Stephensi breeds in water and thrives in congested cities, where unreliable piped-water systems often force people to store water around their homes, and poor trash collection provides ample spots (such as old bottle caps) for mosquitoes to lay eggs. The species is poised to descend on what public health experts describe as a largely malaria-naive human population: Most urban dwellers don’t have immunity from repeated prior exposure and may fall much sicker.
“It’s incredibly worrying: In places with stephensi established, we see cases going through the roof,” said Sarah Zohdy, who heads a task force on the invasive species for the U.S. President’s Malaria Initiative, a United States government program that fights malaria worldwide.
Africa is the least-urban continent, but also the one with the fastest-expanding cities: 50 percent of its population is projected to live in cities by 2030. Since emerging in Djibouti and Ethiopia, stephensi has been found in Kenya and Sudan, where the capital cities, Nairobi and Khartoum, are each home to about six million people, and in Nigeria, where the city of Lagos has a population of 16 million, double that of New York.
Researchers led by a University of Oxford entomologist assessed Africa for suitable habitat for stephensi and concluded that the species’s continued expansion puts an additional 126 million people at risk of malaria.
Fredros Okumu, a Kenyan entomologist and influential thinker on malaria in Africa, said he was waiting for more data that conclusively showed stephensi was driving new cases; there has not been a spike in malaria cases everywhere it has been found, he said, a scientific puzzle that makes it difficult to predict the size of the risk it represents.
Malaria causes high fevers, bone-shaking chills, fierce headaches and vomiting. Without treatment, it can be fatal. It hits small children hardest: They make up most of the 620,000 malaria deaths each year. If a mosquito feeds on a person who already has the parasite, the insect ingests it along with the person’s blood, and the parasite begins a new life cycle in the mosquito’s body. About a week later, if that mosquito bites someone new, it passes on the parasite with its saliva.
One of the biggest challenges with stephensi is that urban health care workers are often inexperienced in diagnosing malaria and can struggle to recognize the parasite in lab tests. Rural clinics, even community health volunteers, are well versed in spotting and diagnosing the disease. But city health care institutions may miss it. By the time people are properly diagnosed, they can be extremely ill.
Shume Tolera, who lives in a middle-class neighborhood of Dire Dawa, an arid city of about a half-million people, developed a surging fever last April, when she was five months pregnant. When she went to the lab in the private hospital where she works as a nurse, staff members tested her blood for malaria. The results were negative. They tested her again and again as she got sicker over the coming week, and kept telling her she was negative.
She grew so weak that her family took her to an emergency room at a public health clinic that traditionally sees a few malaria cases each year in the rainy season. There, she finally received a malaria diagnosis, and treatment.
“I was never so sick in my life,” she said.
The infection had pushed her previously healthy hemoglobin level into severe anemia. It was her first case of malaria, and the first outbreak the family had heard of in the city since moving there a decade before. In the following weeks, Ms. Tolera’s husband, her two children and a sister-in-law who lives with them got malaria too.
As malaria spread through Dire Dawa last year, a team of researchers led by a molecular biologist, Fitsum Tadesse, hurried in. They trapped mosquitoes in the homes and courtyards of people who had malaria, and in the ditches and puddles of water in the narrow alleyways. And before long, they had confirmed their grim hunch: Anopheles stephensi was in the city, and it was spreading the disease.
Malaria traditionally ebbs and flows with seasonal rains in less densely populated rural areas. The mosquitoes that spread it breed in natural habitats, in the pools left by shifting streams and heavy rains.
Stephensi prefers artificial breeding sites, such as drainage ditches, rooftop water tanks and trash heaps where pockets of water collect. It feeds on livestock as well as people, often lives in goat, chicken and cow sheds, and bites humans when it encounters them outside during the day: Sleeping under a bed net, until now regarded as one of the best shields against malaria-carrying mosquitoes, offers no protection.
And Dr. Tadesse’s research showed that in Ethiopia, stephensi was — unusually and alarmingly — transmitting both species of parasites that cause malaria.
Stephensi came from South Asia. In India, it spreads malaria, but there, the disease has been significantly controlled, even in cities, by aggressive contact tracing of cases (so new ones are detected and treated quickly, before the parasite can be spread further), and by killing larvae in the fountains and cisterns where the mosquitoes lay their eggs.
Public health experts say stephensi might be less of a threat now if it had been taken more seriously when it was first discovered in Africa — in 2012, in the seaport at Djibouti, a tiny nation on the Horn of Africa. The country is so small that no one paid much attention — except for a handful of entomologists who anticipated potential disaster. It wasn’t until their warnings began to come true a decade later that governments and major international funders of mosquito-control efforts started to grapple with this new reality. The World Health Organization noted the detection of stephensi in Africa in 2012, but did not convene a meeting on the threat until 2019.
Before stephensi arrived, Djibouti was on the cusp of declaring malaria eradicated. In 2012, there were just 27 cases. But a year after stephensi was found, cases shot to nearly 1,700. Each year thereafter, the number crept up, and in 2020, there was an explosion: more than 70,000 cases, and 190 deaths, most in the capital, Djibouti City, which is home to 600,000 people.
Col. Abdulilah Ahmed Abdi, who heads the malaria program in Djibouti, called his country “a harbinger of what is to come” for other African nations.
“We were right on edge of elimination, and now it’s a whole change of paradigm,” he said. “Every African city is at risk of facing what we’re confronting now.”
While malaria cases were climbing in Djibouti, and stephensi was spreading across borders, the risk was largely lost on the global health community, which was celebrating a sharp fall in malaria deaths in Africa, achieved chiefly through the widespread distribution of insecticide-treated bed nets and the targeted spraying of insecticide indoors during rainy seasons.
Only over the past year — after Dr. Tadesse and his colleagues shared their findings from Dire Dawa at a major global health conference — has the momentum of response picked up, said Dr. Zohdy of the U.S. President’s Malaria Initiative.
There are few quick options to protect people in African cities from stephensi; those that experts say would be most meaningful — better housing and infrastructure, and more efficient municipal government — require significant investment, commitment and time.
And while it poses the biggest threat in urban areas, stephensi, a terrifyingly adaptable malaria host, can also live in rural ones.
“We’re talking about it like an urban vector, but it’s really an everywhere vector,” Dr. Zohdy said. Stephensi is not as good at passing on the parasite as the established mosquito species, but because it thrives in so many places, bites in the daytime, breeds so widely and survives at high temperatures and through dry seasons, it poses as much or more of a threat.
Dr. Tadesse, the lead scientist overseeing the malaria program at the Armauer Hansen Research Institute in Addis Ababa, Ethiopia’s capital, believes stephensi mosquitoes may be traveling on maritime shipping routes from Asia, although the ones found in Nigeria were in the deep interior, perhaps transported on trucks.
The fact that some African cities and countries have yet to find stephensi may reflect only the weakness of entomological surveillance, not the actual absence of the mosquito, he said.
More countries are looking for the species now, but further tracking will be complicated and resource-intensive, requiring detective work of the kind Dejene Getachew, the lead entomologist on the Dire Dawa studies, does. He crawls inside goat sheds, hunts for mosquitoes in the dark corners, then holds the end of a glass test tube above them. The other end of the tube is connected to a rubber pipe; when he gently inhales, the insect becomes trapped inside the tube and he can take it back to the lab to identify the species beneath a microscope. When he’s finished in the goat sheds, Dr. Getachew wades into sewage ponds and drainage ditches with a dipper, looking for larval stephensi, which are easier to spot.
At Dire Dawa University, the main culprit of last year’s malaria outbreak was found in the water treatment plant at the edge of campus: Stephensi was breeding in sewage ponds, Dr. Getachew said, and in puddles made by broken pipes, and in big plastic barrels where students stored water because the municipal supply arrives erratically.
The President’s Malaria Initiative has been killing larvae with chemicals added to the water in sewage ponds, storage containers and other places in the city that were identified as major breeding sites, such as the cisterns at brickmaking operations and construction sites. Those efforts have pushed down malaria rates in Dire Dawa after the wild surge last year.
Yet at the Goro Health Center, near the river that runs through the city, cases have been climbing steadily this year. On a recent Sunday afternoon, every second person who arrived seeking care tested positive for malaria. Ilfe Faye, 31, had just had her third case of malaria in two months confirmed. Two of her three children had it, too. Her intense headache made her wince at the brightness of the late afternoon sunlight while she waited for a new package of anti-malarial medication.
Treating bodies of water to kill larvae is costly, and a long-term commitment, and it would be a significant expense for the Ethiopian government to apply the strategy in all of the country’s urban areas.
The only edge that countries such as Ethiopia have in their fight against Anopheles stephensi is that its preferred habitat is nearly identical to that of the Aedes aegypti mosquito, which transmits dengue, chikungunya and other mosquito-borne viral fevers. Cities that already have expertise or plans to control aegypti can attack stephensi with the same public health messages and steps such as treating stored water to kill larvae.
However, the limited success of dengue control shows just how hard this can be: Households might cover their water tanks and dump out old buckets, but neglect a bottle cap that is a potential breeding site. “In Djibouti, they’re finding stephensi larvae in the drips from air-conditioners,” Dr. Zohdy said.
Dr. Tadesse believes Ethiopia, and other countries, still have a chance to stanch a new malaria crisis.
“You could attack the mosquito from every single direction, crush the population, and then really enforce the bylaws, eliminate the breeding sites,” he said, surveying the chaotic traffic in the center of Dire Dawa on a recent visit. “You need strong government, and resources. But we’ll need to shift the resources in the end, so why not do it now, while there’s still a chance to stop it?”