An invasive, malaria-carrying, insecticide-resistant mosquito that thrives in cities, where malaria has not been a major threat, has moved farther and faster across Africa than even pessimistic scientists had feared. And many public health experts believe it is too late to eliminate, or even contain, it.
A new genomic analysis of the mosquito, called Anopheles stephensi, using specimens collected from 10 countries, showed that those found in Africa had genetic resistance to all of the chemicals currently used in spraying campaigns and other mosquito-control efforts, meaning those insecticides will not kill it.
It is moving with terrifying efficiency and speed across flat, open, windy terrain, pushing westward to Ghana and south through Kenya, from its initial arrival on the continent in Djibouti in the Horn of Africa more than a decade ago.
“The last couple of years there’s less talk of, ‘We really need to contain this invasion,’ because everyone who knows what’s what realizes that genie is completely out of the bottle,” said Tristan Dennis, who studies vector genomics at the University of Queensland in Australia and who led the new analysis, published in the journal Science.
This mosquito alarms health experts because, unlike the species that historically spread malaria in Africa, it thrives in urban as well as rural areas, and is not deterred by dry seasons. This means that malaria, already one of the top killers in Africa, could become a grave problem in megacities such as Lagos and Kinshasa, each of which are home to about 20 million people.
“We’ve not had to worry about malaria in urban settings,” said Dr. Eric Ochomo, the head of entomology for the Kenya Medical Research Institute.
Much of the urban population has no immunity to malaria, and the parasite will make people gravely ill, he said. And when a stable population of stephensi is established, it transmits malaria all year, not just on the rainy season cycle most current malaria programs are structured to address.
“It’s going to really complicate our ability to manage malaria,” Dr. Ochomo said.
In most countries, stephensi is not yet established in populations big enough to detect whether it is affecting malaria rates. But in Djibouti and Ethiopia, the first countries it invaded, it is possible to see the risk it represents.
Before stephensi arrived in 2013, Djibouti was on the cusp of declaring malaria eradicated. In 2012, there were just 27 cases. A year after stephensi was found, cases shot up to nearly 1,700. Each year thereafter, the number crept up, and in 2020, there was an explosion: more than 70,000 cases.
In Dire Dawa, Ethiopia’s second-largest city, stephensi drove a surge of malaria cases in 2022, one that initially baffled health care workers who were not used to diagnosing or treating the disease.
The spread of stephensi is yet another setback in an already sputtering battle with mosquitoes in Africa. In 2024, there were nine million more malaria cases than in 2023. While the full 2025 data is not available yet, and will be less comprehensive due to health program funding cuts, there are clear signs that malaria is resurgent.
Teams of scientists have been working together, often against a backdrop of armed conflict and climate-driven displacement, to combine their bare-bones surveillance efforts and map the dimensions of the new threat.
Mahaman Lamine, a parasitologist in the city of Zinder in the West African nation Niger, trapped a pile of mosquitoes around ponds with a couple of students in 2024. In his university lab, he asked the students to identify the species for a biodiversity survey, and almost as an afterthought reminded them about stephensi, the invasive species that had been detected elsewhere in Africa. A short while later, his students mentioned that they had found some of those in their samples.
“I said, ‘No, no, no!’” Dr. Lamine recalled.
Stephensi had never been found in Niger. But Dr. Lamine rechecked the mosquitoes against one morphological key, and then another. They matched. Soon he dispatched a student on a bus to the city of Kano, across the border in Nigeria, carrying mosquito samples through an area with an armed insurgency to reach a lab that could do molecular confirmation.
The students were right: Anopheles stephensi had reached Niger.
The recently published genomic analysis showed that after arriving in Djibouti, the new African stephensi population split into three groups. One went into Ethiopia, then south into Kenya; one skipped from Djibouti over a narrow channel in the Red Sea and into Yemen; and one went into Sudan and from there headed east across the Sahel to West Africa.
Other scientists have speculated that stephensi has been introduced from South Asia via ports in West Africa in separate incidents, but the genomic analysis provided a compelling case for how efficiently the mosquito had moved across the flat, windy Sahel, expanding its territory by as much as about 300 miles a year.
“We’ve never seen anything like this, this kind of spread. We never imagined a mosquito could spread this fast,” said Dr. Ochomo, who contributed mosquito samples to the study.
A few years ago, he expected stephensi to pose a threat only in Kenya’s very dry north. It has already been found moving steadily south and fanning out through different kinds of habitats.
Stephensi arrived in Africa in about 2013, likely on a ship from Pakistan or India. Researchers in Djibouti identified it as they were scrambling to explain a massive spike in malaria cases in a country that had been on the verge of eradicating the disease.
Everywhere it goes, stephensi encounters malaria-control programs trying to do more with shrinking budgets. The United States, the world’s largest funder of anti-malaria efforts, slashed its support at the start of the Trump administration. Malaria-control budgets were reduced by a third or more in most countries with a high malaria prevalence last year, compared to 2024.
“The first thing cut is surveillance,” Dr. Ochomo said. Yet without data on which mosquito is where, it is harder to make decisions about where to invest in interventions, such as bed net distribution. “If we could do really good surveillance, we could decide where to put the limited resources,” he said.
In Niger, Dr. Lamine is also struggling to continue to track the mosquito. “We do not have any funding, and we have only one very old microscope. But we try to do the work, because we love science,” he said.
Dr. Dennis said stephensi was benefiting from human interaction with the environment.
“They’ve come at a time when there’s massive fragility and instability, lots of displaced people, very little state control in some places, on a really rapidly urbanizing continent,” he said. “And they came armed to the teeth with defenses against the insecticides we can use.”
Scientists fear that stephensi has also reached other countries, including Chad, Somalia, Eritrea and South Sudan, nations that do not have the resources for national vector surveillance. “Nobody is looking,” Dr. Dennis said.
Scientists in Afghanistan, Pakistan, Yemen, Sudan, Ethiopia, Kenya, Iran, the United States and Saudi Arabia collaborated to do the genomic study, to home in on where the African stephensi population originated. Almoevery country had violent conflicts raging when the research began or descended into war over the four years of the work.
Hmooda Toto Kafy, a medical entomologist with the ministry of health in Sudan, contributed samples from his country, collecting the last of them just weeks before the civil war began. Dr. Kafy has been poised to start research on if and how stephensi is driving malaria transmission in the country. “But this is not easily done during the war,” he said.
Regions he hoped his team could surveil are inaccessible because of fighting, while staff members and students left as refugees. And the banking system is in disarray, so it is difficult to pay for supplies. All of it makes the already daunting prospect of hunting for a tiny mosquito in one of the world’s largest countries massively more complex.
In Yemen, Dr. Tarek Sultan Bin Hawail, a public health specialist, supervised a team that collected samples for the study, and shared ominous findings with researchers in Africa. His team found stephensi in the huge camps that ring the Yemeni capital Aden, housing people displaced by the country’s civil war. There were mosquito larvae in the water containers inside people’s homes and tents — living alongside another mosquito, Aedes aegypti, which carries dengue fever and other viruses.
Health workers at clinics overwhelmed with patients with fevers were treating patients with dengue, because malaria was not supposed to be in the area. Stephensi brought it.
Africa is home to nearly half the global total of displaced people; there are 15 million displaced by the war in Sudan alone.
When the global network of scientists had contributed samples, Dr. Dennis carried out the genomic analysis. His findings were bleak. “All of the resistance genes in the invasive population confer resistance to pretty much every insecticide we are using in vector control, so this is actually even worse news than we thought it was,” Dr. Dennis said.
Even with the growing body of evidence about how stephensi is moving and where, there are few signs of resources being shifted to meet it. “You can have these data that tell you a certain thing, but if there’s not the infrastructure to put a response into practice, then it doesn’t help much,” said Dr. Dennis.
Despite this, the scientists who study stephensi speak about the mosquito with grudging admiration.
Typically an invasive species struggles to establish itself in a new place, shrinking down to a small population with limited genetic diversity.
“The fact that this mosquito was able to lose a huge amount of genetic diversity and then still go on to occupy this vast swath of the continent,” Dr. Dennis said. “It took over Africa.”
