A team of trainee sprayers learning how to cover indoor surfaces with insecticide. (Photo: SAMRC).
News & Features
4th March 2026 | Joan van Dyk
Get to know South Africa’s malaria experts as they outrun hitchhiking mosquitoes and pollution-hardy bugs while navigating a regional funding collapse and a spiralling climate crisis.
A month after deadly floods hit parts of South Africa, Thabiso Ledwaba is still on edge.
Others in Limpopo’s provincial government are picking up the pieces of a deadly crisis that has already happened, but for Ledwaba, the disaster only begins once the floodwaters recede, and it unfolds in slow motion.
As the province’s acting malaria manager, Ledwaba knows that initially, fast-moving water washes away mosquito larvae. But when the rain subsides, stagnant pools become perfect breeding grounds. If it’s warm enough, mosquitoes can develop from larvae to adults in just a week.
As the mosquito population grows in the following weeks, some will feed on people already carrying the malaria parasite called Plasmodium. The parasite then needs about a fortnight to develop inside the mosquito before it can be transmitted. Once passed to another person, it will be another week or two before symptoms appear.
This eight-week timeline could coincide with the Easter holiday, a period when South Africa already sees a natural increase in malaria cases in Limpopo, KwaZulu-Natal and Mpumalanga where malaria-carrying mosquitoes are an ongoing presence.
South Africa missed its 2023 malaria elimination target by nearly 2 000 cases and 91 deaths, according to a government review of the programme. Spotlight understands that a new malaria strategy is complete, but the health department didn’t respond to queries about when it will be published.
The risk of malaria infection inside the country’s borders is low despite a small increase since 2022.
In border districts near the Limpopo, Mutale, and Nzhelele Rivers – where transmission is highest – around one in every thousand people will become infected during peak seasons.
The province has logged just 15 to 45 new cases per week after the floods. The four people who died of malaria since January were unrelated, Ledwaba says.
None of this gives him any solace.
The higher-than-average rainfall which has created new breeding sites also sabotaged his strongest defense – indoor residual spraying.
This highly regulated and labour-intensive process involves coating the walls and ceilings of people’s houses with an insecticide that kills mosquitoes before they have the chance to infect another person.
As a precaution, spraying can’t happen while families are sheltering inside from the rain, which began bucketing down just as the spraying season got underway late in 2025.
When interventions like indoor spraying are interrupted, Ledwaba says, a rebound in malaria cases is dangerous because the local population has lost its natural immunity during the period of low transmission. “We’ve lost 30% of our spraying days,” he says.
In pursuit of a parasite
When the weather doesn’t play along, provincial malaria managers try to squeeze in more spraying on the days it doesn’t rain. They also switch their focus to source control, which involves killing mosquito eggs and larvae before they hatch.
Figuring out what’s breeding and where is the weekly task of dedicated monitoring teams.
But even the backup plan is easier said than done after an estimated R10 billion in damages.
“In some places, the damage to roads is so bad that we have to park the car and walk,” says Morgan Mavunda, an environmental health practitioner who works in a malaria hotspot, Limpopo’s Vhembe district.
Mavunda says clinics in the communities he reaches on foot often haven’t reopened because staff can’t get there.
“I wish I could treat people,” says Mavunda, who spends his time in the field hunting for breeding grounds, investigating malaria cases and conducting health education.
Technically, he could treat people. In 2021, on the advice of South Africa’s Malaria Elimination Committee, the Director General of Health introduced a permit that would allow environmental health practitioners to treat malaria in the field. The permits were granted in terms of Section 22(A)15 of the Medicines Act.
Environmental health practitioners must be retrained each year and uptake has varied among the provinces given the high workload in the public sector, explains Karen Barnes, a clinical pharmacologist at the University of Cape Town whose work has focussed on malaria treatment.
In Limpopo, treatment is still done exclusively by nurses and doctors, Ledwaba says.
Mavunda often refers people to nurses in the mobile treatment teams run by the nonprofit Humana People to People. Humana co-operates with the government’s malaria teams as part of the Lubombo Spatial Development Initiative (LSDI).
The LSDI came about in 1999 as a strategy to boost tourism and agriculture in an area enclosed by the Lubombo Mountains, which crosses the borders of South Africa, Mozambique and eSwatini.
The idea was that malaria-free coasts would be more enticing to holiday-goers and healthy farmers would be able to spend more time on their fields and less in a hospital bed.
According to one study on the project, from 2000 to 2011, malaria cases decreased by 99% in South Africa, 98% in Swaziland, and 85% in Mozambique.
When the LSDI’s funding dried up suddenly in 2011, Mozambique battled to sustain the progress. Cases and deaths surged because people there were no longer protected by natural immunity.
In the years that followed, most malaria cases picked up in South Africa and eSwatini were traced back to Southern Mozambique.
In response, a braintrust of 25 malaria experts drew up a solution. They sent Treasury an investment case which showed that it was cost effective for South Africa to expand its malaria control efforts into Southern Mozambique.
Their pitch was that ensuring the financial stability of regional elimination efforts would create a protective buffer designed to stop the parasite before it can travel to areas with low transmission.
Treasury approved a 36% increase for the malaria budget which included recurring ringfenced money for South Africa’s endemic provinces and a co-financing mechanism for southern Mozambique.
The LSDI 2 was born. This iteration includes the three governments, the Global Fund, the Gates Foundation and private sector and non-profit partners including Goodbye Malaria.
Among the partnership’s benefits is that it allows tasks to be divided based on organisational strengths.
Humana and the government’s field operators work as one team, including sharing offices in some areas, but state units stick to indoor spraying and surveillance while Humana handles door-to-door visits and treatment.
But the recent floods were “brutal”, Mavunda says. He worries about the people who haven’t been reached at all.
Delaying malaria treatment increases the risk that someone might need hospital care or that they’ll die, and they’ll also remain a source of new infections.
It could also blunt the government’s ability to prevent a surge in malaria cases, says Ledwaba, because South Africa’s digital malaria monitoring system relies on health workers’ reports.
“There just aren’t enough of us,” says Mavunda.
How does government track the malaria parasite?
Health officials have “almost real-time” insight into dips or spikes in malaria infections, says Basil Brooke, who leads the National Institute for Communicable Diseases (NICD) team in charge of investigating outbreaks caused by parasites and illnesses that spread from animals to humans. He also co-chairs South Africa’s malaria elimination committee.
Malaria is classified as a Category 1 Notifiable Medical Condition, which means every diagnosed case must be reported to the system within 24 hours.
This alert also triggers an investigation by environmental health workers like Mavunda, who will trace the person’s travel history to catch instances that might otherwise have slipped through the cracks.
In combination with the national health department’s parallel database called the Malaria Information System, and specialised training for health workers across all levels of the health system, Brooke says South Africa has precise insight into the parasite’s movement.
“The NICD and the health department are monitoring new malaria cases day-by-day and doing everything possible so that we can respond to an increase in cases quickly,” says Brooke.
The malaria-savvy taxi drivers on SA’s borders
At a taxi rank in Manguzi, northern KwaZulu-Natal, a canopy tent serves as a makeshift office for Humana’s mobile malaria Unit 1.
The team, speaking to Spotlight while huddled around a cellphone inside the taxi rank’s guard house, consists of a community health worker, an environmental health practitioner and a professional nurse.
Stationed just a few kilometers from the southern border of Mozambique, Unit 1 offers on-the-spot testing and treatment for anybody moving through, whether they got their passport stamped or not.
A catch-up with local taxi drivers is usually first on community health worker Lucky Dlamini’s to-do list. The drivers keep him in the loop about the amount of traffic heading to the border.
Next, he speaks to migrants about what symptoms to look out for and where to get help once they reach their destination.
Anyone who tests positive will be treated by Unit 1’s nurse, Lindubuhle Mpontshane, who will also refer people who are seriously ill to government hospitals for treatment, where she says she’s built strong relationships with physicians over years.
Manguzi residents appear to support a stalled Zuma-era border wall project to stem smuggling of stolen vehicles, but Dlamini says there’s none of the Dudula-style animosity about health services that’s prevalent in parts of Johannesburg and Durban.
“People know that malaria can be deadly, they’re happy that we’re making sure everybody is healthy,” she says.
Humana’s programme manager Molatedi Diole says people in Manguzi have long-standing ties across the border. “They have children this side, relatives that side, people inland don’t relate like that.”
The Trump factor
The bigger picture is that malaria is surging across sub-Saharan Africa after years of decline.
The Africa Centres for Disease Control and Prevention flagged dramatic increases in Botswana, eSwatini, Namibia and Zimbabwe in 2025, driven by shifting rainfall patterns, heavy rains and stretched health systems.
Independent biosurveillance networks have reported similar trends in Mozambique, for example, hundreds of thousands of cases and rising deaths in Niassa Province.
It coincides with the Trump administration’s abrupt dismantling last year of foreign aid structures such as the United States Agency for International Development, and withdrawal of funds for initiatives including the Global Fund and Gavi.
Funding cuts in 2025 severely disrupted malaria supply chains across the continent. Countries quickly ran low on rapid tests and the drugs used to treat malaria, while nearly half of planned bed net campaigns and a third of seasonal prevention drives were delayed or scaled back.
The ripple effects of these funding cuts are, once again, reshaping the fate of the LSDI.
South Africa’s contribution towards indoor spraying in parts of southern Mozambique is built into the budget baseline for three-year bursts but there’s no guarantee Treasury will renew or expand it once it expires in 2027, says Rajendra Maharaj, who leads the malaria research unit at the South African Medical Research Council.
The programme has reduced the prevalence of malaria in young children there and has recently expanded spraying into Inhambane province, and any further growth depends on new funding and the success of the spraying projects.
“There’s only so much money in the kitty,” says Maharaj.
The long-term plan is for Mozambique’s health department to take over the work now led by LSDI2’s partners such as Goodbye Malaria.
Mozambique’s End Malaria Committee raised millions following the funding cuts, but Maharaj says the handover feels a long way off.
Why polluted puddles could spell trouble
So far, no province has recorded enough malaria cases to trigger a response from the NICD’s outbreak experts. Nonetheless, some of Basil Brooke’s team members are heading to Limpopo soon. There, they’ll support field teams and run tests to monitor insecticide and drug resistance.
Resistance isn’t widespread in South Africa, but the NICD does frequent spot checks because there is some evidence that mosquitoes and the malaria parasite are gradually getting tougher and finding ways to dodge the country’s preventive tools.
In 2022, the NICD discovered that mosquitoes in northern KwaZulu-Natal showed low-level resistance to four commonly used insecticides.
Research led by the NICD’s Shüné Oliver suggests that insecticide-resistant mosquitoes, once presumed to prefer clean water, are now thriving in contaminated water too. Worse still, breeding in polluted agricultural or urban runoff that pools after the floods might prime mosquitoes to survive the chemicals used in government spray programmes.
Artemisinin-based treatments, which South Africa uses, are also still effective, but Barnes warns the country is facing a rapidly increasing risk of artemisinin-resistant malaria from East Africa and the Horn of Africa.
The markers for resistance to this medicine have already been picked up in Zambia and as close as Namibia, but there are no back-up treatments in South Africa’s programme yet.
“We don’t want to be caught off guard,” cautions Barnes.
A pre-elimination puzzle
A malaria-free South Africa lies on the other side of a paradox.
Because South Africa’s malaria case numbers are low, companies are reluctant to spend years registering a medicine with the country’s regulator when they might sell only a few thousand doses, Barnes says.
Dwindling stocks of the insecticide dichlorodiphenyltrichloroethane (DDT) is one such example. South Africa is one of just three countries that still uses the insecticide with special permission from the United Nations.
Poorer nations have switched to safer but pricier alternatives with the help of donors, but South Africa doesn’t qualify for such support. The only company that still manufactures DDT has warned the health department that it will stop production in 2029, says Maharaj.
This situation has created a frustrating supply chain that is only partly eased by the government’s collaboration with Humana.
Diole says the nonprofit purposely uses the same supplier as the national government so that it can plug any gaps that might appear as a result of the state’s arduous tender process.
But Humana doesn’t do any spraying, so it’s been an uphill battle for Ledwaba to source the extra spraying pumps he’ll need in Limpopo to make up for the time lost to rainy days.
“I hope the new strategic plan will streamline the supply chain,” he says.
Primaquine, a drug that stops transmission, is another catch-22.
Primaquine is not on South Africa’s Essential Medicines List (EML) because it’s not registered by the country’s drug regulator, and companies won’t foot the bill to register it without the guaranteed demand that EML listing would bring.
In the meantime, the malaria programme must rely on bulk Section 21 applications to make the medicine available, and also pays above-average prices just to keep the tool available. Section 21 applications are a legal mechanism for bringing medicines into the country that have not been registered here.
The same problem is blocking access to back-up treatments for uncomplicated and severe malaria, Barnes says. The market for second-line treatments is even smaller than it is for first-line drugs.
Barnes says in the past, the Malaria Elimination Committee has persuaded manufacturers to license malaria treatments despite the small market but even then, South Africa has had to pay much more for such drugs than the world average.
She says: “South Africa is suffering from its own success.”
Why insect stowaways must be apprehended
Hitchhiking mosquitoes or “taxi rank malaria”, will likely be one of the final hurdles in South Africa’s elimination drive.
This is when malaria-infected mosquitoes catch rides in suitcases or vehicles and then bite unsuspecting people in geographic areas where there’s usually no malaria.
Because doctors don’t immediately suspect malaria in these settings, diagnosis is frequently delayed and the fatality rate is 17 times higher than the national average.
A review of 99 cases recorded between 2014 and 2023 shows most infections clustered in Gauteng, often near airports, transport depots and major highways.
The province has stocked up on malaria treatment in all its facilities, Barnes says, but some logistical issues can still get in the way because the system that tracks malaria tests and treatment is not as streamlined as the two databases that monitor cases.
“If someone shows up in the middle of the night, rapid tests may be in the building but are locked in labs or pharmacies that aren’t available after hours,” she says.
Praying for winter
So much rain fell over the festive season that it caused irreversible damage to the ageing Senteeko Dam in Mpumlanga.
Engineers at the national water and sanitation department warned that a million cubic metres of water that would be released should the dam break would devastate farmland, infrastructure and lives.
In stark contrast, an increasing number of settlements and villages in Limpopo are facing water scarcity.
Malaria spraying teams need clean water in abundance.
“It means teams have to drive kilometers further to find a water source to fill the trucks,” Ledwaba says.
His most recent budget proposal includes a request to install tankers in some places to make sure spraying is not delayed by water shortages.
In a changing climate, the unknowns are constant, Ledwaba says, but he’s relieved that the nighttime temperatures have started to drop.
“The feeling of constantly waiting for something to go wrong, it’s not good for the heart,” he says.
Disclosure: The Gates Foundation is mentioned in this article. Spotlight receives funding from the Gates Foundation but is editorially independent – an independence that the editors guard jealously. Spotlight is a member of the South African Press Council.
