[SciDev.Net] The “catastrophic” freeze on US funding for malaria has halted prevention programmes across Africa and also threatens to stall advances in genomic research, says Jane Carlton, director of the Johns Hopkins Malaria Research Institute.
The US President’s Malaria Initiative (PMI) is one of numerous USAID-supported programmes to see its funding terminated under US President Donald Trump’s sweeping reforms this year.
From eco-friendly bacterial pellets that kill mosquito larvae, to gene-drive mosquitoes that suppress wild populations, scientists are developing an arsenal of promising new technologies to combat malaria.
But “without sustained funding, even the best tools stall”, says Carlton, in an interview with SciDev.Net, warning that a retreat from funding could jeopardise decades of progress.
What is the impact of the recent US funding cuts for malaria programs?
The dissolution of the President’s Malaria Initiative [PMI – a five-year programme to combat malaria in 15 African countries] is catastrophic.
Modeling [reported in a leaked USAID memo] shows its collapse could cause 18 million new cases and 160,000 deaths yearly.
Already, Uganda reports clinics rationing rapid tests, and Ethiopia’s PMI office halted bed net distributions mid-campaign.
Stockouts of artemisinin-based drugs are rising and five African countries have less than three months’ supply.
This isn’t just a health crisis; it’s economic. Malaria costs Africa US$12 billion yearly in lost productivity.
With the funding freeze, how do you make a case to sceptics and policymakers in higher-income countries that malaria funding matters to the US?
First, self-interest. Malaria isn’t “someone else’s problem”. The US had 2,000 cases last year, mostly travelers, yes, but Anopheles mosquitoes still thrive here. Florida and Texas saw local transmission in 2023 after decades.
Second, leadership. The US eradicated malaria in the 1950s through swamp drainage and DDT [dichlorodiphenyltrichloroethane, a pesticide used to control insects]. Today, it is a moral duty to share that knowledge.
Finally, security. Destabilised regions breed conflict and healthy populations are more resilient.
How will the PMI funding freeze impact genomic research in malaria control?
When I started, malaria research was like navigating a maze in the dark. Sequencing the Plasmodium falciparum and vivax genomes in the early 2000s was revolutionary, it gave us the first “blueprint” of the parasite. Suddenly, we could identify genes, proteins, and metabolic pathways.
But it wasn’t an instant cure. Genomics laid the groundwork for precision medicine. Today, we combine parasite, human, and mosquito genome data to track drug resistance and outbreaks.
[Genomics] is a foundational tool, not an endpoint. Translating genetic insights into drugs requires massive collaboration. For instance, my team works on “functional genomics” to link genes to traits like drug resistance. It’s painstaking work, but AI tools are now helping automate hypotheses. Without sustained funding, even the best tools stall.
How is artificial intelligence reshaping malaria research?
AI is a game-changer in three areas. First, machine learning models predict outbreaks by analysing climate data, human movement, and historical trends. In Ethiopia, these models helped pre-deploy bed nets before rains triggered outbreaks.
Second, AI-powered diagnostics. Algorithms analyse blood smears to detect parasites, reducing human error. But field validation is tricky, dust on microscope slides or poor lighting can confuse the software.
Third, protein language models like AlphaFold predict 3D protein structures in hours, not years. This lets us design drugs targeting parasite proteins more efficiently. For example, we’re using AlphaFold to study Plasmodium proteins that help mosquitoes transmit the parasite.
What ethical concerns come with AI in malaria?
Bias is a big risk. Most genomic data comes from Africa, but AI models are often trained in Western labs.
If local researchers aren’t involved, tools might ignore regional nuances, like how Anopheles stephensi, an urban mosquito invading Africa, behaves differently from rural species.
Also, AI-driven drug discovery risks prioritising profit over access. Who owns the patents? Will new drugs be affordable in low-income countries? These questions need global dialogue.
What innovations excite you most?
In Zambia, we’re testing bacterial pellets that kill mosquito larvae without chemicals. They’re cheap, eco-friendly, and can be produced locally.
The second are gene-drive mosquitoes. Engineered to block parasite transmission or reduce fertility, they could suppress wild populations.
Trials in Burkina Faso show promise, but public acceptance is a hurdle. The third are vaccines. R21 and RTS,S are being rolled out in 19 African countries. Early data from Ghana shows a 30 per cent drop in severe cases among vaccinated kids.
How can research avoid ‘colonial science’ pitfalls?
True partnerships are key. We don’t fly in, collect samples, and leave. For example, in India, we train local scientists to run genomic labs. In Zambia, community leaders co-design biopesticide trials.
Capacity-building ensures African researchers lead future breakthroughs. But cancelled field visits [due to funding cuts] undermine this.
What gives you hope?
The malaria map is shrinking. Egypt was declared malaria-free in . India slashed cases from 20 million to 2 million since 2000.
With vaccines, gene editing, and African nations like Nigeria stepping up — they just allocated US$200 million [for the health sector] to offset US cuts — we can eliminate malaria.
But urgency is critical, retreating now would waste decades of progress.
This piece was produced by SciDev.Net’s Sub-Saharan Africa English desk.