The story of a devastating disease, scientific breakthroughs, and the race to save a generation of children.
In the world's newest nation, a silent emergency claims thousands of lives each year, most of them children. South Sudan faces one of the world's most severe malaria crises, with the 2025 World Malaria Report revealing the country accounts for a staggering 64% of malaria cases and 46% of deaths in its region. The statistics paint a grim picture: 5.5 million cases and over 4,000 deaths annually place an unbearable strain on a fragile healthcare system. Perhaps most alarming of all, malaria prevalence among children aged 6-59 months has skyrocketed from 32% in 2017 to 52.6% in 2023 – meaning more than half of South Sudan's youngest children are infected with this potentially deadly disease 1 5 9 .
Children infected (6-59 months)
Annual malaria cases
Annual deaths
Malaria's stronghold in South Sudan isn't accidental but fueled by a perfect storm of seasonal flooding, conflict-induced displacement, and weak health infrastructure. These factors create ideal conditions for malaria transmission, with extreme weather events and population movements between 2023 and 2024 alone causing a 20% surge in cases. The human toll is disproportionately borne by the most vulnerable – children under five and pregnant women 1 .
At the heart of this crisis lies Plasmodium falciparum, the deadliest of malaria parasites. Its complex life cycle begins when an infected Anopheles mosquito bites a human, injecting parasites into the bloodstream. These parasites travel to the liver, transform, then re-enter the bloodstream to invade red blood cells, where they multiply until the cells burst, releasing countless new parasites to continue the destructive cycle.
Sporozoites injected into bloodstream
Parasites multiply in liver cells
Merozoites invade red blood cells
Gametocytes taken up by mosquitoes
For decades, scientists believed the malaria parasite quickly left the skin for the liver after a mosquito bite. But in 2010, researchers at the Institut Pasteur made a revolutionary discovery using real-time imaging in mice: up to 50% of injected parasites remained in the skin, with 10% actually developing into infectious forms right in the dermis, epidermis, and hair follicles without ever reaching the liver .
The Institut Pasteur team employed sophisticated imaging techniques to challenge conventional understanding of malaria infection:
The experiment yielded startling results that forced reconsideration of fundamental malaria biology:
Parasites were found not just diffusely in skin but specifically associated with hair follicles
The skin environment supported complete parasite development into infectious forms
Parasites remained viable in skin for several weeks, suggesting possible dormancy
The draining lymph node received antigens from multiple parasite stages, indicating the skin as a critical site for immune response initiation
This discovery has profound implications for vaccine development, suggesting the skin immune response may be harnessed for protection. It also potentially explains some mysterious aspects of malaria biology, including patterns of disease recurrence and variable vaccine effectiveness .
In July 2024, South Sudan launched the R21 malaria vaccine in 28 high-burden counties, targeting over 265,000 children. Initial reach showed promise with 148,878 children receiving the first dose by May 2025. However, a concerning pattern emerged: only 56% returned for the second dose, 34% continued to the third, and a mere 7.6% completed all four doses 5 9 .
Source: South Sudan Ministry of Health 5
This steep decline highlights systemic challenges in healthcare delivery, prompting Health Minister Sarah Cleto Rial to call for "improved service delivery, defaulter tracking, community engagement, and follow-up mechanisms" 5 . In August 2025, South Sudan launched the vaccine's second phase, expanding to 52 counties with a goal of reaching 324,571 children aged 5 to 23 months 5 .
While vaccines represent a breakthrough, they're just one weapon in the arsenal:
Remain crucial, though insecticide resistance is growing
Received new WHO recommendation in 2025, creating protective spaces against day-biting mosquitoes
| State | Malaria Prevalence (%) |
|---|---|
| Western Bahr El Ghazal | 61% |
| Northern Bahr el Ghazal | 56% |
| Warrap | 54% |
| National Average | 52.6% (children 6-59 months) |
Source: 2025 World Malaria Report 1
| Tool/Technique | Function | Application Example |
|---|---|---|
| Gene editing | Modify or remove specific parasite genes | Studying gene function by creating modified strains 4 |
| Real-time imaging | Visually track parasites in living organisms | Discovering skin-stage parasite development |
| Rapid diagnostic tests | Quickly detect malaria infection at point-of-care | Enabling 5 million tests in South Sudan (2024) 1 |
| Spatial repellents | Create protective zones against mosquitoes | New WHO-recommended intervention (2025) 2 |
| Attractive Targeted Sugar Baits | Lure and eliminate mosquitoes using bait stations | Phase III trials in Zambia 2 |
The path to malaria control in South Sudan remains fraught with obstacles. Funding gaps severely hamper efforts, with only 25% of the required $3 million for malaria commodities secured as of March 2025. The climate change threat looms large, with Africa CDC noting "shifts in temperature and rainfall that are expanding the range of malaria-carrying mosquitoes" 2 . Flood-prone states like Jonglei and Unity face particularly high risks in the coming years 1 .
The battle against malaria in South Sudan represents both one of global health's greatest challenges and most urgent priorities. With over half of young children infected, the disease threatens not just individual lives but the nation's future. The complex interplay of biological factors, climate change, and healthcare infrastructure demands equally sophisticated solutions.
Yet scientific progress continues to provide new weapons – from revolutionary vaccines to parasite-killing nets and groundbreaking discoveries that reshape our understanding of the disease itself. As South Sudan expands its vaccination campaign and strengthens its health system, the international community's support remains crucial to close funding gaps and scale up interventions.