In Nigeria, authorities are warning of heightened cholera risks linked to flooding, while Lassa fever continues to claim lives despite a decline in weekly cases. In Togo, the response to polio is being stepped up with a second nationwide vaccination round. Across the continent, humanitarian crises are straining health systems, even as progress is being made, particularly in vaccination and institutional strengthening through the Africa CDC. At the same time, new threats are emerging, including an unidentified disease in Burundi.

An outbreak of an unidentified disease in Burundi has killed five people and sickened 35 others, the Africa CDC reported. First detected in late March 2026, the outbreak is concentrated in the Mpanda district.

Symptoms include fever, vomiting and diarrhea, with neurological and respiratory complications in severe cases. Laboratory analyses have ruled out the main hemorrhagic fevers. According to the WHO, tests have been negative for Ebola and Marburg, Rift Valley fever, yellow fever and Crimean-Congo hemorrhagic fever.

"Although these preliminary results are reassuring regarding the absence of these major diseases, investigations are actively continuing to identify the causative agent," said Dr. Lydwine Badarahana, Burundi's health minister. "All necessary measures are being taken to protect public health and prevent any potential spread," she added.

A multisectoral team has been deployed to identify the pathogen and contain transmission.

Africa: Vaccination Saves Millions, but Gaps Remain

Vaccination programs have prevented nearly 20 million measles-related deaths across Africa between 2000 and 2024, according to the WHO and Gavi, the Vaccine Alliance. More than 500 million children have been protected.

During this period, vaccine coverage improved significantly, with 44 countries introducing a second vaccine dose, raising coverage from 5% to 55%. Campaigns have delivered more than 622 million doses.

These efforts cut measles mortality in half and reduced case numbers by 40%. Programs now cover 13 diseases, up from eight in 2000.

Despite the progress, inequalities persist. Access to care, population growth and humanitarian crises are hampering efforts to reach the target of 90% vaccination coverage by 2030.

Africa CDC Strengthens Capacity and Health Financing

The African Union's Africa CDC reported a 95% budget execution rate and expanded its grants portfolio to $463 million since 2023, according to a recent report by the institution.

Congratulations to our Director General, @Dr_JeanKaseya, on being recognised by Meridian Letters as one of the Top 20 Leaders Shaping Health Across Africa in 2025.

This recognition reflects the growing impact of his leadership in advancing Africa’s health priorities on the… pic.twitter.com/RKHmXm0J6I

— Africa CDC (@AfricaCDC) April 15, 2026

During that period, the institution expanded its activities in emergency preparedness, research and epidemic response. The number of national public health institutes rose from 19 to 36, while emergency operations centers doubled. Genomics capacity grew sharply, from seven countries in 2020 to 46 in 2026.

The agency, currently led by Congolese director Jean Kaseya, said it helped mobilize more than $40 billion for member states. Those advances have enabled better coordination in response to threats including mpox, Ebola and cholera. Looking ahead, the Africa CDC is seeking to consolidate a more autonomous and structured continental approach.

Africa: Humanitarian Crises Strain Health Systems

Africa accounts for nearly 40% of global humanitarian needs, according to the latest OCHA report. Conflicts, climate shocks and mass displacement are weakening health systems across the continent.

Prolonged crises, particularly in Sudan, the Democratic Republic of Congo and the Sahel, are worsening food insecurity and limiting access to healthcare. Droughts, floods and cyclones are compounding vulnerabilities while disrupting already fragile health services.

For 2026, humanitarian agencies are calling for greater funding mobilization and improved access to affected areas to prevent worsening health conditions. That goal remains uncertain as humanitarian financing contracts globally.

Nigeria: Cholera Alert Ahead of Flood Season

Nigeria is bracing for a rise in waterborne diseases as heavy rains are expected this week. The Nigerian Centre for Disease Control and Prevention (NCDC) has warned of a high risk of cholera outbreaks and diarrheal diseases in at least 10 states, including Kaduna, Oyo and Niger.

Health authorities noted that flooding promotes contamination of water sources, also increasing cases of malaria and environment-related diseases. Historically, flood seasons have been associated with epidemic outbreaks in vulnerable areas.

The NCDC recommends the use of treated drinking water, improved hygiene practices and avoiding stagnant water. Communities have been urged to promptly report symptoms including diarrhea, vomiting and fever. Authorities are also strengthening epidemiological surveillance and coordination with states to limit the health impact of flooding.

...While Lassa Fever Persists Despite Drop in Weekly Cases

Separately, Africa's most populous country has reported a Lassa fever death in Oyo State, prompting renewed health alerts. Since November 2025, 685 confirmed cases and more than 4,000 suspected cases have been recorded.

While weekly case numbers are declining, the case fatality rate has risen to 24.8%, up from 18.8% a year earlier. A total of 170 deaths have been recorded in 2026.

The disease remains endemic and affects 22 states. Authorities have activated response mechanisms including contact tracing and enhanced surveillance.

Experts have flagged persistent challenges in early detection and access to care, against a backdrop of sustained pressure on the health system.

Togo: Second Vaccination Round to Contain Polio

Togo launched a second round of polio vaccinations this week to consolidate gains from a first phase that reached 95% of targeted children in March 2026. The campaign targets children aged 0–5 across the entire country.

Health authorities are deploying mobile teams in both urban and rural areas to administer a second dose, which officials say is essential to interrupt transmission. The strategy rests on the principle of herd immunity, which is key to eradicating the disease.

Polio remains a debilitating disease that can cause paralysis or death. Despite progress, it remains under sustained surveillance to reduce the risk of resurgence in the event of a drop in vaccination coverage.

Zambia: Foot-and-Mouth Outbreak Prompts Sanitary Restrictions

Zambia confirmed a foot-and-mouth disease outbreak across seven districts in Western Province. Authorities immediately restricted livestock movement to contain the spread. A total of 35,000 vaccine doses have been deployed in the affected areas.

The highly contagious disease affects cloven-hoofed animals and threatens the livelihoods of livestock farmers. The response aims to limit economic losses and prevent the outbreak from spreading to other regions.

Ayi Renaud Dossavi