Mozambique and Madagascar are struggling to address the after-effects of cyclones and cyclone-related flooding, with huge increases in cholera cases and displaced people.

There has been a seven-fold increase in cholera cases in southern Africa in the first six weeks of 2026 in comparison to the same time last year, with 90% of the 4,300 reported cases in Mozambique, according to the World Health Organization (WHO) Africa region.

Meanwhile, UN agencies warn that 380,000 Madagascans need aid after two cyclones battered the island.

“Mozambique accounts for the majority of reported cholera cases, particularly among flood-affected and displaced populations. Extensive floods due to cyclones have damaged water and sanitation systems, contaminated drinking water sources and displaced communities, creating conditions for rapid transmission of cholera and other water-borne diseases,” said Dr Marie Roseline Belizaire, WHO Africa’s emergencies director. 

Malawi, Namibia, Zambia and Zimbabwe are also experiencing cholera outbreaks.

“The sharp rise in cholera cases in Southern Africa is a clear reminder of how climate-related shocks are intensifying public health risks,” she told a media briefing this week.

“As extreme weather intensifies, displacement rises and infrastructure comes under severe strain, health systems must be equipped to manage multiple overlying risks simultaneously.”

Vaccination campaign

Dr Severin Ritter Von Xylander, WHO’s Representative in Mozambique, told a media briefing this week that 181 health facilities had been damaged and more than 700,000 people displaced by the cyclone that hit the country in mid-December.

The WHO is assisting the Mozambican government to vaccinate 1.7 million people against cholera, now that the vaccine shortage has eased.

“Our risk analysis flags a transmission period from March to August, particularly during floods,” said Von Xylander. 

Cyclone Gezani made landfall near Madagascar’s second biggest city, Toamasina, in mid-February, and officials reported that three-quarters of the city’s buildings were destroyed.

It developed as a result of warm sea temperatures (above 28 °C), wind shear below 20 kilometers per hour, and an unusually moist atmosphere, according to meteorologists with the Joint Typhoon Warning Center.

Madagascar is one of the worst-affected by cyclones in Africa, and the intensity of these is increasing with climate change.

Diphtheria outbreak

Meanwhile, eight African countries are affected by a diphtheria outbreak, with more than 26,000 suspected cases and over 1300 deaths reported. Up to 95% of cases are among unvaccinated or under-vaccinated children, according to WHO Africa.

“Strengthening routine immunisation, expanding the ‘Catch Up’ campaign, improving laboratory confirmation and ensuring access to diphtheria antitoxin remain urgent priorities across the meningitis belt in West Africa and the Sahel,” said Belizaire.