Since late December 2025, heavy rains across Southern Africa have led to a surge in malaria cases.
Botswana: Botswana has recorded 197 malaria cases during the 2025/26 season, including 176 locally acquired and 21 imported cases. In week 3 of 2026 alone, 56 locally transmitted cases were reported.
Likewise in February 2025, following heavy flooding, a significant surge in malaria cases was seen with more than 2’000 in 2025 compared to 290 cases in 2024.
Namibia: Health authorities report a significant surge in malaria during the first four weeks of 2026, with 8’760 confirmed cases, up from 5’229 in the same period last year. Katima Mulilo is the hardest hit (1’448 cases), followed by Outapi (1,287 cases). In total, 20 districts have crossed the epidemic threshold, including Andara, Nyangana, Ncamagoro, Nkurenkuru, Eenhana, Engela, Okongo, Grootfontein, Katima Mulilo, Rundu, Tsumeb, Otjiwarongo, Omuthiya, Tsandi, Outapi, Okahao, Opuwo, Oshikuku, and Oshakati.
South Africa: Mpumalanga’s Health Department warns of a malaria spike after floods, with 314 cases in January 2026 compared to 69 cases in 2025, mainly in Ehlanzeni District’s Nkomazi, Mbombela, and Bushbuckridge.
Given the heavy rain falls and early upsurge in malaria cases in areas outside the seasonal chemoprophylaxis zone (see marked districts below), the Swiss Expert Committee for Travel Medicine has enlarged the region in Namibia where seasonal chemoprophylaxis is recommended. For Botswana and South Africa, the recommendations remain the same. New recommendations, see maps with marks: