Background: The World Health Organization declared a global cholera emergency in 2023 due to an increase in cholera outbreaks, with most cholera-associated deaths reported in Africa. Characterizing large-scale burden patterns can help with monitoring progress in cholera control and targeting interventions. Methods: We modeled the mean annual incidence of suspected cholera for 2011-2015 and 2016-2020 on a 20 km by 20 km grid across Africa using a global cholera database and spatial statistical models. We then examined how 2011-2020 incidence is associated with post-2020 cholera occurrence and investigated the potential reach of prospective interventions when prioritized by past incidence. Findings: Across 43 African countries mean annual incidence rates remained steady at 11 cases per 100,000 population through both periods. Cholera incidence shifted from Western to Eastern Africa, and we estimated 125,701 cases annually (95% CrI: 124,737-126,717) in 2016-2020. There were 296 million (95% CrI: 282-312 million) people living in high-incidence second-level administrative (ADM2) units (≥ 10 cases per 100,000 per year) in 2020, of which 135 million experienced low incidence (<1 per 100,000) in 2011-2015. ADM2 units with sustained high incidence in Central and Eastern Africa from 2011-2020 were more likely to report cholera in 2022-2023, but cases were also reported in sustained low ADM2 units. Targeting the 100 million highest burden populations had potential to reach up to 63% of 2016-2020 mean annual cases but only 37% when targeting according to past 2011-2015 incidence. Interpretation: By revealing the changing spatial epidemiology of cholera in Africa, these 10-year subnational estimates may be used to project OCV demand, characterize the potential of targeting interventions based on past burden, and track progress towards disease control goals.

The authors have declared no competing interest.

JPS, QZ, JK, KZ, MD, RD, DL, STH, JL, AD, ASA, ECL received funding from the Bill and Melinda Gates Foundation (BMGF INV-044856).

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