Background Between 2014 and 2017, successive cholera epidemics occurred in South Sudan within the context of civil war, population displacement, flooding, and drought. Understanding the determinants of cholera spread in complex settings like this can provide valuable insights for mitigating future cholera risk. Methods We analyzed cholera linelist and molecular data to describe the spatio-temporal progression of the epidemics. We explored the role of rainfall, population movement and vaccination campaigns in shaping the explaining incidence and the spatial distribution of reported cases. Findings South Sudan experienced three distinct cholera epidemic waves of cholera ranging from 6-18 months with more than 28,000 cases reported and more than 2 million cholera vaccine doses delivered to curb transmission. The 2014 and 2015 epidemics remained spatially limited while the 2016/17 epidemic exploded along the Nile river. Initial cases of each epidemic were reported in or around Juba soon after the start of the rainy season, but we found no evidence that rainfall modulated transmission during each epidemic. All isolates analyzed had similar genotypic and phenotypic characteristics, closely related to sequences from Uganda and Democratic Republic of Congo. The direction of large-scale population movements between counties with cholera outbreaks was consistent with the spatial distribution of outbreaks. As of September 2020, zero cholera cases have been confirmed within South Sudan since 2017. Interpretation The three epidemic waves were caused by V. cholerae of the same clonal origin despite the periods of no reported cases between waves. While the complex emergency likely shaped some of the observed spatial and temporal patterns of reported cases, the full scope of transmission determinants remains unclear. Timely and well targeted use of cholera vaccine can avert cases and deaths, however, most of the vaccine campaigns occurred after the epidemic peak highlighting the challenges of delivering vaccines quickly in response to an outbreak in settings like South Sudan. These analyses provide a multi-faceted template for examining cholera dynamics through epidemiological, microbiological, climatic, and behavioral lenses.
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