Abstract
SummaryBackgroundBetween 2014 and 2017, successive cholera epidemics occurred in South Sudan within the context of civil war, population displacement, flooding, and drought. We aim to describe the spatiotemporal and molecular features of the three distinct epidemic waves and explore the role of vaccination campaigns, precipitation, and population movement in shaping cholera spread in this complex setting.MethodsIn this descriptive epidemiological study, we analysed cholera linelist data to describe the spatiotemporal progression of the epidemics. We placed whole-genome sequence data from pandemic Vibrio cholerae collected throughout these epidemics into the global phylogenetic context. Using whole-genome sequence data in combination with other molecular attributes, we characterise the relatedness of strains circulating in each wave and the region. We investigated the association of rainfall and the instantaneous basic reproduction number using distributed lag non-linear models, compared county-level attack rates between those with early and late reactive vaccination campaigns, and explored the consistency of the spatial patterns of displacement and suspected cholera case reports.FindingsThe 2014 (6389 cases) and 2015 (1818 cases) cholera epidemics in South Sudan remained spatially limited whereas the 2016–17 epidemic (20 438 cases) spread among settlements 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 analysed had similar genotypic and phenotypic characteristics, closely related to sequences from Uganda and Democratic Republic of the Congo. Large-scale population movements between counties of South Sudan with cholera outbreaks were consistent with the spatial distribution of cases. 21 of 26 vaccination campaigns occurred during or after the county-level epidemic peak. Counties vaccinated on or after the peak incidence week had 2·2 times (95% CI 2·1–2·3) higher attack rates than those where vaccination occurred before the peak.InterpretationPandemic V cholerae of the same clonal origin was isolated throughout the study period despite interepidemic periods of no reported cases. Although the complex emergency in South Sudan probably shaped some of the observed spatial and temporal patterns of cases, the full scope of transmission determinants remains unclear. Timely and well targeted use of vaccines can reduce the burden of cholera; however, rapid vaccine deployment in complex emergencies remains challenging.FundingThe Bill & Melinda Gates Foundation.
Highlights
The seventh cholera pandemic, first recognised in 1961, continues to plague populations without sufficient access to safe water and sanitation across the world
We describe 36 vaccination campaigns providing over 2 million doses of cholera vaccine: we found that early vaccination might have reduced local outbreak sizes, most vaccination activities occurred after the peak week of cases
Using detailed cholera case data collected from 2014 to 2017, we describe the key features of the successive epidemic waves and explore how precipitation, population displacement, and vaccination campaigns might explain the differences in cholera incidence and spatial spread between waves
Summary
The seventh cholera pandemic, first recognised in 1961, continues to plague populations without sufficient access to safe water and sanitation across the world. Estimates of the global burden are uncertain, more than 140 000 suspected cholera cases are reported annually from sub-Saharan Africa.[1] Many of these cases occurred in areas with poor infrastructure including peri-urban slums, rural areas dependent on surface water, and areas with complex emergencies. Universal access to water and sanitation would probably eliminate cholera transmission but is unlikely given the pace of progress and financial commitments.[2]. In 2017, the WHO-led Global Task Force on Cholera Control developed a roadmap to end cholera by 2030, and in 2018, a resolution to end cholera was adopted at the 71st World Health Assembly.[3] The roadmap calls for a geographically targeted approach to use scarce resources in areas with a high risk of cholera, requiring an indepth understanding of transmission across endemic and epidemic settings. South Sudan is one of the 47 focal countries of this roadmap
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