Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
World Health Organization, Juba, South Sudan.
Lancet Planet Health. 2020 Dec;4(12):e577-e587. doi: 10.1016/S2542-5196(20)30255-2.
Between 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.
In 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.
The 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.
Pandemic 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.
The Bill & Melinda Gates Foundation.
2014 年至 2017 年期间，南苏丹在国内战争、人口流离失所、洪水和干旱的背景下相继爆发霍乱疫情。本研究旨在描述这三次不同的疫情波次的时空和分子特征，并探讨疫苗接种活动、降水和人口流动在塑造这一复杂环境中霍乱传播中的作用。
本描述性流行病学研究通过分析霍乱病例列表数据来描述疫情的时空进展。我们将在这些疫情期间收集的大流行霍乱弧菌的全基因组序列数据置于全球系统发育背景下。使用全基因组序列数据结合其他分子特征，我们对每个波次和区域中循环的菌株的亲缘关系进行了描述。我们利用分布式滞后非线性模型研究了降雨和瞬时基本繁殖数之间的关联，比较了早期和晚期反应性疫苗接种活动的县一级攻击率，并探讨了人口流动和疑似霍乱病例报告的空间模式的一致性。
南苏丹的 2014 年（6389 例）和 2015 年（1818 例）霍乱疫情仍然局限于特定区域，而 2016-17 年的疫情（20438 例）则沿着尼罗河沿岸的定居点传播。每个疫情的初始病例都在雨季开始后不久出现在朱巴或其周边地区，但我们没有发现降雨在每个疫情中都能调节传播的证据。所有分析的分离株具有相似的基因型和表型特征，与来自乌干达和刚果民主共和国的序列密切相关。南苏丹有霍乱疫情的县之间的大规模人口流动与病例的空间分布一致。在 26 次疫苗接种活动中，有 21 次发生在或之后的县一级疫情高峰期。在疫情高峰周开始后的接种周内进行接种的县的发病率比那些在高峰前进行接种的县高 2.2 倍（95%CI 2.1-2.3）。
尽管在没有报告病例的疫情间歇期内，同一克隆起源的大流行霍乱弧菌被分离出来，但南苏丹的复杂紧急情况可能塑造了一些观察到的病例时空模式。然而，传播决定因素的全貌仍不清楚。及时和有针对性地使用疫苗可以减轻霍乱的负担；然而，在复杂的紧急情况下快速部署疫苗仍然具有挑战性。
比尔及梅琳达·盖茨基金会。
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