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South Sudan Cholera Fact sheet


Cholera Overview

South Sudan gained independence from the North in 2011. Inter-ethnic conflict and political rivalries has led to a civil war that has been ongoing since December 2013.

Between 2014 and 2017, epidemiological surveillance recorded 28,677 cases with 650 fatalities, a high case fatality rate (CFR) ≈ 2.3%1. Main cholera foci were reported in major cities that host Internally Displaced Persons (IDP) camps and/or protection of civilian (PoC) sites along the border with Uganda and Kenya and in the Sudd Swamp along the Nile River

The country is affected by cross-border outbreaks along its borders with Uganda, Kenya, Ethiopia and Sudan

Cholera Distribution

From 2006 to 2017, suspected cholera cases were first detected in counties close to the Ugandan border (Yei in 2006 and Magwi in 2008) or the capital city Juba (2014, 2015 and 2016). The state of Eastern Equatoria and Juba City in particular seem to play a role in amplification and diffusion of cholera outbreaks along the border with Uganda and Kenya and along the Nile River up to the city of Malakal.

Outbreak patterns changed over time, with outbreak onset during the dry season (January-February) in 2006 and 2008 and during the rainy season (April-June) from 2014 to 2017. Cholera cases were reported during the dry season (November to February) in 2006-2007, 2008-2009 and 2016-20171. An increase in cases was observed during the rainy season from 2014 to 2017.

The states of Central Equatoria, Eastern Equatoria, Jonglei and Unity were affected at least four times and represented 78% of the total number of cases. A high CFR was registered in the Sudd, in areas where access to affected communities was limited either due to conflict or difficult geographical terrain.

Overall, the country appeared to be affected by sub-regional outbreaks implicating border countries such as Uganda, Kenya, Ethiopia and Sudan. However, additional evidence, such as genetic analysis of V. cholerae isolates, is required to confirm the origin and spread of cholera between neighbouring countries.

Strategic Recommendations

High-risk areas along the borders were located in areas where cholera outbreaks spread between neighboring countries such as Uganda, Kenya and Sudan. This highlights the importance of cross-border activities for Central Equatoria, Eastern Equatoria and Upper Nile States.

In cholera hotspots, preparedness and response plans should be developed and implemented including: (1) strengthening early detection and rapid response, including community-based surveillance and cross-border alerts; (2) establishing multi-sectoral and cross border coordination mechanisms; (3) building capacity on outbreak management; (4) targeted pre-positioning of supplies and (5) developing risk communication, social mobilization and community engagement plans as well as harmonizing approaches and messaging.

Sustainable Water, Sanitation and Hygiene and Social mobilization activities should be implemented in 12 priority counties regularly affected by outbreaks of significant duration (Table II – Type 1 and Type 2). In hard-to-reach areas, enhancing access to healthcare especially early rehydration (e.g., community oral rehydration points) would help to prevent cholera-related deaths. Oral cholera vaccine campaigns conducted in border hotspots would help to reduce the likelihood of cholera epidemics in Juba.