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South Sudan - Study in Cholera Hotspots in South Sudan: review and propositions for actions to prevent Cholera in the most affect areas (April 2018)

Cholera continues to represent a major public health concern in the East and Southern Africa region. From 2007 to 2016, approximately 634,000 cases and 14,303 cholera-related deaths were reported in the region with an average case fatality rate of 2.3%. To guide cholera control and prevention strategies, UNICEF established epidemiological studies in the countries of two geographical regions: the Greater Horn of Africa and the Zambezi Basin. The current assignment aims to better understand the dynamics of the disease in South Sudan. Identification of cholera hotspots as well as high-risk populations and practices will serve to guide the decision-making processes and advocacy initiatives.

Cholera continues to represent a major public health concern in the East and Southern Africa region. From 2007 to 2016, approximately 634,000 cases and 14,303 cholera-related deaths were reported in the region with an average case fatality rate of 2.3%. To guide cholera control and prevention strategies, UNICEF established epidemiological studies in the countries of two geographical regions: the Greater Horn of Africa and the Zambezi Basin. The current assignment aims to better understand the dynamics of the disease in South Sudan. Identification of cholera hotspots as well as high-risk populations and practices will serve to guide the decision-making processes and advocacy initiatives.South Sudan has recently gained independence from the North in 2011. Inter-ethnic warfare and politic rivalries has led to a civil war that has been ongoing since December 2013. As a direct consequence of the prolonged conflict, approximately one third of the total population (3.5 of 12 million) has been displaced.

From 2006 to 2017, suspected cholera cases were first detected in the Eastern Equatoria State, either in counties close to the Ugandan border or the capital city Juba. The state of Eastern Equatoria and Juba city in particular seem to play a role in amplification and diffusion of cholera outbreaks towards the east 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) and during the rainy season (April-June). A high case fatality rate was registered in the Sudd, a vast swamp that stretches between Bor and Malakal, in areas where access is limited either due to conflict or difficult geographical terrain.Cholera foci are located in major cities that host large IDP camps and settlements, along the border with Uganda and Kenya, and in the Sudd Swamp along the Nile River. In the past years, specific groups of population were affected such as internal displaced peoples in camps or settlements as well as military or armed groups. During the 2016/2017 epidemic, cholera outbreaks heavily affected displaced and host communities living in the Sudd Swamp and communities in cattle camps.

Cholera transmission was often observed during funeral rituals, around affected households and in facilities that received cholera cases. Open defecation has often been reported as a contributing factor for cholera outbreaks over the past years. Since the onset of the ongoing conflict, the already low WASH indicators have further declined with increases in the cost of safe water in urban areas, damage to water facilities, and continued population displacement.

To control cholera outbreaks in the country, nearly two million doses of oral cholera vaccine were administered since December 2012. Nevertheless, little has been done to substantially improve access to basic services in cholera hotspots. Twelve counties, which host approximately 2,280,000 people (18% of the total estimated population), account for two-thirds of the total number of cases. High priority counties should be assessed and targeted for longer-term WASH, Health and social mobilization improvements taking into account the protracted nature of the conflict in some parts of the country.

South Sudan is situated between two major cholera transmission zones, the Great Lakes Region in the south and the Horn of Africa in the east. Evidence of cross-border spread from and to neighboring countries has been reported, especially involving Uganda and to a lesser extent Kenya, Ethiopia and Sudan. Additional genetic studies of Vibrio cholerae strains circulating in the East and Central Africa region would confirm these initial but limited observations and promote a concerted effort to eliminate cholera.