South Sudan battles cholera, malnutrition as Ebola threat looms

South Sudan is facing a worsening public health emergency as authorities respond to ongoing cholera transmission, severe food insecurity, displacement and the threat of a deadly viral disease spreading across the border in neighboring Democratic Republic of Congo.

The World Health Organization’s latest weekly situation update, covering Aug. 31 to Sept. 6, places the cholera outbreak and protracted conflict and violence at the highest emergency grading. Acute food insecurity and famine risk, as well as circulating vaccine-derived poliovirus, are classified as Grade 2 emergencies, while the ongoing mpox outbreak is rated Grade 1.

South Sudan has not reported a confirmed case of Bundibugyo virus disease, a form of Ebola virus disease, but health authorities are maintaining heightened surveillance because of the outbreak in the Democratic Republic of Congo.

The DRC has reported 6,436 confirmed cases and 3,095 deaths, representing a case fatality rate of 48.1%, according to the update. The outbreak has expanded across 60 health zones, with 92 new cases and 33 deaths reported during a recent 24-hour period in Ituri, North Kivu, Haut-Uélé and Tshopo provinces.

South Sudan has screened more than 1.05 million travelers at points of entry, particularly at Nimule and Kaya. Authorities have recorded 40 alerts, of which 18 tested negative, 21 were discarded and one remained pending. Operational readiness across 15 priority counties was assessed at an average of 56%.

The cholera outbreak remains the country’s most immediate infectious disease threat despite signs that transmission is declining.

Health authorities recorded 61 new cases and no deaths during the reporting week, bringing the cumulative number of cases to 111,912 and deaths to 1,722, with a case fatality rate of 1.5%. About 98.4% of patients have recovered or been discharged.

Transmission remains concentrated in Rubkona, which recorded 31 new cases, followed by Mayom with 19, Renk with eight and Panyijiar with three. In Rubkona, internally displaced people accounted for nearly one-third of the new infections.

Oral cholera vaccination campaigns have achieved high coverage in several affected areas, including Leer at 93%, Mayom at 88% and Rubkona at 80.5%. However, the International Coordinating Group did not approve a vaccine request for Renk, citing insufficient evidence of active transmission based on rapid diagnostic tests and cultures.

South Sudan is also preparing for a national polio vaccination campaign after recording no new circulating vaccine-derived poliovirus isolates during the week.

The country has reported 11 AFP-confirmed cVDPV1 cases and three cVDPV2 cases so far this year. The first round of National Immunization Days is scheduled for Oct. 13-16, with vaccines already available in the country. National preparedness for the campaign currently stands at 48%.

Measles remains another concern, with 1,126 suspected cases recorded cumulatively, including 133 laboratory-confirmed cases. Outbreaks are being investigated or addressed in Pariang, Rubkona, Aweil East, Aweil Centre, Magwi and Wau.

The country’s mpox outbreak has remained relatively stable, with 131 confirmed cases and two deaths. Active transmission has been reported in Yambio, Juba, Ezo and Tambura. A national mpox vaccination plan has been finalized and is awaiting final approval from the Ministry of Health.

There was some improvement in malaria indicators. South Sudan recorded 53,567 malaria cases and 12 deaths during the reporting week, a 39.5% decline from the same week in 2025, when 88,582 cases were reported.

Authorities and partners have distributed about 7.5 million of 9.5 million planned long-lasting insecticidal nets, reaching 79% of the national target ahead of the expected malaria transmission peak.

In Jonglei state, however, health and humanitarian conditions remain particularly severe.

Health facilities in Akobo recorded 4,023 consultations during the week, with malaria accounting for 1,156 cases, acute respiratory infections for 888 and acute watery diarrhea for 630.

Health workers also reported 33 cases of severe acute malnutrition with medical complications, highlighting growing nutritional pressures among vulnerable communities.

Meanwhile, violence in Twic East displaced an estimated 1,301 households, or about 7,806 people, according to an interagency rapid needs assessment. Displaced families reportedly fled with few or no belongings and face shortages of safe water, shelter, food and basic health services.

Humanitarian organizations are working to expand mobile health services in displacement sites, conduct nutritional screening, restore routine immunization services in Akobo and deliver water purification supplies to reduce the risk of further disease outbreaks.

The overlapping health, humanitarian and security crises are placing additional pressure on South Sudan’s already fragile health system, while the outbreak in neighboring DRC continues to pose a significant cross-border threat.

Health authorities and humanitarian partners are maintaining surveillance, strengthening border screening and scaling up vaccination, nutrition and disease-control measures as they seek to prevent further deterioration.