CDC in South Sudan

South Sudan

A group of Frontline-Field Epidemiology Training Program (FETP) participants celebrate their graduation in July 2022. Photo by Gildo Okure/AFENET

The Centers for Disease Control and Prevention (CDC) established an office in South Sudan in 2006 to work on HIV prevention through the U.S. President’s Emergency Plan for AIDS Relief (PEPFAR). CDC partners with the Ministry of Health (MOH) to focus on national responses to HIV, tuberculosis, diarrheal diseases and cholera, Ebola preparedness, measles, polio, and COVID-19. CDC’s partnership and investments help strengthen disease surveillance capabilities, laboratory systems, data and health information management systems, and the public health workforce.

Download South Sudan Fact Sheet [PDF – 340 KB]

CDC Impact in South Sudan

Global Health Security

CDC partners with the MOH to develop sustainable national systems for disease surveillance, emergency preparedness and outbreak response, immunizations, laboratory capacity, strategic information, and workforce development. In response to the 2018 Ebola outbreak in the Democratic Republic of Congo, CDC and the MOH leveraged existing PEPFAR resources to establish the country’s first National Public Health Emergency Operations Center (PHEOC). The PHEOC was critical to South Sudan’s Ebola preparedness and response activities between 2018 and 2020. CDC uses the Extension for Community Healthcare Outcomes (ECHO) Project, a Zoom-based learning platform, to train healthcare workers in epidemiology, disease surveillance, diagnostics, treatment and case management, and prevention. The ECHO Project initially focused on HIV and TB trainings and later expanded to include Ebola and COVID-19 trainings for healthcare workers. Due to existing partnerships and structural investments, South Sudan was prepared to rapidly activate the PHEOC in response to the COVID-19 pandemic.

Icon Covid

CDC’s 15-year partnership with the MOH provided a strong foundation for Ebola preparedness efforts from 2018 to 2020 and during the ongoing COVID-19 response


In 2018, CDC supported the establishment of South Sudan’s National Public Health Emergency Operations Center (PHEOC)

handshake icon

CDC provided technical and financial support to the MOH for a series of trainings for PHEOC staff that focused on the Incident Management System (IMS). These trainings strengthen emergency management capabilities at the national and sub-national levels

Health worker

Participants in the IMS trainings included senior technical staff from 10 states and three administrative areas

Icon Covid

In 2018, CDC also supported establishment of South Sudan’s Public Health Institute (SSPHI) by assisting with the strategic and legal frameworks and operational plan

Icon Covid

CDC supports Ebola response preparedness activities, including epidemiology and disease surveillance, laboratory services, border health screening, infection prevention and control (IPC), and case management

Icon Covid

In June 2022, CDC and WHO supported the MOH to develop and launch a national IPC strategic plan

Icon Covid

CDC expanded the Extension for Community Healthcare Outcomes (ECHO) Project to 54 healthcare facilities since 2018


CDC’s history of PEPFAR partnerships and programs provided the foundation to rapidly mobilize technical support, leadership, and coordination in response to COVID-19. In January 2020, the MOH began preparing for national pandemic response and later activated the PHEOC in March 2020. The first case of COVID-19 in South Sudan was confirmed on April 5, 2020. In the early stages of the pandemic, CDC supported data management and developed surveillance and vaccination reporting modules within the District Health Information Software 2 (DHIS2) platform. CDC also helped leverage existing resources, such as the PHEOC, ECHO platform, and laboratory infrastructure for COVID-19 response. CDC continues to focus support on strengthening disease surveillance, health promotion, laboratory diagnostics and systems, emergency management, communications, and border health. CDC and partners support the MOH’s COVID-19 vaccine rollout through technical planning, coordination of vaccine donations, establishment of a vaccine reporting system, and vaccine delivery.

Icon Covid

With CDC support, South Sudan delivered nearly 1.3 million COVID-19 vaccine doses since April 2021

Icon Covid

Since September 2021, CDC supported distribution of more than 336,000 COVID-19 vaccine doses through COVAX

Icon COVID Chart

In response to COVID-19, CDC supported the PHEOC to establish the Data Management Unit (DMU). DMU is a first-of-its-kind data hub that generates quality outbreak data and informs decision-making, preparedness, and response

Icon Covid

CDC established COVID-19 surveillance and vaccination reporting modules within the DHIS2 to increase availability and visibility of data and inform pandemic response

Icon Covid

CDC supported the decentralization and expansion of COVID-19 testing to more than 36 facilities outside of the National Public Health Laboratory

Corona stats icon

CDC’s laboratory support and leadership resulted in an increase of COVID-19 testing from two tests per week to nearly 1,000 tests per day between April 2020 and the peak of the epidemic in May 2022

Icon training

CDC leveraged the existing ECHO platform to conduct a series of trainings for laboratory staff on COVID-19 IPC

Icon Covid

South Sudan partnered with the MOH to expand existing laboratory infrastructure for COVID-19 testing. This support helped identify more than 17,200 cases and contributed to effective case management

Field Epidemiology Training Program (FETP)

FETP strengthens the capacity of the public health workforce to detect, respond, and control disease outbreaks at the source. Participants at the county, state, and national levels develop critical skills in data collection, analysis, and translation of data into evidence-based recommendations. In November 2021, CDC partnered with the MOH, WHO, and African Field Epidemiology Network (AFENET) to establish FETP-Frontline. CDC plans to expand FETP to include FETP-Intermediate and FETP-Advanced cohorts. FETP graduates are involved in real-time disease surveillance, outbreak investigation, rapid response, and partner coordination.

Health worker

Since March 2021, 48 residents, representing all 10 states, graduated from South Sudan’s FETP

world inspect

In 2022, FETP graduates are leading and coordinating responses to multiple disease outbreaks across South Sudan, including: measles in 6 states, cholera in Bentiu and Rukona, hepatitis in Bentiu, meningitis in Northern Bahr el Ghazal, and anthrax in Gogrial West

Icon Covid

Before establishing FETP in 2021, trainees from South Sudan participated in Kenya’s FETP-Advanced cohort. Fifteen graduates from Kenya’s FETP now hold key positions at the South Sudan MOH, WHO country office, and international non-governmental organizations


As of 2021, nearly 170,000 people live with HIV in South Sudan. More than 9,300 new cases were diagnosed and 8,900 deaths occurred in 2021. As a key implementer of PEPFAR, CDC works with the MOH, WHO, UN, the Global Fund, and other partners to build a sustainable national HIV response program and achieve the UNAIDS 95-95-95 goals for epidemic control. CDC supports comprehensive HIV programs including HIV testing services, prevention of mother-to-child transmission, and anti-retroviral treatment (ART). CDC’s primary goals in South Sudan include:

  • Increasing access to quality services for people living with HIV
  • Reaching high viral load suppression (a low amount of HIV in the body) among people living with HIV by minimizing treatment interruptions and re-engaging people whose treatment was interrupted
  • Enhancing laboratory capacity and coverage of viral load and early infant diagnosis testing
  • Enhancing the quality and availability of HIV program data and use of data to inform program decisions

TB is one of the leading causes of death for people living with HIV. CDC works with the MOH and other partners to screen for TB among people receiving treatment for HIV and ensure that people living with co-infections are treated for both diseases.

Icon Covid

In 2021, CDC adapted HIV strategies to minimize treatment interruptions for people living with HIV during the COVID-19 pandemic. CDC transitioned to a new treatment regimen (TLD) and initiated 6-month ART and community refills

Icon ribbon

In April 2022, the MOH launched the Incident Management System (IMS) for HIV/AIDS to accelerate progress toward HIV control

Icon Covid

In 2021, CDC helped expand the number of facilities with point-of-care testing capacity from 14 to 34 facilities

Icon pills

CDC helped deliver ART to more than 31,000 people living with HIV in 2021


In 2021, CDC screened for TB among all patients who receive HIV treatment. More than 200 people were newly diagnosed with TB co-infection and started TB treatment

Icon Covid

CDC supports HIV service delivery in approximately 70 health facilities. Most of these facilities are in the Equatoria region and Lakes and Western Bahr El Ghazal states

Icon Covid

During the COVID-19 pandemic, CDC identified 70% of the new HIV cases reported by PEPFAR in South Sudan in fiscal year 2021


CDC identified more than 7,700 new cases of HIV in 2021 and linked 100% of the new patients to treatment

Icon Covid

Despite transportation challenges due to COVID-19, viral load (VL) testing continued uninterrupted

Icon Covid

In 2021, CDC conducted 80% of the VL tests documented in South Sudan, which covered more than 60% of all patients. As of December 2021, the VL suppression rate is 86%

Icon training

CDC provided training and mentorship to 26 MOH officers at PEPFAR-supported sites to ensure high-quality HIV service delivery

Icon Covid

In 2021, CDC engaged in nearly 500 site management meetings at 21 health facilities. This support helped identify program challenges and develop action plans to enhance HIV service and programs

Icon Covid

With CDC support, the MOH completed two HIV bio-behavioral surveys that focused on determining the burden of HIV and access to resources for female sex workers. These surveys also helped inform decisions on resource mobilization

Icon Covid

CDC is supporting a 5-year project focused on strengthening national capacity for integrated HIV/AIDS health data collection, use, and dissemination. CDC’s priority is to support the MOH to launch a DHIS-2 and establish an HIV Electronic Medical Record System

Laboratory Systems Strengthening

Since 2006, CDC has partnered with Global Fund to support South Sudan’s National Public Health Laboratory by strengthening laboratory infrastructure, staffing, and technical capacity. CDC and Kenya’s National HIV Reference Laboratory also support the South Sudan MOH to monitor viral load among people receiving treatment for HIV. In partnership with CDC’s country office in Kenya, CDC South Sudan started a quality assurance program for HIV rapid testing. Other CDC-supported activities include implementation of laboratory quality management systems, biosafety, blood safety, staff trainings, and guideline development.

Icon Covid

In May 2018, CDC supported establishment of the first viral load monitoring facility at South Sudan’s National Public Health Laboratory (NPHL)

Icon Covid

In April 2017, CDC began supporting the MOH to monitor VL among patients being treated for HIV. Testing was done at Kenya’s National HIV Reference Laboratory

Icon Covid

With technical support from CDC, the MOH developed and released consolidated national HIV treatment guidelines and five laboratory manuals and SOPs for NPHL staff and HIV/AIDS program staff

Icon Covid

Through PEPFAR, CDC partnered with the MOH and WHO to revise national ART guidelines in South Sudan. These guidelines reflect a transition to a new treatment regimen and the use of innovative approaches to HIV service scale-up in settings with limited resources

Vaccine-Preventable Diseases

Every year, vaccines prevent more than 2-3 million deaths among children younger than age 5. In South Sudan, CDC works with the MOH, WHO, AFENET, and UNICEF to strengthen immunization systems and provide technical support. CDC supports workforce capacity-strengthening for national and state immunization programs as part of the Expanded Program on Immunization. To strengthen workforce capacity and immunization systems, health professionals from across the country participate in trainings on routine immunization, disease surveillance, cold-chain logistics, data management, communication, and other supplemental activities.


As part of the Expanded Program on Immunization (EPI), 56 trainees from across South Sudan were trained in vaccine-preventable disease surveillance, cold-chain logistics, data management, and communication

CDC Staff in South Sudan
  • 2 U.S. Assignees
  • 8 Locally Employed
South Sudan At a Glance
  • Population: > 11.3 million
  • Per capita income: $1,090
  • Life expectancy: F 60 / M 57 years
  • Infant mortality rate: 61/1,000 live births

Sources: World Bank 2021, South Sudan; World Bank 2015, South Sudan; Population Reference Bureau 2021, South Sudan

South Sudan Top 10 Causes of Death
  1. Neonatal disorders
  2. Lower respiratory infections
  3. Diarrheal diseases
  4. Malaria
  6. Tuberculosis
  7. Stroke
  8. Ischemic heart disease
  9. Congenital birth defects
  10. Protein-energy malnutrition

Source: GBD Compare 2019, South Sudan

Related Links

Global HIV & TB Country Profile: South Sudan

Republic of South Sudan | Travelers’ Health | CDC

Video: CDC in Action: Measuring and advancing progress towards controlling HIV – YouTube


Emerging Infectious Diseases Journal: South Sudan Articles All Issues | CDC

HIV and TB: