African regional assistance to South Sudan and Kenya during the pandemic


This project’s previous work focused on mapping the regional response to the pandemic, but important questions remain about the impact of this regional support.  In collaboration with Amref International University Kenya and Amref South Sudan, we explored the impact of AU and Africa CDC support on the national responses to the pandemic in Kenya and South Sudan.  This piece relies on an analysis of primary source documents from the AU and Africa CDC as well as news articles and reports.  In addition, the analysis is supported by a limited number of key informant interviews of with government officials.


COVID-19 in South Sudan

As of early March 2022, South Sudan had officially recorded just over 17,000 cases of COVID-19.  However, accurate reporting can be difficult, and beyond the case numbers, the COVID-19 pandemic has had a significant impact on the economic and political landscape.  The pandemic and social distancing policies impacted economic growth, investment, and market participation in South Sudan. The poverty rate was already very high due to ongoing conflict and development challenges, but it rose in 2020.  COVID-19 also hit South Sudan at a particularly tenuous moment as the country was trying to end its civil war.   The Revitalised Agreement on the Resolution of the Conflict in the Republic of South Sudan (R-ARCSS) was signed in September 2018.  However, the transitional government was not inaugurated until February 2020, and just a few weeks later government officials and ministers were dealing with the impact of the pandemic and often needing to self-isolate themselves.  As of early 2021, the government was significantly behind in implementing the peace agreement.

Regional Support to and Collaboration with South Sudan

As with AU assistance to the entire region, there has been multiple components encompassing political advocacy and solidarity, economic support, and public health expertise and resources.  South Sudan also faced humanitarian disasters during the pandemic, and the AU Commission specifically highlighted its plight and called for increased member state support to South Sudan. This solidarity specific to South Sudan is part of a much larger picture of the AU advocating for member states and raising issues of vaccine inequality and more recently travel bans.

The AU has not only been engaged in advocating for more vaccine equity but in securing additional vaccine doses for African states beyond those provided by COVAX.  The AU reported it secured an additional 270 million doses in early 2021.  Of these, 39 million were slated to be distributed through the East African Community (EAC) with 2.3 million allocated to South Sudan.

Public health support through Africa CDC began very early on in the pandemic.  For example, in February 2020, Africa CDC held a training in Nigeria for representatives from 22 member states, including South Sudan, to build capacity to prevent infection at healthcare facilities and to screen air travellers.  And it has continued throughout.  In summer 2021, Africa CDC, in collaboration with Project HOPE and the West African Health Organisation (WAHO), trained 140 healthcare workers on COVID-19 vaccines.  Healthcare workers from Economic Community of West African States (ECOWAS) member states and South Sudan attended.

There has also been in-kind support coming from African institutions and businesses, international organisations, and charitable foundations, which Africa CDC helped to coordinate and disseminate. In December 2020, Africa CDC delivered mechanical ventilators and oxygen concentrators donated by the Wellcome Foundation to South Sudan. In April 2021, Africa CDC distributed 200,000 PCR extraction kits to 10 member states, including South Sudan.  It is unclear exactly how many went to South Sudan.

Impact of Regional Support

Africa CDC documents and media reporting show many specific initiatives of regional in-kind and training support to South Sudan.  More recently, Africa CDC and the AU have also been instrumental in addressing vaccine inequality and augmenting COVAX with Africa-led initiatives to procure more vaccines for the continent.  The regional health body is also investing in bolstering Africa’s ability to respond to the next pandemic by building capacity in the healthcare professional workforce, investing in laboratory facilities and disease surveillance, and establishing regional approval and manufacturing of vaccines.

However, Africa CDC has not been instrumental in shaping the South Sudan national COVID-19 response.  Africa CDC has put out a significant amount of policy and public health guidance as well as real-time information on cases throughout Africa.  In South Sudan, government officials interviewed for this research, indicated that the Government of South Sudan used this guidance to confirm or strengthen nation decisions, but it was not necessarily the guiding force in crafting government policy.  They also cited many other sources of information, notably the World Health Organisation (WHO) and local authorities.


COVID-19 in Kenya

As of January 2022, Kenya was experiencing its fifth wave of COVID-19, and as of early March 2022, Kenya has officially recorded just over 323,000 cases of COVID-19.  As seen in South Sudan and around the globe, the pandemic also had a profound impact on the Kenyan economy, health systems, and vulnerable populations.

Regional Support to and Collaboration with Kenya

Kenya has supported Africa CDC and one of the key issues for Kenya’s delegates at the Ordinary Sessions of the AU Assembly and Executive Council held in February 2022 was support for the operationalisation of Africa CDC.  Cabinet Secretary Ambassador Raychelle Omamo stating through the Ministry of Foreign Affairs, “In order to be fully prepared to respond (to another pandemic), we must ensure that Africa CDC is properly engineered to live up to its task and fit for purpose”.  Kenya strongly supported the Africa CDC Trusted Travels Platform and was a pioneer country in its development and move to digitize vaccine records, and Kenyan officials praised the continental efforts to respond to the COVID-19 pandemic. Like South Sudan, Kenya also received allocations of vaccines through the African Vaccine Acquisition Trust.  For example, in October 2021, Kenya received 252,000 doses of the Johnson & Johnson vaccine.

Impact of Regional Support

It is clear from Government of Kenya statements and links between Kenya and Africa CDC that there will be ongoing collaboration.  One of the most notable spaces for collaboration will be through the Eastern African Regional Collaboration Centre (RCC), which is hosted by Kenya and headquartered in Nairobi. This RCC was launched on 1 October 2021 with an event discussing effective responses to COVID-19 and future public health threats.

Further Research

This piece offers a window into the impact of regional support to member states.  However, it has limitations. It profiles two states whereas the AU has 55 member states all of which have different needs and capacities and which saw uneven impacts from the pandemic.  It is also based on very limited interviews due to availability of government officials.  However, it provides a basis for further research to understand the utility of the trainings and supplies that were offered and the benefits and lessons from coordination amongst national and regional actors.  Africa CDC has also set the stage for ongoing collaboration through RCCs and for long-term capacity building within the region and national health ministries, which will surely impact readiness to manage future public health challenges.

Disclosure: Amref Health Africa is a partner of Africa CDC and WHO and has aided in the COVID-19 response in South Sudan and other countries.  This research project partnered with the Amref International University, based in Nairobi, Kenya, and Amref Health Africa in South Sudan.

Acknowledgements: We want to acknowledge Rawiyah Aboud, Jackeline Njuguna, Winfrida Mutegi, and  Gilbert Sigei, postgraduate students at Amref International University, for their support in the desk review.

About the authors

Kathryn Nash: University of Edinburgh Law School Old College

Samuel Okaro: Amref South Sudan, Opp UN-OCHA Juba

Ireri Mugambi Edward: Amref International University & Smart Health Consultants Limited Company

Lydia Atambo: Amref International University

Bibliography (sources also hyperlinked above)

Abraham A. Awolich. “COVID-19 and the Political Transition in South Sudan”. The Sudd Institute (6 February 2021). Available at:

Elizabeth Merab. “EAC states to get 39m Covid vaccine doses from AU”. The East African (14 January 2021). Available at:

James Alic Garang. “Will the Impact of the Pandemic on the Expected National Output Persis?”.  The Sudd Institute (3 June 2021). Available at:

Africa CDC and African Union Documents

Africa CDC to launch Eastern Regional Co-Ordination centre. African Union (24 September 2021). Available at:

African Joint Continental Strategy (5 March 2020).  Available at:

Framework for Public Health Workforce Development, 2020-2025.  Africa CDC (10 March 2020). Available at:

Kenya’s Statement on the Africa CDC Trusted Travel Platform.  Africa CDC (25 May 2021). Available at:

Outbreak Brief #9. Africa CDC (17 March 2020).  Available at:

Outbreak Brief #47. Africa CDC (8 December 2020). Available at:

Outbreak Brief #91.  Africa CDC (14 October 2021). Available at:

Outbreak Brief #98.  Africa CDC (30 November 2021).  Available at:

Outbreak Brief #103. Africa CDC (4 January 2022).  Available at:

Partnership for African Vaccine Manufacturing: From Aspiration to Action. Africa CDC (7 December 2021).  Available at:

US $100 million Africa Pathogen Genomics Initiative to boost disease surveillance and emergency response capacity in Africa. Africa CDC (12 October 2020).  Available at:

Member State Documents

Kenya Support the Operationalization of Africa CDC.  Republic of Kenya Ministry of Foreign Affairs (4 February 2022).  Available at: