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Fewer than 0.5% of SARS-CoV-2 sequences available in GISAID are from Africa, despite Africa representing 14% of the world’s population. While some African institutions have access to genomic sequencing technology, this is not widespread due to high upfront costs, a limited well-trained workforce, and limited infrastructure for data systems. 

By creating a collaborative program for genomic sequencing of SARS-CoV-2 in Nigeria, Kenya, and South Africa that supports other African countries, we will spearhead the Africa genomics surveillance revolution. Genomics surveillance aims to transform public health interventions by monitoring genetic changes that impact pathogenicity, diagnostics, therapeutics, and vaccines.

Thie Genomics Africa program’s principal investigator (PI) is Prof Tulio de Oliveira from CERI, Stellebonsch & UKZN. The Co-PIs are Prof Christian Happi from ACEGID and Prof Samuel Oyola from ILRI..

This program will be conducted in close collaboration with the Africa Centres for Diseases Control and Prevention (Africa CDC) and the World Health Organization (WHO). Africa CDC and WHO partnered to create the Africa Pathogen Genomic Initiative (Africa PGI).


This program was created using financial support from The Rockefeller Foundation to Stellenbosch University. The Centre for Epidemic Response and Innovation (CERI) at Stellenbosch University and UKZN in South Africa, the African Center of Excellence for Genomics of Infectious Diseases (ACEGID) in Nigeria, and the International Livestock Research Institute (ILRI) in Kenya. Together we will expand Africa’s capacity to produce extra 20,000 SARS-CoV-2 additional genomes, which will double the number of genomes produced on the continent in 2021/2022. 

To increase capacity in Africa, this project will also launch the Rockefeller Fellowships for Genomics in Africa, which will allow more than 100 scientists involved with Africa PGI to receive hands-on genomics training at CERI, ACEGID, and ILRI. 

In brief, this project will:

1.         Support public health authorities in African countries to develop and implement sampling strategies for genomics surveillance that can guide policy and interventions

2.         Increase genome sequencing throughput through investments in automation and targeted sequencing

3.         Expand and streamline bioinformatics pipelines for SARS-CoV-2 analysis 

4.         Develop and expand the scientific workforce with training fellowships to drive more robust, sustainable genomic surveillance in Africa

This funding will not only help fight COVID-19, but will also provide a unique opportunity to expand the genomics infrastructure in Africa that can be used for pandemic prevention and preparedness. 

 We would also like to encourage funders and philanthropists to help to advance this initiative and allow the genomics revolution to benefit Africa as much it is benefiting other regions of the world! See our donors page for a list of funders.

Contact Genomics Africa PIs: