Accelerating genomics-based surveillance for COVID-19 response in Africa

The use of genomics to support the response to COVID-19 and containment of the virus in Africa is currently low. To address this suboptimal use of genomics, the Africa Centres for Disease Control and Prevention (CDC) Institute of Pathogen Genomics, in consultation with the Africa CDC led African Task Force for Coronavirus Preparedness and Response (AFTCOR) laboratory technical working group.

First, resources are being mobilised to accelerate SARS-CoV-2 sequencing across the continent, leveraging available next-generation sequencing plat- forms within the continent, and resources and technical support is being provided to 16 countries.

Second, a network of sequencing laboratories and genomics and bioinformatics experts is being brought together to share resources, expertise, and data.

Third, protocols are being standardised to ensure generation of representative and reproducible data. Fourth, sample referral approaches are being coordinated, to network countries with limited sequencing capacity with regional laboratories.


Download the manuscript published in the Lancet Microbe.

As well as ongoing mobilisation of resources to support the COVID-19 outbreak response, it is crucial for Africa to develop sustainable approaches, with a vision to change the siloed pathogen-specific diagnostics methods and implement digital and genomic transformation in the public health system.

In recognition of the revolutionary potential of genomic technology and computational power, African researchers are pioneering novel approaches and alliances to advance public health surveillance systems. In addition, the AfricaCDC, SANBI, KRISP and H3AbioNet, among others, have organised weekly training webinar to capacitate researchers and public health officials in Africa. Webinar every Wednesday 2PM East African Time - to register visit:

News date: 2020-08-25


Publication cited

Accelerating genomics-based surveillance for COVID-19 response in Africa. Tessema SK, Inzaule SC, Christoffels A, Kebede Y, de Oliveira T, Ouma AEO, Happi CT, Nkengasong JN, Lancet Microbe (2020),

KRISP has been created by the coordinated effort of the University of KwaZulu-Natal (UKZN), the Technology Innovation Agency (TIA) and the South African Medical Research Countil (SAMRC).

Location: K-RITH Tower Building
Nelson R Mandela School of Medicine, UKZN
719 Umbilo Road, Durban, South Africa.
Director: Prof. Tulio de Oliveira