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Detailed analysis by African scientists of SARS-CoV-2 published in Science
Author: Corporate Communication and Marketing / Korporatiewe Kommunikasie en Bemarking
Published: 09/09/2021

​​​Scientists and public health officials in Africa join forces to expand genomic training and facilities so the continent can respond robustly to the global pandemic. If left behind, Africa could become a breeding ground for new variants.

Science published a detailed analysis of SARS-CoV-2 variants produced by hundreds of African scientists and public health officials across the continent, today (9 September 2021). This is the first major output of Africa's top scientists to increase the continent's capacity to produce and analyse genomic data.

Genomic surveillance has been crucial to identify SARS-CoV-2 variants and guide the global public health response. Unfortunately, when the pandemic started, Africa was soon left behind. Its fragile health and scientific infrastructure, weak purchasing power, and the fact that diagnostics and reagents were being hoarded by developed countries, made Africa the world's least vaccinated continent. It did not have access to the technology required to fight the pandemic.

In order to close this gap, 112 African and 25 international organisations, in close collaboration with the Africa Centres for Disease Control and Prevention (Africa CDC) and the World Health Organisation (WHO), worked together and created a detailed analysis of SARS-CoV-2 variants and lineages in Africa. The detailed Science paper describes SARS-CoV-2 genomic surveillance in 33 African countries and two overseas territories.

It shows that the epidemics in most countries were initiated by importations predominantly from Europe, which diminished after the early introduction of international travel restrictions. As the pandemic progressed, ongoing transmission in many countries and increasing mobility led to the emergence and continent-wide spread of many variants of concern and interest, such as B.1.351 (Beta), B.1.525 (Eta), A.23.1 and C.1.1/C.1.2.

In spite of limited sampling, the African scientists identified many of the variants of concern (VOCs) and variants of interest (VOIs) that are being transmitted across the world. Detailed characterisation of the variants and their impact on vaccine-induced immunity is extremely important. If the pandemic is not controlled in Africa, we may see the production of vaccine-escape variants, which may profoundly affect the African and global population. The findings in this important paper highlight that Africa must not be left behind in the global pandemic response, otherwise it could become a breeding ground for new COVID variants.

“We are deeply committed to using the most advanced technologies in Africa to trace and combat the virus. If the virus keeps evolving on the African continent, this will become a global problem. It is our moral duty to try to protect Africa and the world," says Prof Tulio de Oliveira, a professor of Bioinformatics who hold appointments at Stellenbosch University's School for Data Science and Computational Thinking, its Faculty of Medicine and Health Science and Faculty of Science, and director of the KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP) at the University of KwaZulu-Natal. “This was a very fulfilling collaboration. Not only did we manage to share and analyse our African data together, the collaboration also involved complete sharing of knowledge, with all analysis scripts shared and hundreds of hours of capacity building in analysis and data generation so that genomics can be decentralised and performed in real time in Africa."

“Strengthening genomic surveillance systems across the continent is key for early detection and control of disease outbreaks," says Dr John Nkengasong, director of the Africa CDC. “Since the beginning of the COVID-19 pandemic, the Africa CDC Institute of Pathogen Genomics has been supporting member states to expand their SARS-CoV-2 genomic surveillance for the rapid detection of variants. The Institute is very proud of this collaborative work and will continue to coordinate collaboration among public health, academic and research institutions to strengthen pathogen genomics and bioinformatics capacity in Africa."

Since the production of this manuscript and collaboration, Africa has increased its genomics surveillance and today, 40,000 African genomes are available in GISAID. The increase of sequencing is a challenge that the continent is overcoming with the support of funders, the Africa Union/Africa CDC and the WHO in close collaboration with Ministries of Health, public health institutions and the scientific community that produced this pan-African analysis.

“We ignore mutations and variants at our own peril. The Delta variant is a wake-up call and underlines the importance of genomic information, and of ensuring that African scientists have the necessary resources to analyse the evolution of COVID-19," says Dr Matshidiso Moeti, WHO regional director for Africa. “Without this analysis, variants can spread undetected on the continent and across the globe. This will prolong the acute phase of the COVID-19 pandemic, not just in Africa, but worldwide."

The open-access manuscript is available on the Science website:

Wilkinson et al. A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa, Science, doi/10.1126/science.abj4336, 2021.