Addis Ababa, Durban, Brazzaville, and Stellenbosch, 15 September 2022. A major scientific report from Africa is featured in the journal Science today. This scientific report show how the rapid expansion of genomics surveillance in Africa allowed the continent to describe the introduction and spread of the SARS-CoV-2 variants in African countries in real-time during the COVID-19 pandemic.

The scientific publication includes over 300 authors from Africa and abroad who worked together to describe and analyze over 100,000 genomes and characterize SARS-CoV-2 variants in real-time. This was the largest consortium of African scientists and public health institutions working together to support data-driven COVID-19 response in Africa.

This publication shows how the large investment, collaboration and capacity building in genomic surveillance on the African continent enabled real-time public health response. Particularly it describes the setting up of the Africa Centre for Disease Control and Prevention (Africa CDC) – Africa Pathogen Genomics Initiative (Africa PGI) and the development of the continental network by the Africa CDC and the Regional Office for the World Health Organization in Africa (WHO) to expand access to sequencing and cover surveillance blind spots, in parallel with the growth of the number of countries that are able to sequence SARS-CoV-2 with in the country.

“The publication highlights that sustained investment for diagnostics and genomic surveillance in Africa was needed to not only combat SARS-CoV-2 on the continent, but establish a platform to address the emerging, re-emerging, endemic infectious disease threats, such as Ebola, HIV/AIDS, TB and Malaria. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century.” said Dr. Yenew Kebede, Head Division of Laboratory Systems Acting Head for Surveillance and Disease Intelligence at the Africa CDC

This study was led by two labs that setup the network for genomics surveillance in South Africa, the Centre for Epidemic Response and Innovation (CERI) at Stellenbosch University and the KwaZulu Natal Research and Innovation Sequencing Platform (KRISP) at the University of KwaZulu-Natal, in close coordination with the Africa CDC, WHO AFRO and 300 other institutions across the continent.

“The enormous leap Africa made in genomic surveillance during the past two years is the silver lining in the COVID-19 pandemic,” said Dr Matshidiso Moeti, WHO Regional Director for Africa. “The continent is now better prepared to face down both old and emerging pathogens. This is a model of how when Africans are in the driving seat we can come up with lasting change and stay a step ahead of dangerous diseases.”

“It has been an inspiring experience to share knowledge, support and learn from colleagues in all parts of the continent continuously during the pandemic. We witnessed small

countries with no previous genomics experience become empowered in sequencing and bioinformatics methods, and start to actively participate in regular pathogen genomic surveillance for SARS-CoV-2. I think it will be a real model of how scientists and public health officials across countries can have a unified front against infectious diseases in the future.”, says Houriiyah Tegally, Bioinformatician at KRISP and CERI and first-author on this publication.

The results also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most relevant being the detection of Beta and various Omicron subvariants. The publication highlights that most of the SARS-CoV-2 variants causing epidemic in Africa were introduced from abroad.

The scientists proceeded carefully in analysing genomic and epidemiological data collected in over 50 countries that experienced quite heterogenous epidemics in order to reconstruct transmission dynamics of the virus in the most accurate way. “The phylogeographic methods that we employ to investigate the movement of the SARS-CoV-2 virus and its variants into, out of, and within the African continent account for uneven testing and sampling proportions across countries, arising from the realities of doing genomic sequencing in the middle of a pandemic, often in low resourced settings.”, explains Dr. Eduan Wilkinson, head of bioinformatics at CERI at Stellenbosch University and senior author on this publication.

The initial waves of infections in Africa were primarily seeded by multiple introductions of viral lineages from abroad (mainly Europe). The Alpha variant that emerged in Europe in the end of 2020 ended up causing infections in 43 countries with evidence of community transmission in Ghana, Nigeria, Kenya, Gabon and Angola. For Delta, the bulk of introductions was attributed to India (~72%), mainland Europe (~8%), the UK (~5%), and the US (~2.5%). Viral introductions of Delta also occurred between African countries in 7% of inferred introduction. For Omicron the scientific results indicate more reintroductions of the variant back into Africa, at least 69 (95% CI: 60 – 78) from Europe and 102 (95% CI: 92 – 112) from North America than from other African countries. This was amplified for Omicron BA.2; the results suggest at least 99 separate introduction or reintroduction events of BA.2 into African countries, ~65% of which are from Europe and ~30% from Asia.

“The ironical part of these results is that most of the introductions of variants in Africa were from abroad, but Africa was the most discriminated and penalized continent in the world with travel bans. Instead of unscientific and inappropriate reactions, we should be building on the infrastructure established in Africa so that the continent can rapidly pivot to other epidemics without the fear of being punished” said Prof. Tulio de Oliveira, Director of the two institutes, CERI and KRISP, that lead the consortium analysis with the Africa CDC and WHO AFRO.

“This study is a testament to Africa CDC’s impact in rapidly expanding access to sequencing technologies by African Union Member States, and creating a platform for coordination and collaboration by all stakeholders.” said Dr. Ahmed Ogwell, Acting Director of the Africa CDC

About Africa Pathogen Genomic Initiative (Africa PGI)

In 2020, the Africa Centres for Disease Control and Prevention (CDC) launched a multi-sectoral partnership –Africa Pathogen Genomics Initiative (Africa PGI) to integrate pathogen genomics and bioinformatics into public health surveillance, outbreak investigations, and improved disease control and prevention in Africa. Africa PGI is a collaboration between the Africa CDC Institute of Pathogen Genomics, ASLM, US CDC, the Bill & Melinda Gates Foundation, Microsoft, Illumina Inc, Oxford Nanopore Technologies, and others.

About the Centre for Epidemic Response and Innovation (CERI) at Stellenbosch University.

CERI primary goal is to challenge the status quo on epidemic response and innovation in Africa and allows Africa to control its own epidemics and pandemics. Our vision is to effectively respond to epidemics through pathogen genomic surveillance to enhance biomedical discovery, improve the treatment, diagnosis and prevention of human diseases in Africa. CERI is a centre of Stellenbosch University and its state-of-the-art laboratory are based at the new Biomedical Research Institute Building at the Faculty of Medical and Health Sciences campus.

About the KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP) at University of KwaZulu-Natal (UKZN).

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 Council (SAMRC). KRISP is based on a state-of-art building at Nelson R Mandela School of Medicine at UKZN, Durban. KRISP has one of the world’s most advanced genetic sequencing systems in order to enable and support world-class genomics research in Africa. Our objective is to use Next Generation sequencing and bioinformatics to answer scientific questions that are of local, national and international importance.

About World Health Organization (WHO) African Region (WHO AFRO)

World Health Organization contributes to a better future for people everywhere. Good health lays the foundation for vibrant and productive communities, stronger economies, safer nations and a better world. As the lead health authority within the United Nations system, our work touches people’s lives around the world every day. In Africa, WHO serves 47 Member States and works with development partners to improve the health and well-being of all people living here. The WHO Regional Office for Africa is located in Brazzaville, Congo. Learn more at www.afro.who.int and follow us on Twitter, Facebook and YouTube

For media enquiries to Africa CDC – Africa PGI, please contact:

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For media enquiries to CERI and KRISP, please contact:

Paul Harris Communication Officer

CERI – Centre for Epidemic Response and Innovation Stellenbosch University KRISP – KZN Research Innovation and Sequencing Platform Nelson R Mandela School of Medicine, UKZN, Durban. +27 31 260 4898 +27 82 806 6290 paul@htagmedia.co.za

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