What are the origins of COVID-19 variants in Africa?

Genomic sequencing enables live tracking of the spread of a virus. A Science paper, released on September 15^th, 2022, analyzing more than 100,000 genomes, recalls the benefits of local sequencing while studying the spread dynamics of SARS-CoV-2 and its variants of interest on the African continent. More than 300 authors combined their research including 10 members of the Pasteur Network who shared locally sampled SARS-CoV-2 sequences. The results show that most of the introductions of the virus in Africa were from abroad. They also highlight the critical need to invest in diagnostics and genomic surveillance in Africa to best prepare for and respond to future emergencies and epidemics.

This study reveals a mapping of the transmission dynamics of COVID-19 on the African continent. Increased local sequencing capacity has resulted in improved turnaround times and more regular routine surveillance. Pasteur Network members have shared, via the GISAID initiative, the SARS-CoV-2 sequences in the framework of the REPAIR and AFROSCREEN projects.

The spread of the different COVID-19 variants in the continent was heterogeneous, especially for the Alpha, Beta, Delta and Omicron variants which have followed and still follow distinct patterns of dispersion. The Alpha variant that occurred on the continent emanated mainly from Europe before spreading to 43 countries. Most of the Delta variant introductions (about 72%) came from India, while introductions between African countries of the same variant represented only 7% of cases. As for the Omicron variant, its emergence came from Europe, as well as North America and Asia.

The 200 signatory institutions[1] of this study constitute the largest consortium of African scientists and public health institutions united to respond to COVID-19 using local data. The establishment of the Africa Pathogen Genomics initiatives by the Africa CDC and the continental network by the Africa CDC and WHO AFRO are testament to the intent to expand access to sequencing across the continent. Following the example of this study, sustained monitoring remains essential to maintain quality surveillance of both the circulation of COVID-19 and other emerging or re-emerging infectious diseases that may affect Africa.

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For more information:
The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance
Science, September 15^th, 2022.
Houriiyah Tegally^†, Tulio de Oliveira^*, Eduan Wilkinson^†* and al.
^† These authors contributed equally to this work.
^* Corresponding author.
DOI: 10.1126/science.abq5358
Press release: https://africacdc.org/news-item/a-continent-wide-collaboration-on-genomics-surveillance-show-the-power-of-african-science-and-how-the-majority-of-covid-19-variants-were-introduced-into-africa/

[1] This study was conducted by the Centre for Epidemic Response and Innovation (CERI) at Stellenbosch University, and the KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP) at the University of KwaZulu-Natal, in coordination with Africa CDC, WHO AFRO, and more than 200 partner institutions, including 10 Pasteur Network members: the CERMES Niger, the Institut Pasteur, the Institut Pasteur d’Algérie, the Institut Pasteur de Bangui, the Institut Pasteur de Côte d’Ivoire, the Institut Pasteur de Dakar, the Institut Pasteur de Guinée, the Institut Pasteur de Madagascar, the Institut Pasteur de Tunis, the Pasteur Center in Cameroon.

In June 2021, the Pasteur Network changed its governance to be more participatory and egalitarian. Upon agreement of all its members, a dedicated executive board was created to translate this evolution into concrete actions.

At the end of June 2022, the restructuring of the Pasteur Network begins with the arrival of Rebecca F. Grais, its new Executive Director, whose vision integrates a strong human dimension that is essential to the functioning of a network.

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Rebecca F. Grais was the Director of Research at Epicentre. She has extensive experience in epidemiological research focused on populations with little or no access to care. She was a former co-opted member of the Board of Directors and a member of scientific committees in the network and thus has a good knowledge of the Pasteur Network, its strengths, weaknesses and potential. She will lead its development with a collaborative ethos to address public health issues and improve health equity throughout the world.

Under her leadership, Pasteur Network will unite around a common culture built on the fundamental right of every human being to be in good health ^[1]. Rebecca F. Grais’ vision of the network includes a multi-scale approach: that of the individuals, that of the members and that of the Pasteur Network as a whole. With her, the network will learn to develop and add the strengths of each to improve public health in all its aspects: research, prevention, communication, and training among others.

Rebecca F. Grais will ensure that an environment conducive to the acquisition of knowledge and skills is maintained for both the Pasteurian community and the local populations. The results will be translated and transmitted beyond the scientific and academic literature. This open approach will participate in ensuring community participation and  will contribute to the development of health policies.

The executive management of Pasteur Network will leverage the network’s international presence, collaborative ethos, and diverse expertise to establish its global leadership.

About:

Rebecca F. Grais’ work focuses on prevention of infectious diseases, tropical diseases and emerging infections in low resource settings, particularly low and middle income countries among populations with little to no access to care. She has also focused on population-based studies of the effectiveness of public health interventions and efficacy trials of novel vaccines and therapeutic agents.

An additional aspect of her work concerns professional development, mentoring, and management training for populations underrepresented in research. The goal is to advance their individual careers while contributing to responsive innovations in health care. Rebecca F. Grais completed the majority of her training at John Hopkins University (USA) before obtaining her accreditation to supervise research from the Faculty of Medicine at the Université Paris-Saclay (formerly Paris-Sud) in 2013. At Epicentre, she was the head of the Epidemiology unit before becoming the Director of Research from 2015 to 2022.

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[1]  According to the WHO Constitution “the enjoyment of the highest attainable standard of health is one of the fundamental rights of every human being.”

Original publication on June 23^rd 2022, updated September 27^th 2022.

New appointments took place between July and September 2021 within the Pasteur Network. Six directors where appointed in agreement with the local institute administrations and the Institut Pasteur for a period of at least two years.

These new directors will integrate the various bodies of the Pasteur Network located in the Network four regions : Africa, Americas, Asia-Pacific and Euro-Mediterranean.

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Original publication on November 17^th 2021. Updated on September 27^th, 2022.