INSERM-ANRSAFROSCREEN: a sequencing capacity-building project to detect and monitor SARS-CoV-2 and other emerging pathogens in Africa

In Africa, the COVID-19 pandemic has affected nearly 6 million people and nearly 150,000 deaths have been reported to date. However, it is difficult to determine whether these figures correctly reflect the epidemiological situation, as virology surveillance is still limited in Africa. To date, circulation of the “Alpha”, “Beta”, and “Delta” variants has been reported in many African countries and, like all RNA viruses, SARS-CoV-2 will continue to mutate, which will have a decisive impact on the course of the epidemic.

In light of the urgent need for surveillance of the development of SARS-CoV-2 variants, the AFROSCREEN project has been designed to reinforce the sequencing and screening PCR testing capacities of laboratories in 13 African countries to detect emerging SARS-CoV-2 variants, monitor the dynamics of their diffusion in the population and investigate the epidemiological characteristics of the variants of interest. This will make it possible to track the development, spread, and clinical impact of variants more closely, to quickly alert health authorities and the international community in the event of an outbreak of a variant of interest, and support decision makers in defining public health priorities and preventive measures to control and limit the circulation of variants.

In the long term, the program will consolidate technology platforms to develop a permanent surveillance network for emerging pathogens in Africa, with a “One Health” approach.

Integrated in the French “COVID-19 – Health in Common” Initiative and in line with the G20 strategy, the AFROSCREEN project is funded by the French Agency for Development (AFD) to the tune of 10 million euros over 2 years (July 2021-July 2023).

AFROSCREEN demonstrates a resolute, committed approach focusing on interinstitutional collaborations to tackle major scientific and societal challenges. Indeed, the project is implemented by a consortium comprising three French research partners: ANRS | Maladies infectieuses émergentes, the Institut Pasteur and the National Research Institute for Sustainable Development (IRD), and 21 laboratories and reference centers in 13 sub-Saharan African countries: Benin, Burkina Faso, Cameroon, Central African Republic, Côte d’Ivoire, Democratic Republic of Congo, Ghana, Guinea, Madagascar, Mali, Niger, Senegal and Togo. This consortium, the first between the three French institutions and their laboratory networks, will provide extensive geographical coverage, strong delivery capacity, and technical and scientific expertise.

The project is implemented in close coordination with the Africa CDC and complements the Africa Pathogen Genomics Initiative for variant surveillance on the continent.

“In order to bring an end to the pandemic, it is necessary for all countries to have the tools to identify the emergence of new variants. AFROSCREEN is a pivotal project in the area of virology research and surveillance because one of its major components involves bolstering sequencing and training capacity. This consortium fits perfectly with the missions of the ANRS | Maladies infectieuses émergentes, which revolve around international and interinstitutional collaborations and combine the strengths of different actors working together” – Yazdan Yazdanpanah, Director of ANRS | Maladies infectieuses émergentes and GloPID-R Co-Chair.