The AFROSCREEN project

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Genome sequencing: a public health tool

The establishment of a network for surveillance and sequencing represents an essential public health tool when it comes to detecting and containing pathogens with epidemic potential. Genome sequencing makes it possible to identify pathogens, monitor the emergence and impact of variants, and adapt public health policies accordingly.


The COVID-19 epidemic has highlighted the disparities persisting between the continents in terms of surveillance and sequencing systems. At the end of October 2021, out of the 4,600,000 sequences shared worldwide via GISAID, a public platform accessible free of charge, only 49,000 were from the African continent, representing less than 1% of the COVID-19 cases diagnosed there.

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Creating and developing a genomic surveillance network in 13 African countries


  • Build laboratory sequencing and bioinformatics capacities
  • Monitor the progression of SARS-CoV-2 and other emerging pathogens integrating into each country's national system

By mobilising 22 laboratories and reference centres, the project is expected to enable the performance of around 34,000 sequencings and 54,000 PCR screening tests for variants of interest.

Over the long term, the programme will consolidate technological platforms and will structure a sustainable network to monitor emerging pathogens in Africa, thereby addressing the One Health - Global Health challenges.


    Key figures

    • 1 consortium bringing together 3 partners: ANRS | Emerging Infectious Diseases, Institut Pasteur, IRD
    • 10 million euros over 24 months (July 2021 - July 2023) funded by the AFD as part of the 'Health in Common 2' initiative
    • 13 countries: Benin, Burkina Faso, Cameroon, Central African Republic, Côte d'Ivoire, Democratic Republic of the Congo, Ghana, Guinea, Madagascar, Mali, Niger, Senegal, Togo
    • 25 African partners, including 22 laboratories and reference centres
    • activity streams: capacity building, epidemiology and sequencing

    Partner countries

    carte des pays membres du réseau AFROSCREEN




    Capacity building: fitting out of premises, provision of equipment and reagents, and training, to build the target laboratories’ capacities for sequencing and PCR screening tests for variants of interest 

    Epidemiology: performance of public health surveys and studies to investigate the epidemiological characteristics of the variants of interest

    Sequencing: management and sharing of data and sequences to quickly alert the health authorities and international community of any emerging variants of interest 


    Coordinated by ANRS | Emerging Infectious Diseases in partnership with IRD and Institut Pasteur, and with AFD funding, AFROSCREEN maintains the continuity of three projects coordinated by these institutes and supported by AFD in 2020 ('Health in Common 1’ initiative): APHRO-CoV, ARIACOV, and the support to several Pasteur Institutes in Africa, all three of which have built the capacities of laboratories in several African countries in terms of diagnosis.

    AFROSCREEN is developed in conjunction with the national authorities of each country as well as with the African Pathogen Genomics initiative, initiated by the Centres for Disease Control and Prevention of the African Union for the monitoring of variants on the African continent.  

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    The AFROSCREEN network
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    BENIN (Abomey-Calavi, Cotonou)
    •    Benin Clinical Research Institute (IRCB)
    •    Benin Viral Haemorrhagic Fever Laboratory (LFHV)

    BURKINA FASO (Bobo-Dioulasso, Ouagadougou)
    •    MURAZ Centre
    •    National Institute of Public Health (INSP)
    •    Souro Sanou University Hospital Virology Laboratory
    •    Yalgado University Hospital Virology Laboratory

    CAMEROON (Yaoundé)
    •    Centre for Research on Emerging and Re-Emerging Diseases (CREMER)
    •    Centre Pasteur Cameroon

    CÔTE D'IVOIRE (Abidjan)
    •    National Institute of Public Hygiene (INHP)
    •    Institut Pasteur Côte d’Ivoire
    •    Treichville University Hospital Virology and Bacteriology Laboratory
    •    ANRS Côte d'Ivoire Co-operation Programme (PAC-CI)

    GHANA (Accra)
    •    West African Centre for Cell Biology of Infectious Pathogens (WACCBIP)
    •    Noguchi Memorial Institute for Medical Research (NMIMR)

    GUINEA (Conakry)
    •    Centre for Research and Training in Infectious Diseases in Guinea (CERFIG)
    •    National Institute of Public Health (INSP)
    •    Institut Pasteur Guinea

    MADAGASCAR (Antananarivo)
    •    Institut Pasteur Madagascar

    MALI (Bamako)
    •    National Institute of Public Health (INSP)
    •    Point G University Hospital Virology Laboratory

    NIGER (Niamey)
    •    Centre for Medical and Health Research (CERMES)

    •    Institut Pasteur Bangui

    •    National Institute of Biomedical Research (INRB)

    SENEGAL (Dakar)
    •    Fann Centre for Research and Training in Clinical Care (CRCF)
    •    Institut Pasteur de Dakar
    •    Dalal Jamm National University Hospital Virology Laboratory
    •    Fann University Hospital Virology and Bacteriology Laboratory

    TOGO (Lomé)
    •    Molecular Biology and Immunology Laboratory (BIOLIM)
    •    National HIV-IST Reference Centre

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    About the project :



    About ANRS | EID’ work in fighting COVID-19 in Africa :