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The medical field is increasingly shifting from a one shoe fits all approach to personalized medicine. These developments are informed by new data resulting from improved advances in the genomics field. Unfortunately, although the African continent is home to more than 1.3 billion people with the greatest genetic diversity globally, this diversity remains understudied.

For the continent to enjoy the benefits of the genomic revolution and for the rest of the world to better understand the role of human genes in disease, it is imperative that we extensively study the genome of the African people. The Human Heredity and Health in Africa (H3Africa) initiative seeks to build human capacity and other infrastructure necessary for the African continent to benefit from the genomic revolution.

The greater H3Africa consortium facilitates fundamental research into diseases in the African continent while also developing infrastructure, resources, training, and ethical guidelines to support a sustainable African research enterprise – led by African scientists, for the African people. The $176M initiative is co-funded by the National Institutes of Health (NIH) and Wellcome with the SFA Foundation managing Wellcome’s investments. The greater consortium is managed by the H3Africa coordinating center based at the University of Cape Town, South Africa.

Key achievements of H3Africa in the continent

H3Africa has been successful in delivering on its objectives including cross country collaborations, development of various guidelines relevant for conducting genomics work in Africa (all freely and available online, training of experts and capacity building in various aspects of genomics). There are three H3Africa associated regional biobanks (Uganda, Nigeria and South Africa) that have been a great resource, for example, in providing COVID-19 related services throughout the pandemic period. Many H3Africa Principal Investigators have played a key role in decision making by working closely with governments and regional public health bodies during the pandemic. Importantly, H3Africa equipped labs and associates have been instrumental in the surveillance and spread of the SARs-CoV-2 virus, with the first viral genome from Africa being sequenced from one of the H3Africa labs in Nigeria, the African Centre of Excellence for the Genomics of Infectious Disease (ACEGID)at Redeemer’s University.

Looking Ahead

The SFA Foundation is seeking strategic partnerships in genomic sciences to help continue building on the foundational work that has been initiated by the H3Africa community.

“If we only conduct genomics research with populations of European descent, we limit the ability for genomics to benefit everyone. That is why researchers around the world are working to include people from different ancestral backgrounds!” – Eric Green, National Institute of Health (NIH)


The consortia is made up of collaborative groups from 34 African countries with a total of 51 African projects. This design is intentional to make sure that countries with poor infrastructure and expertise are brought onboard as collaborators.

The funded projects are diverse but are characterized as being of great public health importance to the continent. They include population-based genomic studies of common, non-communicable disorders such as heart and renal disease, as well as communicable diseases such as tuberculosis.

These studies are led by African scientists and use genetic, clinical, and epidemiologic methods to identify hereditary and environmental contributions to health and disease. To establish a foundation for African scientists to continue this essential work into the future work, the consortium also supports many crucial capacity building elements, such as: ethical, legal, and social implications research; training and capacity building for bioinformatics; capacity for biobanking; and coordination and networking.

H3Africa initiative was funded under a 10-year grant cycle which came to an end in July 2022. SFA Foundation is seeking strategic partnerships in genomic sciences to help continue building on the foundational work that has been initiated by the H3Africa community.

Components of the H3 Africa Consortia Model:
  • Capacity building, training, collaboration and networking for Africa Scientists
  • Collaborative groups from 34 African countries with 51 African projects
  • Africa-led research through genetics, clinical and epidemiological approaches in identifying hereditary and environmental factors contributing to disease
  • Population based genomics studies focusing on non-communicable and communicable diseases
Consortia Director: Dr Enock Matovu

Consortia Name: Genetic Determinants of Two neglected tropical diseases (TrypanoGEN+)

Country : Uganda

Focus Area: Trypanosomiasis and Schistosomiasis

The over-arching aim of this network is to improve the health of people living in some of the poorest countries in the world that carry a disproportionate burden of infectious diseases. Human African Trypanosomiasis (HAT) is caused by a single-celled parasite whilst schistosomiasis is caused by a parasitic worm. They are two of the most important of the neglected tropical diseases. Both diseases are targeted for elimination by the World Health Organisation, but the current control strategies are inhibited by failure to target and treat some of the people that maintain the reservoir of infection. The network seeks to apply the latest advances in scientific research to identify these people and understand their response to infection, and in the process train the next generation of African scientists in these advances.

Project Sites: Institute nationale des Rescherche Biomedicale, Human African Trypanosomiasis National Control Program(PNLTHA), Faculty of Science, University of Dschang, Universite Jean Lorougnon Guede, College of Medicine, University of Malawi, Uganda Virus Research Institute, Entebbe,  Rhodes University, University of Liverpool and the  University of Glasgow

Consortia Director: Prof Ambroise Wonkam

Consortia Name: Hearing Impairment Genetics Studies in Africa (HI-GENES Africa)

Country : South Africa

Focus Area: Hearing Impairment (HI)

Hearing impairment remains the most disabling congenital disease, with a higher burden in Africa. Congenital hearing impairment occurs in 6 per 1000 new-born in Africa. Half of congenital hearing impairment cases have a genetic aetiology, of which 70% are isolated and referred as non-syndromic (NS). 

The HI-GENES Africa programme uses whole genome sequencing (WES), to study the largest sample of sub-Saharan Africans from Cameroon, Mali, Ghana, and South Africa with prelingual non-syndromic hearing impairment (NSHI), in order to identify novel NSHI genes and to better understand the genetic aetiology of NSHI in African populations. Identifying novel genes can help doctors to improve their capacity to detect HI early and offer appropriate treatment to children with hearing impairment to maximise their cognitive, social-emotional, speech and language development. The project also seeks to improve genetic screening and in future, prediction of cochlear implant and treatment outcomes in sub-Saharan Africans, African-Americans and Hispanic-Americans of African descent. The network also engages policymakers and support groups on psychosocial challenges experienced by families and people living with HI.

Project Sites: University of Ghana, University of Yaounde and University of Science, Technical and Technology of Bamako

Consortia Director: Prof Alfred Amambua-Ngwa

Consortia Name: Pan African Malaria Genetic Epidemiology Network (PAMGEN)

Country : Gambia

Focus Area: Malaria

Human populations in Africa possess extraordinary genetic diversity in the erythrocyte surface proteins known as glycophorins that are exploited as invasion receptors by the malaria parasite Plasmodium falciparum. The recent discovery of a large structural glycophorin variant that confers resistance to severe malaria in African children, together with the observation that parasite genes involved in erythrocyte invasion are also extremely diverse, suggests that an evolutionary arms race is going on. The network seeks to understand the genetic interactions between host and parasite invasion genes and how they are affected by the environment. With an African led team of scientists, this project is examining human, parasite and vector genomic data from 7 locations distributed across the continent, representing a wide range of ecological and epidemiological settings.

Project Sites: University of Ghana, Addis Ababa University, University of Buea, National Institute for Medical Research (NIMR), Institut Pasteur de Madagascar and the  University of Science Technical and Technology of Bamako

Consortia Director: Dr Kidist Bobosha

Consortia Name: Tuberculosis Genetics Network in Africa (TBGENAfrica) 

Country : Ethiopia

Focus Area: Tuberculosis

Africa has the highest level of genetic diversity amongst all human populations. It also has the highest level of genetic diversity amongst populations of the pathogen that causes tuberculosis.

Building on established links with leading institutions in Europe and the US, the project networks three African Institutions with ambition to develop their mycobacterial and human genetic research capacity to study human health and heredity in East Africa, focusing on host-pathogen genotype interactions in tuberculosis. The scientific goal is to identify molecular targets that will rationalise the development of new drugs and vaccines to control a global epidemic, which disproportionately affects vulnerable East African populations.

Project Sites: University of Khartoum, University of Buea and the Eritrea Institute of Technology