Why investing in Africa’s genomics future is vital

AFRICA bears a disproportionate burden of infectious diseases with malaria, HIV/Aids, tuberculosis, cholera, Ebola, Lassa fever, and other tropical diseases, such as dengue and chikungunya having a profound impact on morbidity and mortality.

Writing in Science, Professo Tulio de Oliveira, director of the Centre for Epidemic Response and Innovation (Ceri) at Stellenbosch University and Dr Cheryl Baxter, head of Scientific Support at Ceri, said various factors contribute to the higher prevalence and incidence of infectious diseases in Africa, including socioe-conomic challenges, limited access to health care, inadequate sanitation and hygiene infrastructure, climate-related factors, and endemicity of certain diseases in specific regions.

According to the authors, a skilled workforce is crucial to addressing these challenges.

“Unfortunately, many countries in Africa often lack the required resources, and aspiring scientists frequently seek educational and career opportunities abroad, leading to a substantial loss of talent and expertise from the continent. This exacerbates the existing training gaps and hampers the sustainability of research within Africa.”

During the Covid-19 pandemic, considerable resources were invested to enable African countries to directly monitor genetic changes of severe acute respiratory syndrome coronavirus 2 (Sars-CoV-2) without relying on international assistance. In particular, the Africa Centres for Disease Control and Prevention and World Health Organization, through the Africa Pathogen Genomics Initiative, invested in increasing the capacity of African countries by providing equipment, reagents and training.

“These investments resulted in an exponential increase in the number of Sars-CoV-2 genome sequences produced in Africa. Remarkably, whereas it took 375 days to produce the first 10 000 African Sars-CoV-2 genomes, it took only 87 days to produce the next 10 000 and just 24 days to produce an additional 10 000.

“Currently, 54 African countries have the capacity to conduct genome sequencing, and these countries have collectively contributed almost 200 000 genomic sequences from Africa, with South Africa contributing about a third of the sequences.

“Although this is only a fraction of the 16 million Sars-CoV-2 genomes publicly available, the monitoring of Sars-CoV-2 genetic changes in Africa played an important role in shaping the global scientific response to the pandemic and enabled the identification of several variants of interest and five variants of concern to date, two of which, Beta and Omicron, were identified by scientists from Africa,” the authors said, adding this success highlights the potential for genomics to help revolutionise disease control and prevention in Africa.

As the Covid-19 pandemic recedes, it will be important to redirect resources on the continent to quickly and effectively characterise other pathogens, Oliveira and Baxter said.

“One of the main lessons from the Covid-19 pandemic is that pathogens do not respect borders and can quickly spread globally. It is necessary to build on the investments already made and use genomics, clinical trial capabilities, and vaccine development as catalysts for responding to other ongoing and future epidemics, particularly those previously neglected, such as tuberculosis and mpox (monkeypox), and those affected by climate change, such as dengue, chikungunya, cholera and malaria.”

The need to build genomics capacity in Africa while simultaneously retaining skilled personnel is critical for several reasons, the authors noted, and the infectious disease burden in Africa is likely to worsen as the impacts of climate change become apparent.

“A recent review revealed that climate change has the potential to amplify more than 50% of known human pathogens. Genomic sequencing could be harnessed to elucidate the origin, genetic diversity, transmission patterns, and evolution of these pathogens.

“Strengthening capacity in genomics will enable researchers and health care professionals in Africa to generate region-specific data and knowledge crucial for understanding disease dynamics and developing targeted interventions, including the evaluation and development of diagnostics, therapeutics, and vaccines to improve public health outcomes.”

Despite Africa carrying 25% of the global burden of disease, African-led research has contributed less than 1% of the scientific literature, the authors said, this discrepancy further highlighting the urgent need to build capacity in science to address the unequal distribution of research efforts and ensure scientists from Africa have equitable opportunities to contribute and lead in Africa.

“Additionally, building local capacity in genomics and bioinformatics analysis enhances the ability of Africa to conduct in-depth investigations into ongoing health problems and identify potential local solutions.”