NEW YORK – While increased research funding and large-scale initiatives have advanced human and pathogen genomics in Africa, poor infrastructure, low wages, limited job opportunities, and reliance on foreign funding continue to stymie further expansion.
Around the continent, a new network of centers of excellence is providing African researchers with cutting-edge genomic technology, advanced training, and salaries more on par with those of peers from high-income countries. In the meantime, large infusions of grant money help fuel continent-spanning genomics initiatives that elevate the profile of African science while providing more opportunities for local researchers.
These research efforts have also spurred the launch of private enterprises, such as genomic research and molecular diagnostic companies, often founded by African scientists returning to their home countries from abroad in a reversal of a longstanding "brain drain" from the continent.
Although job creation continues to lag improvements in training and education in STEM fields in Africa, and perennial issues such as poor infrastructure and uncertainty surrounding genomic data governance persist, some stakeholders see signs that Africa's genomics sector is poised for growth.
"African genomics is flourishing at the moment," said Segun Fatumo, associate professor of genetic epidemiology and bioinformatics at the London School of Hygiene and Tropical Medicine (LSHTM) and founder of the Nigerian Bioinformatics and Genomics Network.
The COVID effect
The COVID-19 pandemic made several African governments realize the value of not only pathogen genomic surveillance in population health but genomics more generally.
Yosr Hamdi is the lead investigator of the Personalized Medicine in North Africa (PerMediNA) initiative, an international collaboration of the "Pasteur Network" of the Pasteur Institutes of France, Tunisia, Algeria, and Morocco, as well as Institut Gustave Roussy and Institut Marie Curie.
"I really think that the COVID crisis helped us to launch this initiative, because before 2020, policymakers … had not really been aware of the importance of genomics in healthcare," she said.
PerMediNA brings together diverse stakeholders from across the precision medicine landscape to develop and implement a translational research program that addresses noncommunicable diseases such as diabetes, metabolic disease, and cancer. Particularly with respect to the program's precision oncology component, PerMediNA researchers seek to employ whole-genome and whole-exome sequencing to better understand the prevalences of different cancers throughout the region's population.
In June of last year, PerMediNA organized a "Precision Medicine Academy," consisting of a series of lectures and practical training sessions, which was attended by policymakers from across North Africa. Hamdi said participants primarily wanted to know more about the relevance of genomics to population health, as well as the economics of implementing precision medicine in healthcare systems. A second Precision Medicine Academy took place earlier this month.
Genomics companies operating throughout Africa also attributed lasting changes in business practices on the continent to the pandemic.
Samantha Beal, associate director of public relations for Illumina, for example, said the pandemic hastened the company's shift toward seeking local distribution partners and conducting more business online. "Africa is part of Illumina's growth development in emerging markets in both human and agrigenomics segments," she said, adding that the firm has invested in a sales and support network to ease access to Illumina technologies, while also "making it possible to keep genomic samples on the continent and develop capabilities of Africans in [next-generation sequencing]."
South of the Sahara, Derrick Edem Akpalu, CEO and cofounder of Ghanaian startup Revna Biosciences, echoed Hamdi's assessment of the pandemic's effects. "A positive impact of the COVID experience is … at the political and social level, there is more appetite to do things in the biotech area," Akpalu said, including vaccine development, which has been accelerated by the ability to sequence the genomes of pathogens quickly.
Ghana, for example, established its National Vaccine Institute in 2021, in direct response to the global pandemic. That institute and others like it, Akpalu said, contribute to the growth of genomics in Ghana and beyond because they include new resources for technologies such as sequencers, as well as training in genomics.
Africa CDC
Genomics institutions and initiatives in Africa have also benefited from strong support from the Africa Centres for Disease Control and Prevention (CDC), the public health agency representing the member states of the African Union. In January 2020, Africa CDC concluded a continentwide assessment of how to leverage genomics, especially pathogen genomics, to support public health. Two weeks after the agency convened a meeting detailing the results of that assessment, COVID-19 was declared a global emergency.
Sofonias Tessema, an implementation science expert with Africa CDC and program lead for one of its projects, the Pathogen Genomics Initiative (PGI), said that Africa's high infectious disease burden creates "competing priorities" for how to allocate resources, but that following the global emergency declaration, "we shifted towards working on COVID."
The agency was able to enlist substantial aid, including for genomics research and equipment, from charitable organizations such as the Bill and Melinda Gates Foundation, public entities such as the African Society for Laboratory Medicine, and numerous companies including Illumina and Oxford Nanopore Technologies. The Gates Foundation, for instance, contributed $100 million in 2020 to expand access to next-generation genomic sequencing tools and related expertise and another $20 million the next year. According to Tessema, the number of countries with next-generation sequencing capacity increased to 40 in 2023 from seven in 2019.
Riding on the tails of this expansion and the renewed public interest in preventing future infectious disease outbreaks, Africa CDC last year launched the PGI with the goal of integrating genomics into pathogen surveillance and early detection of outbreaks. Tessema said that pathogen genomic sequencing has now penetrated "everywhere" in the public health space in Africa. "If today we have an outbreak of Ebola, the first question is, 'Is it sequenced?'" he said.
Additionally, Africa CDC is supporting a continentwide expansion of centers of excellence for genomics, seeking to establish eight more in addition to the two currently in place in Mali and Uganda. While some funding will come from Africa CDC itself, the initiative is also seeking approximately $200 million in funding from individual African governments, philanthropic organizations, private companies, and the African Development Bank.
The centers will target pathogen surveillance, implementation of precision public health, such as interventions for sickle cell disease and next-generation newborn screening, and workforce training and development. They also build research capacity through the acquisition of sequencing platforms, computing cores, and other cutting-edge technology. "We need those," Tessema said of the centers. "We believe [that's] the best way to strengthen the genomics capacity on the continent and [to] address the inequity that we have, especially when it comes to sequencing in human genomics."
Reversing the 'brain drain'
One important knock-on effect of these genomic research initiatives and related investments is that they are attracting African expat scientists back to the continent in a small but consequential reversal of Africa's "brain drain."
"We've seen … experts from the diaspora being attracted to come back and support genomics efforts on the continent," Tessema said, noting that he is one of them, having returned to Ethiopia from the US to support Africa CDC initiatives.
Additional returnees include LSHTM's Fatumo and Revna's Akpalu, along with others who have founded several of Africa's nascent genomics enterprises. "When there are opportunities that we can create in a sustainable way, I think, we can attract those people who are trained abroad and who are working abroad to come and contribute to the development of genomic health [initiatives] on the continent," Tessema said.
Africa's brain drain is a perennial source of concern and topic of debate across the continent, although current statistics on how many African scientists receive advanced degrees within Africa compared to how many leave are scarce. Reports referencing Africa's brain drain often cite a handful of studies from the late 1990s and early 2000s.
A report published by the African Union in 2018, for example, estimated that Africa had been losing 70,000 skilled professionals per year to job opportunities abroad, although this did not separate skilled workers by field. A separate study estimated that roughly 30 percent of African graduates in STEM fields left the continent to pursue further studies between 2022 and 2023.
Indicators of a potential reversal of this trend exist, though. Yaw Bediako, founder and CEO of Ghanaian cancer research firm Yemaachi, said he sees more money available for science initiatives and commercial enterprises in Ghana than there was even 10 years ago, and the quality of science education has improved so the number of qualified local job applicants in STEM fields is rising. "The Wellcome Trust, the Gates Foundation, the NIH have all invested in Africa-specific programs, typically run by African scientists," he said, which drives local capacity building, such as higher-quality education, particularly in the STEM fields.
Abasi Ene-Obong, founder and CEO of Nigerian genomics startup Syndicate Bio and former CEO and cofounder of now-defunct 54gene, which shut its doors last year in the wake of financial struggles and high leadership turnover, said he sees the same happening in Nigeria. "If there is good work in Africa, in Nigeria, what we find is that people are coming back," he said. He agreed that as the quality of STEM training has improved, so has the local pool of skilled applicants. "I think now, more than even five years ago, there's a lot more talent to work with," he said. "There is [a] desire and a hunger to contribute to the life sciences space in Africa."
Persistently low salaries across Africa's biotech sector continue to contribute to brain drain and slow the growth of genomics, though. Governments and private funders are cognizant of this and have taken steps to improve conditions to boost retention.
Nigeria, for instance, in 2014 established the African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), which has become one of the country's premier research and training institutions. ACEGID offers postdocs annual salaries between $50,000 and $60,000, compared to the usual salary range of roughly $20,000 to $33,600 for a trained biochemist in that country. Similarly, the Uganda Medical Informatics Centre (UMIC), established in 2015, pays its postdocs UK salaries to keep them in Africa. "This is one of our strategies for retention," said LSHTM's Fatumo, who also heads genomics at the UMIC, adding that the institution provides its researchers opportunities to work temporarily in the US, the UK, and Germany.
While encouraging, better training and higher-paid positions in genomic centers are not enough to stem the outflow of talent from Africa, particularly as the quality of training and the availability of commensurate jobs do not always keep pace with each other. "I think we're getting to the point where the number of trainees outstrips the number of opportunities for high-level [positions]," Bediako said. In Ghana at least, he sees the country's STEM-oriented business environment as becoming "almost too competitive in the sense that there's just not enough of a pie to go around."
Gert van Wyk, CEO of South African genetic testing startup BioCertica, expressed the same sentiment with respect to South Africa. "People [here] are highly skilled, but … the capacity to employ them is not where it should be," he said.
Nonetheless, Bediako said, large-scale initiatives such as the Human Heredity and Health in Africa (H3Africa) initiative and the African Pharmacogenomics Network have raised the profile of genomic science, demonstrated that it is possible to conduct high-quality genomics work in Africa, and provided evidence of the immense scientific value of African human genomic data, all of which does contribute to greater opportunities for African scientists to remain on the continent. "That's actually what brought me back to Ghana," he said.
Bediako returned to Ghana from the UK in 2019 to work at the West African Centre for Cell Biology of Infectious Pathogens before founding Yemaachi in 2020. He said he feels that Africa's large-scale genomics initiatives remain largely focused on academic training and capacity building, whereas commercial initiatives are more translational and linked to IP, product development, and commercialization.
"While academic initiatives are important, they cannot be the end goal of scientific capacity development," he said. "The end goal must be job creation and product development. Successful commercialization and resultant revenue production provides a path towards sustainability."
He also cautioned that large public genomics projects throughout Africa still rely almost exclusively on international funding, and their continuation beyond the original grant periods is not a given. "Private sector involvement would certainly present a pathway towards sustainability," Bediako said, "but I don't think there has been much development in that direction."
By presenting Africa as an opportunity for overseas investors to do business in Africa, he said, private businesses can tap into more secure funding.
"Even in difficult economic times, investors will continue to seek good investment opportunities, whereas philanthropic giving declines significantly," Bediako said. "In the long term, a strong and profitable African private sector will decrease reliance on external aid and result in greater self-reliance."
Nonetheless, others describe Africa's continent-spanning and externally funded consortia as key elements of the genomics ecosystem that have eased the launch of commercial entities, even if the overall number of such businesses remains small. Biotechnology companies such as the Bioinformatics Institute of Kenya, health-tech firm mPharma in Ghana, and ATCG Solutions and Mara Scientific, both in Uganda, all launched in the wake of H3Africa, for example, which was established in 2012.
"Projects like H3Africa have done a lot to support and promote the practice of genomics both in the academic and private sector settings in Africa," Ene-Obong said, adding that in his private business, he often works with bioinformaticians trained through the H3ABionet program, H3Africa's bioinformatics analog.
Several stakeholders in Africa's public and private genomics sectors said that efforts such as H3Africa and the more recent PGI broaden funding opportunities through increased donor awareness, create more opportunities for scientist training and employment, and increasingly pull state attention toward the value of investing in human genomics.
Governments are increasingly interested in precision medicine initiatives, genomic studies, clinical trials, and the biomanufacturing needed to support those efforts, Ene-Obong said, and both governments and international pharma companies are showing greater willingness to participate in African genomics projects, while governments are more willing to partner with private companies. Syndicate Bio, for example, recently partnered with Nigeria's National Institute for Cancer Research and Treatment (NICRAT) to launch the Cancer Genome Nigeria Project, which seeks to study the frequencies of cancer risk genes in Nigeria. The company also recently partnered with Swiss bioinformatics firm Sophia Genetics to co-commercialize the MSK-ACCESS cancer genomic profiling and disease monitoring liquid biopsy test in African markets.
Collected in Africa, analyzed in Africa
New data centers in Africa have helped genomics projects to be conducted entirely on the continent, with no need to ship data abroad for analysis. Uganda's UMIC, for example, recently installed a high-throughput computing core that Fatumo said makes it one of the largest genomic computational centers in sub-Saharan Africa. Although UMIC still receives funding from the UK Medical Research Council, samples can now be fully processed and analyzed locally.
Collecting, processing, sequencing, and analyzing biological samples all within Africa has been a goal for many African researchers for some time. "We've seen more and more research institutions conducting genomics, more and more pathogens being sequenced on the continent," said Africa CDC's Tessema. "We've also seen a reduction in the number of samples that are sent from Africa to other parts of the world for sequencing, which I think is an indicator that this capacity is maturing on the continent."
Even some foreign genomics companies that do business in Africa are committing to keeping samples on the continent and analyzing them in-country. IndyGeneUS AI, for example, a Delaware-based bioinformatics company, has subsidiaries in Kenya and South Africa in order to comply with its commitment of keeping all genomic samples and information local. In 2022, the company partnered with South Africa's Aurum Institute to sequence up to 3 million human samples in an effort to study infectious and noncommunicable diseases, which will be stored at a biorepository in Johannesburg.
"We're building [a] facility in Johannesburg, South Africa, where we will be able to do sequencing on the continent and preserve [genomic] data sovereignty," said IndyGeneUS CEO Yusuf Henriques. Genomic sovereignty has been referred to as the ability of a nation, people, or state to own and regulate access to and use of samples, data, and knowledge of human genes from its citizens.
Although centers of excellence such as UMIC and partnerships such as that between IndyGeneUS and the Aurum Institute boost local genomics capacity and contribute to better scientist retention, Fatumo said the reliance on foreign funding sources still impedes growth and research independence in the long term. "If the money [for the centers of excellence] had come from the African Union," he said, "African governments would have had to pay more attention." As things stand now, he said, governments "don't care so much about research, which is a shame, really."
Bediako countered that African governments "don't do too badly" in terms of supporting research. "It's just that the state of the problem outstrips the resources they have available. Are you going to build a road or a hospital, or put $10 million into a research fund? You can see which one is going to get voted for in an election."
Another drawback to relying on foreign funding, Fatumo said, is that it makes African researchers more beholden to those funders' research priorities, which are not always aligned with their own. He noted, though, that major funders such as the US National Institutes of Health — which increased its grant funding for African nations from approximately $4.5 million in 2000 to nearly $92.6 million in 2023 — have adopted a more collaborative approach with respect to taking guidance from African grant recipients when setting research agendas. "It's not where we want to be, but [it's] not where we used to be," Fatumo said.
Temesgen Fufa, program director of genomic sciences at the National Human Genome Research Institute, said that the NHGRI actively engages with local stakeholders and ensures that grants are aligned with the priorities of recipient African nations.
"NHGRI has really emphasized a more inclusive and collaborative approach," he said.
Additionally, Fufa said that the NHGRI takes an active role in trying to convince governments to incorporate more research funding into their national health budgets.
"We try to convince the policymakers in each country where we have a presence [that] genomics research, and biomedical research in general, would be a critical aspect of … improving the health outcomes of their citizens," Fufa said.
Fufa added that the NHGRI also works to incorporate provisions for scientist training as well as physical infrastructure, such as biorepositories, into its grants.
Infrastructure everywhere
Outdated and sometimes nonexistent infrastructure has been cited in numerous studies as impediments to conducting population genetics studies and clinical trials in Africa.
A 2020 report on the lessons learned from a clinical trial in Malawi, for example, described unreliable internet connections, lengthy shipping times for lab equipment from outside the country, and a lack of dedicated inpatient treatment space at trial sites as challenges that needed to be overcome in that study. The H3A consortium also conducted an evaluation of implementation challenges across Africa, calling poorly equipped facilities, inadequate infrastructure, and erratic power supply "major impediments" to conducting genomics research.
Although not primarily with scientific research in mind, the governments of several countries across Africa are investing in infrastructure such as better-connected road systems and modernized ports. While these are largely meant to boost economic activity and attract more business, they can also assist researchers by easing access to remote populations and medical centers and reducing wait times for research material. "Everywhere you go, you see infrastructure development," said van Wyk, who frequently travels through East Africa, adding that this part of the continent in particular is on an "upwards trajectory."
East Africa is projected to be the fastest-growing economic region globally over the next two decades, according to the World Bank, with a predicted GDP growth rate of approximately 6 percent through 2040, largely thanks to robust growth in the Democratic Republic of Congo, Kenya, Rwanda, and Uganda.
Governments throughout East Africa have been investing in large-scale transport infrastructure, for instance, to facilitate business between rural and urban areas and between countries. Kenya and Tanzania, for example, recently laid out policy initiatives and development strategies such as reducing transport costs, improving access to affordable water and sanitation services, and increasing agricultural production, collectively meant to spur private sector development and improve human capital.
While many infrastructure projects are in their opening phases, some see genomics' continued growth as an inevitability. Africa is the most genetically diverse continent, Syndicate's Ene-Obong explained, and offers a wealth of genomic research opportunities, with African genomes accounting for only an estimated 2 percent to 7 percent of genome-wide association studies despite the continent housing approximately 18 percent of the world's population and, by some estimates, being on track to account for 25 percent of it by 2050.
Despite Africa's considerable potential and the recent improvement in both commercial and academic genomics research, Ene-Obong remains realistic. "The challenges have not disappeared," he said. "Doing this kind of work requires more money than is typical for, let's say, a fintech or software-as-a-service company. That makes it a difficult space with a high barrier to entry."
Nonetheless, Africa seems more poised for growth in genomics than perhaps ever before. "Africa is the next growth frontier in life sciences," Ene-Obong said.