Emerging genomics hub in Africa aims to transform disease response

Africa’s first genomics hotspot has emerged on the outskirts of Cape Town and it could revolutionize the continent’s understanding of and response to disease outbreaks. The Centre for Epidemic Responses and Innovation, the largest genomics facility in Africa, is housed in the glistening new Biomedical Research Institute on the north side of the campus surrounding Tygerberg Hospital. CERI, which opened in 2001, has already played a key role in detecting mutations in COVID-19 and other diseases. The South Africa Medical Research Council’s Genomics Platform is five minutes south on the same campus. In less than five years, the facility has sequenced 10,000 samples, according to the laboratory manager, Nadia Carstens, making it one of the largest service laboratories by volume in the country. The two facilities share next-generation sequencing capabilities, though their goals are different, with CERI focusing on pandemic response, while the genomics platform assists researchers from universities and foundations. But the development of the two facilities was spurred by a similar impulse: “We just want to make sure that this technology is infiltrated everywhere, and it’s adopted as widely as possible,” Carstens said. Having faster access to information on the genomics of disease could help contain outbreaks by speeding the delivery of appropriate vaccines and diagnostics. CERI, in particular, is trying to position the global south to lead the response to emerging epidemics by updating the way genomics is used on the continent. In the past, Tulio de Oliveira, CERI’s director, said that researchers would send out samples to laboratories in Europe or even further afield and then wait years for the results, which would come too late to have any impact on the actual outbreak. South Africa had already been working to end that reliance, building the genomics capacity that it demonstrated during the COVID-19 pandemic. That included de Oliveira’s work leading the teams that identified the beta and omicron variants of COVID-19. With CERI, the goal is to create enough capacity that “African samples do not leave the continent,” he said. The delivery of genomic data is cut from years to days. “You can understand very quickly the variant that is circulating,” de Oliveira said. This can be crucial in the case of cholera being detected, for instance. Normally a new strain of cholera is needed to cause an outbreak because communities will have grown resistant to a strain they have previously been exposed to. By identifying the strain quickly, researchers better understand the threat the disease presents and can help communities prepare to meet it. “What would be success would be that quick characterization and then that you can get the proper response with diagnostics, therapeutics, and vaccines that are efficient for a pathogen,” he said. CERI’s model has attracted the attention of the Wellcome Sanger Institute, one of the United Kingdom’s leading genomics research centers. The institution announced a partnership with CERI last month that will see the two facilities share their genomics data sets, which will give both of them a repository of information to draw on as they conduct new analyses. CERI will also get details on how to process some of the large genomic data sets that Sanger specializes in. CERI plans to transfer their sequences to Sanger so that the partnership “goes both ways,” de Oliveira said. The center is also rapidly forging partnerships with other researchers and institutions on the continent, primarily through a fellowship program that de Oliveira said has brought more than 500 African fellows to CERI. They are trained on CERI’s protocols and then dispatched back to their countries to set up processes. In addition to expanding genomics capacities throughout the continent, the fellows have become something like partner organizations that are linked to CERI. Over the past few years, as disease outbreaks have occurred around the continent, CERI has pioneered a model of sending reagents out to these researchers. Experts at CERI then work with the in-country researchers to guide them through characterizing the epidemic, without sending samples back to CERI and waiting for results. These kinds of partnerships have led to the characterization of cholera in Malawi, of Rift Valley fever in Kenya, and of dengue and chikungunya, which both Burkina Faso and Senegal experienced. “Normally the samples would have gone to the Sanger and come back years later as a great academic exercise,” de Oliveira said. “Now they could sequence that in a week.” There has not yet been much collaboration between CERI and the genomics platform, though Carstens said the technicians will take advantage of training opportunities at each others’ facilities. But there is congruity in the benefits of the work they are doing. When the genomics platform opened, Carstens said they anticipated they would largely be doing sequencing of human DNA. The genomics platform was initially set up through a joint funding scheme between the South African Medical Research Council, which continues to provide running costs, and the Chinese company, BGI Genomics. But then researchers in other fields recognized an opportunity to take advantage of the new resources the platform offered. There was a surge in interest from the infectious disease community for transcriptomics, which can identify all of the RNA molecules in an entity and can be crucial in vaccine development or diagnosing a disease. And in a country where specialist care is limited and it can be difficult to do clinical testing for a disease, some doctors at nearby Tygerberg Hospital have turned to the platform to determine the genotype of a rare disease, for instance, and worked from there to make a diagnosis and assign a treatment. “We also provide access to diagnoses that you wouldn't have been able to make without that molecular confirmation,” Carstens said. The Bill & Melinda Gates Medical Research Institute has also started sending samples to the platform, using them as a core base for sequencing and then leveraging the results to do their own data analysis. Like the platform, CERI offers sequencing services for researchers across the continent. Both facilities try to keep their costs as low as possible. De Oliveira said that CERI charges for the costs of the reagents they use since the machinery has been subsidized by grants and donors. The institution has drawn funding from a variety of donors, including the World Bank, the Rockefeller Foundation, and the Africa Centres for Disease Control and Prevention. But even that cost is higher than it should be because reagents are imported and cost more in Africa than they do in Europe or North America, he said. Furthermore, some of the robotics they purchase can be double the price they would be charged in Europe or North America. These point to one of the broader challenges that the organizations face as they seek to expand access to genomics across the region. Carstens said that the platform tries to work directly with manufacturers, which can keep costs down. However because of the lack of a market in a region that does not have a plethora of genomics facilities, sometimes they have to purchase through a distributor, which can make the price balloon. “It’s such an expensive space, you need to show feasibility, you need to show sustainability to get bigger investments to come,” she said.