Stellenbosch University is home to the largest genomics facility on the African continent, which is situated in the Faculty of Medicine and Health Sciences’ Biomedical Research Institute (BMRI), and embedded in the School for Data Science and Computational Thinking.
Led by Professor Tulio de Oliviera, who discovered the Beta and Omicron variants of the coronavirus, the facility aims to lead the world in its response to novel epidemic threats by supporting South Africa and dozens of other African countries to characterise and discover new pathogens.
President Cyril Ramaphosa, along with the Minister of Higher Education, Science and Technology, Blade Nzimande, and the biotech investor of NantAfrica (a division of NantWorks), Dr Patrick Soon-Shiong, visited the Stellenbosch University (SU) Biomedical Research Institute (BMRI) last week to view the cutting-edge facilities of the Centre for Epidemic Response and Innovation (CERI), which will provide the genomic sequencing for the development and evaluation of vaccine therapies in South Africa. CERI is to be officially launched later this year.
The centre is envisioned to be the largest genomics facility in Africa and is headed by Professor Tulio de Oliveira, world-renowned bioinformatician and professor of bioinformatics at the School for Data Science and Computational Thinking at SU.
The visit to the centre preceded the launch of the NantSA vaccine production facilities at Brackengate, Cape Town, and the announcement of the Coalition to Accelerate Africa’s Access to Advanced Healthcare (the AAAH Coalition).
Welcoming the president’s delegation were Professors Wim de Villiers, SU rector and vice-chancellor; Kanshukan Rajaratnam, head of the School for Data Science and Computational Thinking; Elmi Muller, dean of SU’s Faculty of Medicine and Health Sciences, and De Oliveira.
CERI at SU is the forerunner of a host of similar facilities at other research-focused South African universities and was established with the support of the Chan Soon-Shiong Family Foundation and The Rockefeller Foundation’s Pandemic Prevention Institute (PPI).
The BMRI, where CERI is located, is a large infrastructural investment of more than a billion rand by SU and the Department of Science and Innovation (DSI). It is on a par with the most advanced biomedical research facilities in the world and plans to host dozens of world-class research groups in South Africa.
Prof De Oliveira’s research is aimed at responding effectively to epidemics through pathogen genomics surveillance. This work enables enhanced biomedical discovery, improved treatment and diagnosis, and better vaccine development to prevent human disease, and has the potential to lead global research in this field and generate significant economic opportunities for Africa.
The next phase will be to launch a fellowship programme that will train African scientists in cutting-edge genomics, bioinformatics, big data and artificial intelligence techniques to support Africa’s scientific advances and industrial revolution.
“The facilities at SU’s Faculty of Medicine and Health Sciences and the large network of collaborations in South Africa, Africa and the world will be a game changer for science in Africa,” said Professor De Oliveira.
“With the detection of the Omicron variant, we already showed the world that Africa is capable of practising world-class science. To date, we have raised around $20 million to support our research, but we estimate that we will need $100 million in the next five years to allow genomics technologies to be used in real time to trace and respond to novel epidemics and pandemics on the continent.”
In addition to large robotic equipment, facilities include two Illumina Novaseq 6000 DNA sequencing platforms, the largest of their kind in the world, and one NextSeq 2000.
Professor De Oliveira showed the president the two Novaseq 6000 platforms, which had been donated by the Chan Soon-Shiong Family Foundation with support from Illumina and The Rockefeller Foundation to build the largest Illumina high-throughput facility in Africa.
Professor De Oliveira concluded: “The expanded laboratories will allow Africa to become a world leader in genomics surveillance and bring technologies to South Africa that can identify new pathogens and human genetic mutations quickly.
“These technologies can save lives through the early detection of cancer and will have a definitive social impact.”
Commenting on this proud moment for SU, Professor De Villiers said the collaboration between the various entities aligned with SU’s vision of being Africa’s leading research-intensive university, globally recognised as excellent, inclusive and innovative, where knowledge is advanced in service of society.
“Establishing purposeful partnerships and inclusive networks is an ongoing and key strategic theme for the University. The collaboration between the various entities is a prime example of our express aim of collaborating at a multi-institutional level.
“The research could potentially have an impact on millions in Africa and, indeed, the world.”
Professor Rajaratnam added that SU would be realising its vision through the world-class science set to take place under this collaboration.
“This will include both innovation in technologies, as well as training future scientist to lead in Africa,” he said.
“Our research agenda at the Faculty of Medicine and Health Sciences is strongly shaped by the major health challenges facing people living on the African continent, and underscored by our diligent and persistent effort to address these,” Professor Muller commented.
Fellowship programme to capacitate science in Africa
CERI and SU have already received 41 fellows from 21 African countries and will expand the fellowship programme in 2022 with support from the Chan Soon-Shiong Family Foundation, The Rockefeller Foundation, the Africa CDC and the WHO.
The aim is to host 100 new fellows to be trained in genomics, bioinformatics, big data and artificial intelligence analysis.
“This advanced training programme builds on the work of the School for Data Science and Computational Thinking, which aims to transform Africa’s ability in data analysis and help fuel the Fourth Industrial Revolution in Africa,” said Professor Rajaratnam.
“Professor De Oliveira’s leadership in identifying the Omicron variant of SARS-CoV-2 and efforts to build a network of scientists to expand genomic surveillance in Africa are, and will continue to be, one of the most notable success stories of the Covid-19 pandemic,” said Dr Rick Bright, PPI chief executive and senior vice-president of pandemic prevention and response at the Rockefeller Foundation.
“We’re proud to partner with institutions such as Stellenbosch University that are at the cutting edge of our collective mission to respond to this pandemic and prevent future ones.”
Professor De Oliveira was recently selected as one of Nature’s 10 – ten people who helped shape science in 2021. He will also be awarded a gold medal from the South African Medical Research Council (SAMRC) in 2022 for his contribution to science.
* More on the work being done
Biomedical Research Institute
The aim of this research initiative is to understand the diseases that have the greatest impact on communities in South Africa and the rest of Africa.
This R1 billion facility, which is set to be completed at the end of 2022, is one of the most innovative and advanced biomedical research centres in Africa and will advance SU’s capacity to undertake world-class research on the leading health problems affecting African and South African people.
It will also contribute considerably to building research capability on the African continent.
The new BMRI is on a par with the most advanced biomedical research facilities and allows for the immediate expansion of SU’s current research activities, including bioinformatics, surgical sciences, and solutions to addressing the Covid-19 pandemic.
NantWorks is a multinational, California-based conglomerate that is leading the digital revolution in healthcare, technology and media through the harnessing of science, digital infrastructure, supercomputing and communication.
It is an ecosystem of companies with a deep understanding of a wide variety of complex industries, from medical science to physics, data to artificial intelligence, and communications to mobility.
SU School for Data Science and Computational Thinking
The School was launched in July 2019 with a vision to be a world-class institution in data science and computational thinking in and for Africa.
Through partnerships with government and private entities, such as the generous sponsorship from Standard Bank, Capitec Bank and others, the School is working on innovative technologies and data methods that would improve quality of life across the country and the continent.