​Die nuwe, hipermoderne Instituut vir Biomediese Navorsing (BMNI) is onlangs by die Fakulteit Geneeskunde en Gesondheidwetenskappe bekendgestel. Tydens ʼn genomika-simposium, wat as deel van die bekendstelling gehou is, het topwetenskaplikes van regoor die wêreld die belangrikheid van genomiese waarneming vir onder meer die opsporing van verskillende patogene, die behandeling van seldsame siektes en die hantering van toekomstige pandemies beklemtoon.

• Lees 'n artikel oor die geleentheid deur Sue Segar, 'n vryskut wetenskapskrywer, hieronder.

Africa has the potential to “leapfrog" over the rest of the world in the field of genomic surveillance in the next few years, Stellenbosch University bioinformatician Professor Tulio de Oliveira has told a symposium of global scientists. Having excelled globally during COVID-19, African experts can, and should, now build on their success in COVID-19 genomics to expand to other pathogens such as influenza, H5N1 and climate-amplified pathogens.

Speaking at the university's Biomedical Research Institute Inauguration Genomics Symposium,

De Oliveira said the continent's experience in genomic surveillance of pathogens in Africa evolved to “unheard-of" levels during the COVID-19 pandemic. “We've been trying to advance genomic surveillance in Africa for the past two decades, and when the pandemic came, we had the right expertise to deal with viruses and respiratory pathogens such as tuberculosis, so we were able to pivot for SARS-CoV-2. In the end, South Africa and Africa became the example to follow on genomic surveillance for the whole world," said De Oliveira, who is globally recognised for detecting the Beta variant of SARS-CoV-2 in 2020 and the Omicron variant in 2021.

“All the investments we have made in genomic surveillance for COVID can now be leveraged, and advanced to other areas of genomics in Africa …including for rare diseases, for cancer diagnostics and human genomics," he said.

“Finally, we have the tools and the equipment, as well as the support, to do advanced genomics in Africa, as we have dreamt of doing for the last twenty years."

His sentiments were echoed by a range of top scientists at the symposium, which formed part of the historic launch of the university's state-of-the-art Biomedical Research Institute (BMRI). The institute positions Stellenbosch University as a leading institution in biomedical sciences, with a particular focus on African diseases.

It brought together some of the world's top experts and companies working in the field of genomics, including Professor Nicola Mulder, head of the Computational Biology (CBIO) division at the University of Cape Town, and principal investigator for the H3ABioNet Bioinformatics Network, which was established to develop bioinformatics capacity in Africa and specifically to enable genomics data analysis by researchers across the continent.

Value of African genomics

Professor Mulder, whose research lies in the area of applying genomics to human diseases of relevance in Africa, spoke about the rich value of African genomics.

“African populations have the biggest diversity on the planet and this provides an enormous opportunity for improving our knowledge on genetics and human diseases," she said.

“In a study a few years ago, we looked at a few human sequences and found enormous diversity in a handful of African populations.

“Everyone is talking about genomics. We, in Africa, need to work on what is specific to our population and what we need." 

Professor Mulder described African genomics as “the most exciting field. “There are so many opportunities in human genetics, for novel discoveries that can take, not just for Africa, but for the world, in terms of what is hidden in the African genomes - the humans, plants, viruses, and animals. All our diversity is just waiting for novel discoveries. There are enormous opportunities for novel discoveries and to address the Sustainable Development Goals."

But, she added, it is essential to use the right tools. “We need to be using tools that are appropriate for African data but also for African settings in terms of the limitations we have in internet, in data and resources. We need to adapt. We need a robust infrastructure and … a diverse workforce so that we can have African ownership of African data and so that we can develop our own solutions for our unique organisms and diversity."

Monika Moir, a bioinformatics Postdoctoral Researcher at the Centre for Epidemic Response and Innovation (CERI) in the School for Data Science and Computational Thinking at Stellenbosch University, spoke about CLIMADE Africa, which has the vision to create an African consortium to generate knowledge, develop localized tools and inform public health action for early warning and timely/targeted response to pathogens amplified by climate change.

Moir said CLIMADE Africa's key objective will be to fill critical knowledge gaps and blind spots of disease transmission predicted to pose increased threats in the future. The initial activities in CLIMADE-Africa will be used as leverage to apply for further funding to expand the CLIMADE consortium and to ensure the sustainability of the initiative. Importantly, the analysis of the data for CLIMADE Africa will be supported by partners in the Global North.

In her presentation, Professor Vanessa Hayes, Petre chair of Prostate Cancer Research at the University of Sydney, said Southern Africa has the highest genetic diversity within and between populations in the world, “yet Africans make up only two percent of all the data out there. The data is still heavily biased towards Europeans, which means that the drug market is not tailored to our populations."

​Professor Hayes, whose presentation was titled Generating a roadmap for precision medicine in South Africa, said Africa has “been left behind … in terms of precision medicine where a person is treated based on their genome profile."

She said all her research is based in South Africa, and that she works mainly in rural communities in her studies on prostate cancer. “It has a massive genetic ethnic disparity," she said, in emphasizing the need for a focus on genomic medicine.

“We have to be inclusive," she added. Professor Hayes referred to the late Archbishop Desmond Tutu, who lent his genome to science in 2010, and who suffered from prostate cancer himself. “He had a saying, that 'there comes a point where we need to just stop pulling people out of the river. We need to go upstream and find out why they are falling in'.

Accelerating access

Professor Zané Lombard, Principal Medical Scientist in the Division of Human Genetics at the University of the Witwatersrand spoke about the importance of accelerating access to genomic-based healthcare in Africa through research. She said most of South Africa does not have access to genetic services and the picture is worse in the rest of Africa.

“Genomics can improve the healthcare services we can offer to people in South Africa and Africa and there really are no more excuses for us not to be offering that locally. We need to make it happen now. It's happening globally and we can't have Africa left behind," she said.

Professor Lombard highlighted the importance of offering answers to patients with rare diseases, thus ending the “diagnostic odyssey" which some patients and their families have to go on to get diagnoses for their conditions. “It's not only about getting a diagnostic answer. Some people go through mental health anguish for years when they don't know the reason for their child's disorder. We need to serve the rare disease community in a better manner – and genomics can help," she said.

Marco Salemi, professor of Experimental Pathology at the Department of Pathology, Immunology and Laboratory Medicine at the University of Florida College of Medicine, said Africa and the world need to be “proactive, rather than reactive" in the battle against future epidemics.

“We really need to invest for more research and more monitoring in the human/animal interface. South Africa has done an amazing job in showing how much can be gained by epidemiological monitoring in real-time. It put Africa on the map in research and allowed South Africa to face the COVID epidemic better than any country in the world. If we want to prevent the next epidemic, we need to understand how many viruses out there affect animals, and how often they can jump from animals to humans. We need to act before the epidemic starts."

Professor Salemi, who is also the Holloway Chair for research in Chronic and Infectious Diseases said the world is currently focused on monitoring the COVID pandemic. “But we forget this is this huge reservoir of pathogens out there which we know so little about and which can become more and more of a threat, especially because of climate change - so we need to understand more about all these pathogens in the wild, in animals, and their potential to jump to humans, especially with the rate of globalization on the planet …

“Events of zoonotic transmissions will become more and more frequent. We need to face it."

John Sillitoe, the Head of Surveillance Operations at the Wellcome Sanger Institute in the United Kingdom said that the COVID era demonstrated the power of genomics. “The challenge now is to continue that journey at pace, balancing what is relevant to public health versus what is relevant to research. It all needs to come together and it will only succeed if all countries can move forward and do a lot of this work locally rather than in just a few select places."

Sillitoe said the institute was set up outside of the research programmes at Sanger to support the transition of genomic surveillance into public health and to support countries around the world to integrate genomics surveillance into public health.

“There has also been huge investment made during the pandemic into genomics. We need to demonstrate that that investment can be used to generate a lot of value outside of the pandemic to maintain government interest, else we run the risk of going backwards in terms of government attention and investment into genomic surveillance and how it can help and support disease control in public health," he said.

Collaboration

De Oliveira said, besides collaborating with scientists, his team wants to collaborate with public health leaders as well as companies.

Kathryn Reeves (Senior Vice President, Chief Marketing Officer at Illumina, Inc., a global company working to improve human health by unlocking the power of the genome through technology, said

the genomic diversity of Africa will help “all of humankind".

“We celebrate the progress of African scientists doing genomic research in Africa and for Africa. We feel privileged to have the opportunity to support Africans doing science for Africans and to see a partnership between our company and these great scientists.

Mary Rodgers, principal scientist, and manager of the Abbott Global Surveillance Program, said the world needs to be preparing more for a new potential pandemic building tools for virus discovery.

The Abbott Pandemic Defense Coalition works to sense and respond to emerging viruses to protect public health.

Abbott's Global Surveillance Programme, established more than twenty years ago to detect and actively monitor emerging HIV and hepatitis strains around the world, monitors the diversity of current epidemics and the next public health threats.

Scientists and corporates interviewed at the symposium used adjectives like “phenomenal", “cutting-edge", and “truly world-class" and “perfectly geared for the genome era", to describe the BMRI, whose construction process was done by SU's Facilities Management division.