​World-renowned bioinformatician Prof Tulio de Oliveira, Director of the Centre for Epidemic Response and Innovation (CERI) in the School for Data Science and Computational Thinking at Stellenbosch University (SU), delivered his inaugural lecture on Tuesday 5 September 2023. The title of his lecture was “Two decades of genomics excellence: Illuminating health, fostering innovation, and cultivating transdisciplinary research in Africa".

De Oliveira, who is also a professor of bioinformatics at the School for Data Science and Computational Thinking, spoke to the Corporate Communication and Marketing Division about how his work in genomics helps us to plan for future pandemics and also detect new emergent epidemics, especially in Africa.

Tell us more about your research and why you became interested in this specific field.

I work in Genomics which is a broad field of research that focuses on the structure, function and analysis of genomes, that is, the complete set of genetic material present in an organism's cells. Genomic sequencing technologies (laboratory techniques and scientific processes used to determine the building blocks of DNA or RNA) help public health specialists and researchers understand pathogens in greater detail, allowing them to better monitor and respond to localised outbreaks and the spread of infections. Next-generation sequencing offers a more efficient, accurate and cost-effective way for researchers to track genetic changes. Furthermore, genomics surveillance can assist with the ongoing assessment of diagnostic accuracy, which may lead to more effective treatments. With the potential to revolutionise healthcare in Africa, genomics is increasingly being used to understand diseases and epidemics, especially those that are prevalent in the continent.

I was born and raised in Brazil where I majored in molecular biology but also did some scientific computing. When my mother, an international development consultant, returned to Africa in 1997, I joined her, and ended up doing an undergraduate degree at the University of KwaZulu-Natal (UKZN). As an intern at UKZN, I began to produce genomic sequences of HIV. But I soon realised that my laboratory skills weren't so great. So, I decided to do my PhD in bioinformatics at UKZN. Bioinformatics is the art of using computers to analyse genomic sequence data. After graduating, I joined the best viral evolution research group in the world at the University of Oxford, where I learned how crucial it is to track viral evolution. We used genomics to solve a case of HIV-1 and hepatitis C transmission in a Libyan hospital, where five medical doctors were wrongfully accused of and jailed for infecting children. Our findings saved the lives of these doctors.

How would you describe the relevance of your work?

During the Covid-19 pandemic, we saw what important role genomic surveillance can play in shaping the scientific response to diseases, especially in Africa. Even before the pandemic, genomics was used to respond to epidemics such as HIV-1, tuberculosis and arboviruses such as chikungunya, dengue, Zika and yellow fever.

Early in the pandemic, my team and I recognised the important role that genomic surveillance could play in responding to SARS-CoV-2. We then created a highly effective consortium in South Africa, namely the Network for Genomic Surveillance South Africa (NGS-SA), which monitored genetic changes that affect pathogenicity (the ability of an organism to cause disease), diagnostics and therapeutics and vaccines, and managed to identify two of the five SARS-CoV-2 variants of concern circulating in South Africa.

Despite the rapid expansion of genomic sequencing capacity and increased genomic surveillance during the pandemic, the global response to SARS-CoV-2 illuminated the barriers that prevent the world from having readily available, reliable and comprehensive genomic data to aid public health decision-making. Specifically, the ability to rapidly analyse and interpret the data for public health impact is severely limited. We need to plan for future pandemics by increasing genomic surveillance to other pathogens in Africa to be able to quickly detect new emergent epidemics.

You have received international acclaim for your breakthroughs with Covid-19 variants. What were the most satisfying aspects of this endeavour?

Despite the terrible toll of Covid-19, scientists in South Africa have worked relentlessly to produce some of the science that has driven the global Covid-19 response. Scientists in Africa identified some of the most important SARS-CoV-2 variants (beta [B.1.351] and omicron [(B.1.1.529]) and ran a successful trial of a Covid-19 vaccine with almost 500 000 healthcare workers. This trial proved the effectiveness of a vaccine and protected South Africa's health workforce before a large wave of infections hit the country. Despite several setbacks and, against all the odds, we persevered and are a leading country in SARS-CoV-2 genomics surveillance.

Our efforts were recognised by the World Health Organisation and the Africa Centres for Disease Control and Prevention (Africa CDC), while the Centre for Epidemic Response and Innovation at Stellenbosch University as well as the KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP) at UKZN were appointed as specialised genomics facilities to support genomic surveillance expansion in Africa. We also received local and international media coverage for our groundbreaking work, which showed the rest of the world that African scientists can be major role players in health responses to epidemics and pandemics, lead global consortiums, host large grants and events and guide the global scientific agenda. All we need is support, respect and a chance to lead.

I have to say that when you look beyond the recognition and accolades, the most satisfying aspect was that we were able to save lives – lives that are close to us, lives of people whose names, families and communities we know and who we keep in our hearts.

As a world-renowned bioinformatician, you boast many prestigious accolades. What has been the driving force behind your success?

I have always had that activist spirit; the desire to make the world a better place and to stand up for the underdogs. I guess I inherited this from my parents. This could perhaps also explain why I ended up in a field where I can use my expertise to save lives.

What also drives me is to train the next generation of African scientists and reverse the scientific brain drain of top young African talent to train at overseas institutions – from which many don't return. I want to offer opportunities for emerging local scientists and make the rest of the world take notice of Africa as a scientific powerhouse. My dream is to show the world that the global South – Africa, Latin America, and Southeast Asia – is the best place to identify new pathogens and control them. African scientists can indeed help the world to prepare for the next pandemic.

You have spent many years in the challenging environment of higher education. What keeps you motivated when things get tough?

I am driven by the belief that our work can have a positive impact on the world. By contributing to the understanding and control of infectious diseases that affect millions of people worldwide, we can reduce human suffering.

Tell us something exciting about yourself that people would not expect.

I was an avid skateboarder as a teenager and for my first job, I worked in a skate shop after school. Oh, and I love my hair.

How do you spend your free time?

I enjoy spending time in nature, especially taking long hikes with my beautiful wife, cycling and doing outdoor activities with my children. I also read a lot and one of my favourite books is Let my people go surfing by Yvon Choiunard. Another thing I enjoy is watching Formula 1 and football. And my favourite movie is The Godfather.

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