Searching for clues in pandemics

In COVID-19 history, Stellenbosch University (SU) bioinformatician Prof Tulio de Oliveira will be remembered for first detecting the Beta variant of SARS-CoV-2 in late 2020, and then the Omicron variant a year later. The latter happened a few months after he moved from the University of KwaZulu-Natal (UKZN) to SU’s School for Data Science and Computational Thinking and Centre for Epidemiological Research and Innovation (CERI).

It was at the start of the pandemic already, when he mapped the origins and transfer path of the first South African cases, that De Oliveira was first thrust into the scientific limelight.

He was subsequently named as the 2022 recipient of the South African Medical Research Council’s Gold Medal, and received visits from World Health Organization (WHO) director-general Dr Tedros Ghebreyesus, South Africa’s president Cyril Ramaphosa and South African-born medical business leader and philanthropist Dr Patrick Soon-Shiong.

Also in 2022, his team’s work on identifying and tracking COVID-19 variants was listed among the year’s top 10 technological breakthroughs by the Massachusetts Institute of Technology’s MIT Technological Review. He was furthermore awarded the Ministerial Special COVID-19 Award at the 7th National Batho Pele Excellence Awards of the South African Department of Public Service and Administration. De Oliveira also received this year's German Africa Award in November 2022.

He serves on the WHO’s highest possible technical working group on the detection of new viruses and variants, is linked to the world’s strongest scientific networks, and leads the national genomics surveillance network of eight South African universities and the National Institute for Communicable Diseases.

In 2021, De Oliveira was named one of science journal Nature’s 10 most influential scientists for standing up against vaccine hoarding, so-called ‘vaccine apartheid’, and the way that some countries used strict travelling sanctions to punish others that had made significant COVID-19-related scientific discoveries. He used floods of worldwide media enquiries to highlight the significant science being produced in South Africa, and to advocate for more respect for researchers working in Africa.

“South Africa and Africa at large do not have to be mere followers in the science world. The long-term objective is to reverse the brain drain, to attract leading experts and to grow local talent. And to be a big exporter of the best technologies related to vaccines, therapies and diagnostics to help the world,” says the ponytailed professor who holds joint appointments in SU’s Faculty of Science and that of Medicine and Health Sciences.

A COVID-19 leader

At the beginning of the pandemic, De Oliveira’s KRISP team (short for ‘KwaZulu-Natal Research Innovation Sequencing Platform’, the research team he established in 2016) could quickly pick up the new virus’ tell-tale genetic clues because they were experienced at monitoring and analysing HIV strains and diseases such as tuberculosis, Ebola and yellow fever through genomic sequencing.

His team at CERI continues to sequence the genomes of known pathogens and unknown variants.

“Most of our ‘big questions’ relate to epidemics: COVID-19, HIV and TB. Then there are lesser-known diseases that commonly occur in Africa, such as yellow fever, Zika, Lassa, dengue, Ebola and the chikungunya virus,” says De Oliveira.

His first computer only had 16 KB of RAM as memory capacity. That is laughable compared to the mammoth computer clusters and state-of-the-art laboratories with automated DNA extraction robotic equipment that he now has access to. These facilities are based in the billion-rand, world-class Biomedical Research Institute (BMRI) of SU’s Faculty of Medicine and Health Sciences on the Tygerberg campus.

The BMRI houses two Illumina Novaseq 6000 DNA sequencing platforms, the largest of their kind in the world. These were donated by the Chan Soon-Shiong Family Foundation.

Such technology allows the transdisciplinary and transorganisational CERI team to do vaccine-related research and sequencing work on behalf of other research groups running clinical cohort trials. Genomics surveillance work is also done for 21 other African countries, and high-level training is provided to their scientists. CERI staff furthermore support the WHO mRNA vaccine technology transfer hub in Cape Town – the first facility of its kind in Africa.

In early 2022, De Oliveira also offered CERI’s help to President Ramaphosa in the fight against another South African epidemic: gender-based violence. Training provided to South African Police Service forensic staff will hopefully help reduce severe backlogs in the analysis of crime-related DNA samples that are needed to put perpetrators behind bars.

Experience

De Oliveira’s interest in analysing disease outbreaks started in 1997 in a virology research lab at UKZN. One of his first projects was to co-author software to classify HIV variants. After receiving his PhD from UKZN, he spent valuable research time in Belgium at Leuven Catholic University, and in the UK at the Wellcome Trust Sanger Institute in Cambridge (as a Royal Society Newton Fellow) and at Oxford University (as a Marie Curie Fellow).

Since then, his insights have informed WHO policy briefs. He serves on local and international committees and councils, and has raised 50 million dollars in research funding.

De Oliveira is currently raising 100 million dollars so that the BMRI and CERI, through real-time genomic research, can enable African scientists to trace and better respond to new epidemics and pandemics.

De Oliveira is an affiliate professor at the University of Washington’s Department of Global Health, and still serves as director of KRISP and as a senior research associate of the Centre for the AIDS Programme of Research in South Africa (CAPRISA) at UKZN.

The early years

When given the chance, De Oliveira cycles to work, in an effort to strike a better work-life balance.

“Each time we double our pressure, we also double our basic mental health processes. Otherwise, one cannot handle that kind of pressure,” notes the professor who doesn’t much like hierarchical structures or being called by any title other than his name.

This ethos was instilled in him by his civil engineer mother, Maria, when he was placed in a programme for gifted children in Brazil at the age of six. She ensured that he made time for tennis, skateboarding and basketball in between learning about computing, programming and artificial intelligence.

While flying his way through school and university, he often heard that he was “too rebellious”. Still, De Oliveira often uses words such as ‘fun’ and ‘laughter’ in describing his day job, through which he combines his interest in biological and health sciences with his IT prowess.

He’s called South Africa home since the age of 21, when he and his two sisters decided to start studying in Durban after Maria returned to Mozambique for work reasons.

Saving lives

About the political and economic ramifications following Omicron’s detection, De Oliveira says: “As scientists, we had the OK from the President to announce it. He said we needed to be transparent, and that fast responses in this pandemic would save lives.

“We were able to quickly help the world, including South Africa, prepare their response. We ended up with a much less deadly wave. We showed how acting rapidly and seriously on an epidemic can make all the difference.”

The threats that De Oliveira and others in the South African medical fraternity received were by no means a new experience for this scientist who gets through his day by cracking jokes.

In 1998, he helped prove the innocence of six foreign medical workers who were due for execution in Libya. They were accused of infecting more than 480 children with HIV. An analysis of DNA samples proved that the children were already infected prior to the medical staff’s arrival in Libya. The results, with De Oliveira as first author, were published in Nature. More than 100 Nobel Prize winners endorsed it.

After international pressure secured their release, De Oliveira met the former captives – for the first time, he was able to put faces to the names of people his work helped save.