Prof Tulio de Oliveira: saving lives by 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. In November 2021, a few months after moving from the University of KwaZulu-Natal (UKZN) to SU's School for Data Science and Computational Thinking, he also detected the Omicron variant.

Even before the latter made international headlines, De Oliveira was named as one the ten most influential scientists of 2021 by the top science journal, Nature, for the way he has been fighting vaccine apartheid and vaccine hoarding. He is quite vocal in opposing the way some countries have punished others with strict travel sanctions because of their Covid-19 related scientific discoveries.

He is the 2022 recipient of the Gold Medal from the South African Medical Research Council. In March, his team's work to identify and track Covid-19 variants was listed as one of the 10 top technological breakthroughs of 2022 by the prestigious MIT (Massachusetts Institute of Technology) Technological Review. Towards the end of March, he received the Minister’s Special Covid-19 Award at the 7th National Batho Pele Excellence Awards (Dept of Public Service and Administration).

De Oliveira is quick to highlight that science is indeed a team effort. Over the past 20 years, he has nurtured a worldwide network of collaborators – from computer scientists, mathematicians, statisticians, bioinformaticians and infectious diseases clinicians to theoretical physicists and quantum computing scientists.

De Oliveira was already thrust into scientific limelight when the pandemic started, and he mapped the origins and transfer path of the very first South African cases. Thanks to years of doing genomic sequencing work to monitor and analyse HIV strains and diseases such as tuberculosis, Ebola and yellow fever, his KRISP team (short for KwaZulu-Natal Research Innovation Sequencing Platform, the research team he established in 2016) quickly picked up the new virus' tell-tale genetic clues.

This year, De Oliveira and other leading SU health researchers have already hosted numerous high-level delegations at the billion-rand world-class Biomedical Research Institute (BMRI) of the SU Faculty of Medicine and Health Sciences (FMHS). Visitors have included the likes of World Health Organisation (WHO) director-general Dr Tedros Ghebreyesus, South African President Cyril Ramaphosa and South African-born medical business leader and philanthropist Dr Patrick Soon-Shiong.

From this building on the Tygerberg campus, staff of the soon-to-be-launched Centre for Epidemic Response and Innovation (of which he is director, while he also holds appointments in the FMHS and SU's Faculty of Science) will continue sequencing the genomes of known pathogens and unknown variants. This work and that of others will help to develop and produce vaccines in the new WHO mRNA vaccine technology transfer hub in Cape Town – the first facility of its kind in Africa to manufacture Covid-19 vaccines.

Finding balance

De Oliveira is currently raising 100 million dollars towards real-time genomic research through BMRI and CERI, so that the African continent can trace and respond better to new epidemics and pandemics. He has already secured a fifth of what is needed over the next five years.

When visiting him in his office, there is no sign of the dapper suits he dons to meet dignitaries and media people. In a pair of comfortable shorts, he cycled to the Mostertsdrift offices of the South African Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA) in Stellenbosch. That's where he and members of his research team currently share office space, just the way he likes it.

As he fidgets in the open-plan office to install a new security gadget for his bicycle, he muses how important a work-life balance is.

'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, as a six-year-old, he was placed in a programme for gifted children in Brazil. It saw him make time for tennis, skateboarding and basketball in between learning about computing, programming and artificial intelligence.

He was ten when he received his first computer from his uncle – one that still used a television as screen. Its petty memory capacity of 16 KB of RAM is laughable compared to the mammoth computer clusters and state-of-the-art laboratories with automated DNA extraction robotic equipment that he nowadays has access to.

BMRI's newest 'residents', two Illumina Novaseq 6000 DNA sequencing platforms, are the largest of their kind in the world. These were donated by the Chan Soon-Shiong Family Foundation.

It 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 are done for 21 other African countries. High-level training will be provided to their scientists.

'Being spread across different faculties and campuses brings science to the edge. By bringing medical doctors, lab technicians, scientists and big data people together, we can answer the big questions we are interested in,' says De Oliveira in his trademark Portuguese accented English.

'Most of our 'big questions' relate to epidemics: Covid-19, HIV and TB. Then there [are] lesser-known ones that commonly occur in Africa, such as yellow fever, Zika, Lasa, dengue, Ebola and the Chikungunya virus.'

He's also offered CERI's help to President Ramaphosa to fight another South African epidemic: gender-based violence. South African Police Service (SAPS) forensic staff will receive training. This is to help cut back on severe backlogs in the analysis of crime-related DNA samples needed to see perpetrators behind bars.


His interest in analysing disease outbreaks started in 1997 in a virology research lab at UKZN. As a junior student he soon raised his first grant. Together with American bioinformatics expert Rob Miller he wrote software to classify HIV variants. He received his PhD from UKZN, and has spent time at Leuven Catholic University, 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 committees and councils and has raised 50 million dollars in research funding.

Along with his professorship in the SU School for Data Science and Computational Thinking, De Oliveira (among others) is an affiliate professor at the Department of Global Health at the University of Washington. He still serves as director of KRISP and senior research associate of the Centre for the AIDS Programme of Research in South Africa at UKZN. He sits on the highest possible technical working group that detects 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.

Early years

De Oliveira often uses words such as 'fun' and 'laughter' while chatting about his day job, which allows him to combine his interest in biological and health sciences with his IT prowess. While flying his way through school and university, he has, however, had his fair share of teachers and academic superiors who have described him as 'too rebellious.'

He has called South Africa home since the age of 21. Durban and its coastline won when in 1997 he and his two sisters decided where to study after their mother relocated from Brazil to Mozambique. In her younger days she was a freedom fighter in the war-torn country, and post-apartheid she returned to her country of birth to work for the United Nations.

Saving lives

He uses the floods of worldwide media enquiries to highlight the significant science being produced in South Africa, and to advocate for more respect for researchers working on the continent.

'South Africa and Africa do not have to be mere followers in the global science world.''

'Our 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.'

About the political and economic ramifications following Omicron's detection, he 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 save lives.

'We could quickly help the world to prepare their response, including South Africa. We ended with a much less deadly wave. We showed that how acting quickly, seriously and rapidly on epidemic responses made the difference.'

The threats that De Oliveira and others in the South African medical fraternity received post-Omicron was not a first for the pony-tailed scientist who gets through his day with many jokes up his sleeve.

In 1998 he helped to prove the innocence of six foreign medical workers set to be executed in Libya. They were accused of infecting more than 480 children with HIV. An analysis of DNA samples from the children proved that it had happened prior to the medical staff's arrival in Libya. The results, with De Oliveira as first author, were published in Nature and endorsed by more than 100 Nobel Prize winners.

Months later, after international pressure secured their release, he met the former captives – and for the first time could tangibly put a face to the lives his work has since helped save.

This article was written by ?Engela Duvenage

News date: 2022-04-11


KRISP has been created by the coordinated effort of the University of KwaZulu-Natal (UKZN), the Technology Innovation Agency (TIA) and the South African Medical Research Countil (SAMRC).

Location: K-RITH Tower Building
Nelson R Mandela School of Medicine, UKZN
719 Umbilo Road, Durban, South Africa.
Director: Prof. Tulio de Oliveira