“Not you again, Tulio!” President Cyril Ramaphosa would say when virus sleuth Tulio de Oliveira called during the pandemic. De Oliveira and the national network he co-founded were the first to warn the world about Omicron, within days of the Covid variant appearing in hospitals.
For their contribution to Covid-19 decoding and surveillance, bioinformatician De Oliveira and medical virologist Sikhulile Moyo, then director of the Botswana-Harvard HIV Reference Laboratory, were named among the 100 pioneers of 2022 by Time magazine.
This month Time again singled out De Oliveira, 48, as one of the world’s 100 health leaders, for his work in tracking the pathogens that cause infectious diseases and advancing genomics in Africa.
“Tulio is a good leader of a good team which gets results and he deserves the credit,” said Prof Glenda Gray, president and CEO of the South African Medical Research Council. “He acknowledges that he could never do this work without the team and got them all to stand up when they got [a major award last year].
“He is part of this country’s science ecosystem and very important for the scientists of Africa, beyond our borders. He is hard working and inspires trust, bringing collaborators together,” she said. “He’s quirky, friendly and always has a smile.”
He is part of this country’s science ecosystem and very important for the scientists of Africa, beyond our borders. He’s quirky, friendly and always has a smile
— Glenda Gray
More like a pirate of the Caribbean than a scientist in a lab, with long hair and a swashbuckling walk, the Stellenbosch professor met me at the newest institute under his leadership — the Centre for Epidemic Response & Innovation (CERI) — which was launched at the university in 2021.
The “dream team” of scientists at CERI are his not-so-hidden treasure — De Oliveira spent half the interview boasting about them. Five of the team have worked with him for decades, having been with him at the first institute he got off the ground in Durban, the KwaZulu-Natal Research & Innovation Sequencing Platform (Krisp).
He has helped to place South Africa at the cutting edge of genomics surveillance and sequencing by establishing these two institutes — which have attracted well over R1bn in funding — and by forging an alliance with the Wellcome Sanger Institute (WSI) in the UK, the global front-runner in genomic sequencing.
“When they [WSI] headhunted me in January to become their chief scientific officer, I said, ‘Let’s join forces to invest and grow the genomics programme here,’ and said they must come to South Africa to discuss it.
“Their jaws dropped when they saw our state-of-the-art labs,” said De Oliveira, a practising Zen Buddhist who rides his bike to campus. He is now part-time deputy director of WSI’s genomic surveillance unit.
De Oliveira, whose work has saved countless lives, was born in Brazil and began his studies surrounded by bones. A gifted student who got into computers young, he studied paleontology before switching to molecular biology and genomics.
As to how he shifted from a fossil- to a virus-hunter, he said: “Both of them deal with evolution: one is about the morphological evolution of bones and skulls and the other about the evolution of DNA.
“Pathogens [viruses, bacteria, fungi and parasites] are fantastic models of evolution because they change so fast,” he said. Computer tools developed in his lab — such as “the genome detective” — facilitate the rapid identification of viral mutations, which was particularly crucial during the Covid pandemic.
De Oliveira moved to South Africa in 1997 and identifies as an African scientist. “I’ve had multiple offers elsewhere but I like being here,” he said.
He has no hesitation throwing his weight around to secure grants, though his “egotism” irks some of his peers.
Moyo, director of the first lab to sequence Omicron and a former student of De Oliveira’s, told the Pulitzer Centre when it profiled him: “[Tulio] is identified with Africa, and I think we are identified with him, regardless of his colour. He’s raising a lot of black African scientists.”
CERI’s team has grown from 20 to 120 since its launch and most of them are based in the university’s School for Data Science and Computational Thinking. Here they work alongside De Oliveira in cubicles in an open-plan office, on the first floor of a building where bicycles are stacked outside the sliding glass doors.
For many, heading up what is the largest genomics centre in Africa would have been enough; but in January last year De Oliveira co-founded a new global consortium called Climade, which, working in 16 countries, focuses on epidemics and diseases that are likely to get worse with climate change.
“Nearly 60% of known pathogens will be amplified by rising temperatures and extreme events, like floods. This work is not just about science but about intervention in public health policy,” De Oliveira said.
Recent examples include a new cholera strain that broke out in Malawi after Cyclone Freddy hit in February-March last year and has since caused thousands of deaths, and a major outbreak of Dengue fever in Italy in August-October last year.
De Oliveira, who is also an associate professor at Washington University, wants CERI to be a magnet for young scientists in Africa, and Climade is part of this drive.
More than 1,900 scientists have applied for 15 fellowships being offered at CERI in June and its grant-writing programme is a hit, said De Oliveira. “We want to spread the knowledge of grant writing, not have it restricted.”
De Oliveira has been involved in the genomics training of more than 500 scientists from 48 other African countries, several of whom now head labs across the continent. “We have trained heads of [labs and programmes] in Senegal, Cameroon, Mozambique, Zimbabwe, Botswana and Kenya,” he said.
He also works to reverse the scientific brain drain and recently persuaded South African epidemiologist Frank Tanser to return from the UK to a post at Stellenbosch University where he now leads one of CERI’s four research programmes.
He was willing to go the extra mile and was passionate, and we funded him. We must try to keep scientists like him in the country
— Glenda Gray
After earning a PhD in bioinformatics at the University of KwaZulu-Natal, De Oliveira studied at Oxford University, with a top viral evolution research group, and saw the power of sequencing when the group’s work helped to win a reprieve for the six foreign medics who were sentenced to death in Libya 20 years ago for allegedly infecting children in a Benghazi hospital with HIV and hepatitis.
The Oxford scientists proved that the strains detected were present in the hospital before the foreigners — five Bulgarian nurses and a Palestinian doctor — ever arrived. That was the first time De Oliveira received death threats related to his work, but not the last.
In 2009, De Oliveira returned to South Africa, becoming director of what was then the Wellcome Trust Africa Centre’s genomics programme in Mtubatuba, in rural KwaZulu-Natal. In 2017 he co-founded Krisp at the UKZN medical campus in Durban; he is still the institute’s director and their collaboration continues.
Gray remembers flying into Pretoria one Tuesday night and De Oliveira asking to meet her at 10pm to pitch Krisp. “He was willing to go the extra mile and was passionate, and we funded him. We must try to keep scientists like him in the country.”
The year 2017 was momentous for De Oliveira, who was lead author on a milestone study on HIV transmission. This research found that older men were infecting younger women, influencing the country’s prevention strategies. De Oliveira’s parents-in-law, leading HIV scientists Salim and Quarraisha Abdool Karim, were co-authors on that study.
De Oliveira and team members have had more than 300 publications in top journals. “We are good at finishing things and we want our scientific output to guide public health,” he said, adding that public health was more important than publishing for him.
The networks in which he’s pivotal, such as the National Genomics Surveillance Network in South Africa, help to protect the public day by day as health threats emerge, including relatively routine ones such as the annual flu season.
“Eight months ago, we prepared our labs to respond to the flu. We have sequenced the variants and, if there is a new lineage, it will be quickly detected. Flu is seasonal and expected to last eight to 12 weeks,” De Oliveria said.
He said it has taken the US “months” to release only limited genomic data on the outbreak of bird flu currently sweeping dairy herds on farms across a large part of the country. Reports that a farmworker with conjunctivitis had been infected — he has since recovered — suggest the virus crossed the species barrier.
X, formerly Twitter, has provided De Oliveira with a platform to call out what he sees as the self-interest of the Global North and its double standards, and he’s stirred up controversy. When the UK and EU imposed travel bans on South Africa after the announcement of the Omicron variant in 2021, De Oliveira slammed them as stupid and called for compensation for the losses.
He grew up with an activist role model: his Mozambican born mother, Maria João Nazareth, who rebelled against the dictatorship in Brazil, later moving back to Africa as an international development consultant. Last year the grandmother of three graduated with her master’s from Stellenbosch University and De Oliveira appears to have inherited her indefatigable nature.
But he also believes in a work-life balance, noting the rise in breakdowns during the pandemic. CERI has started a tennis club, and its team hikes together. “We have started a football club for men and women, which has joined the local league, and the team trains every Friday,” said De Oliveira.
Following our interview he was due to travel to an strategic health summit with health leaders like World Health Organisation chief, Tedros Ghebreyesus, and Bill Gates, and to an international conference in Denmark where he is delivering a keynote address this week on the surveillance and screening of blood-borne pathogens.
De Oliveira sees a time when the principal investigators in major research projects will no longer routinely be based in Western institutions such as Harvard or the London School of Tropical Medicine.
“Our big vision is for African researchers to lead global studies and be the principal investigators,” he said. “We want to challenge the status quo of how science has been done and for the Global South to be the best at detecting new pathogens and tracking them.”
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