Meet Professor Tulio de Oliveira, forging a genomic surveillance partnership

Professor Tulio de Oliveira has a passion for launching new scientific ventures. “It’s quite fun,” he says, a light in his eyes. “I find it exciting to go from setting up the operations, the science, funding things, all from scratch.”

Tulio has established two scientific institutes in his home of South Africa, both with catchy acronyms. First came KRISP – the KwaZulu-Natal Research Innovation and Sequencing Platform – founded in 2017 to support his team’s investigations of viral outbreaks across Africa. Then, in 2022, CERI – the Centre for Epidemic Response and Innovation – was launched at Stellenbosch University in the wake of the COVID-19 pandemic. Tulio led the team that first identified the Beta and Omicron variant in 2020 and 2021.

“When I moved to Stellenbosch to create CERI I left every single piece of equipment I had in the other lab [in KwaZulu-Natal] to start again from scratch, to create a team of scientists, many of them from top scientific organisations in South Africa and from abroad,” says Tulio. “In addition, we also created a team of professional grants managers, scientific writers, and chartered accountants, allowing us to attract and manage large projects and grants.”

CERI is now the largest genomics operation in Africa, with facilities as advanced as any across the globe.

World-changing partnership

Tulio’s latest venture isn’t quite so from the ground up. He is in the UK to launch a new strategic partnership between CERI and the Wellcome Sanger Institute’s Genomic Surveillance Unit (GSU). Both labs have impressive pedigrees already, but he sees the opportunity for “a bigger thing, with scientists and product developers that sit across the two centres.”

Tulio has worked with Sanger at least twice before, from South Africa as part of a five-year UK Royal Society Newton Advanced Fellowship, and also while working in the UK at the University of Oxford. To cement the new relationship, Tulio will now become deputy director of the GSU, alongside his existing work in South Africa.

The GSU team didn’t need a huge amount of convincing to visit the beautiful Stellenbosch University campus, nestled among vineyards and mountainous nature reserves. As Tulio had hoped, they were impressed by the CERI labs.

“We have great hopes for this new partnership with CERI, and are incredibly proud to welcome Tulio on-board,” says John Sillitoe, director of the GSU. “Our institutes may be thousands of miles apart, but our aims and thinking could not be closer: genomic surveillance is critical to making informed decisions on public health.”

Tulio agrees: “I believe this can be a really world-changing partnership, which brings genomic surveillance to the next level across the world. I think that’s possible with the technical expertise of both centres. We can act more quickly. And we can have two surveillance sites and training bases, one here and one in South Africa.”

Expertise at the two institutions complement each other neatly. The Sanger Institute has two decades of experience in malaria genomics, while Tulio and his colleagues have been using genomics to investigate virus outbreaks across Africa over a similar time period, including tuberculosis, hepatitis B and C, dengue, yellow fever, and HIV/AIDS. Both turned their attention to COVID-19 and became world leaders during the pandemic, scaling up genome sequencing to monitor emerging threats from new variants.

Life-saving hospital investigations

Tulio recently revisited the many chapters of his storied career in his inaugural lecture at Stellenbosch (worth a watch here). This included his part in a particularly dramatic investigation in Libya in 2007, which saved six foreign medics from a likely death sentence. They used genetics to prove they had not infected children with HIV at a Benghazi hospital, as Libyan authorities had claimed.

He still investigates hospital outbreaks, and recalls a case during the COVID-19 pandemic in South Africa where 35 hospital patients had died from the virus in two days. The investigation recommended a system of colour-coded zones to limit transmission of the virus. “After that we trained 10,000 medical doctors on how to redesign their hospitals.”

Training is another of Tulio’s passions, and CERI has invested in a large fellowship programme, so far training over 500 fellows from 42 African countries. The GSU also supports bioinformatics analysis courses in Africa for malaria genomics. Tulio wants this focus on building skills to be central to the new partnership. “I see a big step forward in what we want to do. So not only African scientists come to the UK to get trained, but also the other way round.”

Climate and health, a historic moment

Between building up CERI and forging the GSU partnership, Tulio has also been instrumental in the birth of another scientific venture, complete with catchy acronym. CLIMADE – Climate Amplified Diseases and Epidemics – is a global consortium which will predict, track, and control diseases and epidemics that are amplified by human-caused climate change in the most affected countries in the world. Tulio and a CLIMADE team presented a global report on climate change and epidemics at last year’s COP28 summit in Dubai, appearing at the annual event’s first ever ‘Health Day’ linking climate change to public health – a decision Tulio describes as “historic”.

“The event was well attended, with many health ministers from multiple countries. The director general of the Africa Centres for Disease Control and Prevention (Africa CDC) and head of the WHO Africa Region (AFRO) delegation were both there. It was good to see the impact of our work starting to cross disciplines, from genomics to climate change. COP is a very intense event, where one meets dozens of health ministers and policy makers. We were very tired at the end!”

In this post-pandemic moment, global interest in the role of genomics to monitor and contain infectious diseases is rapidly growing. A network of scientific institutes and public health bodies is taking shape across the globe, and the partnership between CERI and the GSU is an important piece of the jigsaw.

But when asked if his career has been leading to this point, Tulio smiles: “It’s just the beginning.”