INTERVIEW | “Guys, I think it’s a new variant” – de Oliveira looks back on 2 years chasing the Covid-19 virus

  • Professor Tulio de Oliveira led the team that detected the beta variant of SARS-CoV-2 for the first time in 2020.
  • He was recently chosen as one of Time Magazine’s 100 Most Influential People Award.
  • He is adamant that scientists in Africa have key contributions to make in advancing global health.

South African bioinformatics expert Professor Tulio de Oliveira still hasn’t decided whether to travel to New York next month to accept his Time Magazine’s 100 Most Influential People Award.

De Oliveira keeps a tight schedule. Returning from Stockholm, where he addressed the world’s top Covid scientists at the Nobel Symposium in Medicine, he led the team that in 2020 first detected the Beta variant SARS-CoV-2, the virus that causes Covid-19. De Oliveira and his team also detected the Omicron variant last year.

“So it was 26 scientists, invited from all over the world to Stockholm,” says de Oliveira. “The leading scientists who identified the virus, created the vaccines, evaluated all major therapies, identified variants and led the world’s best clinical vaccine programs.”

Sitting in “meeting room 2” – an outdoor bench flanked by lemon trees next to the South African Center of Excellence in Epidemiological Modeling and Analysis (SACEMA), housed in a restored Cape Dutch building in Stellenbosch – De Oliveira is dressed of knee-high shorts and a K-Way jacket. The man who runs the cutting-edge local labs that first identified Beta and Omicron – the Center for Epidemic Response and Innovation (CERI) at the University of Stellenbosch and the Platform for Innovation and KwaZulu-Natal Research Sequencing (KRISP) – has a surprisingly unchanged behavior. Tendrils of hair escape from his ponytail as he laughs.

Behind the variant discoveries

Speaking to Spotlight, De Oliveira, in his Portuguese accent, recalls the details of their discovery. “We run a very efficient system, what we call the Genomic Surveillance Network in South Africa. [NGS-SA]. When we find something new, we can transport hundreds and hundreds of samples from hundreds of clinics in South Africa, to all major laboratories capable of rapid genomic monitoring. I run the two main ones, KRISP and CERI.

“What people don’t understand is that finding the first genome [the complete set of genetic information in an organism] It’s not difficult. The most difficult thing is to validate that it is a worrying variant, very quickly. And that’s what we did very well with the Omicron.

KRISP, CERI and the Botswana-Harvard HIV Reference Laboratory all released the first Omicron genomes on Tuesday, November 23, 2021.

“At that time, I was sitting in Durban,” De Oliveira says. “I just WhatsApped everyone saying ‘guys, I think this is a new variant.’ is almost like a commando team, a SWAT team [Special Weapons and Tactics], you look at each other, and everyone knows exactly what to do. OK. You go, you do this. Everyone is very well trained, they have received the best training in the world.

“He was emerging in Johannesburg. So I asked the people in charge of the two big labs there – one is based at the University of Pretoria, the other at Wits University – and the samples arrived less than six hours later, in our labs,” he says. “We received the samples at 6 a.m. on the 24th. And by the end of that day, we had all the genomes analyzed.

“Thursday morning 25, we presented to our two ministers, Blade Nzimande [Minister of Higher Education, Science, and Technology] and Joe Phaahla [Minister of Health]. Then we spoke to the president at 10 o’clock.

How did President Cyril Ramaphosa react?

De Oliveira laughs. “Oh President, I spoke to him several times. Half the time he says ‘not you yet, Tulio!’ He said “this is not good news”. But it is better that we are transparent, otherwise it will leak very quickly in the media. Better that we give all the information quickly. Thus, at noon, the Minister of Health had called for an urgent press briefing. He chaired that and asked us to present the information. On Friday we had an urgent meeting with the World Health Organization,” De Oliveira recalls.

Chasing viruses amid stigma

Initially dubbed by some “the South African variant”, Omicron quickly became the dominant variant of the virus globally, identified in 87 countries within three weeks. Its discovery brought stigma and animosity, with world leaders closing their borders to South Africa and local scientists even receiving death threats.

“However, it soon became clear that although the variant was discovered in South Africa, it did not originate here, and the security measures seemed more punitive than preventive,” says De Oliveira. “They were absolutely useless and ineffective.”

Over the years, De Oliveira (46) has worked on global viral epidemics including HIV, hepatitis B and C, Zika, yellow fever, dengue and chikungunya. Reflecting on the Covid pandemic, he says: “The pandemic has been a terrible thing from a health point of view, also from an economic point of view, and psychologically. But on a scientific level, it was phenomenal to see how we could identify a new emerging virus within days, and then develop diagnostics, develop vaccines, and track vital signs in real time.

In April, de Oliveira noted the discovery of two new Omicron sublines on Twitter: “New Omicron BA.4 and BA.5 detected in South Africa, Botswana, Belgium, Germany, Denmark and UK Uni… No reason for alarm as no major spike in cases, admissions or deaths in South Africa,” he wrote.

In a published piece in the medical journal The Lancet last week he called on world health leaders to recognize – instead of punish – researchers in Africa.

“During the Covid-19 pandemic, the lives of many loved ones and colleagues have been lost,” he wrote.

“Despite the terrible toll of Covid-19, in South Africa scientists have worked tirelessly to produce some of the science that has driven the global Covid19 response. But the researchers faced challenges, including the foreign travel ban that was imposed on South Africa for much of the pandemic and deeply affected the local economy. Some researchers in South Africa have received death threats and at one point even needed armed guards outside our labs.

“It is time,” he says, “to enter a new global phase where researchers in Africa are recognized and not punished for their scientific discoveries. Scientists in Africa and other LTICs [lower middle-income countries] have key contributions to make in advancing global health, particularly in areas such as epidemic response and infectious disease.

Young, talented and Brazilian

De Oliveira was born in Brasilia, the capital of Brazil. His family later moved to Porto Alegre, where he was placed in a program for gifted children at the age of six. Here he would learn computers and programming. He received his first 16K RAM computer from his uncle when he was ten years old – a computer that still used a television as a display.

It recalls its roots. “My mother, Maria Joao, an architect and civil engineer, was from Mozambique. She was involved in the liberation movement there. She went to Brazil because it had become very dangerous with the civil war; she basically went into exile. And then the day that Mandela became president, she came to dinner and said, “We’re going back to Africa.” She knew the war would end in Mozambique because it had been funded by the apartheid government. She therefore returned to Maputo to take up important positions in the United Nations to help rebuild the country. Me and my two sisters went to university in Durban.

De Oliveira completed a PhD at the University of KwaZulu-Natal [UKZN], before continuing his studies in institutions such as the University of Oxford, United Kingdom. Today he is a professor at UKZN and the University of Stellenbosch, and an associate professor at the University of Washington in the United States.

Despite his titles, De Oliveira likes to be called by his first name. He prefers small towns to big cities and regularly cycles to work from his home in Brandwacht, in the suburb of Stellenbosch. His wife Astrid works at the Africa Open Institute for Music, Research and Innovation at the University of Stellenbosch. They have three children.


About monkeypox, De Oliveira says: “Yes, it’s another emerging virus. So at the moment we have just received an article with a colleague from Oxford accepted in The Lancet Infectious Diseases. We are part of a global collaboration that tracks it in real time. So far, this is a rapidly evolving epidemic. Today [May 27, 2022], I think there have been more than 250 cases in 25 countries. We just produced the graph.

He scrolls his phone, enlarges a graphic on the screen, adding: “We don’t think this is going to become global, affect everyone. But this is the first time that these large epidemics have occurred in so many countries at the same time. Also, with monkeypox, it is very unusual to have direct human-to-human transmission. Normally it passes through intermediate hosts, which are normally rodents or squirrels.

He points to an oak nearby. “Yeah, people don’t realize it, but they’re a natural host for monkeypox. The beautiful little squirrels we have here.

It’s a Friday afternoon and he has another meeting after our interview. “I prefer to drink wine,” he laughs.

Recognized by time

De Oliveira was nominated for Time The magazine’s prestigious annual list of the 100 most influential people in the ‘pioneers’ section, alongside its former doctoral student, Dr Sikhulile Moyo, director of the Botswana-Harvard HIV Reference Laboratory at Gabarone. Moyo received his doctorate in medical virology in 2016. Others on the Time The list of 100 for 2022 includes Ukrainian President Volodymyr Zelensky.

On its website, Time says, “Scientists in Africa were monitoring and sequencing pathogens long before the pandemic. The world benefited from this network when scientists including Sikhulile Moyo and Tulio de Oliveira identified and reported the emergence of the Omicron variant last November. It was a transformative moment and a paradigm shift…”

In a first for South Africa, Stellenbosch will host the Physics Nobel Symposium on “predictability in science in the age of artificial intelligence” in October, with De Oliveira due to address delegates.

*This article was published by Projector – public interest health journalism.

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