"So we're just gonna go in a freezer," says Tulio de Oliveira.
We're at the institute that he directs, the Centre for Epidemic Response and Innovation at Stellenbosch University near Cape Town, South Africa. And he's taking me to a cold storage room chilled to 20 degrees below freezing.
He calls over his deputy, Yeshnee Naidoo, to lead the way.
"This is the lab queen," jokes de Oliveira. Because she's in charge of lab operations.
Naidoo pulls hard on the freezer door.
"You need muscle here," she says with a grunt.
Naidoo and de Oliveira want to point out an important delivery that's just arrived.
Hidden viruses: how pandemics really begin
NPR is running a series on spillover viruses — that's when animal pathogens jump into people. Researchers used to think spillovers were rare events. Now it is clear they happen all the time. That has changed how scientists look for new deadly viruses. To learn more, we traveled to Guatemala and Bangladesh, to Borneo and South Africa.
We have a quiz to test your spillover knowledge. But we'd also like you to quiz us. Send your questions about spillovers to goatsandsoda@npr.org with "spillovers" in the subject line. We'll answer questions in a follow-up post when the series concludes in mid-February.
It's a plastic box containing 300 samples extracted from cerebrospinal fluid taken from patients a continent away.
"Very close to the Amazon Forest in Colombia," says de Oliveira.
The key to spotting new pathogens
De Oliveira is a co-discover of the omicron variant of COVID. And he's one of a slew of disease hunters from middle- and low-income countries who are now racing to spot new pathogens before they can balloon out of control.
He says, when it comes to stopping the next brewing pandemic, the world's best hope is to look to scientists from this part of the world – what's often called the "Global South."
Why? Well it starts with these samples from Colombia sitting in the freezer.
De Oliveira explains that the patients who gave the samples all had high fevers.
But the health workers at the clinic near the Amazon couldn't figure out what was making them sick.
"They tried all the diagnostics and they failed," he says.
So now de Oliveira's lab is going to use a cutting edge process to see if they can figure out, what exactly was the virus or bacteria infecting the patients?
"We do what we call meta-genomic sequencing," he says.
Meta-genomic sequencing essentially means they run the samples through machines that analyze all the foreign DNA and RNA in there and then use sophisticated computer programs to identify the genetic code or "sequence" of any organisms in that cerebrospinal fluid.
"These methods can sequence up to 11,000 viruses," explains de Oliveira. Then they compare the results to check if they match any of a long list of known pathogens. "And we see, is it something new?"
Because, he says, if the pathogen is new, the early warning could be key to preventing it from sparking another pandemic — by giving scientists the jump on creating diagnostics, therapies and vaccines.
"We want to identify [new pathogens] and have the tools to control them before they hit you," he says.
That's why the fever clinic near the Amazon is just one in a global network of clinics that are forwarding fluid samples from their mystery cases.
And it's why the fever clinic effort, which began about two years ago, is just one of multiple international virus hunts the lab is involved with — including another project that's just started focusing on places where climate change might cause new flare-ups.
Rethinking the way we collaborate
This effort is a truly global collaboration – with plenty of partners and funding from wealthy countries as well as big companies such as the diagnostics powerhouse Abbott. But de Oliveira says that scientists from the Global South countries – South Africa, Brazil, Senegal, India, Thailand – are the most central players.
Indeed, the Cape Town center has become a hub for scientists from across the Global South. They're coming together to develop new processes that will advance genomic sequencing even further.
In a room just beyond the freezer, the latest team is at work: Three scientists visiting from Malawi, Kenya and Botswana respectively. The Botswana-based scientist, Wonderful Tatenda Choga, uses a pipette to transfer some fluid into tiny tubes that will be run through one of the sequencing machines.
"The beauty of this is that whatever we develop here we can go and implement it in our home countries," he says.
And the Cape Town center is actually the second institute that de Oliveira leads. The first — the Kwazulu-Natal Research Innovation and Sequencing Platform, or KRISP — is on South Africa's other coast, in Durban.
De Oliveira says it's hardly surprising that the Global South has such a deep bench of infectious disease specialists. Spotting sudden epidemics is a forte of the Global South.
He cites the COVID pandemic as a case in point:
"One good example was how long it took the United States to have an effective genomic surveillance network. It took years."
By contrast South Africa set up its surveillance network to look for COVID variants within months.
And it was the first in the world to detect the most threatening variant yet: omicron.
Naidoo, who was then part of the lab team at KRISP in Durban, still remembers how they swung into action at the first sign of the new strain — racing in before dawn to process a final set of samples that would confirm the findings.
"Believe it or not, we were in position at the door waiting for the samples to arrive," she says with a laugh. "Literally at the door. Just like, 'Are the samples here? Do you see the courier yet?' "
Twenty four hours later — on Nov. 25, 2021 — South Africa was able to alert the whole world.
The only other country to detect omicron as fast was Botswana — even though it turned out that the variant was already circulating in many other parts of the world, including the United States.
Naidoo Africa's speedy record on omicron makes it all the more galling when the rest of the world greets findings by African scientists with skepticism.
"It's a stigma that's attached with Africa," says Naidoo. "It's like, 'Oh, it's from South Africa, I don't think the results are viable.' Why can't Africa produce the best results? I mean, Come on! We can!"
In fact, de Oliveira says that compared to the wealthy nations of the Global North, countries of the Global South actually have a leg up: "We have more experience dealing with epidemics in the Global South," he says. He gives a rueful chuckle. "It's one of our only scientific advantages."
It's why Brazil has some of the foremost experts on mosquito-borne outbreaks like Zika and Chikungunya. Why Uganda is so good on viral hemorrhagic fevers like Ebola.
In South Africa the scourge has been HIV. To deal with it de Oliveira didn't just study up on genomic surveillance, he helped pioneer its use. "Yeah, very early on," he says. "Probably in 1995. When the field was just starting."
In other words, it wasn't a fluke that South Africa stood up their COVID genomic surveillance so fast. They were building on years of prior work.
De Oliveira says those early efforts included developing methods to minimize the number of samples that clinics would need to send in so that South Africa's already strapped health workers could contribute.
And yet, de Oliveira says, the burden those health workers face is something many of his Global North colleagues overlook.
"They come with these great ideas of setting up these really advanced computer systems in the clinic."
De Oliveira's response: First try spending a day at one of our rural clinics.
"Most of them just burst into tears during the process," he says. "And they're like, 'Oh! I didn't realize that that clinic would have like, 500 people in the queue. And like, people almost dying and the doctors didn't have the tools. And that if I put in an advanced computer system that tries to get [hundreds of samples], not only is it going to have no effect, but it will disturb the clinicians who are overworked.' "
And so as the world mobilizes to catch future pandemics, de Oliveira has a request: Let the Global South take the lead.
"Why not take advantage of the knowledge of the Global South?" he says. "If we work together this way, then we can protect the whole globe."
