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Scientists race to detect new pathogens before they can spark another pandemic


Infectious disease researchers in South Africa were the first to identify the omicron variant of the COVID-19 virus. Now scientists there are racing to detect new pathogens before they can spark another pandemic. They're drawing on decades of experience dealing with the AIDS epidemic. As part of a new NPR series called Hidden Viruses, global health correspondent Nurith Aizenman has the story.

TULIO DE OLIVEIRA: We're just going to go in a freezer.

NURITH AIZENMAN, BYLINE: I'm at Tulio de Oliveira's institute, the Centre for Epidemic Response and Innovation, 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.

DE OLIVEIRA: This is the lab queen.

AIZENMAN: Queen because she's in charge of lab operations.

YESHNEE NAIDOO: Hi. How are you?

AIZENMAN: She pulls hard on the freezer door.

NAIDOO: I need muscle, yeah?

AIZENMAN: They want to point out an important delivery that's just arrived.

NAIDOO: Yeah. This is what we have it in.

AIZENMAN: A plastic box containing 300 samples extracted from cerebrospinal fluid. This fluid was taken from patients a continent away.

DE OLIVEIRA: Very close to the Amazon forest in Colombia.

AIZENMAN: After we scurry out of the freezer...

DE OLIVEIRA: Oh, it's cold.

AIZENMAN: ...De Oliveira explains that these patients all came to that clinic with high fevers, but the doctors there couldn't figure out what was making them sick.

DE OLIVEIRA: They tried all the diagnostic, and they failed.

AIZENMAN: 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.

DE OLIVEIRA: We do what we call metagenomics sequencing.

AIZENMAN: Metagenomic sequencing essentially means they run the samples through machines that analyze all the foreign DNA in there and then use sophisticated computer programs to identify the genetic code, or sequence, of any organisms in that cerebrospinal fluid.

DE OLIVEIRA: These methods can sequence up to 11,000 known or unknown viruses.

AIZENMAN: You literally...


AIZENMAN: ...Just check. You're like, let's run it against what you know.

DE OLIVEIRA: What you know and what you don't know. We can see, is that something new?

AIZENMAN: Because, he says, if it is new, the early warning could be key to preventing those pathogens from sparking another pandemic by giving scientists the jump on creating diagnostics, therapies and vaccines against them.

DE OLIVEIRA: We want to identify them and have the tools to control before they hit you.

AIZENMAN: That's why the health center near the Amazon is just one in a global network of clinics that are forwarding fluid samples from their mystery fever 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 climate change might cause new flare-ups. This lab is in the midst of a multimillion-dollar expansion.

NAIDOO: And then I'll introduce you to our babies.

AIZENMAN: Back outside the freezer room, Naidoo, the lab head, points out some of the new equipment.

NAIDOO: These are the Novaseq 2000s.

AIZENMAN: This is your baby, this machine.

NAIDOO: These two are called the twins.

AIZENMAN: Making this the largest facility for genomic sequencing in all of Africa. Now, this effort is a global collaboration with plenty of partners and funding from wealthy countries and big companies like the diagnostics powerhouse Abbott. And yet, arguably, the most central players are scientists like de Oliveira and Naidoo in the middle- and lower-income Global South countries - South Africa, Brazil, Senegal, India, Thailand. De Oliveira says spotting sudden epidemics is their forte. He says, consider the COVID pandemic.

DE OLIVEIRA: One good example was how long it took United States of America to have an effective genomic surveillance network. It took years.

AIZENMAN: By contrast, South Africa set up its COVID surveillance network within months, and it was the first in the world to detect the most threatening variant yet - omicron. Naidoo still remembers how the lab team swung into action at the first sign of it, racing in before dawn to process a final set of samples that would confirm the findings.

NAIDOO: Believe it or not, we were in position at the doorway waiting for the samples to arrive. And...

AIZENMAN: Wait. You were literally at the door?

NAIDOO: Literally at the door. We're like, has it come in yet? I'm like, no, it's not yet. I don't see the courier (laughter).

AIZENMAN: Twenty-four hours later, 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 omicron was already circulating in many other parts of the world, including the U.S. Naidoo says this makes it all the more galling when the rest of the world greets findings by African scientists with skepticism.

NAIDOO: It's a stigma that's attached with Africa. It's like, oh, it's from South Africa; I don't think the results are viable. Like, why can't Africa produce the best results? I mean, come on. We can.

AIZENMAN: And de Oliveira says, in fact, compared to the wealthy nations of the Global North, countries of the Global South actually have a leg up.

DE OLIVEIRA: We have more experience for dealing with epidemics in the Global South. It's one of our only scientific advantages.

AIZENMAN: 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 helped pioneer the use of genomic surveillance.

DE OLIVEIRA: Very early, yeah. To be specific, probably in 1995. And that's when the field was just starting.

AIZENMAN: In other words, it wasn't a fluke that South Africa stood up their COVID DNA surveillance so fast. They were building on years of prior work. De Oliveira says that included developing methods to minimize the number of samples that clinics would need to send in so that the arrangement would actually be doable for South Africa's already strapped health workers. And yet, de Oliveira says, the burden those health workers face is something many of his Global North colleagues overlook.

DE OLIVEIRA: They come with these great ideas of setting up these really advanced computer systems in the clinic.

AIZENMAN: De Oliveira's response? First, try spending a day at one of our rural clinics.

DE OLIVEIRA: Most of them just burst into tears during the process, and they're like, well, I didn't realize that that clinic would have, like, 500 people in the queue, like, people almost dying, and the doctors didn't have the tools.

AIZENMAN: Such that introducing some complicated sampling program would only make things worse. And so as the world mobilizes to catch future pandemics, de Oliveira has a request - on this one, let the Global South take the lead.

DE OLIVEIRA: Taking advantage the knowledge of the Global South to protect the globe.

AIZENMAN: Because he says that's what's at stake here - protecting the whole globe.

Nurith Aizenman, NPR News.

(SOUNDBITE OF SUN-EL MUSICIAN'S "TO THE WORLD") Transcript provided by NPR, Copyright NPR.