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What we know about the omicron variant

MARY LOUISE KELLY, HOST:

The worrisome omicron variant of the coronavirus has been turning up all over the world. It has not been found in the United States yet. But as the president's chief medical adviser, Anthony Fauci, told NPR today...

ANTHONY FAUCI: It could be that it's here in such a very, very low level that it could be still at the point of it being a needle in a haystack.

KELLY: Lots of questions about just how big a problem this new variant will be and whether vaccines will hold up against it. Here to talk about what we do know are NPR science correspondents Joe Palca and Michaeleen Doucleff. Hi, you two.

JOE PALCA, BYLINE: Hello.

MICHAELEEN DOUCLEFF, BYLINE: Hi.

KELLY: Hi. So, Michaeleen, you start. We've been hearing a lot about the high number of mutations on this variant, which, of course, has implications for how effective vaccines may or may not be against it. What do we know?

DOUCLEFF: First off, I want to be clear. We don't know yet if omicron will spread in the U.S. the way it has in South Africa. The populations are very different in terms of things such as age, vaccination and exposure rates. That said, all the scientists I talked to agree that the efficacy of the vaccines will likely take a hit, probably a big hit, when it comes to stopping infections of omicron - so stopping mild or moderate cases. But protection against severe disease and hospitalizations is likely to hold up.

KELLY: Which is good news, if true. But how would scientists know this so soon? - because researchers just discovered this in South Africa and Botswana a week ago.

DOUCLEFF: That's a great question. The short answer is while omicron is super new, its mutations, in many ways, aren't. Many of these mutations have shown up in other variants across the globe, just not all at once. And over the past year, scientists have been intensely studying these mutations. They found that many of them weaken the ability of antibodies to fight the virus.

One group of scientists at The Rockefeller University even wondered what would happen if a virus had a bunch of these mutations all together, a bit like what we're seeing with omicron? So they put together about 20 mutations into the infamous spike protein. They call it a polymutant. Paul Bieniasz helped to lead this research. He says they then took blood plasma from people who had been vaccinated or infected with COVID and checked to see if these people's antibodies could knock out this polymutant protein.

PAUL BIENIASZ: This polymutant spike protein was almost completely resistant to the neutralizing antibodies in those two sets of plasmas.

KELLY: OK, so hold up. Let me just see if I can put this in plain English. Is what he's saying, Michaeleen - is what he's saying that the antibodies triggered by vaccines won't work against omicron?

DOUCLEFF: Yeah. So studies like this are why scientists believe that the vaccine efficacy will likely take a hit, yes.

KELLY: Joe Palca, let me get you in here because that prompts the question of what vaccine manufacturers are going to do about it. If we think the vaccines might not work as well, they would want to change them, right? How's that going?

PALCA: Well, all the manufacturers are moving aggressively to deal with omicron. For example, I spoke with Mikael Dolsten. He's the chief scientific officer at Pfizer.

MIKAEL DOLSTEN: We have a three-pronged plan that we think will help us feel confident that we can get through this troubling situation.

PALCA: So the first part of the plan is to see if people who have been vaccinated, either with two doses of the Pfizer-BioNTech vaccine or three doses, to see whether the people from those - the blood from those people contains antibodies that can prevent the real omicron virus, not the polymutant protein virus-like thing that Michaeleen was talking about.

KELLY: Yeah.

PALCA: But to see if it works against them - and Dolsten says that work has already begun.

DOLSTEN: We remain cautiously optimistic that after three doses, you will have some meaningful protection.

KELLY: Joe, cautiously optimistic sounds just that, not quite as optimistic as one might want.

PALCA: Yeah, I wouldn't put it in the bank, as they say. But Dolsten says they're taking the attitude that, yes, this is going to be possibly not working at all. They don't think that's the case - but possibly not working at all. And so what they're going to do is they're just going to start all over again and make a wholly new vaccine directed toward the omicron variant. And they're going to pull out all the stops, and they could be ready with a vaccine for testing in humans as soon as soon as 60 days.

KELLY: In soon as 60 days. OK. And just to follow up on something else he said, he talked about a three-pronged approach. What are the three? What's that third one?

PALCA: Yeah. Well, Pfizer has developed a new kind of drug called - they're calling Paxlovid. And unlike a vaccine or a monoclonal antibody, Dolsten says it shouldn't be affected by mutations in the spike protein.

DOLSTEN: We feel very confident that our new oral Paxlovid drug is going to be highly active against omicron.

PALCA: He also says in addition to using the drug to treat COVID-19 infections, it could be used as a prophylactic. In other words, you would take the drug for a few days if you had - if you thought you've been exposed to someone with - infected with the omicron variant. And that would prevent the virus from establishing a beachhead inside your body. And I have to say quickly that Paxlovid has not yet received authorization from the FDA.

KELLY: Michaeleen, a booster question for you because that is still the big push. The Biden administration came out yesterday and said, get a booster. Get a booster. It will help protect against omicron. Why? Why would three doses work better than two?

DOUCLEFF: Yeah, and this is actually really good news. So scientists are just starting to understand that a booster doesn't just return your antibody levels to what they were after the second shot, right? It actually likely goes beyond that. The booster can actually help broaden out your defenses in a way that you can fight off not just one variant of SARS-CoV-2 but many different versions of it. Pei-Yong Shi is a virologist at the University of Texas Medical Branch in Galveston. He works with Pfizer and has been studying this effect in the lab.

PEI-YONG SHI: After the third dose boost, our antibody profile inside our body is more capable to block the variants, so that adds another value of taking the booster.

DOUCLEFF: Yeah, so this research is really new, but it looks like the booster may be your best chance of offering protection at this moment.

KELLY: That is NPR's science correspondents Michaeleen Doucleff and Joe Palca. Thanks to you both for your reporting.

PALCA: You're welcome.

DOUCLEFF: Thank you. Transcript provided by NPR, Copyright NPR.

Joe Palca is a science correspondent for NPR. Since joining NPR in 1992, Palca has covered a range of science topics — everything from biomedical research to astronomy. He is currently focused on the eponymous series, "Joe's Big Idea." Stories in the series explore the minds and motivations of scientists and inventors. Palca is also the founder of NPR Scicommers – A science communication collective.
Michaeleen Doucleff, PhD, is a correspondent for NPR's Science Desk. For nearly a decade, she has been reporting for the radio and the web for NPR's global health outlet, Goats and Soda. Doucleff focuses on disease outbreaks, cross-cultural parenting, and women and children's health.