Omicron Is Here. What That Means For The Winter : Consider This from NPR It was only a matter of time before cases of the COVID-19 omicron variant started popping up in the U.S., and now, it's here. Although it's too early to tell how this virus strain will spread, the threat it poses has already lit a fire under public health messaging.

President Biden announced a new strategy to avoid a winter surge of cases that involves free at-home testing, a vaccine booster messaging campaign and heightened international travel safeguards.

Meanwhile, the race is on to detect how omicron is already spreading in this country. NPR reporter Will Stone gives us a look into what's happening in labs right now across the country.

And Saad Omer, director of the Yale Institute for Global Health, discusses what we know about how effective travel bans are scenarios like this.

In participating regions, you'll also hear a local news segment that will help you make sense of what's going on in your community.

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Omicron Is Here. What That Means For The Winter

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Well, it was only a matter of time.


UNIDENTIFIED REPORTER #1: City health leaders say they're not surprised that the omicron COVID variant was detected here in San Francisco.

CORNISH: The omicron variant is here.


UNIDENTIFIED REPORTER #2: Another case of the omicron variant in the U.S. - the CDC tracking a confirmed case in Minnesota.

UNIDENTIFIED REPORTER #3: The breaking news that we're following - the first detected case of the omicron variant of the coronavirus has been found here in Colorado. Here's what we are...

UNIDENTIFIED REPORTER #4: But because this case was community-acquired, health officials believe it could have been spreading already here in Hawaii.

CORNISH: And while we still don't know how quickly omicron may spread or how much protection vaccines will provide, we'll know a lot more in a few weeks. But already, the threat of the new variant has lit a fire under public health messaging.


PRESIDENT JOE BIDEN: I've seen more - (laughter) - of Dr. Fauci than I have my wife. We kid each other, but...

CORNISH: On Thursday, President Joe Biden announced a new plan to combat a COVID winter surge.


BIDEN: And it doesn't include shutdowns or lockdowns but widespread vaccinations and boosters and testing and a lot more.

CORNISH: Biden announced stricter testing guidelines for international travel, a pledge to send millions more vaccine doses to countries in need and a push for booster shots among the 100 million fully vaccinated adults who haven't yet gotten theirs...


BARACK OBAMA: I want to let you know that all adults are now eligible for a COVID-19 booster shot. I got mine.

CORNISH: ...Which is why you might be seeing more ads like this one, featuring former President Obama.


OBAMA: So if you were vaccinated before June, it's time to get a booster.


CORNISH: The White House is also requiring health insurance companies to reimburse people who buy at-home tests and providing tests for people without insurance.


BIDEN: The bottom line - this winter, you'll be able to test for free in the comfort of your home and have some peace of mind.

CORNISH: But with all COVID messaging, there's always the underlying question of whether enough people will fully understand the guidance or want to actually follow any of that guidance at all.


BIDEN: I know COVID-19 has been very divisive in this country. It's become a political issue, which is a sad, sad commentary. It shouldn't be, but it has been. Now, as we move into the winter and face the challenges of this new variant, this is a moment we can put the divisiveness behind us, I hope.


CORNISH: CONSIDER THIS - with vaccines and boosters, we should have what we need to avoid a winter surge like we saw last year. But an unpredictable variant and a predictably clunky public response might make that difficult.


CORNISH: From NPR, I'm Audie Cornish. It's Friday, December 3.

It's CONSIDER THIS FROM NPR. As we've said, it's hard to know how the omicron strain will spread in the U.S. since we're in the very early days of this. But maybe if we ever had anything close to a crystal ball, we could try to predict the future by looking overseas.

WOLFGANG PREISER: Sequencing labs around South Africa are frantically analyzing samples as we speak.

CORNISH: Wolfgang Preiser is head of medical virology at Stellenbosch University in South Africa. It was South Africa, of course, where the omicron variant was first detected.

PREISER: What I do know is that these early outbreaks in Gauteng were largely younger people and therefore also healthier people.

CORNISH: Preiser told NPR that's probably why the majority of cases have been mild.

PREISER: It does, however, not mean by any means that this virus is not able to cause also severe disease should it affect people who belong to the risk groups.

CORNISH: Since the first detected case, Preiser says the overall numbers are low. But...

PREISER: It now constitutes the majority of newly infected people.


CORNISH: So omicron accounts for the majority of new cases in South Africa, and tracking whether the U.S. is headed for a similar trajectory the next few days is critical. NPR's Will Stone has been following the race to detect the spread.

WILL STONE, BYLINE: Dr. Charles Chiu suspected the sample being sent to his lab might be omicron. It was 3 p.m. on Tuesday. And Chiu, who is a virologist at UC San Francisco, had just received an email from the local health department. It said that a positive COVID-19 case had been identified in someone who'd recently traveled to South Africa.

CHARLES CHIU: They wanted to get an answer very quickly. I realized that there was certainly a possibility that this is a case of omicron.

STONE: Chiu's lab does genomic sequencing to understand what variants are circulating in the Bay Area.

CHIU: We managed to get the sample in the laboratory by 6 p.m. We did actually two analyses simultaneously.

STONE: The first was a PCR test - what's generally used by labs to diagnose a COVID-19 case - except this particular PCR test happens to be good at screening for omicron because it can pick up what's called a spike gene dropout.

CHIU: The idea behind spike gene dropout is that PCR tests - they typically look for multiple targets on the virus. One common target is a spike gene. But what's interesting about omicron is omicron has a deletion - specific deletion in the spike gene.

STONE: That deletion causes the PCR tests to look different. This is the result of a mutation in omicron.

CHIU: We are fortunate in that at least spike gene dropout is a very good screening tool, but it doesn't prove that it's omicron.

STONE: You still have to sequence it, which can take a bit more time. For that, Chiu used a small, pocket-sized sequencer. And by close to midnight, he had confirmed his suspicions.

CHIU: It's very likely that this is the tip of the iceberg.

STONE: Scientists in the U.S. already had a sense of how to look for omicron thanks to an early heads-up from South Africa and Botswana. Earlier in the pandemic, the U.S. had struggled to ramp up its surveillance for variants, but Alexandra Phelan at Georgetown Center for Global Health Science and Security says the country is definitely in a better place now.

ALEXANDRA PHELAN: We've actually had quite a significant increase in our capability to conduct the genetic sequencing and then to be tracking what's going on with variants. But right now this is really, I guess, the first full test we have of that system being up and running.

STONE: This week, the CDC director said about 1 in every 7 positive PCR tests are now being sequenced in the U.S. That's a big increase, but Phelan says one challenge is that not everywhere in the country is doing the same amount of it. Some places, like California, are doing a lot of sequencing. But in others...

PHELAN: In some states, we're, you know, sequencing, you know, less than 1%. Getting a bit more consistency across the nation will be critical.

STONE: The more testing that's done, the better positioned the U.S. will be to track the spread of omicron. But the testing is a mix of PCR tests and rapid antigen tests. Dr. Alex Greninger at the UW Medicine Clinical Virology Lab in Seattle says these rapid tests are great and convenient.

ALEX GRENINGER: At the same time, they're not as good at that next portion. They don't get reported to public health as much. They don't get sequenced. And so as that growth is a growing share of testing the United States, that's an area that we're sort of dark to.

STONE: No one wants omicron to be in the U.S., but Dr. Chiu at UCSF says there's a silver lining to finding it here. We can now study it more easily.

CHIU: Whether it's more infectious, whether it's more transmissible, whether it may affect vaccine protection.

STONE: And that is critical for figuring out what needs to be done to stop it.

CORNISH: NPR reporter Will Stone.


CORNISH: So the emergence of the omicron variant may feel like one of the many moments of deja vu we've experienced during the pandemic. Another one is this very specific response to an apparently highly infectious virus strain - the travel ban. The U.S. restricted flights from several African countries in the days after omicron was first detected. And even though dozens of countries all over the world have reported the variant in patients, those limits on travel from southern Africa remain in effect.

PREISER: I can sympathize with the knee-jerk reaction that, if you hear there is something new and potentially nasty, you want to keep it out.

CORNISH: Again, virologist Wolfgang Preiser in South Africa.

PREISER: The problem is that South Africa at this stage feels very much the victim of their own good deeds.

CORNISH: What Preiser means is that it feels like South Africa is being punished for doing the right thing. They had a COVID surveillance system to check for new variants, and they've been transparent about their findings, alerting the rest of the world right away. And the risk, according to him and others who study this kind of thing, is that countries may want to stop being so transparent about detecting new strains.

PREISER: This is actually enabling other countries to look out for it. But the effect is that the travel bans are devastating now our second tourism season for international tourists. I would very much hope the world can move to a cleverer system.

CORNISH: But is there a more clever system? And does a system involving travel bans even work the way world leaders hope they will to stop the spread of COVID? Well, to get at those questions, my co-host Ari Shapiro spoke with Saad Omer, director of the Yale Institute for Global Health.

ARI SHAPIRO, BYLINE: Setting aside the specifics of these travel restrictions, can you say broadly whether shutting down flights can be an effective response in a pandemic?

SAAD OMER: Well, shutting down flights can work theoretically to only delay the arrival of a significant virus. Moreover, in order for a travel ban to work, it has to be really early, and it has to be so drastic as to shut down all travel into a country by 90 to 95%. So, yes, theoretically, it can work. But it can't be a selective ban of flights from a few countries. And it can't be at a time when, you know, this current travel ban happened.

SHAPIRO: We know now that even though the omicron variant was first identified in South Africa, there's research suggesting that it was already in Europe at that point. So what did you think when you heard President Biden announce these restrictions on travel from eight countries in southern Africa?

OMER: I was a bit surprised. The ban, even in the early part, was a bit perhaps unwarranted because it was unlikely to even delay the arrival of the virus, which was the rationale given because it wasn't shutting down - and for understandable reasons - 90, 95% of the traffic coming into the U.S. It was only focusing on a few countries when even there were very early indications that the virus was already in multiple countries. On top of that, part of the concern is that this is not a policy without cost because we know that it discourages countries from reporting new variants. And it's in all our interest to find out not just the existence but the intensity of circulation of any new variant.

SHAPIRO: Yeah. We are now seeing leaders in southern Africa saying, we're basically being punished for having been good global citizens - doing the science, reporting the new strain - because of these travel bans. So do you think that as the pandemic continues, other countries where new, perhaps more dangerous strains might emerge could be less likely to reveal that to the world, having seen what happened in South Africa?

OMER: Yeah. That's the fear because if you think about it, if you are a health minister in central Africa and you are seeing some initial data and you have that incentive to say, why do I have to be the first one to report? - because if I do so, I will face domestic pushback for being a little too naive to report this and then having restrictions imposed on my country selectively. The selectiveness of that ban is very concerning to a lot of these countries and sets a really bad example.

SHAPIRO: Last year the U.S. banned travel from China, where the virus first emerged, and then we saw many coronavirus cases come to the U.S. from Europe. And so do you think we could see something similar here with the omicron variant?

OMER: We are already seeing that. So it's like not only closing the barn door after the horse has left the barn. It's closing the barn door in the next farm over. It's not rational to do so, and it has costs. So, yes, we can see a similar phenomenon here.

SHAPIRO: Are there things you think the U.S. could do in terms of international travel that would help limit the amount of omicron coming over from other countries short of sealing the borders and not letting anybody in?

OMER: There are a few things the U.S. can do - more rational and stringent testing in terms of testing on departure and arrival and quarantine for a select number of individuals - perhaps not everyone - and making sure that during the travel people are safe and there is a low probability of infection, for example, by making sure that, you know, there's a masking requirement. It's OK to add on top of testing - or, actually, desirable to add vaccination requirement. But the long-term solution - we can't get out of this pandemic, at least without a lot of harm, without vaccinating high numbers of people all around the world. There's no shortcut to that.

CORNISH: That was Saad Omer. He is the director of the Yale Institute for Global Health.

It's CONSIDER THIS FROM NPR. I'm Audie Cornish.

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