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Stanford Infectious Disease Expert: What We Do and Don't Know About Omicron

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A young girl wearing a mask gets vaccinated.
Eight-year-old Ava Onaissi receives a pediatric Pfizer COVID-19 vaccination during a vaccine clinic at Emmanuel Baptist Church on Nov. 3, 2021, in San José, California. (Justin Sullivan/Getty Images)

While much remains unknown about the omicron coronavirus variant, we do know it’s in Northern California.

On Wednesday, federal, state and local officials announced that scientists at UCSF had detected the nation’s first confirmed case of omicron, in a San Francisco resident who returned from South Africa, where the variant was first discovered, more than a week ago. By Wednesday evening, additional cases had been reported in Colorado, Minnesota and New York.

Officials said the infected San Francisco resident is fully vaccinated — though has not yet received a booster — and has mild symptoms that are improving.

During a Wednesday news conference, San Francisco Public Health Director Dr. Grant Colfax said the city is well positioned to respond to new variants.

"Our vaccine rate is high. More boosters are going into arms every day," he said, noting that kids age 5 to 11 are now getting vaccinated at a rapid pace. "Our masking and vaccine requirements are among some of the most stringent in the country. These efforts have been very effective in helping slow the spread of the virus."

To find out more on the few knowns and many unknowns about the omicron variant, KQED's Brian Watt spoke on Wednesday morning to Dr. Julie Parsonnet, a Stanford University infectious disease expert and professor of medicine, epidemiology and population health.

The following interview has been edited for brevity and clarity.

Brian Watt: It's probably no surprise to you that the omicron variant has been detected here, right?

Dr. Julie Parsonnet: No, not at all. We [the Bay Area] are one of the most diverse populations in the world. We have a lot of travel and we have a lot of people who move around and come into the area. We have a very rich economy that permits that to happen. And we have actually excellent testing here. So if there were a variant that appeared, we would find it.

The person who was detected with this variant was fully vaccinated, not boosted, had mild symptoms and is already doing better. The people known as close contacts of this person have tested negative. What does this set of facts tell you about omicron?

We've known for quite a while that asymptomatic people and people who are generally immune can carry this virus. Even before omicron existed, we knew that there were going to be people vaccinated who carried this virus asymptomatically, vaccinated and unvaccinated. So it's not a surprise that we might find omicron in a vaccinated person.

I feel very reassured that it wasn't transmitted to their family, and I'm also very reassured that this person had mild symptoms. We're hearing rumors that perhaps this is not causing very severe symptoms, but we still have yet to really learn the spectrum of disease that this particular variant is going to cause.

We expect viruses to develop mutations, but just how long does this happen in the life span of a virus? Is there an endpoint to this process?

Yeah, absolutely. So, everything mutates. All animals, they have mutations in their systems when their cells replicate. When you have an organism that has DNA, which is the great majority of organisms, we have repair systems. So in a human, when our cells turn over, the DNA gets repaired if it has a mistake in it. So every time you replicate the DNA or you copy it, you can have a mutation. But there are enzymes that clean those up.

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RNA viruses, which don't have DNA — but they have RNA — don't have those enzymes that clean up the copy that's being made. And so they have mutations all the time. So every virus in every cell is going to be mutating all the time. They're going to have mistakes all the time. The great majority of those mistakes are going to be lethal — the virus can't survive. It can't do its functions with those mutations. It just kills it.

Many of them that also occur don't do anything. They don't create a variant.

And then there are some mutations that actually survive. They usually take about 10 days for those to survive and to actually go in a way that it can move in through the population. So even if you have a mutation, for example, the immune system may not allow it to go forward or another form of the virus may outcompete it in the host.

So there are all these things that go on. Most mutations don't do anything, but some of them survive, and we're going to continue to see that happen. Viruses can do this infinitely, forever.

What lessons can be drawn from delta as you and other scientists around the world learn more about omicron?

I think that we should not get caught too much in the trap of just counting cases. For instance, we don't count cases of the common cold and we don't count cases because it doesn't really matter, right? It's important for us to know where this virus is, and it's important for us to really look at serious disease and death, which is what we've had to do with delta as well, and not get too wrapped up in finding each individual case.

So we don't really know yet with omicron what the concern is. We know that it's likely to outcompete delta. We know, at least from South Africa, it appears that's going to be the case. We know that it may be the dominant form. But we don't know how much it's really going to matter in the various ways that we've protected our population.

We don't know whether it's going to cause significant illness. We don't know how well the vaccines will work, how well the drugs will work, how well the monoclonal antibodies will work.

There's still a lot that we have to learn. And so far, I don't think the signals are terribly worrisome in that regard, but we have to be really vigilant to figure that out.



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