Omicron: From Vaccines to Transmission, Here's What We Know (and Don't)

Federal health officials confirmed Wednesday that the first U.S. case of the COVID-19 omicron variant was detected in San Francisco. According to the CDC, the infected individual — a traveler who returned from South Africa on Nov. 22 — was fully vaccinated. The San Francisco Department of Public Health later confirmed the individual is a San Francisco resident.

The individual is currently self-quarantining and has mild symptoms. In a joint statement, state and local health authorities said that the case was identified thanks to viral sequencing technology from UCSF.

“We must remain vigilant against this variant, but it is not a cause for panic,” the statement said. “To help detect and prevent the spread of this new variant, the State of California is increasing COVID-19 testing at our airports for arrivals from countries identified by the [CDC].”

The case was found after federal health officials announced they were expanding the search for the variant across the country, including at San Francisco International Airport.

As health officials proceed with contact tracing to gauge the spread of infection, researchers race to understand the variant. There are still many questions about omicron: whether it’s more contagious, whether it’s more deadly and how the vaccines hold up against it.

Earlier this week, The Bay spoke with Dr. Chaz Langelier, assistant professor of medicine at UCSF to better understand how the virus mutated and how the Bay Area has prepared ahead of the variant’s arrival.

The following interview has been edited for length and clarity. You can hear the extended version in the latest episode of The Bay.

The Bay’s Ericka Cruz Guevarra: There are many COVID-19 variants out in the world, and we know that some are more concerning than others, like the delta variant earlier this summer. Why are health authorities especially concerned about the omicron variant?

Dr. Chaz Langelier: Well, there’s a couple of reasons, but one of the reasons is because it contains more new mutations than have ever been seen before in a single variant. Many of the mutations that have been observed have been studied before and have been found to make the virus more transmissible and better able to evade the immune response. So not only were there a lot of mutations, but several that are known to be bad actors. So all of a sudden we had some of the worst mutations, all in one virus, coupled with many more that had never been seen before.

Do we know how the virus mutated into this particular variant?

We don’t. What we do know by studying the coronavirus is that on average, approximately on a monthly basis, the virus would be expected to accumulate two new mutations. What likely happened here was some type of accelerated evolution, and that most commonly would be expected to happen within a single individual, as opposed to the virus acquiring mutations [while] being transmitted through a population.

We don’t know where it happened nor when it happened, but most likely there was some type of incubation in an individual with some type of suppressed immune response, where the virus just wasn’t able to be cleared effectively. So [the virus] had that opportunity to continue to evolve and try to evade the weakened immune response that existed in that person.

Do we know whether it is even more deadly or more severe?

We don’t know that either. That is certainly a second key question, in addition to, is it more infectious and transmissible … We do know from a number of the few reported cases that the infections seem to be mild, but we just don’t have enough information yet in terms of exactly what things will look like across a broader population.

Are fully vaccinated people protected?

We know that some of the people who have been infected with omicron have been vaccinated, so it does appear to have the ability to cause breakthrough infections, but so does delta. What we know from looking at delta and from our experience with other variants is that the vaccines we have work well against a number of variants, even though they weren’t originally designed to work against those variants.

So, for instance, the vaccines by and large were designed against an original coronavirus lineage that didn’t have all the mutations yet [and] still may confer excellent protection against severe disease and death.

We still don’t know exactly to what degree omicron might evade our immune response, vaccine-induced or otherwise. But I think most people suspect that vaccines, in particular vaccines plus boosters, will give an important degree of protection and probably protect against severe disease.

How concerned should we be about the new variant here in the Bay Area?

It’s important to be aware. It’s important to be moderately concerned, but also important to recognize that we are fortunate in the bay to live among people who by and large have done a very good job at getting vaccinated. Throughout the Bay Area, 75% to 85% of people are vaccinated. Let’s say if it is more transmissible than delta, it will give us that extra degree of protection.

But globally, in terms of how concerned we should be, the whole world is a bit on edge because there are still so many unknowns. I think that this really emphasizes the fact that nobody is truly safe from COVID-19 until everybody is safe and vaccinated. When we have regions in the world where very few people have had access to vaccines, that really increases the risk of everyone for being exposed to a new variant that might develop and spread more rapidly than would otherwise happen in a highly vaccinated population.

Looking ahead, what are the big questions and thoughts on your mind about omicron and just the next few weeks of this pandemic?

I think there are three three main questions. No. 1, is omicron more transmissible, and will it outcompete delta and cause another surge? To what degree will it evade our immune responses, vaccine-induced or natural? And to what degree might it evade some of the monoclonal antibody therapies that are currently being used? And then, No. 3, will it cause more severe disease?

We’re still very early on understanding how this variant works. Exactly when will we know answers to the questions we have about omicron?

Well, within a few days of identifying the omicron variant, scientists were already testing the impact of this new variant on immune responses. So those experiments are underway. In most cases, they take several weeks to generate an answer. But I think we’ll probably start getting our first clues in terms of the impact of some of these mutations on evading the immune response within a couple of weeks.