UC Davis microbiome expert weighs in on the Omicron variant and shares his evolving thoughts on eating out, indoor events and long Covid


The Omicron variant is now spreading throughout the world at an alarming rate, and Sacramento County has seen a massive spike in recent weeks, hitting four-month highs. So we spoke to Dr. Jonathan Eisen, director of the UC Davis Microbiome Special Research Program, who is an expert on microbes—organisms such as bacteria, fungi and viruses—which are normally invisible without a microscope, but play critical roles (good, bad and in-between) in every ecosystem on the planet. 

Of particular interest to him these days is the SARS-CoV-2 virus, which causes Covid-19. He holds degrees from Harvard and Stanford, and previously held appointments at Johns Hopkins University and The Institute for Genomic Research. He is currently a professor at UC Davis with appointments in the department of medical microbiology and immunology, the department of evolution and ecology, and the Genome Center.    

He was also profiled in Time magazine in 2020 as one of 16 people or groups “Fighting for a More Equal America,” for his work on trying to increase female representation at scientific conferences. 

We spoke to Dr. Eisen about how the Omicron variant is different from its predecessors, his recommendations for the community, and what precautions he’s taking in his own life to stay safe.

What kind of risk are we looking at right now with Omicron?

The Omicron variant is way more infectious [than Delta]. It’s horribly contagious. Even people who are boosted are still getting infected. [The vaccine] does not seem to provide a huge protection against getting infected. I think that’s part of why it’s spreading so fast—people who have been vaccinated and/or boosted have mistakenly thought they were not going to get infected, and so they were going maskless everywhere. But if you have five times as many people infected, that’s going to create havoc, and that’s what is happening in New York and the Northeast, where the hospitals are full. They’re already sending people away who have any other types of emergency or nonemergency health needs. I think we’re in for some tough times; that’s my prediction. 

You’re saying that vaccines may not provide much protection against getting infected with Omicron, but is it still true with Omicron that vaccines are very effective at preventing serious illness and death?

All the evidence right now shows that vaccines are incredibly effective in reducing the risk of severe illness and death from Covid. And this is true even for new variants such as Delta and Omicron, even though the vaccines were not specifically designed for them. One can reduce the risk of severe illness even more by getting a booster shot. This reduction in risk is very, very clear from all the data. The one issue with Omicron that is different than with other variants is that just getting the regular vaccine dose (e.g., two Pfizer shots) does not reduce the risk of severe illness as much as it did for other variants. In other words, to reduce the risk of severe illness or death, it seems that a booster is very important here.  

Hautamaki Andria Jonathan Eisen

Dr. Jonathan Eisen in his lab at the UC Davis Genome Center. (Photo by Andria Hautamaki)

What are some things we can do to slow the spread?

What I’m hoping is that people do a lot of behavioral intervention that can slow down the spread of the Omicron variant. It goes back to the whole “flattening the curve” thing from before, and there are many things we can do. If you’re in crowded indoor spaces, you can avoid doing things where you have to take off your mask—so, no eating. But even with your mask on, not all masks are created equal. There’s new guidance that has come out in the last few days that cloth masks just aren’t going to cut it against Omicron. They just do not, on their own, filter enough particles out to reduce your exposure when airspace is getting filled with virus. What you want is a KN95 or N95 mask.

So is it safe to say that you’re not eating indoors at restaurants?

I am not eating indoors at any place. Absolutely not. No fricking way. If I’m inside a restaurant, and someone is 40 feet away, they’re still putting virus into the air in that space. And if the air is not filtered, you’re going to get it. This “6 feet apart” thing is completely wrong. That guidance was put out ages ago when there was this idea that the virus is transmitted in these big droplets, but the virus is also transmitted in what are called aerosols—little droplets that get suspended in the air. If you don’t have good air circulation and you’re sharing an indoor space with someone who’s infected, you’ll get exposed no matter how far away they are.

What about outdoor patio dining? Has Omicron changed that for you? Will you now avoid patio dining during Omicron’s wave over the next month or two?

As for patio seating, yes, Omicron has changed that too. I think I would generally avoid this myself unless the seating was really spaced out. If it was crowded but outdoors, that would not be good enough. I would want a decent amount of space to limit exposure. If someone is near you, and is infected, the virus they’re releasing gets dispersed pretty fast, and you can still get it if you’re really close to them.

What about contracting the virus through surfaces? You’ve studied this.

That was a mistaken assumption made by many people in the medical and infectious disease community based upon other pathogens. And it looks like [the danger] is virtually zero [with Covid]. It’s almost completely a nonissue. I mean, it is true that if someone is infected, and they cough and it gets on a surface, and if you go and lick your hand or that surface, then yeah, you can pick it up. But we can find almost no documented cases of transmission [via surfaces]. It doesn’t mean it doesn’t happen, but it’s not something to worry about. If you estimate the risk of getting Covid from the air versus getting Covid from a surface, I would estimate that something like 99.9% of transmissions happen from the air and 0.1% happen from surfaces.

Where is your thinking right now in terms of working indoors with others or going into other indoor places?

Prior to Omicron, I was starting to go back into the office, wearing a mask all the time. So that seemed reasonably safe. And we were all doing it in my lab. With Omicron, I’m definitely going to avoid indoor spaces whenever I can. I mean, I’m shopping—I went out today to the Co-op and into a bike shop, and I’m not completely isolating myself. But I’m not going into a place where I’m going to take off my mask, and I’m not going into a place where they don’t require masks. And I’m only going in for short periods.

Do you think that large indoor events are safe to attend if you wear an N95 mask the whole time? 

I think if you wear an N95 mask in an indoor event for the whole time, it would definitely reduce your risk. But it does not eliminate risk, since the virus can still get by the mask, just at a much lower rate than without the mask. Personally, I would not feel comfortable right now, with the rate of Omicron spread, at any high-density indoor event like a concert or a sporting event. I would assess each situation as best I could, but from what I know right now, with upwards of 10% of all people in some areas infected with Omicron, going to a large gathering indoors seems unwise right now. I think that likely will change in a month or so, since in many places, Omicron has swept through very fast and then diminished reasonably fast too. So skipping a few indoor events for a month and seeing how things play out seems wise.

What about flying right now?

I wouldn’t do it right now, probably. But I think you can do something like that and be reasonably safe if you wear an N95 mask the whole time, and if the airline is making sure everybody has masks.

Does that mean you would advise against taking off your mask for food service on a cross-country flight?

This is a great question. If you take off your mask for 10 seconds, that is very different than if you take off your mask for 10 minutes. Sadly, you can get sick from 10 seconds if you get a massive dose of virus from the air. So personally, I would try to not take off my mask at all. But again, the risk goes up the longer your mask is off, so if people really feel like they need to have some food while on the flight, I would consider the context. If the plane is crowded and people are wearing crappy cloth masks and some are not keeping them on much and not covering their noses, I would not take off my mask at all. But if the plane was not so crowded and people seemed to be wearing good masks mostly and wearing them carefully, then it would not be a massive risk to remove one’s mask for a bit to eat. Again, with the crazy high rates of Omicron right now, I would recommend against this. But I would certainly feel safer removing my mask in the second scenario than in the first.

One of the growing concerns with the virus is long Covid, where symptoms can far outlast the initial infection. What are your thoughts on that?

That is one of my biggest concerns with this attitude of not worrying about Omicron too much because it might cause less severe symptoms. We know that long Covid is a problem for the other variants. It’s a big problem that is poorly understood medically, but is very clearly a real thing. These are real medical problems that people are having for months to now years after infection. Some people are saying everybody is going to eventually get Omicron, and that’s just the wrong attitude. We can make it so that not everybody gets it, and therefore reduce the risk of long Covid in too many people. We can’t just let it spread to everyone on the globe, because that’s going to be a medical catastrophe. Now is not the time to do nothing and hope for the best. It is the time to take measures while at the same time trying not to damage people’s lifestyles and lives and the economy.

This interview has been edited for clarity and length. Follow Dr. Eisen on Twitter at @phylogenomics.