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Breaking Down Omicron

UCSC infectious disease ecology professor Marm Kilpatrick addresses questions about the Covid variant

The County of Education and local school district distributed some 80,000 test kits to students and staff across Santa Cruz County in hopes of slowing the spread of the Omicron variant of Covid-19. PHOTO: Tarmo Hannula

Just when it started to feel like many parts of life were returning to normal, everyone and their mother got Covid-19. 

Health officials first identified cases of the Omicron variant in Santa Cruz County on Dec. 21 from tests taken on Dec. 16 and 17. Shortly after that, the average number of new daily cases in the county skyrocketed from around 40 to over 110—an increase of more than 187%. 

Models forecast that new daily infections will continue increasing in the near future. Some reports suggest the new variant causes more mild sickness—especially in vaccinated people—but its transmissibility still makes it likely to overwhelm the healthcare system.

In a Jan. 5 press release, county officials urged people with mild to moderate cases to stay home and consult outpatient primary care providers rather than crowd emergency rooms. 

In the same release, Santa Cruz County Deputy Health Officer Dr. David Ghilarducci emphasized the importance of getting vaccinated.

“The best defense against serious illness and hospitalization from Covid-19 is to get vaccinated. If you have not gotten vaccinated or boosted and are eligible, please do so now. Do it for yourself, your family and your community, including the health care workers we depend on to be there when we truly need emergency care,” he said. 

Wearing masks and getting tested can also help keep numbers down. Santacruzhealth.org lists testing locations, but recent surges have overwhelmed some sites.

As cases increase and information changes, it can be tough to keep track of the latest recommendations. UCSC infectious disease ecology professor Marm Kilpatrick has kept an eye on and contributed to Covid-19 research throughout the pandemic. He recently sat down to answer some common Covid-19 questions over email. His answers have been slightly edited for clarity.

What makes Omicron so easily transmissible? How is it different than past variants?

MARM KILPATRICK: Omicron appears to be both inherently more transmissible, and is much better able to infect people that have immunity from vaccination or previous infection.

How long are people contagious for? The CDC currently recommends isolating for five days. Is that enough? 

There isn’t great data from transmission studies on this yet, but available data indicate that a non-trivial fraction of people is infectious for more than the five days implied by the CDC recommendations. The CDC recommendations were a pragmatic move to make it easier for organizations—businesses, hospitals, schools, etc.—to continue to operate when 5-15% of their staff are testing positive in a single week. That’s why California rightly includes a negative test taken at least five days after testing positive before stopping isolation.

Was the current spike caused by holiday travel, and is it expected to calm down anytime soon?

The current spike is a combination of the spread of the new variant (Omicron) plus holiday gatherings and travel. But even without holidays, Omicron is so transmissible—including in vaccinated or previously infected people—that it will continue to spread rapidly in January. Models suggest the Omicron surge will likely peak in late January or early February in many parts of the U.S., including California. But there is substantial uncertainty because human behavior can slow down or speed up transmission substantially.

Why is Omicron harder to detect with tests? Is a throat swab better than a nasal swab?

It’s not harder to detect Omicron, except if tests use a single gene marker where Omicron has a mutation. Antigen tests are likely not less sensitive, in contrast to FDA reports. There is growing evidence that a combination of the throat and nasal swabs is better at detecting the virus, especially earlier in infection. There are many videos circulating on how to safely do a throat swab.

[Kilpatrick references a Dec. 28 Twitter thread from Michael Mina, a former Harvard Medical School epidemiologist and immunologist who recently became Chief Science Officer of at-home testing company eMed. Mina called the FDA’s statement that rapid tests may have reduced sensitivity to Omicron “insane,” and counters the announcement with two main points: 

1) Antigen, or rapid tests, detect a part of Omicron that is not mutated. 

2) Given equal amounts of Delta and Omicron, the tests perform the same. But on day one of infection, there might be less of Omicron to detect. So all types of tests will have a harder time detecting it on the first day—not just rapid tests. A few studies have suggested that early on, the variant appears more in saliva than in nasal mucus, which is why some officials now suggest throat swabs over nasal swabs.]

How long after being exposed should people get tested, and are rapid tests still reliable?

This question has a complex answer and depends on whether people are vaccinated or not, and which variant. Omicron appears to have a shorter incubation period—the time from infection to symptom onset. But a simple [answer] is that if people wait until day seven and then get tested, most—but not all—infections will be detected.

We’ve seen advice about masks—what type to wear, when to wear them, how often to change them or clean them, etc.—change over the course of the pandemic. How can people best protect themselves and their communities against this variant? 

There is a gradient in mask quality (worse to better): gaiters, cloth masks, surgical/procedural masks, N95/KN95. But at least as important as the mask is how well it fits your face. If most of the air you breathe is passing through the mask, then it is doing its job. If it’s passing around the mask (i.e. out the sides/top) then even an N95 will be relatively ineffective.

Is anyone working to develop more effective vaccines for different variants? Are there predictions about what the virus might look like in the future? 

Yes, the big vaccine companies are making Omicron-specific vaccines. But these haven’t been tested for efficacy yet, and it will likely be several months before they are available if they turn out to be substantially more effective than the current vaccines. It’s also possible that Omicron will be replaced by another variant by the time they are available.

How do vaccines and herd immunity affect the evolution of new variants? 

Immunity reduces transmission of the virus, which reduces the evolution of new variants. But if protection isn’t complete then their immunity can select for variants that evade immunity and enable infection. However, our immune system has multiple arms, and some of the arms that prevent severe disease (e.g. T-cells) are much more effective against a range of variants than the part of our immune system that stops infection (antibodies).

If someone who has not received a booster or a vaccine tests positive for Omicron, should they still get a shot once they recover? 

Definitely. There is very strong evidence showing that people who have been infected but not vaccinated have some protection, but those that have been vaccinated after being infected have much stronger and broader protection.

Are there any common misconceptions about this variant you’d like to clear up? 

Probably too many to mention.

In the spring of 2020, you made a point of emphasizing that outdoor activities were safe. Are they less safe now? 

People have been asking if they should wear masks on their outdoor walks, even if they’re not encountering many people. As noted above, Omicron is more infectious and can infect immune individuals much more easily. So, all activities are less safe. However, outdoor activities are still much, much safer than indoor activities. So people should still meet non-household members outdoors whenever possible, and if they can’t maintain a little bit of space (i.e. if they are going to talk face to face less than 3 feet apart) then a mask could help. But going for a walk when you don’t stop to talk to a person up close is still very low risk.

In 2020, there were certain sectors singled out as high-risk: hair salons, gyms, movie theaters. Has your view of the risk at any of those changed? With Omicron, do they now seem any riskier than other indoor locations?

The relative riskiness of different activities has not changed. All activities where you spend sustained time inside breathing air that other people have breathed are higher risk, and activities in which you spend more time or people breathe more heavily are higher risk. But, as noted above, with Omicron, the risk of all activities is higher.

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