The Omicron Variant

27 November 2021

This post was written on November 27th, and last updated on Jan 4, based on information available at the time. I am linking to primary sources: virologists, epidemiologists, researchers.

I’d also recommend reading a great writeup of the current state (as of Dec 17) by Derek Lowe at He links to primary sources.

This post is written in a question-and-answer (Q&A) format.

Caveat - I am not a doctor, virologist, epidemiologist, public health expert. I spend a lot of time listening to them, trying to make informed + thoughtful choices.


Q - How much faster does Omicron spread compared to Delta?

A - Best guess, 4-6X faster. So far, when it’s not the dominant strain, it doubles the number of people infected every 1.3-2 days. We know this from several different sources:

Omicron could be spreading faster due to being more transmissible, and/or being able to evade antibodies (immune escape). We don’t know which yet. Dr. Trevor Bedford goes into detail about this.

This leads to truly crazy spread, like 1 in 10 people in London having Covid on December 19th

Q - What will this winter (winter 2021->2022) wave look like?

A - Best guess, this could be the biggest wave yet. An IHME model]( projects more COVID-19 cases in the next 60-90 days than there have been in the last 2 years combined, over 3 billion.

This will put immense strain on already stressed/breaking health care systems. If there was ever a time to ‘flatten the curve’, it is now.

Q - Why does Omicron spread faster?

A - We’re not sure yet. A Honk Kong study suggests Omicron reproduces up to 70x faster in the upper respiratory tract (i.e. nose + throat), and yet more slowly in the lung. Stat has a good writeup.

Recall that the original Covid strain was confusing, because most people weren’t highly contagious. So the spread was mostly due to a small percentage of super-spreaders.

Omicron appears to have a large percentage of super-spreaders.

Updated 12/28

Q - What does it mean if my city/county has ‘high’ transmission? What’s the practical difference between 100 cases per 100K people and 1000 cases per 100K people (over 14 days)?

A - The short version? The higher the number, the higher the chance of your friends & family getting infected, all else being equal.

For example, the difference between 100 cases/100K and 1000 cases/100K is that in the latter, you are 10 times more likely to get infected doing the same things. That means your risk at the grocery store, in the office, at a restaurant, is ten times higher than it would be otherwise. The odds are 10 tens worse.

The other factor to consider is the ‘attack rate’, a.k.a the test positivity ratio. If more than 5% of tests are coming back positive, that means the spread is even higher than the case numbers indicate, because there’s not enough testing going on.

To measure your personal risk, I’d recommend a risk calculator. The best one I’ve found is microCOVID. A ‘micro-covid’ is a 1-in-a-million chance of getting infected with Covid-19.

Q - If I’m exposed to Covid, how long before I test positive? How long before I’m infectious?

A - The timeline from ‘exposure’ to ‘symptoms’ is called the incubation period. It was about 5 days for Alpha, and 4 days for Delta. With Omicron, it’s down to about 3 (72 hours).

Based on that knowledge, the best time to get tested for Covid is 48-72 hours after exposure (if you know you’re exposed).

Hospitals + Health Systems

Q - Will Omicron cause worse symptoms than Delta? A higher fatality rate?

A - The latest study finds Omicron isn’t quite as severe as Delta. However, there are some things that make that number misleading (Simpson’s paradox, if you’re curious)

Worse, Omicron is far more transmissible. That will cause higher fatality rates. It will strain hospitals even further. Hospital staff will have to do triage, give less care per person. A higher fatality rate becomes inevitable.

The fact that ‘most cases are mild’ doesn’t mean much because that’s true of all Covid variants so far. When a small percentage of a large population gets sick, the numbers are still large.

Oh, and the idea that viruses become less deadly over time? It’s a myth.

Updated 1/4

Q - What is Omicron going to do to the number of hospitalized patients?

A - Bad news. It depends on three things: a) how many people get infected at once, b) how severe their cases are, and c) how quickly their cases become severe.

A) We already know Omicron is far more transmissible, so a lot of people are getting infected all at once.

B) The latest studies show Omicron cases become just as severe as Delta.

C) Finally, both Denmark and the UK are seeing a faster hospitalization rate than with Delta, suggesting that people who get Omicron become sick more quickly.

The conclusion? A massive wave is coming. Keep in mind that we’ve already broken our hospital systems.

I’m seeing reports of increasingly full ERs, decreased hospital staffing, often because they’ve tested positive and need to isolate for 10-14 days. This is happening all over the world

When I look at first-hand sources, like r/nursing, I see increasingly dark, despairing, despondent, and death-filled posts.

Updated 1/4

Q - How will we know if our local hospitals are getting full?

A - There are several ways. One indicator is when hospitals cancel/suspend elective surgeries, like the UW on January 1.

Another is when you see reports of hospitals going on ‘diversion’, meaning they can’t accept ambulance patients. What’s worse is when multiple hospitals go on diversion, meaning patients in ambulances have to be driven farther, or sent to beyond-capacity ERs.

Long waiting times in the ER are another clue.

You can look at the number of available ICU beds, though that data may be a little old/out of date.

Vaccines & Testing

Updated 1/4

Q - Will rapid tests & PCR tests detect Omicron?

A - Yes, mostly. Rapid tests are more accurate if you swab both your nose & throat. Here’s a useful video

FYI, 3 PCR tests don’t work for Omicron, meaning they return a negative result even if you’re positive. However, by this point I expect they’re mostly not used.

Q - I’m vaccinated. Can I catch Covid from the Omicron variant? Can I pass it along to others?

A - Yes, you can catch Covid from Omicron, and you can pass it along to others. This was true even with Delta, and Omicron is even better at evading your antibodies.

Remember, Covid is an airborne disease. The 6-foot-distance rule is less useful now than it was before.

There is one report (from Hong Kong) showing vaccinated people (two doses of Pfizer) can get Omicron, and with relatively high viral loads. One person (from S Africa) infected another (from Canada) who was in an adjacent hotel room. This is clearly airborne transmission (no surprise there).

There are also reports of fully vaccinated (3 doses) people transmitting it to other 3 dose people, in Israel.

Immune Erosion/Evasion

Q - I’m fully vaccinated (but not boosted). What’s my risk of getting sick (symptomatic) from the Omicron variant? What’s my risk of severe disease (hospitalization) or dying?

A - Bad news. 2 doses of Pfizer gives you 34-36% protection against symptomatic Covid for the first 15 weeks. That’s not great. AstraZeneca is worse (5.9%).

The latest research shows 2 doses of Moderna gives you better protection against Omicron than Pfizer protection. However, we don’t have a % number. I would guess Moderna is in the 40% rang, but I have no data for that.

Your protection against severe disease (hospitalization) and death is about 70% with 2 doses of Pfizer, and somewhat higher than that with Moderna.

Get boosted!

Q - I’m fully vaccinated and boosted. What’s my risk of getting sick (symptomatic) from the Omicron variant? What’s my risk of severe disease (hospitalization) or dying?

A - Good(ish) news. With 2 doses of Pfizer + booster, you are 76% protected against getting symptomatic Omicron. Your protection against severe disease will be higher, but the numbers aren’t known yet.

3 doses of Moderna (2 + booster) gives you better protection than that. A study found 3x Moderna (boosted) had 6.5X lower antibodies against Omicron than 2x Moderna against Delta.

J&J, Sputnik, Sinopharm, and Convalescent plasma have effectivity of basically 0% - they don’t protect you at all.

However, you can still (super)spread Covid even if you’re boosted.

Q - How long does booster efficacy last?

A - We don’t know for sure yet. 15 weeks (~4 months) at least seems likely, but a lot more research is needed here.

Some countries aren’t taking chances. Israel is moving towards giving high-risk people a 4th dose.

Q - What does a drop in antibody effectiveness mean for a greater risk of getting sick from Omicron?

A - That’s simple question with a complex answer. We don’t know yet. The studies being done right now (like the one above, by the Sigal Lab) looks at neutralizing antibodies, which are an important part of the human immune response, but it’s not the only thing.

Also important is the T-cell antibody response, which is much harder to study. I need to learn about CD8 and CD4 T-cells, which are apparently the relevant types.

Our best bet is to look at the spread of Omicron in a population, and see how people respond to its spread. That means our best information is going to come from South Africa, with its current Omicron wave and excellent public health system. Here’s an example, looking at preliminary Omicron impacts on the Tshwane District.

Q - What does a ‘mild’ case of Covid/Omicron look like?

A - Good question. The definition of ‘mild’ in the US means ‘not admitted to a hospital’. That can include pretty bad symptoms, including: emps up to 103, severe shaking racking chills, sweating enough to soak the sheets 1-2 times daily, severe coughing, vomiting their guts up, severe myalgias.

Q - What about Long Covid?

A - That’s a good question with a complex answer. There isn’t even a good defintion of Long Covid, it covers so many different symptoms. There are large studies looking at it.

Among other things, a Covid infection can lead to long-lasting neurological damage, and can linger all over the body for months. It’s also quite common.

I’ve heard that being vaccinated reduces your risk of long covid, but I haven’t found the relevant studies yet. So for now I’m treating that as conjecture.

This is just as frightening as hospitalization to me. I’m boosted, so I’m not likely to end up in the hospital. I don’t know my risk of getting long covid.

Q - I previously caught COVID-19 and recovered from it. Am I immune to Omicron?

A - NO. Omicron is re-infecting people who are unvaccinated but have recovered from COVID-19. This includes people who have recovered from Delta. Some people are getting infected by Delta & Omicron at the same time.

Get vaccinated and boosted. Your disease-acquired antibodies provide little protection.

This is conclusive proof that the idea of ‘letting people get sick to achieve herd immunity’ won’t work, in addition to being highly unethical.

Treatment, If You’re Sick

Updated 1/4

Q - What should I do if I test positive for Covid?

A - Several things.

  1. Do everything you can to isolate at home for 10 days. The 5-day guidelines from the CDC have no supporting scientific/medical evidence, and have significant flaws.
    • If other people live with you, isolate from them as best you can. If you can get your own bedroom/bathroom, that’s ideal. Try to maximize ventilation and air filtering to protect your loved ones.
  2. Tell your friends and family. It’s natural to feel embarrassed, but this is everywhere. Ask for their support (grocery drop-off, getting meds, phone calls)
  3. Tell everyone you’ve been in close contact with (shared indoor air for more than 15 minutes), tell them to quarantine. Tell them when you tested positive, and when you first had any symptoms.
  4. If you’re fully vaccinated or boosted, prepare for a rough week or two.
  5. If you’re not fully vaccinated or boosted…prepare for a very rough time. Make sure you have a trusted loved one with a healthcare power of attorney, a list of your current medications / allergies / medical history. Put together a contact list of the most important people in your life, and make sure a few key people have it.
    • In your shoes I would fill out a will and put my affairs in order. A very, very large number of people have died from Covid-19, and that number is going up quickly.
  6. Read the CDC guidelines on quarantine & isolation. It has some useful information, even if the 5-day timing is wrong.

Updated 1/4

Q - What should I do if a friend / family member / close contact has Covid?

A - Have you shared indoor air with them in the 4-5 days before they tested positive, or first had symptoms? If so, you’ve been ‘exposed’ and should quarantine.

Also, keep in mind your friend/family/contact is going to need support. Try and help them get it from other, non-quarantined people.

If they live with you (if you share air with them), read this, make a plan, and quarantine.

Q - What treatments exist if I get sick with Covid?

A - There aren’t as many as we’d hope. Pfizer’s new Paxlovid drug, a protease inhibitor, seems to do well. It was approved for use in the US (an EUA) on Dec 22. However, we won’t have enough supply to do much for the Omicron wave.

Many monoclonal antibody treatments don’t work against Omicron. Sotrovimab, from Vir/GSK, appears to be the exception. Note that it was designed to be a last resort against variants, and it was designed partially based on SARS-CoV-1 (the original SARS).

There is a new COVID-19 vaccine, SpFN, developed by Walter Reed, that apparently works against Omicron and all other variants. It just finished up a phase 1 clinical trial to prove efficacy. Given that phase 2 & 3 trials haven’t started, it’ll likely be 6-8 months minimum before it could get an EUA & thus be given to people.

The WHO page on therapeutics lists other known-good treatments, including certain monoclonal antibodies, IL-6 recepter blockers, and systemic corticosteroids. This depends on how severe your case is.

I’m keeping an eye on colchicine, which is currently being researched by the WHO.

Prevention / Preparation

Q - How can I protect myself from Omicron?

A - There are several things you can do. Since no one step is perfect, I recommend doing multiple things: less shared air, masks, vaccines/boosting, reducing exposure, and prophylactic measures.

Less shared air


Vaccines + Boosting

Reduce exposure


Q - It’s been less than 6 months since I had my 2nd dose of Pfizer/Moderna. Can I get a booster? Is it safe? Will it help?

A - Well, the UK is offering boosters to people 3 months after their second dose. Australia is may shorten the delay to 4 months.

Personally, I would get boosted if it’s been 3+ months since my second dose. I’d be willing to deceive a vaccine clinic/doc to do that. Thankfully I didn’t have to.

Updated 1/4

Q - I have kids in school. What can I do to protect them, and myself, from getting Covid-Omicron?

A - Wear masks, and add ventilation to the schools. There’s a great Swiss study showing how better ventilation reduces kids+teachers’ risk of getting Covid.

Band together with other parents, your PTA, if you need to. Find some like-minded parents and build CR (Corsi-Rosenthal) boxes for all of the classrooms in your kids’ school.

Pediatric hospitalizations are at an all-time high.

More practically, prepare for your school to shut down with little notice. The level of spread is so high that large numbers of schools will have no choice but to close.

Q - I want to see loved ones this winter, and it’s too cold/wet/miserable outside. What can I do?

A - There are several things you can do. Since no one step is perfect, you need to do several things.

The World Health Network made a great guide for steps you can take to have a safe holiday.

Personal Decisions

Until there’s solid data on the impact of Omicron against vaccine-induced immunity, I am reducing my risk of potential exposure:


Q - What relevant lessons were learned earlier in this pandemic, and previous ones?

A Several:


Old / Less Relevant Questions

Q - What do we see about antibody level drops

A -

We’re starting to get some useful lab data now. For blood from Pfizer-vaccinated people, an initial study shows a 41x (!) drop in antibodies against Omicron, from 1321 to 32. The study was done by the Sigal Lab - here’s their site & the associated paper.

Pfizer reports a 25x drop in antibodies…but they put out a press release, not a scientific paper, and not the data+methodology. I’ve spoken to a couple of virologists, and they’re pretty annoyed; this is the sort of thing that makes sensational headlines but obfuscates the underlying research. We don’t need more of that.

However, a 41x drop in neutralizing antibodies doesn’t mean the vaccine is 41x less effective. There’s more to a human’s immune response than neutralizing antibodies alone. For example, T-cells play an important role.

Background: There has been a lot of research into what different mutations in the COVID virus could mean for immunity. Based on that knowledge, the mutations are worrisome.

Moderna’s CEO suggests (without numbers) current-generation vaccines may not be as effective against Omicron. They’re planning on having updated vaccines in spring/summer.

Q - Is the Omicron variant in the United States right now?

A - Yes, all over the place. The first documented case was on a traveler who arrived in San Francisco on November 22 from South Africa. More cases have been found in NYC and Minnesota. The Minnesota case is domestic spread, from someone who went to the Anime NYC 2021 at the Javits Center, between November 19-21. That event had 53K attendees.

We’re seeing evidence of community transmission around November 20th. It has been circulating since before Thanksgiving.

Cases were identified in western Washington on Dec 4, for people who tested positive on November 29th.

The countries that have found Omicron cases (South Africa, Denmark, UK, Hong Kong, Israel) have highly competent quarantine + monitoring programs. They’re not unlucky, they’re the ones looking. It is everywhere already. Cases have been found in many other countries, including Australia, Austria, Germany, Brazil, the Czech Republic, and more.

Q - Will travel bans help?

A - At this point, they’re largely useless.

They can only buy time in the early stages, if done correctly. That ship has sailed.

Country-specific travel bans are useless. There are cases from people who haven’t been in sub-Saharan Africa, meaning it’s too late. You’d have to do what Israel just did, isolate from the world for a time.

Q - What’s happening with the push for at-home testing?

A - The idea is pretty simple; if tests were cheap ($1) or free, people could test themselves & their families more easily. At that point you can test everyone you meet socially, easily. It would be a good way for people to slow down transmission.

One downside - home test results usually aren’t reported to public health agencies, so published case numbers would become inaccurate.

Q - Are you scared?

A - Now and then. It helps to find primary sources and think through the implications. This isn’t the end of the world. We know a lot more, individually + collectively, than we did in March 2020.

Q - Does Omicron spread faster than Delta?

A - Yes, it spreads faster. We know this from many different sources: