Omicron

If you look at the graph of COVID-19 infections in the U.S., the “omicron wave” is rather obvious:

Yes, it’s that giant spike in the infection rate at the end, the one that has hit us this year.

Let me plot that data again, as a blue line, but reduced by a factor of 100. I’ll also delay it 20 days. That way, we’ll see what 1% of daily infections looks like, when it’s delayed 20 days. But I’ll expand the y-axis so that it covers such a small region, the huge “omicron spike” this year spills over the top of the graph!

That’s because I’ll also plot, as red triangles, the mortality rate, the number of deaths per day (per million population).

And that’s the point. UNTIL NOW, the death rate from COVID-19 in the U.S. has always been higher than 1% of the infection rate delayed 20 days. UNTIL NOW.


Omicron is quite different from other variants in the way it infects the body. It rarely even gets to the lung tissue, instead it wreaks havoc on the upper respiratory system — like a terrible cold. That’s a genuine threat to the young, the old, those with co-morbidities, but it’s nothing like the other variants of COVID-19 which shred your lungs and bring a much higher risk of hospitalization and death.

It’s also quite different in that it’s far more infectious. That’s not because the other variants aren’t highly infectious, they are, it’s because omicron is “off the scale” of infectious.

The good news: because omicron is a variant of COVID, it has so many of the same active proteins in its structure that when your body learns to beat omicron, it’s “locked and loaded” to fight off every COVID. In fact, it’s the most effective vaccine you can get.

And if you are vaccinated, then if (I’m tempted to say “when”) you’re exposed to omicron, you are far less likely to require hospitalization … or a body bag.


If we zoom in on the time axis, and add yet another line (in green) showing one half of 1% of the infection rate delayed 20 days, we get this:

I’m hopeful that this is a portent of things to come: that the death rate from COVID-19 will continue to be less that 0.5% of the infection rate (delayed 20 days), and that the infection rate will continue to fall because omicron is so infectious, we’re going to reach “herd immunity.”


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15 responses to “Omicron

  1. It looks like the anti-vaxxers are going to get vaccinated (by Omicron) whether they want to or not.

  2. As always, thank you for your excellent and timely post! One possible bug: I’m unsure whether infection by Omicron provides better immunity than full vaccination. I’ll look for data and comment again.

  3. The Danish household study of its overlapping Delta/Omicron wave shows that Omicron isn’t more intrinsically infectious than Delta. The R0 of both variants should be equal, roughly 6.0 or whatever (there’s actually some debate about that). The massive number of infections is due to Omicron being an escape mutant so it reinfects and breaks through vaccination a lot better than Delta or any other variant ever did before. Combined with the fact that so many people are “done with covid” and aren’t really being as cautious and pretty much all we did for Omicron was wear masks in supermarkets. The Omicron wave of infections looks a lot more like what would have happened in the start if nobody took any precautions at all (ish).

    Click to access 2021.12.27.21268278v1.full.pdf

    Furthermore it isn’t clear that Omicron is inherently less virulent in humans. Since Omicron is an immune escape variant it is infecting lots of people who already have T-cell immunity and their CD4+/CD8+ responses to the infection is going to keep them out of the hospital/morgue even though it cannot prevent infection. We do know that it is less inherently virulent in mice and hamster models, which is good news if you’re a mouse. That doesn’t necessarily translate to humans. And studies that try to tease the effects apart come up with Omicron being 3.5x less virulent than Delta. Since Delta is generally though to be 2x more virulent than D614G that means that Omicron is a little over 1/2 as virulent as D6146. Half of D614G is still bloody awful and is why Omicron is still packing hospitals with the unvaccinated, even though we must be getting down to only around ~10% or less of the population that is totally immune naive to SARS-CoV-2. That reduction of severity compared to Delta isn’t enough to matter.

    Its still better to focus on what we can do to change the viruses severity (just get vaccinated which is a 10x effect or more) compared to intrinsic changes in the viruses severity (factor of 2 one way or the other compared to D614G). And that paints a more accurate picture in that the better we do with vaccination the better the IFR is going to get and that population immunity and behavior control the severity of waves. The immune escape behavior of Omicron is the thing worth talking about (and the fact that it may have spilled over from a reservoir species). Which points to the fact that the virus isn’t going away. On a long enough timeline we do need to figure out how to live with the virus (although given the health care overload during Omicron we seem to have decided to not care a little bit too soon for my taste).

  4. I guess we are lucky that Omicron has such a low mortality rate! I refuse to think about a combination of high infectiousness and hight mortality…

  5. I’m afraid that the sequelae and the long covid, the blood clot anomalies and other problems that show up, even weeks after a “recovery” are not so inconsequential. This is a system disease, not just a disease of the lungs, and if it all the same to you, I’d rather not risk ANY of them ;-)

  6. Interesting lag there and it appears to clearly show reduced virulence of omicron.

    However, there is something interesting happening in New Zealand (where I live). On case data alone, the “fully vaccinated” (2 or 3 doses – about 30% of the population has had the booster) are just as likely to be infected as the unvaccinated. For hospitalisations, the unvaccinated are 10 times as likely to be hospitalised. But the interesting thing about hospitalisations is that there is a suggestion in the very little data about this, is that hospitalisation from Omicron (not completely sure it’s omicron but the data is suggestive of that) is likely to last longer for the vaccinated than the unvaccinated.

    I’d take that last statement with a pinch of salt due to lack of clear data but most days, the people currently in hospital with COVID-19 are overwhelmingly fully vaccinated, even though the unvaccinated are far more likely to need some hospital treatment. This suggests a longer stay for the vaccinated. Impossible to say whether it is mainly omicron hospitalising people, given the lag with cases and the fact that omicron only entered our community about 3 weeks ago. But, even if most hospitalisations are delta, it’s an interesting observation.

    We have very little data on the vaccination status of the few deaths we’ve had.

    For cases, there may be mitigating circumstance which skew the figures (for example, the fully vaccinated can go to cafes, restaurants, bars, gyms and swimming pools unmasked). But I haven’t figured out possible reasons for the hospital lengths of stay, if that’s a real thing.

  7. One factor may be that New Zealand appears to have nearly 100% vaccine coverage in older age groups (e.g. over 75s). Older age groups might be expected to spend longer in hospital than younger groups regardless of Covid related issues. There may well be delays in discharge for recovered elderly patients where there is concern about risks to social care settings.

    • Good point, Astringent. Maybe that’s part of the explanation but, and I hadn’t mentioned this, the average age of those currently hospitalised is usually given. This changes quite a lot with the small numbers we now have (only a dozen or so in hospital currently) but is usually around 50 with the average age yesterday (10th) being 55, Still, with small numbers, the average is probably not helpful (it could be skewed markedly by a 10 year old being hospitalised). I long for better or more accessible data.

      • The broader point is that you’re selecting for vaccinated people who wind up in the hospital. That means you have to consider all known and unknown selection effects. Generally people with vaccine breakthrough infections who wind up hospitalized will be in worse health than the rest of the population which makes matching them with unvaccinated cases difficult. You may also be missing the effects of things like HLA subtypes where the people who are vaccinated who wind up hospitalized likely have immune systems which just aren’t as good as fighting off this particular coronavirus. Once you’ve done all that matching though you’ve likely got low numbers in all your different matching buckets and you have so many matching buckets you have to start worrying about p hacking effects.

        The useful question is to look at the population hospitalization rate of unvaccinated vs. vaccinated and their load on the hospital system, which is 10x larger for unvaccinated. That’s the only really useful statistic for public health. The question of why some people seem to be intrinsically more vulnerable and other people seem to be intrinsically hard to infect is very difficult and doesn’t have much public health impact, and probably has low clinical impact (at least in the short term — by the time we sort it out the pandemic will be over, but it might inform the next pandemic).

        And the clinical questions are going to be inherently messy to sort out because we can’t do randomized clinical challenge trials which send some fraction of the human participants to the hospital/morgue like we can with mice. And any effect that you think might be tied to vaccination status should be treated skeptically and assumed to be selection effects first (because it probably is).

      • I didn’t understand your first sentence, lamont-granquist, but I think you’re spot on with your last! There has been very little public discussion of this stuff and so no serious analysis. The good thing, sort of, is that for the last two days, the percentage of doubly vaccinated currently in hospital has moved down and is now at 45%, which is much easier to think about. Good point about the breakthrough cases probably being more in the less well.

        Another factor, for the case data apparently showing equal risk of becoming a case whether fully vaccinated or not vaccinated, is that the unvaccinated may be less likely to be tested. As per this small study: https://www.medrxiv.org/content/10.1101/2022.01.17.22269450v1

  8. Combination of infection with vaccination greatly increases antibodies over vaccination alone: https://www.science.org/doi/10.1126/sciimmunol.abn8014. But that study did not compare to unvaccinated people after infection recovery; I still intend to look for that comparison versus vaccinated and not infected.

  9. Reinfections with omicron are occurring at a much quicker rate than with previous variants. Reports of reinfections after 3-4 weeks are becoming more common by the day.
    Being a systemic disease, it is not just the respiratory organs that can be affected, but rather every organ that has ACE2 receptors (and that is most, including the brain).
    https://www.nature.com/articles/d41586-022-00403-0
    https://www.researchsquare.com/article/rs-1201481/v1
    While much less likely to attack the lungs, virus load in the upper airways is much higher, and the virus will enter the brain via the olfactory bulb.
    Brain fog (issues with short term memory) is one of the most widely reported symptoms of an omicron infection.
    Colleague of mine got infected with omicron right before New Years and is still struggling with ‘Alzheimer like’ lack of short term memory, and he is far from the only one. His wife also had it for a while, but thankfully improved.
    https://alz-journals.onlinelibrary.wiley.com/doi/10.1002/alz.12558
    https://www.nature.com/articles/s41582-021-00593-7

    Click to access 2022.01.31.478476v1.full.pdf

    It seems that omicron is more likely to cause micro clotting of the blood, and that can cause issues like strokes and pulmonary embolisms.
    Many of the covid induced ailments that are not directly linked to the respiratory tract/lungs are likely to receive a ”with covid” rather than a ”of covid” designation, even though the infection was the direct cause of the issue.
    Long Covid is defined as symptoms lasting for more than 12 weeks, and the first omicron cases were reported around November 25th, so we don’t have any official statistics on omicron induced as of yet, but it seems that long term effects could be considerable, and with lots more people affected.
    With reinfections happening after as little as 4 weeks, and a possible compunding, negative effects on organs (brain/heart/kidneys/blood vessels/etc), the individual and societal long terms effects of the current spread could be considerable.
    https://www.nature.com/articles/d41586-022-00414-x
    https://www.nature.com/articles/s41591-022-01689-3
    https://medicalxpress.com/news/2022-01-omicron-amps-covid.html

  10. Much of the disinformation (including disinfo about omicron) that we have seen since the start of the pandemic stems from a source that we unfortunately are way too familiar with:
    https://www.dailyposter.com/how-the-koch-network-hijacked-the-war-on-covid/