Omicron Now 73% of US COVID Cases [Or Not?]

That didn't take long.

Three weeks after its discovery, the newest COVID variant has become far and away the predominant form spreading in the United States.

Axios (“CDC: Omicron accounted for 73% of recent COVID-19 cases“):

The Omicron variant accounted for more than 73% of recent COVID-19 cases in the U.S., according to Centers for Disease Control and Prevention’s updated data released on Monday.

[…]

These numbers are stark, but they’re not surprising,” said Rochelle Walensky, the CDC’s director, adding that the growing infections reflect what has been seen in other countries.

[…]

President Biden on Tuesday will deliver a speech outlining new steps the administration will take to address the rapid spread of the new variant.

NYT (“Omicron accounts for nearly three-quarters of new U.S. cases.“):

The extremely contagious Omicron variant is now the dominant version of new coronavirus cases in the United States, according to the Centers for Disease Control and Prevention, and has prompted the resumption of mask mandates in some cities and states in the Northeast, where the growth in new cases has been particularly steep.

Omicron, first discovered overseas around Thanksgiving and identified in the U.S. on Dec. 1, now accounts for more than 70 percent of new U.S. cases, according to federal estimates released Monday.

The estimates underscored the rapid spread of the new variant. Two weeks ago, the C.D.C. said Omicron accounted for just 1 percent of U.S. cases; a week ago, it was about 13 percent. Delta, which for months had been the dominant form of the virus, accounted for about 26 percent of new cases over the last week, the C.D.C. estimated.

Omicron, discovered thanks to its distinctive combination of more than 50 mutations, has turned out to be highly transmissible — two to three times as likely to spread as Delta — and less susceptible to vaccines than other variants. Early cases raised hopes that it may cause milder disease than other variants, but scientists say more research is needed.

[….]

The tens of thousands of new cases in recent days have included prominent politicians and lawmakers, such as Larry Hogan, the governor of Maryland, and Senators Cory Booker of New Jersey and Elizabeth Warren of Massachusetts.

The surge is coming as many hospitals have reached capacity and governors in several states have mobilized the National Guard to help with hospital staffing shortages. As Covid-19 cases crowd into hospitals, leaders of health care facilities in multiple states have taken out newspaper ads begging local residents to get vaccinated.

We’re starting to see closures again with, for example, the National Hockey League becoming the first sports league to suspend play again. At the same time, though, people are far less cautious than the last go-round. The latest Spiderman movie is doing boffo box office.

Even though this variant seems more likely to cause breakthrough cases than Delta, those who are vaccinated are mostly just going about their lives. And those who aren’t vaccinated were pretty much doing that all along.

UPDATE: Ari Allyn-Feuer who describes himself as “an Artificial Intelligence engineer at a major pharmaceutical company” and who purports to hold a Ph.D. in Bioinformatics from the University of Michigan, says this is simply a technical glitch that the news media has jumped on.

There was some kind of bug in an automated statistical algorithm at the CDC, known as the variant proportions Nowcast.  Omicron isn’t really dominant in most of the USA yet (although all evidence continues to indicate it will be soon).  And the bug in Nowcast went from a quiet database update on a quiet CDC web page, to a national press sensation, in a matter of hours.

No humans at the CDC stood up in front of a podium and announced the 73% number, or wrote a press release.  It came from the CDC’s automated COVID data tracker website.

But it’s also not a statement of hard data, it’s the output of an algorithm called the Nowcast.

[…]

All the press coverage has focused solely on the top level, nationwide number.  But digging into the regional and time series numbers, and comparing them with the hard data from two weeks ago, the national and regional case numbers, and what we know about Omicron’s rate of growth from other contexts, shows clearly that something is fishy with this update of the Nowcast.

From the top down, we can look at the national numbers. The last two weeks of data say that Omicron made up 0.0% of cases sampled (regionally adjusted) in the week ending November 20, .1 in the week ending on November 27, and .7% in the week ending December 4.  Then, the Nowcast says these numbers shot up to 12.6% in the week ending December 11, and 73.2% in the week ending December 18.

That is, the Nowcast is not saying Omicron is making up 73% of US COVID-19 cases now.  It’s saying that Omicron was already making up 73.4% of cases during the average day in a week that began all the way back on December 12.  And that it escalated from .7% to 12.6% in one week, and from 12.6% to 73.2% in another week.  Assuming, as data has indicated, that Delta cases stayed approximately constant during this time, these numbers correspond to Omicron case numbers growing approximately twenty fold in one week, a doubling time of approximately thirty six hours, sustained over a two week period.

This is out of touch with what we know about Omicron.  Responsible estimates of the growth rates of Omicron in populations with better data (like the UK and Denmark) and prior data on the USA, have suggested doubling times in the range of two to four days.  This has caused us (and the real experts) to characterize its rate of growth as “explosive,” and to say in late November and early December that it might attain dominance in the USA in a matter of weeks.  And that’s all true.  But a doubling time of 36 hours, sustained for over two weeks, is out of step with all the other data.  It’s not credible.

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James Joyner
About James Joyner
James Joyner is Professor and Department Head of Security Studies at Marine Corps University's Command and Staff College and a nonresident senior fellow at the Scowcroft Center for Strategy and Security at the Atlantic Council. He's a former Army officer and Desert Storm vet. Views expressed here are his own. Follow James on Twitter @DrJJoyner.

Comments

  1. MarkedMan says:

    “Less cautious” may not be the best way to put it, at least not for everyone. Our kids are home for the holiday and the four of us are vaxed and boosted. We recognize that, given its almost surreally rapid spread, it would take almost a total lockdown for us to avoid exposure. On the other hand, it seems that for those of us who kept up on the jabs, the odds are very good that if we get infected our cases will be mild. So we have decided that we won’t go into lockdown mode.

    That doesn’t mean we aren’t taking precautions, mostly in an attempt to reduce the quantity of any exposure. This is based on the medical consensus from the first variant back in 2020 that there was a correlation between the amount of virus inhaled during exposure and the severity of the resultant infection. So we continue to mask indoors except where we know everyone is vaxed. Medical grade masks, N95 in our case. (No one should still be wearing filterless cloth masks at this point!) We make an exception to that for bars and restaurants while we are eating but avoid such places if they are anywhere near full. We’ve walked over to our local Christmas market in Baltimore’s Inner Harbor several times, which is packed but outside with a wind blowing in from the bay. We only went inside the tent during the soft opening week, when there weren’t any crowds, and now stay outside. Tonight we will walk over there again for a drink, and then to the National Aquarium, but that is for a special after hours members only viewing and they are controlling the number of people allowed in, so no crowded halls, and we will be masked.

    So all in all we are not in lockdown mode but I wouldn’t say we are less cautious. It’s the circumstances that have changed, not our caution.

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  2. James Joyner says:

    @MarkedMan: Even in the highly-vaccinated DC suburbs of NoVa, masking is way down and those who are wearing them are still in cloth or, increasingly, the cheap surgical ones. I hardly see any N95 or equivalent.

    1
  3. Jen says:

    In the little corner of NH in which I reside, there’s very limited masking unless it’s required. Our town had a significant increase in cases so the select board reinstated the mask mandate for town buildings and there are some who are…not reacting well at all. You’d think the town requested a kidney from each resident.

    Because we’re also in the midst of developing the town budget for next year, I’m required in a bunch of meetings, and am wearing the Korean equivalent of KN95 masks. I’m seeing a mix of the thin surgical masks, homemade cloth ones, and completely ineffective “solutions” such as scarves.

    I’m vaxed and boosted, and am somewhat resigned to the fact that I’m likely to get this bug at some point. I just hope my case is mild, doesn’t f&ck with my sense of taste or smell, and doesn’t leave me with long covid. I am most worried about a family member with an autoimmune disease. He’s vaxed & boosted too, but no guarantees of a mild case.

  4. Mikey says:

    @James Joyner: I still see probably 90% mask use in stores here in Fairfax, but we generally go to the same few stores so maybe my sample size isn’t very high. Both my wife’s and my job require masks as well.

    We have changed from cloth to KN95 though.

    3
  5. Michael Cain says:

    Good that we’re still under a public indoor mask mandate here, and that conformance is pretty good. Down the road, just a bit under three million people are expected to go through Denver International Airport between yesterday and Jan 3. Figure on that being a super spreader event, masks or not.

    2
  6. MarkedMan says:

    @James Joyner: I was about to write that cloth masks are horrible, but I just came across a paper that says otherwise. To be honest, I’m a bit dumbfounded. I assume the sodium chloride aerosol they mention is produced according to the NIOSH standard, and the equipment at my company generates that same aerosol and then measures filtration efficiency. Back in March and April of last year we grabbed a bunch of cloth samples and tested them and found that the efficiencies were less than 10%. This paper says a fricking bandana is 50%! That makes no sense to me. And however they are testing, they are taking fit into account, but our tests were with the material clamped in jig, which is the equivalent of perfect fit, so their tests should be worse, not better. I’m gong to do some experimenting today.

    3
  7. Kathy says:

    @MarkedMan:

    Well, even 10% is better than 0%

    At work masks are still mandatory. In common areas people wear them. Inside at their desks most don’t. I keep my KF-94 on at all times. Yes, most have been vaccinated, few boosters as yet, but so what? the number one lesson of the pandemic is you never lower your guard against the trump virus.

    4
  8. grumpy realist says:

    …off to get my booster today….just in time for Xmas travel.

    1
  9. Michael Reynolds says:

    I have not found any mask, let alone an N95, that fits well enough to allow me to open my mouth enough to speak. But I’m pretty close to being a hermit, so there are few opportunities for exposure. My kids are coming down though, so in all honestly I expect a possible breakthrough. Fukkin Christmas.

    On the plus side, 30 minutes from now we reach the solstice. The darkness will slowly begin to give way to the light. Pity Christians stole the solstice, the return of the sun is worth celebrating.

    2
  10. JKB says:

    Double vaccines with boosters doesn’t keep one from getting the Omicron Variant (OV). They still throw in the “vaccines are likely to reduce the risk of severe illness” but never offer any actual data. Niall Ferguson, the historian, announce on the Goodfellows podcast that he, double vaccinated/boosted, had just tested positive for Omicron and sounded as if he had a cold. It was their last podcast of the year, but he should be over it now as that was on the 14th, more than 5 days ago.

    But the Omicron cases are in steep decline in South Africa after a short steep rise. And during that time, the deaths in SA remained flat. But then SA has a low vaccination rate.

    By the time even the paranoid take any real action, Omicron will be in the past. And the panic mongering will be exposed as being just that further undermining the legitimacy of the purveyors.

  11. grumpy realist says:

    @JKB: Just look at the breakdown of people with Covid-19 in the ICU. How many of them are vaccinated vs. unvaccinated? Vaccination helps. Even if you get a breakthrough case, your body reacts better than if you hadn’t had the vaccination at all.

    Or are you one of those idiots who absolutely refuses to look at facts?

    Face it, if you don’t have the guts to admit you’re wrong when confronted with contrary evidence, you’re a coward.

    8
  12. Sleeping Dog says:

    @Michael Reynolds:

    My niece is having the extended family over xmas eve, the other day she issued the order that we all should home test before coming over. No one objected as we are all in agreement on vaccine and mask wearing.

    Not a bad idea for anyone getting together.

  13. Jen says:

    @JKB: A few things.

    First, omicron emerged in a country with a median age of 27. The US’s median age is a decade older. Age has an impact on outcomes, indeed one of the concerns about assuming that omicron doesn’t cause severe disease is that it appears to be spreading/infecting younger people which has the potential to skew outcome results. Denmark does extensive testing and they are concerned.

    Next, the US has recorded its first known omicron death. It was an unvaccinated man in his 50s who had previously had covid and recovered. Something to watch.

    It is very, very evident that the unvaccinated are the predominant group being hospitalized.

    5
  14. Michael Reynolds says:

    @JKB:
    Why did your cult leader get the booster?

    In the coming schism are you Team T or Team Q?

    2
  15. MarkedMan says:

    @MarkedMan: I downloaded the entire paper I mentioned above, and I just don’t know what to make of it. First, their methodology for testing efficiency is one that is meant to be used with a dummy head, not a real person, but using it on a real person should give worse results, not better. (People breath out as well as in, and therefore bring up all kinds of particles from the lungs as they do. Dummy heads don’t breath at all.) I went back and looked at our numbers and we didn’t come across any cloth material that you could actually breath through that performed better than about 15% efficiency and most were in the single digits. I can’t see any way that stitching those materials into a mask would cause them to get better results. On the other hand, the procedure mask material we test has 80% or higher efficiency. I can certainly believe that an ear loop mask could dramatically reduce that due to leaks, but the idea that a bandana outperforms it is ridiculous. You can hold a bandana up to the light and actually see the holes in the weave! To something the size of a COVID particle, well, it’s like a bee flying through the Holland Tunnel. I can’t tell you exactly why they are getting such good results from cloth, but I can tell you there are at least two questionable facets of their setup. And we have actually tested cloth samples per the NIOSH standards on certified equipment and gotten much worse results than they did for media clamped in a fixture, which should yield the best possible results for that material.

    Bottom line, I’m going to stick to my guns. You should be using N95 masks or at least procedure masks. Cloth masks stop droplets, but not individual virus particles.

    2
  16. Joe says:

    @Sleeping Dog: While I feel fine, I am about to go get tested at the request of my fiance whose father is coming for the holidays as well as all of our 20-something kids. All of us are vaxed, boosted and at least moderately careful about masking. Still have my fingers crossed that a positive (whether false or true) will sink the week.

  17. Sleeping Dog says:

    @Joe:

    The extended family is vaxxed and boosted so that base is covered. My nieces husband had a breakthrough case before thanksgiving and their 4 yo also caught it. Neither were particularly ill, but it’s about being careful.

  18. OzarkHillbilly says:

    @JKB: further undermining the legitimacy of the purveyors.

    Something you will never have to worry about.

  19. @grumpy realist:

    you’re a coward.

    Come now, how can you say that?

    He is always brave enough to drop some comment and then run away!

    2
  20. grumpy realist says:
  21. Mikey says:

    @Steven L. Taylor:

    He is always brave enough to drop some comment and then run away!

    The Tale of Brave Sir Robin

    4
  22. Gustopher says:

    @Michael Reynolds:

    I have not found any mask, let alone an N95, that fits well enough to allow me to open my mouth enough to speak.

    Hallelujah!

    On a more helpful note, I have some N95s that loop around the back of the head — they are a pain to get on and off, but the direction they pull is better for letting me talk. And less ear nuisance. I think they are just 3M.

  23. Gustopher says:

    @JKB:

    They still throw in the “vaccines are likely to reduce the risk of severe illness” but never offer any actual data.

    Lots of places have breakdowns on infection, hospitalization and death rates among vaccinated and unvaccinated. The data is there.

    Here’s King County. https://kingcounty.gov/depts/health/covid-19/data/vaccination-outcomes.aspx

    Your lies are transparent, but your purpose is not.

    2
  24. Just nutha ignint cracker says:

    @Gustopher: I’m not sure that I would call JKB’s posts purposeful to begin with. I’ve always thought that he was simply spouting contrary sources for the sake of propelling the argument.

  25. Kathy says:

    @Gustopher:

    3M, as I gather, is like the gold standard for respirators.

    @Gustopher:

    What’s your proof that someone who needs hospitalization is more severely ill than someone who doesn’t?

  26. JohnSF says:

    @JKB:

    Double vaccines with boosters doesn’t keep one from getting the Omicron Variant

    Actually, if you care to look at the data, they do, generally.
    They just don’t do so infallibly.

    Similarly, if infected, the vaccinated generally suffer less severe case; but again, not always.
    This is as for other variants also, but with considerably increased (re)infection likelihood for omicron.

    Immunity escape is a feature of a lot of virus vaccination, and particularly so for coronaviruses.
    Vaccines are not an off off switch, never were, never will be.
    Why do you imagine the concept of “herd immunity” is so important in all vaccination programs ? (not just covid, but diptheria, measles, polio, varicella, rubella etc etc)
    As with all things related to disease, it’s a question of shaving the odds, of reducing replication, of mitigation.
    This really is absolutely basic.

    It is to be hoped that Omicron does turn out to be mild and to burn out rapidly.
    This is not certain; the best we know, rather than hope, is that it no worse than other variants in severity, but much more transmissible.
    It would be foolish to “hope for the best” on the basis of highly caveated South African data.

    Especially when surge mitigation is fairly easy to do: get boosted, wear masks in crowded conditions, exercise a little bit of caution. Shave the overall social odds.

    As an uncontrolled surge can lead to massive short run pressures on intensive care, as even a small percentage of a very very large number is still a very large number.
    It can block others who need intensive care being among intensifying triage.
    Inevitably some will die who need not have died, of ICU level covid or other ICU emergency cases.
    Why let that happen if you can avoid it?

    It rather seems you are using selected data to support a prior preference.
    As with the drunk and the lamp-post: you are using it for support, rather than illumination.

    2
  27. Jax says:

    @JohnSF: Bless you for tryin, but he ain’t listenin. You’ve given him too much data, it does not compute.