No, 73% of US COVID-19 cases aren’t Omicron yet: how the press got it wrong

From Dec 14. Omicron exploded, but to 3% of total cases, from half a percent the week before. Still phenomenal.

https://www.google.com/amp/s/www.cnbc.com/amp/2021/12/14/omicron-now-makes-up-almost-3percent-of-us-covid-cases-according-to-the-cdc.html

Ari specifically lists Florida as one of the few places that Omicron is already dominant. Even if focusing only on new cases, Ari is correct that Omicron is not yet dominant in most of the US, though that is likely to change soon.

The issue is timing. Anyone who believes those CDC projections will look at the case numbers, see that it is not having much effect, and think maybe Omicron is no big deal after all. Then a week later, when Omicron actually does become dominant, they will see what that looks like. Case numbers will explode.

Everything in CDC’s projections will happen. They just got the timing wrong. And too many people took their projections at face value instead of thinking.

That’s a reasonable way to start thinking about it. And it’s probably similar to the reasoning behind CDC’s NowCast projections, which are based on data from several weeks ago. But you can also look at more recent measurements to determine that this can’t actually be true right now. If Omicron suddenly became 75% of the cases, wouldn’t you expect the cases per day to go up by at least a factor of 4? Instead they’re edging up a little in some places, flat in others… Current data needs to be given higher weight than projections based on old data, and Ari has correctly pointed out these discrepancies.

Omicron is coming. It will be at 75% prevalence soon enough, perhaps within a week, but not yet.

Yes, it is coming. Did you look at the links given? Most of them specified that the 73% was referring to new cases, with the vast majority of active but somewhat older cases still being Delta. Both are probably true. I think the point is the exponential growth. On Dec 1, one percent of new cases was Omicron. Now it’s apparently 73% of new cases which is Omicron. We’re planning to stay at home except to get groceries for the foreseeable future, but so far Omicron continues to look not that dangerous. The first Omicron death in the US was just announced in a man in his fifties with comorbidities. That’s already much less dangerous than Delta, which immediately started causing many deaths when it arrived. As did Alpha and Original. Would we rather see Delta double every few days?

There were ~120,000 new cases of Delta on December 3rd. 0% were Omicron.

There were ~140,000 new cases of COVID (Delta + Omicron) December 20th. Some unknown percentage were Omicron.

If NowCast is right, and 73% of the new cases ending the week of December 18th were Omicron, that means Delta went from infecting 120,000 people per day to something like 38,000 (27% of 140,000) per day. That makes no sense.

By contrast, if total case numbers were 440,000 it would make sense, because it would imply that Delta was still chugging alongside Omicron.

“By contrast, if total case numbers were 440,000 it would make sense, because it would imply that Delta was still chugging alongside Omicron.”

Bingo! That’s the main way we know Omicron isn’t dominant in US as a whole yet. The cases just aren’t rising fast enough for that.

If you want to see what it looks like when Omicron becomes dominant, look at the new cases graph in Florida. You can see here that new cases per day suddenly doubled between Dec 15 and Dec 17. That’s what happens when Omicron hits 50% prevalence. Then on Dec 20 the new cases per day double again. That’s 75% prevalence. That’s the shape of graph that you see when Omicron hits 75% prevalence. You won’t find a similarly fast rise for USA cases overall, because USA overall hasn’t hit this prevalence yet.

This first plot is new cases in the United States.  That “zoom” exponential takeoff started around Dec 15th.  Same time as Florida (second plot).

This indicates to me (along with sequencing data now available) that US hit 50% prevalence of Omicron sometime around ~Dec 16th.  This is consistent with UK data, showing 55% on Dec 14th across the kingdom (2395 of 4385 sequences Omicron).

Last plot is Houston/Harris County hospital system testing, showing Omicron >70% prevalence by Dec 13th.

In both Dallas county and Harris (Houston) county, Omicron was ~75% by Dec 15th.   This according to sequencing data from area hospital networks.  Genotyping in N Texas was done using an 8-factor PCR test that can identify the currrent most common variants circulating.

I think this author has it wrong, grossly underestimating Omicron prevalence.

Below is Harris County followed by N Texas.

The logistic growth model you showed for Harris county indicates that Omicron prevalence reached 50% at 15 days (Dec 12) and 75% at 17 days (Dec 14). Daily new cases in Texas jumped from 5k to 10k on Dec 19-20, suggesting that prevalence reached 50% around that time. That’s roughly a 7 day difference in result depending on which of these approaches you take to estimating Omicron’s prevalence in Texas. Any idea why the cases per day in that state would take an extra week to reflect the prevalence changes that a Texas hospital was seeing?

Note that Texas is not representative of the entire country. For USA as a whole, cases had been steady at around 150k, and we should expect cases to hit 300k per day around the time USA reaches 50% Omicron prevalence. As of Dec 23, that still had not happened, and it looks like USA as a whole will probably hit 50% around Dec 24-25.

Remember the original projection that Ari is arguing against. NowCast indicated 73% prevalence in the week of Dec 12-18. That’s consistent with the timing you found in Texas, but case counts show that Texas cases rose almost a week earlier than cases in the US as a whole.

Also true that the vast majority of those getting Omicron are not counted because they never get sick enough to enter the system. Many are caught by asymptomatic testing, but most are not. 

Two more things to consider. It has always been unusual to do genomic testing, so most people don’t know which serotype of Covid they got. Which means that everything they say is an estimate. 

Also, the strains which infect more people eradicate those less infective quickly. A year ago, the more infective Alpha completely replaced Original. Only a couple of months later, Delta did the same to Alpha. We are assuming there are as many cases of Delta as there were, now competing with Omicron, but Delta may be losing ground faster than we think.

“Two more things to consider. It has always been unusual to do genomic testing, so most people don’t know which serotype of Covid they got. Which means that everything they say is an estimate.”

CDC sequences a small random subset of positive tests. The resulting estimates are actually very accurate, but the measurement process is slow, so we only have that data for samples collected three weeks ago. CDC fills in the gap over the last two weeks with their mathematical model, and everyone reports on it as though it’s real data… But Ari analyzed more reliable data to determine that the projections were incorrect. You’ll see confirmation of that in two weeks when CDC releases actual data for last week, or earlier when CDC just acknowledges that their algorithm made a mistake.

“Also, the strains which infect more people eradicate those less infective quickly.”

Only when the antibodies from one strain can prevent infection by the other strain. That doesn’t happen between Delta and Omicron (immune escape) so they will co-exist as though we now have two separate pandemics.

I listen to Dr. John Campbell talks in the evening. He’s reported on several places where Omicron is actually displacing Delta rather than just massively adding to the total. Delta cases are diminishing fast in those places. It may be that, as has been suggested, that infection with Omicron protects against infection with Delta.or it may be that the majority has protection against Delta from either natural or vaccine immunity. There are increasing indications that Omicron is a much milder disease, and even though it’s extremely infective, it is not causing a surge in hospitalizations.

Dr John Campbell seemed like a good source of information earlier in the pandemic. More recently, he’s been promoting Ivermectin (which is not effective for COVID) and claiming that anyone who disagrees with him on this must have ulterior motives. While this is my only complaint about Dr Campbell, it is enough for me to be very careful about what he says on other topics, and I no longer consider his videos to be a good use of my time.

I’ve seen a few studies that indicated Omicron was a little bit milder. In each case, they hadn’t accounted for the portion of cases with previous infection or vaccination, which is a big enough effect to fully explain any difference in severity that they observed.

My impression is still that Omicron has similar severity to Delta. I would need to see strong evidence of reduced danger before I would consider reducing my own precautions.

I’m thinking about whether my daughter should still get a third dose a week from today. Delta cases in the US fell by about thirty-six percent, Omicron increasing by the same amount, the week before Christmas and more since then. I’m thinking that within a few weeks, Delta will be gone. Those I’ve heard about who were positive only had cold-like symptoms.                           

I’ve read a lot about Ivermectin and HCQ in many cases successfully treating Covid. And about a few late-stage cases in which the patient died anyway. I have no reason to doubt the veracity of these reports. Dr. Campbell has read similar information.  I continue to trust him as a source of information. He believes that COVID as an often-deadly disease is very likely on its way out.

HCQ and Ivermectin are both completely useless for treating/preventing COVID. The research on both could not be more clear. Both have also been pushed by substantial disinformation campaigns.

I’m sure you’ve also heard many times over the last two years that COVID is like a cold/flu and not dangerous, even as it rose to the leading cause of death… Ironically, Omicron’s greatest strength (immune escape) made that false claim easier to believe, because an immune escape variant will tend to have more breakthrough cases, and breakthrough cases are far more likely to be mild.

The common theme to these three false claims was to convince people not to take precautions against the virus… And if they were successful, more people would say…

“I’m thinking about whether my daughter should still get a third dose a week from today.”

I have been taking all the precautions for almost two years now. I have kept up with all the new information very carefully and we have never stopped wearing masks. 

Im sure you’ve seen the many studies at this point showing that Omicron doesn’t infect the lungs very much, where the earlier variants did. And I’m sure you’ve seen the statistics on O being extremely transmissive, but nearly always cold-like, without severe symptoms. Most of those who were diagnosed with O in S Africa were unvaxxed, young, and had mild cases. 

I am thinking carefully what to do in our case. You have to read many sources very carefully to separate information from disinformation, and it cuts both ways. There is reliable information suggesting that contracting O prevents Delta. If that turns out to be true, a case could be made that my double vaxxed daughter (Pfizer) might benefit from a natural case of O, and it might protect her from a possibly more serious case of Delta. I am triple vaxxed, two Pfizer, one Moderna. I am unlikely to get a severe or fatal case of any serotype of Covid, but might benefit from exposure to O if either of us got it. I think the best we can do is balance mights and possiblys. New information is being released every day on O. I think I must make this decision now, because the possible benefit of my daughter contracting O soon, protecting her from Delta (probably), is one to be sought now rather than later. 

Dr. Campbell became quite testy in one of his programs several months ago one in which he discussed the effectiveness of Ivermectin. He believed the public had been ill-served by the official line which had been taken. 

Regarding Omicron mildness, I think you will find this explanatory Twitter thread very helpful.

A sketch to explain how a new variant may appear milder even with no change in underlying virulence. This can occur because, when calculating the fraction of cases that are severe, the denominator now includes many re-infections that had previously been averted. A thread. 1/8 pic.twitter.com/XxrYHnb6XY

— Natalie E. Dean, PhD (@nataliexdean) December 9, 2021

Consider the hypothetical case of a variant that has the same severity as Delta for someone who is unvaccinated with no previous infections, but has much more “immunity resistance” and therefore infects a larger number of vaccinated and previously infected people. This Twitter thread will help you to understand what that would look like, and why it would appear more mild to people who didn’t understand and correct for this issue.

My reply has been awaiting moderation for five hours. Fauci said yesterday that all indications are that O is mild. Caution is warranted, of course. I had a link to what he said, maybe zi shouldn’t have. I’m sure you’ve seen it in any case.

Trying to avoid talking past each other…

Please carefully read the entire Twitter thread that I sent you, and let me know if you understand how Omicron’s strength (immune escape) can give the illusion of it being weaker (mild) when its severity is actually the same as Delta’s. Without that understanding, too many of the facts of this discussion tend to be misunderstood.

I just read through the entire thread, with the comments. I think the term re-infection is misleading. The last comment, at this time, asked her on what she bases the assumption that re-infections are milder. As you said before, O is a new disease, related to Original, but different enough that immunity to earlier variants, whether from natural exposure or from vaccine protection, is not very helpful, if at all. 

i understand that she is saying that even though a far higher percentage of cases of O are mild, that its numbers are so huge and it seems to infect everyone in its path, that even if, say, a quarter of a percent of symptomatic cases died rather than the two percent of overall with older C variants, if you have one billion all infected at once, that means a larger number of fatalities. 

I’d say there’s not much we can do. Anyone who wants to try additional boosters against Original should be allowed to do so, and we’ll get info on how much good it does. So far it looks like not much. 

For the vast majority of individuals, it is mild, and that appears to be the case even for the unvaxxed. I think the most interesting thing is that it has been observed that natural infection with O seems to protect against the more dangerous D.

It has required a Herculean effort to get to where we are now. It will not be possible to give everyone in the world the vaccine du jour every six months. I think we need to get statistics on how protective recovery from the natural disease Omicron and how long-lasting. 

I think the pandemic is ending. I understand that it has tsunamied the world, but I think we have no choice but to let it go on a societal level. In a few weeks it will be over. People are burned out and will not massively flock to stadiums to be vaccinated for a mild disease which is only fearsome in the large numbers affected and the dire results only for a very small percentage. 

It is the case that I have protested the silly 99.98.% infection survival meme, and have said But it’s 2% mortality in symptomatic cases, which is very high. But I think in this case there’s nothing anyone can do. Sure, introduce variant-specific vaccines. They were supposed to keep up with their simple plug and play technology. But they haven’t, and now it’s slipped out of their grasp. The good thing is that it’s not the Spanish flu. Also good that, as in S Africa, it will probably hit huge spikes and then fall just as precipitously, probably leaving millions of O-immune people in its wake. And then we get to recover as individuals and as a society. When even Fauci says it’s mild, you know the game is over.

After looking at the CDC chart on proportion of D to O in every region of the US, and seeing that Missouri, in Region 7, is in the area with the lowest proportion of O to D, 70% D to 30% O, I’ve decided to take my daughter to Walmart to get the Moderna third dose on Friday, as originally planned. I guess the Midwest is an island slow for the flood of O to reach.

“I’ve decided to take my daughter to Walmart to get the Moderna third dose on Friday, as originally planned.”

I think that is the right decision. It will help a lot to entirely prevent infection for Delta and to substantially reduce severity for Omicron.

Immunity from previous variants (whether due to vaccine or infection) is weaker against Omicron but still important. That booster is very effective against hospitalization/death for Omicron, but is not very effective at all for preventing infection. We don’t yet know about Omicron’s long COVID risk, with or without vaccines, because not enough time has passed yet to see that.

My family’s current COVID protections:

• Three Moderna shots
• Work from home
• No indoor or crowded social gatherings
• Wear full face mask (3M 6900 with P100 filter) for shopping, pharmacy visits, etc

No one needs to follow the same precautions. That was my family’s choice based on our understanding of the risk.

we take similar precautions, but just an N-95 or cloth mask. I think that’s enough to reduce the viral load, which I think is enough. I’m no longer worried about Omicron. My daughter is only 21 and heathy. I’m worried about Delta, but don’t think it will be around much longer. 

i just saw this article, it may be from Argentina, saying that omicron is a vaccine for the unvaccinated. Getting it is not usually dangerous and then it essentially immunizes them. It projects that O is so contagious that soon everyone will be immunized and the pandemic will probably be over by summer. That would be nice!

As dot com La inesperada vacuna que puede poner fin a la epidemia

Fauci just said that all indications are that O is milder than D: https://www.google.com/amp/s/www.cnbc.com/amp/2021/12/29/covid-variant-fauci-says-data-suggest-omicron-less-severe-than-delta-.html

The tweet you linked was very confusing, and, as the author said, her sketch did not try to be proportionate when proportion in this matter is vital to know.

i have read both that the vaccine (against Original, which no longer exists, and is very different in many ways from D and O) nevertheless protects very well, at least against severe or fatal illness. I’ve also read that the vaccine does little good and even the vaxxed are readily infected with O. I think they will soon introduce the (adjuvanted) pan-COVID vacvine and also one or more variant-Spector vaccines. But I think at some point we’ll have to consider whether the disease feared is dangerous enough to take more vaccines.

How many in the world have had no exposure at all, either natural or vaccine, to any Covid variant? That number or percentage would have to be established to make the case that they are still in great danger even from O. I don’t see how they could do that. It may have to be left up to every individual in an already majority-vaxxed world to decide what his risk is and what he wants to do about it.

It was already believed two years ago that the pre-SARS human serotypes of coronavirus had started out being very severe, often deadly, then evolved to become milder and cold-like. That may be what is happening now.

Edit: I misinterpreted the paper. See correction in my followup comment.

“Fauci just said that all indications are that O is milder than D”

I just read the paper that Fauci referenced, and was pleasantly surprised to see that they did account for the effect of previous infections. If this paper is correct, Omicron is about 50-80% less likely to put a person in the hospital, compared to the same person getting infected by Delta. There’s a lot of uncertainty due to small sample size, but this is definitely a good sign.

https://www.research.ed.ac.uk/en/publications/severity-of-omicron-variant-of-concern-and-vaccine-effectiveness-

https://www.pure.ed.ac.uk/ws/portalfiles/portal/245818096/Severity_of_Omicron_variant_of_concern_and_vaccine_effectiveness_against_symptomatic_disease.pdf

“I just read the paper that Fauci referenced, and was pleasantly surprised to see that they did account for the effect of previous infections.”

This was incorrect. The researchers collected all the right data to account for vaccination and previous infections, then didn’t actually use it. So actually this paper does not provide any evidence of Omicron having reduced severity.

Fauci said the same thing if you listen carefully. He said that the reduced severity could be due either to Omicron actually being less severe OR due to a difference in previous immunity. A difference in previous immunity is more likely because Omicron is a partial escape variant.

Most of those diagnosed in South Africa were young, unvaxxed, and had a mild case. You could say it was because they were young and at low risk regardless, or because they had had previous exposure to some form of the virus and so had previous familiarity with it which protected them to some degree. But this is true now of virtually everyone in the world now. Measles was a serious disease when it first emerged, and in virgin populations which had not previously had it. Once a disease is common, it usually causes specific immunity on recovery and non-specific immunity from its becoming a background environantal influence. By 1960, measles had become a mild, routine childhood disease in all developed, well-nourished nations of the world, causing an average of 450 deaths out of three to four million cases a year in the US alone. 99% of children had had it by 18, before the vaccine, as per testing on new military recruits. 

A number of studies now have concluded that Omicron is usually mild. It would probably not be possible to compile a study group of individual who had never had a Covid vaccine nor had experienced even an asymptomatic Covid infection. Antibodies may fade over time (though not necessarily), but humoral immunity from T- or B- cells, and others, May have developed and remain. Would it be important to try to discover if Omicron might be dangerous in the small number who might not have acquired any of these protections? Why not just introduce an Omicron specific vaccine for those who think it might benefit them because of their age or impaired health?

i listened to a new talk by John Campbell last night in which he discussed new studies which found that infection with the milder Omicron protects against infection with the more dangerous Delta. Not the other way around: infection with Delta does not protect against Omicron. 

Delta will drop soon because it was going to do that anyway, with or without Omicron. The remaining question is whether it returns in 6 months due to waning Delta immunity. That’s what it would have done without Omicron, and it’s unclear how much Omicron will affect that.

Still no clear sign of Omicron having different severity than Delta. South Africa had fewer hospitalizations as percentage of infected because so many of the infected were either vaccinated or previously infected.

Yes, we actually do have tools that work on Omicron. One of the antibody treatments is still good (out of 20 or so), but in short supply. Newly approved Paxlovid is great, but in short supply. Vaccine and previous infection still help with severity, just not with preventing infection. Also, nothing’s getting through my full face mask. 

The confidence intervals between the two estimates don’t even overlap! (34-94.9 last week, 15.4-31.5 this week.) Ari hitting homers for two years straight now. 🙂

EDIT: It’s also disappointing to see that some of the various public health gurus who pushed this 73% number are acting as though it’s the CDC’s fault. Look, Walensky shouldn’t have tweeted it out. But this was just an automated tool and these guys are supposed to be experts! Surely, even if they couldn’t follow Ari’s logic here, they should seen the 34-94.9% confidence interval and thought “hmm, maybe I shouldn’t make too many strong statements about this.” But set aside that, at least they shouldn’t be turning around and saying stuff like “wow CDC wrong again”… that’s just actively eroding public trust.

Plenty of blame to go around. Reporters should have read the footnotes on the CDC page before copying the “according to CDC” story from other news agencies. COVID gurus on Twitter should have noticed that the Omicron prevalence they were repeating didn’t match the case count growth. CDC should have corrected the misunderstanding that had been so widely reported and attributed to them, especially after seeing their own director tweeting about it. 

While I thoroughly agree that trust in public health authorities is important, those authorities also need to be worthy of that trust. I’ve too many times needed to oppose misinformation that originated from public health authorities. Back in Mar 2020, I was trying to explain to people why they should wear the best mask they could get, cloth now and N95 when they’re available, while WHO was actively pushing the “masks make you sick” line just because they wanted to save them for professionals. The social damage from that misinformation continues to this day, long after WHO did a 180 on that issue. And it’s only in the last few months that WHO finally started promoting airborne precautions. CDC has been a little better than WHO in shifting from promoting contact/droplet precautions to promoting airborne precautions, but has made this change at glacial speed and still isn’t quite there after two years.