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

Something extremely odd happened this afternoon.  The press, including the New York Times, the Washington Post, CNN, the Wall Street Journal, USA Today, and Axios, reported that the CDC had announced that 73% of US COVID-19 cases were now being caused by the Omicron variant, and major public health gurus like Ashish Jha, Eric Topol, Florian Krammer, Eric Feigl-Ding, and Scott Gottlieb circulated the reports at face value.

But that’s not really what’s happening.  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.

What actually happened?

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.

The Nowcast algorithm is based on the CDC’s variant proportions data.  Every week a small percentage of US COVID-19 cases are subjected to genome sequencing, which identifies them by strain.  Right now it’s about 3.6%, but it varies by state.  The CDC collates this data to produce weekly reports on the prevalence of each variant in each of ten regions of the continental USA.  However, the genomic data takes time to generate and process, then get deposited into genomics databanks, then get analyzed by the CDC, so the newest data is about two weeks old at each weekly refresh (today, sixteen days old; the week ending December 4).

To display an estimate of current prevalence, the CDC uses an algorithm it calls a “Nowcast,” to project forward from two weeks ago and give an estimate of current prevalence for different strains.  The Nowcast algorithm has been remarkably accurate and useful in the past; I followed it with great interest as Alpha, Gamma, Delta, Mu, and other strains washed across the USA from early 2021 until Delta attained total dominance in the summer.  It’s a significant achievement for the CDC, and I celebrate them for it.

But something is on the fritz now.  In this week’s update, which dropped Monday afternoon, the Nowcast algorithm is presenting results that don’t make sense.

How we know the Nowcast is wrong in this case

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.

And a quick look at the regional numbers shows that something truly crazy is going on.  Region 10 is composed of Oregon, Washington, and Idaho.  The last week of data (ending December 4) shows a 0.0% prevalence for Omicron there, but the latest Nowcast says that jumped to 43.4% in the week ending December 11 and 96.3% in the week ending December 18.  Region 10 has the lowest numbers in the actual data, but the highest numbers in the Nowcast.  When the data say 0.0% in the latest week, what algorithm could accurately extrapolate 43.4% the following week?

And this points to another big problem.  These numbers don’t comport with the national case numbers and what we know about how variants interact.  While huge case surges have been seen in the states in Region 2, which was already 2.4% Omicron in the latest measurements (the week ending December 4), as well as other Omicron-dominant areas like the UK, they haven’t been seen in most states elsewhere in the country.  This pattern was also seen as Delta took over from Alpha in the USA this summer, but we’re not seeing it in most of the USA now.

Until the last few days, national case numbers were flat, and have since grown by only a few percent, as a result of explosive growth in just a few states.  If Omicron were already nationally dominant last week, this would imply that Delta happened to nationally completely implode (with R suddenly dropping to near zero) at the exact same moment and exact same speed that Omicron exploded.  And that Omicron’s explosion suddenly slowed down at the moment Delta cases hit (near) zero, since we have not seen an explosive increase in national case numbers yet.  Region 10, which supposedly saw the fastest growth and highest prevalence of Omicron, has even had decreasing numbers over this period.

But in reality, none of this is true.  The CDC’s Nowcast algorithm has some kind of bug, and the prevalence of Omicron nationwide wasn’t really 73% in the week ending December 18.  Take that to the bank.

What does this mean?  What will happen now?  What can we do about this?

A few things to take away from this:

  1. You will see this walked back.  The CDC will explain what happened.  The Twitter experts will have to walk back their initial tweets.  The press will have to publish a new round of articles clarifying their prior wave of headlines.  It might happen tomorrow, later this week, or some time next week, but it will happen.  This result won’t stand.
  2. None of this should be taken to impugn the CDC.  They didn’t announce this.  It was an automated algorithm, and one that had a good record prior to this.  But the emergence of Omicron has reset the speed of events back to “fast,” and the modern infrastructure of COVID-19 genetic surveillance, including the Nowcast algorithm, hasn’t yet been vetted in a period of extremely rapid exponential growth like December 2019-March 2020, and now.  It was inevitable that bugs would come up, and this one just happens to have suddenly turned into a media sensation after hours.
  3. The press missed the boat on this one because they’re not keeping track of the details.  The few outlets with a record of reporting on variant prevalence data in depth, like Science magazine, Endpoints, and the MIT Technology Review (along with yours truly) haven’t run this story (that I know of).  Although, disappointingly, Stat News has run it, and so has the Financial Times.  The outlets that are running it are probably encountering the Nowcast for the first time, don’t really understand it, and didn’t dig into the details before running the topline number.  Twitter pundits, including some genuine experts who should have been more careful, then fed off of this initial round of unsophisticated media coverage.  The press has a lot of failings in covering science issues generally, which go over the head of most journalists, and during the pandemic, this general issue has manifested as a serious systemic problem with press coverage.  This is just another example.
  4. Omicron really is growing explosively, and almost certainly will dominate the entire USA pretty soon.  It is probably already dominant in certain areas, like New York and New Jersey, Florida, Hawaii, and Puerto Rico, which are seeing explosive growth in overall case numbers.  This algorithm bug and media frenzy have jumped the gun, but in the long run, they are just a blip.  The overall story on Omicron is still that it’s growing explosively, will take over, and should be an imminent object of concern.

So, what should you do?

  1. Still prepare for Omicron to become dominant in your area within weeks (or already).  That’s real, and it’s still on.
  2. Enjoy watching this story get revised.
  3. Continue to be careful about what you read.


    • July LewisContributor

      You guys pay attention!! Interested to see the updated reports.

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    • brownfox-ffContributor

      Very insightful analysis. Thank you for sharing – both as useful news, and as a good example of using critical thinking and not blindly believing everything we read.

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    • Cia

      I noticed that last night, reports apparently saying that 73% of Covid cases in the US were now being caused by Omicron. Astounding, I was about to put it on a friends WhatsApp. Then I reread it and noticed that it said 73% of NEW cases, which it said were about 3% of the total. It was 73% of 3% caused by Omicron at this time. A horse of a different color.

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    • Cia

      I just saw Stephanie’s link to an article saying that nearly 100% of Covid virus found in Orange County, Florida, waste water was Omicron. So it seems credible that 73% of new cases should be Omicron, although new cases are only 3% of the total however they define that, meaning that Delta is still preponderant in active, but older, cases.

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      • Eric Cia

        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.

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    • Jeff Bullard

      Omicron represented 11% of US cases on Dec 9th. That’s from GISAID data, 45 of 426 sequences from that specimen date. 

      Using known growth rates from UK and Denmark would put the US at 75% Omicron by Dec 18th.

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      • Eric Jeff Bullard

        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.

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      • Cia Eric

        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?

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      • Josh Hug Cia

        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.

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      • Eric Josh Hug

        “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.

        Screen Shot 2021-12-21 at 8.26.36 PM

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      • Jeff Bullard Eric

        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.



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      • Jeff Bullard Eric

        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.


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      • Eric Jeff Bullard

        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.

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    • Josh Hug

      I’ve been so puzzled by the CDC announcement from the moment I saw it — the idea that Omicron was suddenly 73% of new cases, but with only a small increase in total cases just makes no sense. I felt like I was taking crazy pills since pretty much all the high profile folks I follow were not discussing this odd fact. It’ll be interesting to see what actually happened.

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      • Cia Josh Hug

        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. 

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      • Cia Cia

        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.

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      • Eric Cia

        “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.

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      • Cia Eric

        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.

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      • Eric Cia

        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.

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      • Cia Eric

        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.

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      • Eric Cia

        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.”

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      • Cia Eric

        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. 

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      • Eric Cia

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

        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.

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      • Cia Eric

        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.

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      • Eric Cia

        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.

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      • Cia Eric

        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.

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      • Cia Cia

        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.

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      • Eric Cia

        “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.

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      • Cia Eric

        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

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      • Cia Eric

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

        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.

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      • Eric Cia

        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.

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      • Eric Eric

        “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.

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      • Cia Eric

        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. 

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    • mikepow

      Ari, Thank you for outlining this so clearly.  I have been following the data, and it did not add up.

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    • Cia

      Eric Topol said last night that 80% of new cases are Omicron, while over 2100 died yesterday of Delta, most unvaxxed. I think deaths from Delta will soon plunge if for no other reason than that the virus will soon run out of tinder. Omicron continues to cause very few deaths, and hosp in South Africa are plunging. It looks like nothing does much good against Omicron, none of the vaccines, not antibody treatments as presently constituted, not immunity from previous infections with other variants. I think there’s a good chance that lower hosp and deaths are because it’s a milder virus.

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      • Eric Cia

        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. 

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    • Mar Tam

      Ari, I always appreciate your insights (and was excited to see we went to the same university!), but I have to admit I let myself be skeptical about this one because I saw that Walensky had tweeted out and I thought “surely they would’ve double checked this one before they pushed it out.” But no, you’ve been proven right! Per NYT, the CDC is saying that the estimate for that week was actually 23%, and that their estimate for the present is 59%. 

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    • DaveH

      Ari, Thanks for posting this, here’s the latest:

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    • Eric

      A week after Ari warns us that the CDC’s estimate of 73% was unrealistically high, NYT reports breaking news that CDC reduced their own estimate down to 23%.

      Omicron is rising fast, and will no doubt pass the 90% mark soon enough, but that forecast was off by more than a week. It was really strange seeing that 73% figure repeated by so many news outlets and even top public health officials over the last week.


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      • Mar Tam Eric

        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.

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      • Eric Mar Tam

        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.

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    • EzlyAmuzzed

      Congrats Ari on making such a bold speculation and being right!

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    • Greg Green

      Climatology has been ruined by computer modeling, now it appears virology is being destroyed by computer modeling as well. Always trust real data, not virtual data.

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