Category: COVID through 2022

I thought that we’d break the U.S. record for daily new COVID-19 cases today.  But we’re just a touch short.  Looks like we’ll almost certainly break it tomorrow.

Data source for this and other graphs of new case counts:  Calculated from The New York Times. (2021). Coronavirus (Covid-19) Data in the United States. Retrieved 12/28/2021, from https://github.com/nytimes/covid-19-data.”  The NY Times U.S. tracking page may be found at https://www.nytimes.com/interactive/2020/us/coronavirus-us-cases.html.

The good news is that the official hospitalization counts out of the CDC show no proportionate rise in hospitalizations.  Note that, as scaled, this is the first time in the pandemic where the hospitalizations line is below the new cases line.

Source:  CDC COVID data tracker.

You’re going to see people dismiss this as “too soon to tell”, but my best analysis says that’s incorrect.  (Or, for that matter, just look at the peak from January — looks like the lines were pretty much in sync then.)  I went over all this a coupe of posts ago.  There are significant lags between (e.g.) infection, symptom onset, and hospitalization.  But that’s not the point.  Near as I can tell, on average, for the two lines shown above, reported new hospitalizations lag reported newly diagnosed cases by one day, on average.

For sure, people are still being hospitalized and dying.  But at a lower rate, per case, for Omicron than for prior variants.

The problem is, while the hospitalization rate is lower, it doesn’t appear to be anywhere near as low as early research suggested.  But I think I have the answer for that, in the next post.

That said, this wave isn’t stopping, it’s continuing to accelerate.  And before the words “post-Christmas-surge” leave your lips, please note that a) this wave started before Christmas, and b) owing to the typical lag between infection and reporting, the cases showing up today were infected well before Christmas.

My expectation of a short, sharp wave, based on what occurred in South Africa, appears incorrect.  Sharp, yes.  But so far, no strong indication that this is going to be sort.  South Africa and Norway did indeed have a short, sharp peak.  Great Britain and Denmark did not.  As of today, it looks like the U.S. is going to fall into the “not” group.

We can hope that this last uptick is some sort of reverse holiday effect.  Maybe a lot of people decided to get tested before joining relatives for the holidays.  If so, that would be unique to this year.  That certainly didn’t happen last year.  But if so, that will wash through the data in just a few days.

As you can see from this final chart, cases are up in all regions.  The daily new case rate has not-quite-doubled since the start of the Omicron wave on 12/17/2021.

 

Bottom line:  The holidays don’t seem to be making a dent in the growth of reported new U.S. COVID-19 cases this year.

Tomorrow, when all the states report new data, you’ll see that the U.S. has broken the record for daily new cases, set at the peak of the last winter wave. 

For now, here’s my best guess for the U.S. trend through 12/26/2021.  This is the actual U.S. average through 12/23.  Beyond that, it’s based on the growth observed in the ten states that consistently reported data from 12/23 to 12/26.

Based on that hybrid estimate, daily new cases have now roughly doubled in the nine days since the start of the Omicron wave.  Best guess, as of today, the U.S. averages about 76 new COVID-19 cases / 100K / day.

We will get actual data from almost all states tomorrow, at which point I’ll replace this “hybrid” estimate with the actual data.

Data source for this and other graphs of new case counts:  Calculated from The New York Times. (2021). Coronavirus (Covid-19) Data in the United States. Retrieved 12/27/2021, from https://github.com/nytimes/covid-19-data.”  The NY Times U.S. tracking page may be found at https://www.nytimes.com/interactive/2020/us/coronavirus-us-cases.html.

That said, I think it’s finally dawning on a lot of people that the simple count of cases doesn’t tell you much, if you’re replacing Delta with a far-less-virulent Omicron.  I’ve made that point here, and I’m now seeing that in mainstream media (example).

As far as I can tell, there has still been no commensurate surge in hospitalizations.  The CDC still has not updated its COVID-19 data tracker, so this graph is my calculation from the US DHHS hospitalization data itself.

Source for hospital data:  Calculation from this U.S. DHHS file.

I believe this is consistent what what’s being observed in those states that produce timely hospitalization data.  So far, even for states where new cases are skyrocketing, there has been, at most, am increase in hospitalizations that is far less-than-proportionate to the increase in newly diagnosed cases.

Main result

As of Christmas Day 2021, there had not yet been any jump in U.S. COVID-19 hospitalizations to match the recent jump in cases.  Continue reading Post #1367: COVID-19 hospitalization trend to 12/25/2021. No big uptick, and other surprising aspects of U.S. COVID hospitalization data

 

My wife just invited her sister over for Christmas Day.  Without bothering to ask if I thought that was advisable.  Said sister-in-law having possibly been recently exposed to COVID at work.  My son is going out to the local bar to hang out with his buddies.  Ditto.  I’m still going grocery shopping in person, where maskless customers remain an increasingly common sight.

Meanwhile, the U.S. trend for new Omicron cases where I live (Washington DC suburbs) remains more-or-less vertical.  As it is in several other locations around the nation.

I think I can connect the dots.

At six days into the Omicron wave, we ought to be close to our darkest hour, based on what we’ve seen in other countries.  And that’s working out for me. Continue reading Post #1366: COVID-19 trend to 12/23/2021.

 

The bottom line is this:  There were a lot of new cases of COVID-19 diagnosed yesterday.   But you probably already knew that.  What’s more newsworthy is that there aren’t a lot of new hospitalizations.  Not anywhere you look.  Consistent with the best available research at this time.  And, while it’s too soon to count the deaths, it’s a good guess there won’t be many deaths, either.  As I see it, with Omicron, our winter wave of COVID has morphed into something akin to an unbelievably bad flu season.  Lot of people sick.  Lot of work time lost, events cancelled, business closed, and other economic losses.  But not a lot of severe illness or deaths, per infection.

Despite Omicron’s lower case severity compared to prior strains, it remains a really good time to do what you can to avoid exposure.  Because nobody wants to be sick.  But the odds of getting extremely sick, if infected, seem to be vastly lower under Omicron than under the prior strains.

See Post #1364 if you want the straight-up crude comparison between Omicron and flu, in terms case hospitalization rates.  The big difference now is that Omicron spreads ten times faster than flu.  (Literally:  R-nought is about 1.25 for seasonal flu, but between 10 and 15 for Omicron).

Tomorrow will likely be the last day we get any clear data on what’s happening in the U.S.  Not only are states shutting down reporting for the holiday’s, even the CDC’s COVID data tracker website won’t update tomorrow.  So after this, everything will be guesswork until after 1/1/2022

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As has been my practice for the past few days, I’d like to offer a few calming thoughts before discussing today’s trend data. Let me do that by focusing on the worst U.S. states.

What the heck is “calming” about about focusing on the hardest-hit states?  Well, for one, you can be glad you’re not there.  But more to the point, they provide a great illustration of what you’re not reading in the news, despite the incredibly rapid growth in cases.  You’re reading about the huge increase in cases.  But you aren’t reading about overflowing hospitals and morgues.  And that’s a good thing, as these things go.

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Worst in the nation today:  Washington DC, 166 new COVID-19 cases / 100K / day, seven-day moving average.

Source:  New York Times.

Omicron appears to be hitting metropolitan areas first, and spreading from there.  That follows prior waves of new variants.  They enter the U.S. via international travel from already-infected areas.  And so appear first and in greatest number in places with lots of international travel.

The worst hit area, so far, by far, appears to be Washington DC.  That’s depicted above, via the New York Times.  As you can see, the daily new COVID-19 cases shatter all prior records for the city.  They are very nearly as high as have been observed in any state over the entire pandemic.

That’s so nearly vertical that I would normally think it was a data error, but there’s Maryland right alongside it.  And about half the population of Maryland lives in the DC Metro area.

That’s what you’ll see reported.  But as important is what you’re not seeing:  Reports of overflowing hospitals.  And you aren’t seeing that because it’s not happening.

I downloaded DC’s data from their dashboard.  They track “patients in hospital”, which is the number of persons who are inpatients, and have COVID-19.  They don’t appear to track daily new admission to the hospital, for COVID-19.  Here’s the picture of last year’s winter wave, and the Omicron wave:

Source:  Calculated from Washington DC COVID-19 dashboard, accessed 12/23/2021.

In Washington DC, for the past seven days, the count of persons:

• diagnosed with COVID grew about 1000 per day.
• in the hospital with COVID grew about 7 per day.

That’s probably a slight understatement of the seriousness of the situation.  Plausibly, some of the persons just diagnosed were not sent immediately to the hospital, but will show up in a few days.

But I think that’s the gist of it.  At the Delta hospitalization rate, the current rash of Omicron cases would have been an unprecedented public health disaster.  By contrast, at the Omicron hospitalization rate, it’s not even close to maxing out hospital resources.

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Second worst state:  Rhode Island:  125 new cases / 100K / day.

Unlike DC, Rhode Island had been in the grip of a serious Delta winter wave before Omicron came on the scene.  Accordingly, what you see in their data is a blending of rates, as Omicron displaces Delta.

And, as Omicron displaces Delta, despite rising new case counts, the number of COVID-19 cases in Rhode Island hospitals has started to fall:

Source:  Rhode Island Department of Health

If you wanted to be contrary, you could point to the short timeframe of the decline.  It could be a blip.  But Omicron has only really taken off in the U.S. in the past week.  So that short timeframe is about right.

Honorable mention:  New York City

New York state is third in the nation, with 110 new COVID-19 cases per 100K per day.  And, much like DC, it wasn’t having much of a Delta wave prior to the onset of Omicron.

But the center of the wave in New York is New York City.  Let’s look there.

By now you know the drill.  Below is a graph of new cases, followed by a graph of new hospitalizations for COVID-19.  The hospitalization data are incomplete.  And it’s a short timeframe.  But when you see the same thing time and again, it’s probably real, and not an error in the data.

Source:  Government of New York City.

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U.S. trend to 12/22/2021

Data source for this and other graphs of new case counts:  Calculated from The New York Times. (2021). Coronavirus (Covid-19) Data in the United States. Retrieved 12/23/2021, from https://github.com/nytimes/covid-19-data.”  The NY Times U.S. tracking page may be found at https://www.nytimes.com/interactive/2020/us/coronavirus-us-cases.html.

The rate of U.S. new COVID-19 cases / 100K / day is now up 37% since the start of the Omicron wave on 12/27/2021. 

If we go back to the pre-Thanksgiving basline, cases are rising at an average rate of 16 percent per week.

As I stated in a just-prior post, it makes no sense to compare the simple count of Omicron cases to Delta cases.  It’s like comparing a count of $5 bills and $1 bills, without noting that the $5 bills matter a lot more.

But it’s what everybody does.  And all the better information — hospitalizations, deaths, and possibly some other indicators of morbidity — all arrive with some time lag.  So I’m counting cases, along with everybody else.  Even though it makes no sense.

 

The F-word in this case being flu.

This whole debate about how COVID-19 compares to influenza has been so poisoned by the nut-o-verse that it’s hard to have a rational conversation about it.

But things have changed a lot since that early disinformation regarding COVID being no worse than flu.

COVID hospitalization and mortality rates in the U.S. have fallen since that initial New-York-centered outbreak.  And now, it appears that the latest mutation of the virus is resulting in far fewer hospitalizations and deaths.

And so, what was once a right-wing fantasy (“no worse than the flu”) is, in my opinion, no longer so far fetched.

Without beating this into the ground, I’m just going to show you the numbers that have me thinking about this.

First, you have to look up what the CDC gives for the closest analogs of case hospitalization rate and case mortality rate for the flu.  You can find the CDC estimates at this link.

There are significant differences in methods between a “case hospitalization” or “case mortality” rate for COVID versus the flu.  For COVID, a case is a formally diagnosed case — more or less, a positive test result.  By contrast, the CDC’s “case” for flu is an estimate of all symptomatic cases.  So the denominators differ.  One is all persons with a positive test, the other is an estimate of all persons that had symptomatic disease.

The deaths for COVID are fairly straightforward, but deaths for flu involves considerable estimation, as reporting of flu diagnoses on death certificates is not as clear-cut.

So there are difference in methods.

That said, let me just lay out what appear to be the facts.

Per the CDC, eyeballing their chart, I estimate the following for a typical flu season:

• Flu case hospitalization rate 1.2%
• Flu case mortality rate 0.1%

For Delta, most recently, this is my recollection of the current rates:

• Delta case hospitalization rate 6.5%
• Delta case mortality rate 1.2%

If those aren’t exactly right, they’re close.

But now, per the South African study released today , the current estimate is that Omicron has about one-fifth the case hospitalization rate of Delta.  If that’s true, then for the U.S., we should eventually find that:

• Estimated Omicron case hospitalization rate, 1.2%

Compare to flu above.

Further, I’ve already noted the near-total lack of deaths in South Africa from Omicron.  So while I won’t attempt a formal case-rate calculation, it’s not beyond the pale to suggest that the Omicron case mortality rate is at least 80% lower than Delta, if not more.

Let me sum up.

Once upon a time, nobody was vaccinated against COVID, nobody had any immunity, and there were no effective treatments for it.  Hospitals didn’t really know how to treat it.  By contrast, just about everyone except newborns had some prior exposure to flu, 60% of the population got a modestly-effective vaccine each year, and hospitals had decades of experience treating the worst cases.  During the initial outbreak, in the U.S., the case hospitalization rate for COVID was easily 10x that of flu, case mortality rate was nearly 100x that of flu.  At that time, people who said that COVID was no worse than flu were just flaming idiots.

At present, most are vaccinated for COVID, others have some immunity via prior infection, hospitals have gotten considerably better at treating it, and there are some modestly effective treatments (monoclonal antibodies, anti-viral-replication drugs) available.  Even then, with that, if you’d said Delta is no worse then flu, you’d have been an idiot.

Looking forward, if Omicron really results in cases with such lower average severity, you know, I don’t think I’m at all crazy for saying that Omicron’s case hospitalization and case mortality rates are starting to look flu-like.

There’s still an issue of total illness burden.  Not just because a third of our population still has no immunity to it.  But also because there is no comparison in this simple-minded analysis that looks at the average symptomatic-but-non-hospitalized case.  Nobody talks about “long flu”, for example, but “long COVID” is a real thing.

That said, at some point, it looks like we’ve going to have to live with this in circulation.  Assuming Omicron sticks around, and the South African estimates pan out, we probably need to start thinking of this the same way as flu.  Get your vaccine every fall, stay home if you’re sick, and hope for the best.

I hope it remains legal and customary to wear face masks during winter flu/COVID season.  This is common in Asian countries, and in hindsight now just seems like common sense.  I don’t want to be denied the right to give myself a little extra protection.

But the bottom line is that if it reaches the point where the risks from flu and COVID are not so different, and the population has some resistance to it, we’re going to have to start using the F-word in this context, and just ignore the history behind that.

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The CDC’s revised Omicron numbers.

I’m an economist by trade.  Economists take a lot of criticism for routinely making bad predictions.  But we can’t hold a candle to epidemiologists in that regard.

The CDC’s announcement yesterday — that Omicron already accounts for more than 73% of U.S. cases — was unexpected.  By about a factor of four.  (I was expecting something around 12%, based on last weeks announcement).

In this section, let me try to work through all of that.

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1:  What is that number, really?  What is Nowcast?

First, the 73%-Omicron pronouncement is from the CDC’s “Nowcast” model.  It’s a prediction, not a measurement. 

I don’t think I have ever seen a complete writeup of what, exactly, CDC does to make that “Nowcast” prediction.  Here’s what I have pieced together.

Nowcast makes a projection for the most recent past week, using data that are from a much earlier time period, and an estimated rate of growth.  In the case of these variants, CDC variously says that it takes between two and three weeks for the data to come in.  So CDC is projecting the current situation, based on what they think they observed for level and growth of Omicron roughly two weeks earlier.

You can clearly see that if you go to the CDC COVID data tracker website and turn off Nowcast.

Nowcast off, most recent data is week ending 12/4/2021. Omicron was estimated to be about 0.7% of all new cases that week.  This is the actual data.

 

Nowcast on, CDC projects the two-week old data to the week ending 12/18/2021.  Omicron was projected to be 73% of all new cases in that week.  This is the CDC’s forward projection of the actual data.

When something is growing that fast, even a modest mis-estimate of the growth rate, compounded over two weeks, can lead to substantial error in the projection.  I’m fairly sure the CDC understands that.  In any case, you can see the column labeled “95%PI”.  I’m pretty sure that flags that as an estimate of the overall error of the entire data-and-model framework.  (That is, it’s not just a standard statistical sampling error of the underlying data.)

In any case, note the range there.  What the CDC actually said yesterday is that they are fairly sure that, as of last week, the Omicron accounted for somewhere between 34% and 95% of all new U.S. COVID-19 cases.  This is not a slam on the CDC, it’s just an acknowledgement of the wide confidence interval associated with that 73% projection.

It’s 73%, plus or minus.  Plus or minus quite a bit.

In addition, the CDC revises the historical data as more tests get counted.  That appears to have been a primary driver of the change between last week’s estimate of 2.9%, and this week’s estimate of 73%.  Between the two weeks, CDC revised last weeks estimate upward to about 13%.  So what we thought was 2.9%, going into this latest revision, is now said to be 13%.

2:  Count your time lags as carefully as you can.

Now let’s assume that the CDC’s 73% estimate is perfectly accurate.  (We might as well, because as far as I can tell from press reporting, just about everybody else does).

What does that imply for the rate today (12/21/2021).  And is this in sync with the data reporting for the count of cases?

Today’s rate.  The CDC Nowcast is an average for the week ending 12/18/2021.  Given the rapid rate of growth, my best guess is that CDC’s projection actually hit that level around 12/15/2021.

So as of today, it’s six days after the U.S. passed that 73% mark.  Nowcast shows the percentage increasing more than five-fold in the past week.  And while I can’t do the detailed math, I’m certain that puts the estimate for today well into the high 90%s.

In other words, based on the CDC’s projection for last week, and the growth rate, the CDC’s 73% estimate from last week means that virtually 100% of cases tested today should show up as Omicron.

There is a caveat.  I’m pretty sure the CDC is tabulating all of that by sample (test) date.  That’s the only firm date that can attach to the set of swabs they used for their full genetic breakdowns of the virus.

Roughly a week elapses between test date and the cases are counted fully in the seven-day moving average of new cases.  Best guess, about four days elapses, on average, between the time you get tested, and the time that test is reported by your state public health agency.  The raw daily counts should run about four days behind the test dates.  And then we take a seven-day moving average, which in a crude sense amounts to an average 3.5 days additional time lag.  The upshot of all of that is that the seven-day moving average of new cases ought to be about a week behind the CDC data.

And so, as far as that goes, it’s a case of very nearly offsetting errors.  The CDC’s 73% really is for swabs that were taken six days ago, on average, or circa 12/16/2021.  Today’s new case count (for 12/20/2021 data) comes from swabs that were taken circa 12/13/2021.  And so there should be something like a three-day difference between the CDC’s 73%, and whatever is driving today’s increase in cases.

Given the rapid rate of growth, this means that, even if the CDC 73% is absolutely correct, today’s seven-day moving average of new cases actually reflects a substantially lower percentage.  Given the growth rate, plausibly half that or less.

So the seven-day average of new case growth reported on 12/20/2021 (today’s data) reflects something like 40-ish percent Omicron in circulation.  If the CDC’s 73% estimate is correct.

It’ll all be moot in a week anyway, given the growth rate.

3:  Does the regional variation in Omicron match the regional change in new case growth?

Near as I can tell, the match between where CDC says Omicron now dominates, and where the rapid case growth is, is only so-so.  First, here’s the CDC’s chart, via Nowcast:

Source:  CDC COVID data tracker, accessed 12/21/2021.

Based on the CDC estimates, Region 10 (Pacific Northwest, mostly) should be hardest hit by the Omicron wave.  Followed by Region 2 (mid-Atlantic) and Region 4 (South Atlantic)

Now case growth, based the same NY Times data source as above, just split into the 10 U.S. DHHS regions.

The only thing that really stands out is Region 2, the mid-Atlantic region.  Region 10 has seen more-or-less no excess case growth in recent weeks.

I judge that to be a mediocre correlation at best.  Perhaps the estimates of the Omicron share are that bad.  Perhaps other factors (e.g., weather) are driving case growth.

4:  Note if the CDC is right, most of what Omicron has done so far is to displace Delta.

I remain fascinated by this phenomenon.  Once again, the main impact of the newer, more-easily-spread variant is to kill off the prior variant.  And spread a bit faster.  How, exactly, Omicron manages to kill of Delta, I cannot quite fathom.  But this is just a repeat of what Delta did to Alpha, and what Alpha did to the native (Wuhan) strain in the U.S.

I still remain hopeful that case growth will remain low enough, and top out early enough, that Omicron will be a net bonus for the U.S.  As of the last time I checked, more than one percent of diagnosed Delta cases were still ending in death in the U.S.  More than 6% were ending up hospitalized.  As long as Omicron’s case rates are well below that — and I believe that, on balance, the data pretty strongly suggest that — I think the Omicron wave in the U.S. will end up reducing the harm from COVID, compared to letting a Delta-based winter wave play out.

New COVID-19 cases are now spiking in some areas of the U.S.

Before I get into all that, perhaps a bit of a calming exercise is in order.  Continue reading Post #1361: COVID-19 trend to 12/20/2021, looks like the U.S. Omicron wave is here.

Party naked.

Well, that’s a surprise.

Seriously, if what’s being reported this evening is correct, then we’re done with COVID for the time being.  In particular, we’re done with Omicron.

Normally, the CDC releases updates on its estimate of variants, as a proportion of the circulating COVID-19 infections, on Tuesday.  Says so right here:

I had been hawking this Tuesday’s release, because I had predicted an estimate of maybe 12.3 percent. Per this post, from just two days ago.

But here we are on Monday, and we see that Omicron is estimated — on Monday — to be 73% of US cases.  Here’s a reference, but it’s all over the internet.

But, but, but  …

I’m not going to go into the detail.  In particular, how the CDC has revised the 2.9% estimate from last week to 13%.  A four-fold error?  That does not sync with (e.g.) estimates from Europe.

But, well, they said what they said.

But if that 73% is real, then the U.S. is already over the Omicron wave, and hey, hallelujah.

Let just try to explain that.  If it was 73%, on average, for the week ending 12/18/2021, then it actually hit 73% on or about 12/15/2021.  And if the unrestrained doubling time is under two days (which you can’t extrapolate out once the percentage gets this high, but let me just cut the residual 27% in half every two days), then as of today (12/20/2021), Omicron already accounts for something like 94% of all new cases.

The remarkable thing, if the CDC is right this time, is that Omicron became the dominant variant with no notable increase in cases.  With no notable change in hospitalizations, one way or the other.  And with, so far, no notable increase in deaths.

So if that’s true, we’re well and truly done for the time being.  And Omicron is a total dud here.  Versus South Africa.  Or Great Britain.  Or Europe in general.

Okey dokey.  Looks like an error to me.  I think we’re still in process, and we have not yet seen our Omicron wave.  But I’ll try to sort it out in the morning.

As I said, if true — if somehow Omicron has take over here, with no marked increase in daily new cases — then we’re good to go.  Party naked, COVID-wise.