Category: COVID through 2022

What is wrong with this picture?

Source:  Carnegie-Mellon University COVIDcast, accessed 1/1/2022

This post is more-or-less a followup on the just-prior post, where I found out that we’re now admitting as many people to the hospital under Omicron as we did at the peak of the Delta wave.  We’ve managed to offset the lower virulence of Omicron with a vastly higher number of cases.  And the peak of the Omicron wave is nowhere in sight.

And, near as I can tell, other than hospital workers, people just don’t seem to care.  Which I find odd and irrational.  But it is what it is.

And that’s the topic of this post.

Along with COVID in children.  For which, I will say up front, Omicron does not appear to disproportionately affect children.  In Virginia, there was no change in pediatric share of COVID-19 cases over the month of December.

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Background:  The shifting situation

People tend to fuzzy-think their way through a lot of situations in life.   They get hold of an idea that sounds good, and they don’t bother to take a hard and objective look at it, as long as they are comfortable with it.

By now we’ve all heard that Omicron is less virulent than Delta.  And so, I guess we are each, individually, thinking that we’re in some sense a lot safer now with Omicron than we were with Delta.

Let’s call that a warm-and-fuzzy-thinking view of Omicron.  It’s not so bad, on a per-case basis.  Lot better than Delta, say, which had a reputation for virulent infections.

But those of us capable of doing simple math reach a different conclusion.  My likelihood of ending up in the hospital under Omicron is now just about exactly what it was at the peak of the Delta wave.  That’s because my odds depend on two factors:

• Odds of hospitalization = odds of infection x odds of hospitalization, once infected.

For sure, the second term is lower under Omicron than Delta.  Maybe one-third as large.  But give it another couple of days, and the odds of infection term will have more than offset that.  The current situation is best described as:

• Odds of hospitalization, Omicron = 3*Delta X (1/3)*Delta
• Odds of hospitalization, Omicron = Odds of hospitalization, Delta.

Oh, and cases are now doubling roughly every week.  And two doses of vaccine does almost nothing to prevent Omicron infection.   And reinfections are common among those who have already recovered from some prior variant.

And nobody seems terribly concerned.

Doesn’t that strike you as odd?

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And yet, nobody seems terribly concerned

Let me just start with my home town.  As documented in Post #1377, three days ago they were blithely going to shut down a drive-through COVID-19 testing center in town.  Which, as it turns out, would have reduced local testing capacity by about a third.  (Although I am almost sure they didn’t bother to figure that out first.)  Based on news reports, Town officials appeared absolutely unconcerned about the impact that might have.  Only after significant citizen protest did common sense prevail, and the Town bureaucracy agreed to allow the testing site to remain open another month.

In my state of Virginia, it looks like the Governor’s emergency orders all ended with the end of 2021.  The only mask requirements are that masks must be worn in schools and on public transportation.  (I’m pretty sure the second one is a Federal requirement).  There’s no talk of (e.g.) limiting occupancy of bars and other high-transmission-risk areas.

Schools?  Again, I’m seeing no talk of virtual schooling in my area, for grade schools.  My daughter’s college (and many others) are going to require a booster shot for return to campus, for those eligible, and will require mask use in commons areas.  So far, it doesn’t look like they will require a negative COVID-19 test prior to return to campus.

And, noted at the top of the post, about a third of people who were wearing masks last winter can’t be bothered to put them back on this winter.

In short, almost no COVID hygiene will be enforced, aside from masks in schools (in Virginia, anyway).    Private academic institutions seem to be moving to a standard of masks and booster shots.  Beyond that, a lot of people aren’t going to undertake that hygiene voluntarily, and it sure looks like, with a few exceptions, there isn’t a whole lot of lifestyle modification going on.

Against a background where new cases are doubling every week.

I wonder what’s going to happen when everybody goes back to school?

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A quick look at pediatric COVID cases.

Let me start by reminding you of what happened when U.S. kids went back to school this past fall:  Nothing.  For sure, nothing happened in Virginia, because I tracked that pretty carefully (e.g., Post #1268).  And, I think that with a few exceptions in the upper Midwest, pretty much nothing happened anywhere.  There was some above-average spread among sports teams (a high-risk group due to close physical contact).  A few outbreaks.  And not much else.

I’ve never found a timely national data set showing new COVID-19 cases by age.  CDC will give you that information with a couple of weeks lag, based on their own case-reporting system.  But when cases are doubling every week, that might as well be a couple of years.

So I’m turning to data from Virginia.  We’re a middle-of-the-road state, we currently have 118 new COVID-19 cases / 100K / day, and the state Department of Health provides excellent, timely data, including a breakout of cases by age.  The data source is this file, updated to 12/30/2021.  If there’s been some big shift in COVID-19 cases, it should show up here.

There has been no change in pediatric share of cases under Omicron, in Virginia.  As Omicron has begun displacing Delta in Virginia, there has been no noticeable shift in the share of new COVID-19 cases that is for pediatric (under-age-18) cases.

Source:  Calculated from Virginia Department of Health data cited above, accessed on 1/1/2022.

Not quite tongue-in-cheek, I’ll also provide this information as a service to parents of Virginia school-age children who may be worried about the impending return-to-school.

Source:  Calculated from Virginia Department of Health data cited above, accessed on 1/1/2022.

There are about 1.7M persons under the age of 18 in Virginia.  There was one COVID-19 death in December.  Over the entire course of the pandemic, there have been 12 pediatric deaths attributed to COVID-19, for a risk of death, for persons under age 18, of about 0.0004% per year.

That said, this is is non-negligible risk of hospitalization.  Combining Federal and State data for December, the COVID-19 case hospitalization rate for the pediatric population of Virginia was just over 1 percent.  So while risk of death is vanishingly small, risk of being hospitalized with COVID is currently about one-in-100 diagnosed pediatric infections, in Virginia.

But what about rising pediatric hospitalizations under Omicron?

In the U.S., as was seen in South Africa and elsewhere, it looks like there’s a significant increase in hospital admissions for children with COVID-19.  I did the graph just a few days ago, for the U.S.:

Source:  Calculated from U.S. DHHS Patient Impact and Hospital Capacity by State Timeseries

(I would love to redo this now, for Virginia, but the pediatric admissions data are too sparse.  In a typical December 2021 day, pediatric (under age 18) admissions for COVID-19 were in the single digits.  The resulting pediatric fraction of cases is all over the map.)

My most plausible answer for the apparent increase in pediatric admissions for COVID-19 is that it may be due to persons admitted with, but not for, COVID-19.  I went through this distinction in Post #1351, principal versus secondary diagnosis of COVID-19.  And maybe that shows up disproportionately in the pediatric population because the COVID hospitalization rate is so low?

And yet, every time I try a back-of-the-envelope calculation, I’m not sure I can justify that.

But I will note, as a matter of fact and not speculation, that pediatric admissions rose as a fraction of total at the peak of the Delta wave as well:

So, at the very least, this isn’t the first time this has happened.  And the speed of increase in the pediatric share appears to correlated with the speed of increase of total cases in the population.

So I have to speculate that this “increased pediatric share of admissions” might be an artifact of the high prevalence of COVID-19 in the population.  That, somehow, those “stray” cases of people hospitalized “with-but-not-for” COVID disproportionately affect pediatric admission counts.

I just can’t find a way to prove it.  But at least now I can tell you that this happened in the last COVID-19 wave as well.

Let us all now collectively hold our breath as children everywhere return to school next week.  Given how fast Omicron moves, by mid-January we’ll know whether that’s a mistake or not.

For sure, this wouldn’t be my choice of ways to greet the new year.  But it is what it is.

We’re now two full weeks since the 12/17/2021 start of the Omicron wave in the U.S., and there’s still no letup in sight.  The U.S. daily new COVID-19 case rate doubled last week.  Continue reading Post #1378: COVID-19 trend to 12/31/2021, to infinity and beyond? No, just to the day after tomorrow.

The U.S. is now averaging over 100 new COVID-19 cases per 100K population per day.  Still no sign of a slowdown for the country as a whole.

Continue reading Post #1376: COVID-19 trend to 12/30/2021 – still vertical.

 

Source:  CDC COVID data tracker, accessed 12/30/2021

From time to time I’ve been tracking COVID-19 hospitalizations from a data file collected and maintained by the U.S. Department of Health and Human Services.  You can see a daily summary of the data by state, at this link.  DHHS also provides a weekly report showing individual hospitals, at this link.

In addition to counts of COVID-19 admissions and patients, that file also gathers some measures of how stressed the hospital system is.  For example, it captures the fraction of hospitals that report having a critical staffing shortage; it can be used to show the fraction of beds and staffed ICU beds currently occupied; and so on. Continue reading Post #1375: U.S. hospital bed and ICU bed use over the pandemic.

 

This has been yet another morning of looking at the COVID-19 numbers and saying “never seen that before”.

In any case, I’m sure you won’t be able to avoid hearing all the bad news, so let me be brief about that.

The U.S. is now averaging more than 90 new COVID cases per 100,000 population per day.  Here’s how the case counts look, compared to last year: Continue reading Post #1374: COVID-19 trend to 12/29/2021. I reject your reality and substitute my own.

 

The point of this post is to try to get some handle on the actual, as-observed average severity of Omicron, compared to Delta, in the U.S.A.  The bottom line is that the U.S. results look more like research from Scotland and England — the case hospitalization rate for Omicron is about one-third that of Delta.  They don’t look as good as the results from South Africa, which suggested that the case hospitalization rate was one-fifth that of Delta.

The same analysis verifies that there has been an uptick in pediatric hospital admissions with COVID-19, as a fraction of the total.  Not a huge increase, but a marked increase that coincides with the Omicron wave.  Given that we have no national database that shows current new cases broken out by age, there’s no way to tell whether that’s just an artifact of higher infection rates among the pediatric population.

Finally, I think it’s too soon to say much about U.S. mortality rates from Omicron compared to Delta.  The well-aged South African data seem to show a case mortality rate for Omicron that is about one-fifth that of Delta.  But data from European countries — which may or may not be well-aged enough to provide a valid estimate — show a much smaller difference.

All told, this means that Omicron is not quite as benign as the flu.  Best guess, with current data, case hospitalization rate is about twice that of flu, and my guess for a case mortality rate would be about four times that of typical seasonal flu in the U.S.

You can see my original comparison of Omicron and flu in Post #1364.  If our results had matched those of South Africa, then Omicron would have had a flu-like case hospitalization rate.  Now that it’s looking like our results aren’t that good, the best estimate is that Omicron has not-quite-double the case hospitalization rate of typical seasonal flu.

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U.S. case hospitalization rate

Let me start with the case hospitalization rate.   That is, the fraction of newly diagnosed COVID-19 cases that are admitted to the hospital.

Below is the crude case hospitalization rate.  The plot is the seven-day moving average of new adult and pediatric admissions with confirmed COVID-19 at time of admission, divided by the seven-day moving average of new COVID-19 cases.

Source:  Calculated from U.S. DHHS unified hospitalization data set, and new case counts from the CDC COVID data tracker.

You can clearly see what appears to be the Omicron impact circled in red.  I date the Omicron wave to 12/17/2021.  Before that, the case hospitalization rate was about 6.5%.  As of the last day show, it has plummeted to 4.0%.  That fairly abrupt change certainly has all the earmarks of cause-and-effect, given the relatively stable rate prior to that point.

That’s the easy part.

The hard part is guessing what the Delta/Omicron mix is, corresponding to that 4% case hospitalization rate.  And here, I’m not going to get all fancy.  That’s a seven-day moving average ending 12/27.  So the median day is somewhere around 12/23 or 12/24.  Which is roughly contemporaneous with the last CDC estimate of Omicron’s share of cases (week ending 12/25).  So I’m just going to take the CDC’s number.  I’m just going to assume that 59% of those cases were Omicron.

The rest is just a bit of trial-and-error with Excel.

• If the case hospitalization rate under Delta was 6.5%,
• and the case hospitalization under a 31%/59% Delta/Omicron mix is 4%,
• then the case hospitalization rate for Omicron must be 2.3%

To sum that up, it looks like Omicron’s case hospitalization rate is about one-third of Delta’s rate.  That’s in the ballpark of more careful estimates from Scotland and England.  But much higher than the South African estimate that Omicron had just one-fifth the case hospitalization rate.  Plausibly, that would depend, in part, on differences in propensity to hospitalize persons in those countries.

A little sensitivity analysis is called for.  By far, the most uncertain aspect of this is the fraction of newly-diagnoses cases that are Omicron.  The CDC didn’t actually say that Omicron accounted for 59% of cases.  The CDC actually said that there’s a 95% chance that Omicron accounted for between 42% and 74% of new cases.  Like so:

Source:  CDC COVID data tracker, accessed 12/29/2021.

We can use the range of the CDC’s confidence interval for the percent of  cases that are Omicron to show how this calculation of the estimated case hospitalization rate would change.  Same algebra as above, just a different set of assumptions.

I think the important lesson is from the bottom line of the table.  At worst — using the upper bound of the CDC’s confidence interval for its estimate of Omicron as a share of cases — the case hospitalization rate for Omicron is less than half that of Delta.

Some caveats.

Is it too soon to say anything meaningful about Omicron’s case hospitalization rate?  No.  I already dealt with the objection that hospitalizations lag new cases in prior posts.  There are plenty of real-life lags between (e.g.) date of infection, symptom onset, and hospitalization.  But as-reported, with all reporting lags included, the new cases and new hospitalizations series are very nearly exactly contemporaneous. The average lag between changes in reported new cases and changes in reported hospitalizations is one day.

Is this estimate going to mistake changes in vaccination rates and such with differences between Delta and Omicron?  No.  Because Omicron has grown so quickly, I can compare the U.S. today to the U.S. just a couple of weeks ago.  More-or-less the same population, more-or-less the same vaccination rate.   Not much changed in the past couple of weeks.

It’s possible that there may be significant demographic differences between the Omicron-infected and the Delta-infected.  But a) I doubt that, and b) there’s no timely data source in the U.S. that would tell us that.  So that remains a caveat.

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Footnote:  Pediatric admissions as fraction of total.

There have been a lot of stories about increased pediatric admissions for COVID.  But, you know, anything having to do with dying children always gets a lot of press coverage.  So the question is, for the U.S. as a whole, is it true that pediatric admissions with COVID-19 have increased disproportionately?

The short answer is yes.   Below you see that pediatric admissions have gone from about 2.5% of admissions with COVID-19 to about 3.5%, over the course of the Omicron wave so far. As with the graph above, that short, sharp increase has all the earmarks of being cause-and-effect.

Source:  Calculated from U.S. DHHS unified hospital admission data. accessed 12/29/2021.

In terms of the absolute number of cases, this amounts to about 350 children per day admitted to the hospital with COVID.

There are two things to keep in mind.

First, we don’t know what fraction of those are admitted for treatment for COVID, versus admissions where the COVID is an incidental finding.  Near as I can tell, the U.S. data track something akin to “COVID present on admission”.  They are not tracking cases with COVID as the principal diagnosis (the reason for admission, see Post #1351).

Second, we don’t know what fraction of new cases are pediatric cases.  This might just be tracking the trend in new cases, for all we know.  There is no timely national data set that breaks out the new case counts by age.

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Case mortality rate.

I can’t even hazard a good guess here.

In addition to the case hospitalization rate, I’d like to have some idea of the case mortality rate. What fraction of diagnosed Omicron cases go on to die from it?  In the U.S, for Delta, for the most recent period, that number has been just over 1 percent.

It’s too early to see Omicron’s impact on the U.S. case mortality rate.  There’s roughly a two week lag between reported new cases and reported deaths, and two weeks ago Omicron was barely on the horizon in the U.S.

Instead, I looked at three countries where Omicron hit earlier than it did in the U.S.  It’s not clear that any of these provides a good comparison.

In South Africa, the most recent data are all Omicron.  Between they had a material increase in vaccination rate between their prior (Delta) and current (Omicron) waves.  The apparent five-fold reduction in case mortality might be due, in part, to concentrating vaccinations among the highest-risk (e.g., elderly) population.

For two other countries where we can plausibly compare the mortality rates (Great Britain,  Norway), you really can’t see much of an impact of Omicron on the case mortality rate.  I don’t really know why.  I can only guess that this remains an artifact of the long time lags required to gather the mortality data.  In both cases, we’re looking at new cases that appeared in late November/early December.  Even with those countries, Omicron probably wasn’t a big enough factor to have generated large changes in the mortality rate yet.

At the end of the day, in the U.S., all I can do is take a guess.

I’m going to guess that we’ll see about the same effect on case mortality as we see on case hospitalization.   Probably, the ultimate case mortality rate for Omicron is going to end up being somewhere around a third that of Delta.   (I say that mostly because that’s how the Virginia numbers look, for vaccinated versus unvaccinated persons, under Delta.  The reduction in the mortality rate due to vaccination is always similar to the reduction in the hospitalization rate.)

If so, that will make Omicron considerably deadlier than seasonal flu.  A one-third reduction relative to Delta would result in a roughly 0.4% case mortality rate for Delta in the U.S., compared to a 0.1% case mortality rate for flu in the U.S.

My conclusion is much the same as for hospitalizations.  Omicron appears much less virulent than Delta.  But it’s an exaggeration to say that it’s no worse than flu.  Best guess, given what I can get my hands on today, it’ll result in about twice the hospitalization rate and four times the death rate of flu.

(And, of course, those who claim COVID is no worse than “a cold” are just ill-informed.  First, “a cold” is not a single well-defined disease, but refers to the symptoms of any number of upper respiratory viral infections.  Second, near as I can tell, you can’t even find a case mortality estimate for “a cold”, presumably because deaths attributable to complications of a cold are so rare.  Third, the same goes for a case hospitalization rate for “a cold”.  People who claim COVID is no worse than a cold have probably never even tried to look up the actual case hospitalization and mortality data.)

In short, if you’re in one of the higher-risk populations, I think it’s still well worth your while to avoid this strain of COVID.  It’s as prevalent in the population now as it was at the peak of last year’s winter wave.  And while your odds of hospitalization and death, if infected, are lower now than they were then, they are still non-negligible.  Best guess, as of today, if you get infected, you’ve got a better than 1-in-50 chance of ending up in the hospital.

 

We’ve now topped the record for U.S. daily new COVID-19 cases, set at the height of last year’s winter wave.  And the growth in that number isn’t even slowing down yet. Continue reading Post #1372: New U.S. COVID-19 record, no reduction in new case growth.

I’m just trying to get a handle on where things are likely to be headed in the U.S. for the near term.  I’m just going to present the last three months of new cases, with a little commentary.  These plots all come from Google searched for COVID and the country’s name.

Here’s the game I’m playing:  How hard is it to interpret what you are seeing as a peak in new cases?  In other words, how much wishful thinking is required to say that a country has already passed its Omicron peak.

South Africa is an example of a short, sharp peak.  No wishful thinking required.  There were almost no cases of COVID-19 in circulation just prior to the Omicron wave there, so that’s pretty much a pure Omicron wave.  And it’s receding at just about the same rate that it grew.

Norway has peaked, but more gradually than South Africa.  Again, not much imagination required to interpret the graph below as showing a peak.  But Norway was already having a winter wave of Delta when Omicron came along.  The early part of that wave is Delta, the latter part is Omicron.  That might explain the relatively slow ramp-up compared to South Africa.

Denmark hasn’t reported post-Christmas data yet.  Too soon to tell.  Maybe a hint of a peak just prior to Christmas.  But with no post-Christmas data, it takes a lot of wishful thinking to call that a peak.

Great Britain’s first post-Christmas data looks high, but that one bar is three days’ worth of data.  With just a bit of wishful thinking — break the last bar into thirds and fill in last three slots with that — yeah, maybe that looks peak-ish.  But it’s too soon to tell.  That relatively low first post-Christmas data point might be an artifact of testing availability and behavior over the holiday.

Canada’s COVID trends tend to mirror those in the U.S. (or vice-versa, depending on which side of the border you reside).  I can see a peak there, if I just focus on the shape of the blue bars, not the seven-day-moving average line.    Another few days ought to determine that one way or the other.

U.S.A. data reporting is so ragged, it’s hard to say much.  But, trying to be positive here, take that last blue bar, break off a piece to fill in the reporting hole two days’ prior, and things haven’t really changed much in the last six days.  Sure, the seven-day moving average is still rising sharply.  But it’s not completely out of the question that (e.g.) growth in new cases has at least slowed.

 

As you may recall, about a week ago, the CDC announced that Omicron accounted for an estimated 73% of new U.S. COVID-19 cases, for the week ending 12/18/2021.  Continue reading Post #1370: CDC estimate of Omicron share revised sharply downward