Post #1184: COVID-19 trend to 7/23/2021: A ray of light.

 

This was no material change in the trend in new cases today.

New COVID-19 cases increased just over 60% in the past seven days.

Louisiana and Florida are virtually tied for the #1 spot, with 51.6 and 51.7 new COVID-19 cases / 100,000 population / day, respectively.

The U.S. as a whole now stands at 15.5 new cases / 100K / day.

Accordingly, I’m sticking with my prior predictions for this wave of COVID-19.  This is shaping up to be the worst ever in the U.S.  If current growth in new cases persists, Louisiana will hit its all-time record for daily new COVID-19 cases next week.  Florida will do so the week afterward.  If nothing changes, this is going to get ugly, soon.

Continue reading Post #1184: COVID-19 trend to 7/23/2021: A ray of light.

Post #1183: COVID-19 trend to 7/22/2021: Que sera sera.

 

Today’s case counts show no reduction in the rate of growth of new COVID-19 cases.

My estimate is that the U.S. is now at 14 cases / 100K /day, seven day moving average.

As of today, Louisiana has the highest rate in the nation with a seven-day moving average of 47 new cases /100K /day. Continue reading Post #1183: COVID-19 trend to 7/22/2021: Que sera sera.

Post #1181: COVID-19 trend to 7/20/2021

 

Today’s COVID-19 status update meets expectations.

  • New COVID-19 cases grew just under 50% over the last seven days.
  • Florida swooped into the #2 spot with 38 new cases per 100,000 per day, just a hair below the rate in Arkansas.
  • Unvaccinated people are the minority of the U.S. population but make up the vast majority of those requiring medical care and those dying from COVID-19.
  • New cases are up everywhere, and growth rates cluster tightly around that national rate.  When that happens — when there’s no dispersion across the states, and everybody’s headed in the same direction, at the same rate, that has been a signal that we can expect this to continue for some time yet.
  • CDC came out with updated estimates of the prevalence of the Delta variant.  It’s much higher than it was.  And still rising.  Who would have guessed?
  • Americans are still sleep-walking into this wave.  Maybe we’ve hit a bottom in terms of (e.g.) mask use, maybe not.  Not enough to matter, anyway.

I once said that this fifth wave couldn’t possibly be as bad as the third (winter) wave.  My reasoning was simple.  So many people were already immune, the virus would run out of bodies before it got that bad again.

Now, I’m not so sure.  This wave seems to be combining an extra-infectious virus with some extra-special willful stupidity.  Stupidity at a level that we really haven’t seen in the U.S. since the start of the pandemic.  And in the race between stupidity and vaccination, it seems to me that stupidity is winning. Continue reading Post #1181: COVID-19 trend to 7/20/2021

Post #1180: COVID-19 trend to 7/19/2021

The majority of states reported data for Monday 7/19/2021.  Based on the states that reported data (and an assumption of no change in states that did not), daily new COVID-19 cases rose 51% in the past seven days.

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 7/20/2021, 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.

Although today’s seven-day trend is lower than it was at the end of last week, by eye, there’s no inflection point in the curve yet.  I suspect that the seven-day trend number will continue to bounce around quite a bit, due to the choppiness of the data reporting.  As of today, Florida has not yet reported new data, and several other states appear to have reported token (implausibly low) case counts.  My best guess is that some further “catch up” reporting will occur over the next few days and that the seven-day trend number will move back up toward 70 percent or so.

To put this fifth U.S. COVID wave into perspective, below is the national daily-new-cases number for more-or-less the entire pandemic.  (I don’t have the start of the first wave shown because I don’t routinely tabulate the data back that far.)  This is a log-scale graph, so the slope of the line shows the percentage rate of growth.  I’ve sketched in red lines to highlight the growth rates for waves two to five, showing that this is the fastest rate of growth in new cases (steepest red line) so far in this pandemic.

That rapid growth in the U.S. average is occurring not only because cases in individual states are increasing rapidly, but also because this fifth (Delta, Indian variant) wave is hitting all the states at once.  Over the past two weeks, new cases counts have risen in literally all 50 states and the District of Columbia.  No state had stable or falling new case counts.  By contrast, prior waves were piecemeal affairs, starting with a few states and then sometimes spreading to a broader set of areas.  That fact that all the states are contributing ton an increase is one reason that the U.S. average is rising faster now than it has in prior waves.

In absolute terms, the U.S. number is still pretty low.  We have just 11 new cases per 100,000 per day.  But let me update my “simple projections” table, assuming that today’s seven-day rate of growth (51%/week) continues.

I can still say that if today’s rate of growth continues, in two weeks this wave will have been worse than all the prior ones except the third (wintertime) wave.


CDC is still MIA with CYA

In Post #1175, I did an entire song-and-dance about when the CDC should rationally reverse its May 13, 2021 change in guidance.  That’s the date on which CDC said that vaccinated people can go back to their pre-pandemic lifestyles.   No masks needed.

If that May 13, 2021 change in guidance was based on some objective measure of risk of infection, then the CDC should already have reversed that change.  By all but the most simple-minded estimates, the risk of COVID-19 infection is now higher than it was on May 13, 2021.

Today marks the date on which even the most simple-minded rule suggests that the CDC should reverse that May 13, 2021 guidance.  Today’s 11 new cases per 100,000 per day matches the new case rate on May 13, 2021.  Even if we ignore the fact that Delta is more contagious (so risk of infection per existing cases is higher than on May 13), and that cases are rising sharpy (so that, with reporting lags, the actual incidence of new infections in the community is far higher than on May 13, 2021) — even if we ignore that, and stick to the dumbest possible rule, we’ve now reached the point where risk of new infection now exceeds the May 13, 2021 level.

But here’s the bureaucratic angle on this.  The CDC’s recommendations on masking always have a caveat.  It’s a long sentence, the effect of which is, “unless your local government says otherwise”.  So the CDC can hide behind that and say, with a straight face, that nothing about their recommendation prevents states or localities from re-imposing mask mandates.  And, legally, they are quite correct.

Meanwhile, various states and localities look at the CDC recommendation and say that prevents them from imposing of enforcing mask mandates.  Most recently, when Los Angeles re-imposed a mask mandate, the local sheriff  refused to enforce it on the grounds that it was “not backed by science“.  Meaning, that the CDC did not recommend it.

So it’s a classic case of a difference between what they say, and what they hear.

What the CDC literally says is this:

Fully vaccinated people can resume activities without wearing a mask or physically distancing, except where required by federal, state, local, tribal, or territorial laws, rules, and regulations, including local business and workplace guidance.

What state and local governments hear, willfully or otherwise, is this:

Fully vaccinated people can resume activities without wearing a mask or physically distancing, except where required by federal, state, local, tribal, or territorial laws, rules, and regulations, including local business and workplace guidance.

And so the CDC has given itself sufficient CYA that it feels it may remain MIA on this issue.  Despite risk of infection being vastly higher now then when they made that change in guidance, they express no interest in reversing that change.

Why does this matter?  In my opinion, the only thing that influences COVID-19 hygiene is social pressure.  If everybody in your community is wearing a mask when in indoor public spaces, that gets the message across that masks are expected. 

And if that’s what it takes, then vaccinated individuals have to wear masks.  Partly for their own protection, but mostly because everybody has to wear masks if mask wearing is to be enforced.  And thanks to inertia at the CDC, states and localities must now (appear to) go against CDC guidance to do that.  They have to require everybody to wear masks, which the popular press immediately writes up as requiring vaccinated individuals to wear masks.  Which is, duly noted, against CDC guidance, kind of.  Except for the phrase in tiny type above.

FWIW, around here, this past week, everybody seems to have masked up again, even though there is no requirement.  At least, that’s my observation, based on not a whole lot of data.  But this is a high-income, high-education, high-achievement part of the country.  (Fairfax County, VA always makes the list of highest-income counties in the U.S.)

That’s just by way of saying that some people will figure out that we need to resume COVID-19 hygiene without the government telling them that.  But it’s not really something you can count on in most places.  Or with most people.

This is why the CDC needs to reverse its guidance, as cited above.  It needs to do that now, almost regardless of what the CDC thinks the science says about risk of harm to vaccinated individuals.  As a matter of public health policy, the only way to get masks on the unvaccinated population that is spreading this variant is to get masks on everybody.   And, despite any bureaucratic weasel-wording, the current CDC mask guidance is preventing that from happening.

Here’s the current disconnect, in one simple graph.  That’s mask use, via the Carnegie-Mellon Covid Delphi project.  Shown on the same page as the seven-day moving average of daily new COVID-19 cases.

Post #1179: COVID-19 trends, rounding out the week

 

I’ve tracked the trend in daily new COVID-19 cases every day for the past week.  Today I might as well finish out the data week, even though the story remains unchanged.  There won’t be any new information on the trend in new cases until next Tuesday, as most states don’t report that information over the weekend.

U.S. total daily new COVID-19 cases rose 68% over the past seven days.  Judging from how erratic the data reporting has gotten, I don’t think that’s materially different from the 75% increase for the seven days ending yesterday.

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 7/17/2021, 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.


John Q. Public remains oblivious.

The U.S. public doesn’t seem to be too worried about this.  At least, not enough to affect behavior.  We can turn to the Carnegie-Mellon CovidCast website, where they use a large-scale survey of Facebook uses to track some COVID-19 related measures.

Here’s a map showing mask use rates as of July 1, July 7, and July 15, 2021.  Darker = more, paler = less.  The map is almost uniformly paler, showing that use of masks continues to decline, even as this wave gathers steam..  Mask use hasn’t picked up even in the states significant outbreaks.  Let alone as a preventative measure in the states where new case rates are still low.

Source:  Carnegie-Mellon CovidCast website

Here’s a map of the fraction of people who went to a bar two Saturdays ago, and last Saturday. Bars are among the riskiest indoor locations, and typically were the first sites shut down and last sites re-opened during various lockdowns.  Darker is more.  Looks like bar business picked up a bit last week, compared to the week before.

Source:  Carnegie-Mellon CovidCast website


Driving factors

At this point, this is obviously attributable mostly to the rise of the Delta variant.  The greater infectiousness of that variant has to be the main reason behind the unprecedentedly rapid increase in cases.

In addition, I think seasonality is playing some role.  Last year, at this time, we managed to have outbreaks in several hot-climate states, at a time when Delta didn’t even exist.  That summer 2021 outbreak was attributed to more time spent in dry, indoor air-conditioned spaces.

What I think I’m seeing, as I look at the data, is that the combination of high Delta prevalence in a hot-climate state leads to a particularly high rate of growth.  Using the most recent update from CDC on incidence of Delta (this table, accessed 7/17/2021), I can compare the top eight states from last year’s outbreak (first chart below) to the top eight states in terms of the CDC’s estimate of prevalence of Delta as of about a month ago (second chart below).

If anything, I’d say the first chart (hot climate) looks at least as bad as the second one (high Delta).  But maybe I’m just seeing what I want to see.  And at this point, if I picked any random set of eight states it might look just like that.

Finally, conventional wisdom says that the worst Delta outbreaks have been occurring in areas with low vaccination rates.  That would certainly make sense, as this is almost entirely a wave of infections among the un-vaccinated.  Here’s a contrast of the states with highest and lowest vaccination rates.

While the absolute level of cases is far lower in the high-vaccination states, it’s not clear by eye that the rate of growth (slopes of the lines) in this last week has been any lower.  Best guess, even in the states with high vaccination rates, this more-infectious variant has no problem in spreading among the un-vaccinated.

Restated, while this wave is definitely due to the un-vaccinated, it’s infectious enough that there is no shortage of targets, even in states with high vaccination rates.


On a more personal note

Post #1163 is rescinded.  My wife and I talked it over.  Even though the measured new-case rate here is quite low, and we’re vaccinated, working out in a gym, un-masked, doesn’t seem prudent right now.

As of June 23, my best guess is that one trip to the gym in every 7.5 years would pose a significant risk of infection.  But now, if I just take current Virginia prevalence and account for data lags, keeping growth at the current level, the estimate is down to a little under once a year.  Or to put that differently, if we keep going to the gym, under current conditions, sometime this year, we’d expect to get a good, solid dose of the virus.

More to the point, if conditions persist, that mean-time-to-infection-event interval shrinks.  Two weeks from now, if the growth of new cases continues at the current pace, that will be down to one significant exposure event every four months.   Seems like it’s better to quit while we’re ahead.

A final factor is that his rec center is the site of several County-run day camps.  As a result, the facility has a lot of little kids running around in it.  Those kids are by definition un-vaccinated. The risk of exposure from them isn’t really quantifiable, but given the number of kids in the building, it’s probably non-negligible.

So we’re back to walking around the block and calling that exercise.  For now, at least.

Post #1178: Does the Delta variant have a lower hospitalization rate?

The simple answer is no, it doesn’t.  At least, not as far as I can tell from any consistent and available data source.  Not yet, anyway.  The U.S. COVID-19 hospitalization case rate is not materially different from what it was months ago.  And anybody who makes that claim is probably just making it up.

What about mortality rate?  Again, no.  Not from the data that are available so far.  And for that one, anybody who makes that claim is either making it up, or doesn’t know enough to account for the average lag between diagnosis and death for COVID-19 (discussed below).

For this work, I was getting all geared up to do a sophisticated age-adjusted analysis to account for change in the COVID-infected population over time.  In theory, the average COVID-19 infected individual is younger than was true ase historically.  And because both hospitalization and death are strongly concentrated among the elderly, I expected to see those rates fall.  I was expecting to have to do an age-adjusted set of rates to get an apples-to-apples comparison on the virulence of Delta versus prior variants.

To be clear, there hasn’t been much change in how COVID-19 is treated, over the past few months.  Pretty much everything used to treat COVID-19 has been known and available for a year now.  Based on the state of the medical care, you’d expect to see no change in hospitalization or death case rates.  That is, the fraction of diagnosed who are hospitalized or die.  The only material change in health care has been the vaccines, and overwhelmingly the impact of those has been to prevent infections, and only secondarily to reduce severity of illness when infected in a “breakthrough” infection.)

But in fact, nothing about the crude (un-adjusted) hospitalization and death rates has changed.  Yet.  If you look at the end points of either curve, they are well within the “normal variation” that has occurred over time.  Neither the hospitalization case rate nor the mortality case rate is materially different now from what it has been over the past nine months or so. 

I now believe that’s because much of the age shift in new cases occurred before the onset of the Delta variant.  This is now a young person’s pandemic, mostly.  But it’s been that way for a long time now.  And, for sure, there hasn’t been some huge shift in age mix in the past two or three weeks, which is pretty much the extent of the Delta wave so far.  I just can’t lay my hands on a national data file that will allow me to show that.

As I discuss below, this is all about the data.  I’ve used three internally-consistent data sources, from Federal agencies, to do this calculation.  If there’s anything wrong with what I’ve done (and I don’t think there is), it’s consistently wrong for the entire time period.  Based on the Federal data sources cited below,  it’s still true that about 1.5% of people diagnosed with a COVID-19 infection die from it, and about 10% of people diagnosed with a COVID-19 infection are hospitalized for it.


But wait, if this is still as deadly as before, and causes as much hospitalization as before, why haven’t we been hearing about that lately?

Total case counts have been low.  It doesn’t make the news because there aren’t bodies piling up in morgues, and there aren’t hospitals turning away patients.

But that’s NOT because the disease has gotten less virulent.  Or medicine has gotten better at treating it.  That’s just because the total count of cases was down.

Now step back and ponder that in light of the current growth rate of new cases.  In the last two weeks, the situation really has changed, and I don’t think that’s quite sunk in yet.

We’ve got a disease that still kills 1.5% of the people diagnosed with it, and new cases are growing 75% per week

What in the world is our public health bureaucracy waiting for?  We ought to be hearing alarm bells ringing.


Citation as to source of data and methods

This is one of those questions that is all about the data, and the dates.  Where do the counts come from, how do they count them, and what date are they using to track the information?

Getting a count of newly-diagnosed cases is easy enough, from any of several different sources.  I took mine from the CDC COVID data tracker, show cases as reported to the CDC, by the data when reported to the CDC.  Following the current standard, this is (for almost all states) going to be the sum of positive PCR tests and positive antigen tests, even though the positive antigen test cases are categories as “suspected” COVID.  https://covid.cdc.gov/covid-data-tracker/#trends_dailytrendscases

Getting a count of deaths is likewise fairly straightforward.  Same CDC data source.  These are deaths as reported to the CDC, on the date reported.  Exactly what is included in the death counts is a bit murkier, and you’d need to read the extensive footnotes to the table to be completely clear about what you’re getting.  I’m not giving a URL for this because it’s the same as the one above, just reset to show deaths, not cases.

BUT:  On average, for those who die from COVID-19, it takes about two weeks for them to die, and to have that death reported, following the reporting of the diagnosis.  You can see that by overlaying the deaths and cases data, and see that the peak of deaths follows the peak of cases by about two weeks.  Given that, if the data are shown by date of report, you should divide today’s deaths by the count of cases reported two weeks ago.  Which is what I did in the graph above.

If you don’t do that — if you simply divide today’s deaths by today’s cases — you’ll get an erroneous drop in the death rate whenever there’s a sharp uptick in cases.  That’s because the deaths associated with the newest set of cases haven’t occurred yet.  They’ll occur a couple of weeks down the road, on average.

Finally, it’s hard to get any consistent data on hospitalizations.  Almost all of that information comes out of private-sector state hospital associations.  For whatever reason, it’s hard to get any consistent set of data across all the states.  And when anyone presents that data, they tend to present it as a graph, with no access to the underlying data.   For example, CDC does that — you can get a nice graph of daily hospitalizations, but not a data file.

For hospitalizations, I finally settled on a Federal government dataset, apparently controlled by DHHS, based on individual hospital reporting of new cases.  My guess is that this bypasses the state hospital associations, but with the risk of having incomplete reporting.  Once you get to September 2020, the file shows close to 6000 hospitals reporting on a daily basis.  As I recall, that accounts for more-or-less the entire universe of short-term general non-federal hospitals in the U.S.  That’s why the graph above starts in September 2020.  That file also stops on 7/10/2021.  The data source is:  https://healthdata.gov/Hospital/COVID-19-Reported-Patient-Impact-and-Hospital-Capa/g62h-syeh

Unlike deaths, hospitalizations are shown by date of admission, and so should be very nearly contemporaneous with the count of new cases.  Also, it appears that the suspected and confirmed case counts are a double count, so I have used sum of confirmed adult and pediatric cases from that file.

Finally, I should emphasize that the “case rate” uses the number of diagnosed cases as the denominator.  You’ll see people trying to make the comparison to common flu all the time and mess this up, either intentionally or accidentally, by using some estimate of total infections instead of people actually diagnosed with the disease.  If you are going to compare to flu, you you have to compare case rates to case rates.

Post #1177: COVID-19 trend to 7/15/2021: Tempus Fugit.

 

It looks like the data reporting has finally settled down enough to give a solid fix on the current rate of growth of daily new COVID-19 cases.  With just three small states not reporting on 7/15/2021, the one-week increase in new COVID-19 cases for the U.S. was 75%.

I should probably explain, briefly, why I’m so concerned by the growth rate.  Why I making such a big deal about the fact that we’ve never had new case growth as rapid as this before?

I’m not trying to fear-monger here.  I’m just explaining why this unprecedented rate of increase has caught my eye.  Unless you are in the habit of playing around with compound growth rates/exponential growth, it might not be clear to you how compressed the timeframes can become when the rate of growth is high.

Here’s a comparison between the peak rate of daily new cases for the first four U.S waves of COVID-19, and a simple projection of the current wave assuming this growth rate keeps up:

Fully realizing that all health care is local — so maybe the U.S. average isn’t really the best number to focus on — my point is that, for the U.S. as a whole, if this growth keeps up for two weeks, we’ll have exceeded the daily new case rate of every wave of COVID-19 except for the third (winter) wave.

In other words, at the current rate of increase, we have less than two weeks until this becomes the second-worst wave of COVID-19 in the U.S. ever, in terms of daily new cases.

Now recall that the rate of increase for the next two weeks is already locked in.  Nothing we do now will affect it.  Why?  Because of the lags that I have discussed several times on this blog.  The people that will be showing up in the statistics 16 days from now were, on average, infected today.

So, for the next two weeks, all we can do is wait and see what happens.  Any actions we take today will affect the rate of growth after that.

And it’s not as if many people are taking action anyway.  It doesn’t look like many governors are bothering to do anything about this.  Nor have I seen any change in guidance from the U.S. CDC.

After a year and a half of this, is our strategy really to hope that it goes away on its own?  My recollection is that that didn’t work out so well the first time we tried it.  If not, what is our public health bureaucracy waiting for?

And just to finish this off, if this rate of growth keeps up for more than three weeks, this will end up being the worst wave of COVID-19 ever, in the U.S., in terms of daily new cases.

There is one large mitigating factor, which is that the most medically vulnerable populations have high rates of vaccination.  So each new case in this wave does not represent the same type of morbidity and mortality burden that each new case did during the third wave.  Even if we reach new-case rates in excess of what we saw in the third wave, that does not necessarily imply that hospitals across the U.S. will be overflowing.  But it doesn’t imply that they won’t, either.

Post #1176: COVID-19 trend to 7-14-2021

 

The sporadic nature of most states’ data reporting is adding some variation to the estimate of the trend.  The estimated increase in new cases for the past seven days is only 74% today, not the 92% that came out of yesterday’s calculation.

That said, there have been exactly two instances in this pandemic when the seven-day growth in U.S. new COVID-19 cases exceeded 74%.  Those were the seven-day periods ending yesterday, and the day before yesterday.

Just to say it plainly, for the U.S. as a whole, this rate of growth in new cases is unlike anything we’ve seen so far in the pandemic.

Continue reading Post #1176: COVID-19 trend to 7-14-2021

Post #1175: COVID-19 trend to 7-13-2021

 

New COVID-19 cases are up 92% compared to one week ago.  That increase was so hard to believe that I took the raw data and calculated the rates for a few states by hand.  Just to double-check.

What put it over the top, compared to yesterday, is that Florida finally reported fresh data, coming in with a seven-day moving average of over 27 new cases / 100,000 / day.  That’s higher than Missouri, which was, at one time, the epicenter of the U.S. fifth wave.

It really says something, I think, that we’re still setting new records more than a year into the pandemic.  I checked the data all the way back to April 2020.  That 92% increase is the largest one-week percentage change in new U.S. cases since the start of the pandemic.

And yet, we are still sleepwalking into this U.S. fifth wave of COVID-19.

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 7/14/2021, 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.

Continue reading Post #1175: COVID-19 trend to 7-13-2021