Category: COVID through 2022

All my various postings tracking the COVID-19 pandemic through the end of 2022.

Post #1508: COVID, now 25/100K

 

Now 25 new cases per 100K population per day, up 30% in the past week.  A week ago, it was 19.

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 5/10/2022, 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

 

I was going to attribute the increased growth rate to Pennsylvania, a large state that did some catch-up reporting yesterday.  But the graph says otherwise.  Things ticked up pretty much across the country.

I don’t want to make too much of a one-day increase, but this is interesting in that it seems to be nation-wide, or nearly.  And yet, it’s bad science to make up plausible explanations for it after-the-fact, if it turns out to signal an inflection point on the curve.  So maybe it’s better to speculate on possible causes ahead of time.

Given the lags involved (between infection, symptoms, care-seeking, testing, lab turnaround, reporting, and then a seven-day moving average), today’s reported uptick, if real and not just a data-reporting issue, is a consequence of an increase in infection events that occurred around the very end of April.

As far as I can tell, that correlates with absolutely nothing.  It’s too late for Spring Break and associated religious holidays, for 2022.

The only rational explanation is that we somehow angered Hygeia on or about 4/30/2022.  (Or one of the myriad health deities.  Seems to be a fair bit of competition for the god/goddess of health gig.)

In short, there appears to be no rhyme or reason to this particular uptick.  At least none that I can see.  Perhaps it’ll disappear tomorrow.

That said, a comparison against the last two years shows what an impious lot we have become.  A year ago, an upturn like this would have evoked at lot of prayerful pleas, I think.  Now, we’re like, don’t cancel the barbecue on account of a little thing like that.

Post #1507: COVID, now 23/100K. I reject your reality and substitute my own.

 

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 5/11/2022, 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

In related non-news, mask use is at a pandemic all-time low.   In the past, there was an average one-month lag between changes in the new case rate, and changes in mask use.  But mask use has always been driven primarily by peer pressure.  So I’m betting that mask use does not recover until this winter’s wave.  Not because that makes any sense, but because we don’t associate nice spring weather with spread of disease, but we do associate winter weather with colds and flu.  Masking up only for the winter wave is not rational, but to most it will feel more normal.  And so, I’m betting that’s what we do.

Source:  Carnegie-Mellon COVIDcast.

Hospitalizations are up, some.  The CDC COVID data tracker website currently shows 2500 admissions per day.  Doesn’t sound like much, except that at an average cost of around $25K per admission, that represents about $60M/day (or $22B per year) in additional health care spending.  Because the U.S. doesn’t spend enough on health care already.

Deaths are still not up.  I attribute that to the waning of immunity of the vaccinated population, and the resulting shift in infections such that a greater fraction of those with any infection are vaccinated.

How safe are you if you have gotten a booster?

Caveat:  In terms of timely data on vaccine effectiveness, out of CDC, all we have is observational data.  That is, all they can do is observe the rates of infection, hospitalization, and death among the populations that chose to get a booster or not.  The resulting “real-world” or “bottom-line” numbers will reflect not only the effectiveness of vaccine booster, but also the characteristics and behavior of those who chose to get the vaccine or not.

It’s all we have to go by, for better or worse.

That said, as of February, the CDC showed that risk of dying from COVID-19, for the vaccinated and boostered was about 5% of that for the un-vaccinated.  (Shown as “20X” on the graph below):

The same chart shows that, by February 2022, boosters didn’t appear to do much to stop any infection.  (Hence the mere 2.0X for the risk of testing positive.)

The only national information from CDC that’s more timely than that is for risk of hospitalization.  Here, I’m focused on those who got a booster shot, so I am only looking at the 65+ population (because, as I recall, they were the only ones who had carte blanche to get a booster in the U.S.  For all others, the only eligible populations were high-risk population).

Here’s how that looks. As of February/March 2022, the risk of hospitalization for the boostered, relative to the unvaccinated, is around 10%.  So the booster remains roughly 90% effective against hospitalization from COVID-19.  (Among the elderly, at least.)

Source:  Calculated from CDC COVID data tracker, accessed 5/11/2022.

The level shown above for boostered people —  in February, they were about 10% as likely to be hospitalized for COVID-19 as the un-vaccinated — is a pretty good match to the CDC mortality estimate (that they were only about 5% as likely to die from COVID-19).  The result is a consistent story about booster effectiveness.  After a few months, the booster does almost nothing to prevent a mild case of COVID-19 (50% reduction, relative to unvaccinated).  It does a pretty good job of preventing a case severe enough to require hospitalization (90% reduction, relative to unvaccinated).  And it does a slightly better job of preventing a case so severe it kills you (95% reduction, relative to unvaccinated).

But, as the data clearly seem to show, immunity wanes over time.  In this case, for the boostered population, effectiveness at preventing hospitalization appears to wane at about 2.5 percentage points per month.  (The start date of the curve corresponds to the peak week of booster shot delivery, so despite the fact that it took a couple of months to deliver all the booster shots, that’s still a pretty good estimate for the speed at which immunity wanes for any one boostered individual).

The upshot is that, as of now, regarding getting a case of COVID severe enough to land you in the hospital:

  • Vaccination reduces your risk by about 75%
  • Vaccine and a well-aged booster reduces your risk by about 90%
  • Vaccination and a fresh (second) booster arguably reduces your risk by about 97%.

Make up something that’s wrong, pretend that it’s true, then complain when reality fails to match your imagination.

As far as I can tell, this is just standard operating procedure for some classes of individuals.  If you don’t have any solid argument grounded in reality, just make something up, and use that as if it were true.  So that you can complain about something.

I first noticed this when reading newspaper article comments about climate change.  My favorite crazy comment being that this topic used to be called “global warming”, then the United Nations IPCC had to rename it “climate change”, because the earth isn’t warming.  Not realizing that the IPCC has been around for four decades.   And that the CC in IPCC doesn’t stand for carbon copy.

But what I really marvel at is the constancy and pervasiveness of this tactic.  For the decades that I have been tracking reporting on climate change, as the earth’s mean surface temperature has continued to rise, completely in line with predictions made three decades ago, I still get to read that “scientists said such-and-such, and that never happened, so climate change is nonsense”. Where the “such-and-such” is inevitably something completely fictional. 

So the world divides into two types of people.  For people like me, when the preponderance of evidence suggests that something is true, I am forced to accept it as true, whatever my preconceptions.  But, unfortunately, a whole lot of people live by Adam Savage’s dictum:  I reject your reality and substitute my own.  Because, for a lot of people, it’s just easier to make up “facts” than to change their minds.

If you read comments on news articles regarding a second COVID booster, the stupider portion of the American public seems dumbfounded that boosters are required to keep up immunity.

Apparently much of right-wing American has forgotten getting a tetanus booster as a kid, or getting a flu shot each year.  Or they’ve never had kids, and so don’t realize that most vaccines against childhood diseases are given in multiple doses.

In fact, if you just glance at the CDC’s schedule of recommended vaccines for children, you’d be hard-pressed to find any vaccine that only requires one dose.  Even among these highly-effective vaccines against the formerly-deadly diseases of childhood.

Source:  Adapted from CDC.

If you think that all vaccines should only require one shot, should last a lifetime, and be 100% effective, the problem isn’t with the COVID-19 vaccine, it’s with your understanding of vaccines in general.  Few fit that model. Most don’t.

In any case, it is what it is.  You want the additional immunity, you get another shot.  That’s the deal.  If you are surprised by that, then the fault is in your understanding of reality, not in reality itself.

Although, to be clear, I wish reality were different in this case.  But it’s not.  So I deal with it.

To me, the sole question is whether the benefit is worth the cost and risk.  Most of the harm reduction you are ever going to get from COVID-19 vaccination, you already got from being fully vaccinated.  Boosters are gravy.

But in my case, the vaccine is free and harmless.  I get a sore shoulder for a day or so, that’s all the adverse reaction I’ve every had.

I got my second booster yesterday, as did my wife.  It seemed like the rational thing to do.

Two weeks from now, we’re going to be in a lot of crowds at our daughter’s college graduation.  I want to spend the least amount of time possible thinking about COVID-19.  Hence, second booster now, rather than waiting for the likely winter 2022-23 winter wave of COVID.

Post #1506: COVID-19 at William and Mary, no better, no worse.

 

Source:  Calculated from William and Mary COVID-19 dashboard, accessed 5/9/2022

William and Mary updated their COVID-19 dashboard last night.  The most recent new infection rate in the student body is about 100 per 100K population per day.  Roughly speaking, the uptick that started a few weeks back is not getting any worse.  But neither has it disappeared.

I looked at last weeks numbers and didn’t get a booster shot.  I figured I’d wait to see if this weeks numbers resulted in any greater clarity.  No such luck.

So now, push comes to shove on the question of getting a vaccine booster before attending graduation ceremonies, because those are now less than two weeks away.  We’re about at the time limit, as it takes some time for antibodies to build after a booster shot.

To boost or not to boost?

Time for some guesswork calculation.

First, I want to guess the likelihood that I’m going to be in the same room as somebody who is infectious with COVID-19.  At that stage, that’s not the odds of getting infected.  (Being in the same room does not guarantee infection).  It’s just a way to start getting a handle on the riskiness of the situation.

For that, I need two figures:  How many people are involved, and what fraction of them are likely to have an active COVID-19 infection?

I expect to attend three small indoor graduation ceremonies, with an average of maybe 100 student and 200 family members each.  Call that a total cumulative crowd of 900 people with whom I’m be sharing an indoor space. 

Currently, Virginia is averaging 27 new cases per 100K population per day.  If we stick to our current trend, that’ll be around 50, two weeks from now.  Taking the weighted average of that (for the family members) and 100 new cases per 100K (for the students in attendance), I come up with an expected average of 67 known new cases per 100K population per day.

You have to multiply the new-case rate that by two factors — one to account for cases that are not officially reported, and one to account for the number of days an infected person typically remains in circulation and capable of infecting others.  At various times, I’ve guessed estimates for both of those.

At the low end, I’d multiply the current new-case rate by six.  That’s a factor of two, to account for cases not counted in the official statistics, and an average of three days walking around in an infectious state (combining both symptomatic cases and asymptomatic cases).  But I could easily see a factor of nine, if you figure there are three true cases, now, for every one that gets officially diagnosed and reported.

So, take either a nine-fold rule or a six-fold rule as a reasonable way to estimate the number of actively infectious individuals in a crowd, based on the current official daily new case rate figures.

Now I do a lookup on a chart I worked up a few months ago.  Once you accept either a nine-fold or six-fold multiplier above, the rest is just math.  So the chart itself is nothing but a bunch of arithmetic, tabulated.

Without belaboring the assumptions behind the “N-fold rule”, I think it’s a foregone conclusion that I’m going to end up in the same room as somebody who has an active COVID-19 infection. 

I don’t think that’s a surprise, given that this boils down to hanging out in a crowd of about 1000 people in the middle of a modest new wave of COVID-19 cases.

How may people would I expect?  Maybe four or five actively infectious individuals, total, in the crowds I’ll be part of two weeks from now.  Same assumptions, just slightly different math.

Now comes the less-quantifiable part.  What are the odds of being infected, given that?  Let’s say there’s a roughly 0.5 percent chance (4.5 persons out of 900) that any one seat in that room is occupied by an infected individual.  And, in total, I expect to spend about three hours in situations of that type.

Literally the only quantitative analysis I have to go on is a study of Chinese train passengers from early in the pandemic.  This has the multiple disadvantages of being a) train service, and b) the original Wuhan version of COVID, for which the R-nought (basic infectiousness) is at least five times lower than the current strains (BA.2 and BA.2.112.1).

Whatever.  This is the best I’ve got.  This is a study of known infected individuals who took a train trip, and the subsequent infection rates of the people seated around them.  I infer from the writeup that these passengers were not wearing masks.  I’m just going to fuzzy-up the details, and state the following.

On average, for a relatively short exposure, risk in that study was only observed for persons sitting within two rows and two columns of the infected individual.  That means 5 x 5 = 25 seats, less the two occupied by myself and my wife, or 23 strangers sitting within range of me, at each of three one-hour ceremonies.  If, by contrast, W&M leaves every-other-seat empty, then that would mean sitting next to roughly 13 strangers.

Looking at Figure 4 from that study, at the one-hour mark, averaged across all nearby sites, the risk of infection was 0.14 percent per hour, for all those seats.   And, luckily for me, that’s by far highest from the person sitting next to you, on the same row, which will be my wife.

But that was for the Wuhan strain.  There’s no direct way to translate it, but the R-noughts of the current strains are at least five times greater than that.  So, as a rough cut, let me multiply that baseline infection (attack) rate by five, to yield 0.7 percent per hour risk of infection, accounting for the far greater infectiousness of BA.2 and BA.2.12.1 relative to strain B.

Worst case:  When I grind through the numbers, I estimate that if we weren’t vaccinated, and if we didn’t wear masks (the conditions for the Wuhan train study), and W&M does not leave every-other-seat empty, we’d have about a 1-in-400 chance of contracting COVID-19, sometime in the course of three one-hour sessions, given the current new case rates in Virginia and within the W&M student body.

Obviously, that’s a rough cut, but some estimate is better than no estimate.

Now you have to factor in the effects of wearing a properly-fitted N95 mask, and of vaccination and booster.  But you also have to figure that every meal we eat, over that time period, is going to be in a packed restaurant.  And indoor dining is well-established as a relatively high-risk situation for COVID-19 transmission.  If I had to guess, on net, I’d guess that our net risk of all that is at least four-fold smaller than the one-in-400 cited above, due mostly to mask use.  (Per prior post, impact of vaccination on probability of getting any infection is now quite small, due to decline in circulating antibodies over time).

Finally, if we only get one booster, we have to figure out whether or not this is the most risky thing we’re likely to do in the next half-year or so.  If so, might as well use up our one allotted additional booster shot now.  Or, conversely, figure out whether they’ll allow yet a third booster shot this fall, as we get the expected winter wave of flu-and-COVID.

Conclusion

When I put all that in the blender and give it a whirl, the upshot is that my wife and I have made appointments to get our second booster shot this afternoon.  Obviously, YMMV.  We’re in our 60’s and overweight.

Despite the thin veneer of rationality above, really, I think the deciding factor is probably nowhere near as quantitative as the discussion would suggest.  In the end, the less I have to worry about @#$(!@ing COVID-19, the more I can enjoy watching my daughter graduate from college.  And for me, that’s well worth getting my last allotted booster shot before we attend those ceremonies.

Post #1505: COVID-19 trend to 5/9/2021, now 22 cases per 100K

 

Now 22 new cases per 100K population per day, rounded to the nearest digit, up 22% in the past week.  The latest strain — BA.2.12.2 — still is not yet the dominant strain in the U.S.  Deaths still are not rising.

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 5/10/2022, 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

Source:  CDC COVID data tracker.

Since the start of this latest COVID-19 wave (the BA.2.12.2 wave), cases are up 150 percent, hospitalizations are up 50%, and deaths are down 50%.  The calculated average length of stay (per COVID-19 case) is well under 5.5 days now.

Source:  Calculated from CDC COVID data tracker.

A common mis-interpretation of the data

You might start thinking that this latest version (BA.2.12.2) is “weaker” than Omicron (BA.2) itself.  You can see numerous popular press articles that naively look at the raw numbers and say exactly that.

I think that’s incorrect.

Sure, average cases severity appears to be declining.  But I don’t think that has anything to do with changes in COVID-19.

Instead, I think this is a consequence of the increasing share of cases occurring among the vaccinated.  At this point — well after the last wave of booster shorts — vaccine and booster do little to prevent an individual from having any COVID-19 infection.  But they still work quite well to prevent severe infections. Here’s a CDC graphic I’ve shown before:

Source:  CDC COVID data tracker.

As a consequence of that loss of immunity against any infection, the vaccinated and boostered will now make up a larger share of all new cases.  So a larger fraction of the infected population has vaccination-acquired resistance to severe infection.  And so, per observed case, severity is declining.

That doesn’t mean “the virus is getting weaker”.  It just means that vaccination is now working mostly to reduce severity, not to prevent illness.  And by drawing an increasing share of the vaccinated into the overall pool of reported infections, the average observed severity of illness is falling.

Unfortunately, the CDC’s data split by vaccination status is ancient.  The most recent observation is from the end of February.  At that point, for sure, the case mortality rate for Omicron, for the unvaccinated, was two percent.  That is, as of the end of February, Omicron was still killing one-in-fifty of unvaccinated individuals with a reported infection.

The only point I want to make from the chart above is that even a modest shift in the mix of vaccinated and unvaccinated among new infections could account for a declining case mortality rate.  (And, for that matter, a reduced hospitalization rate).

 

Post #1501: COVID-19 trend to 5/3/2022

 

Now 18.5 new cases per 100K population, up 26 percent in the last 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 5/4/2022, 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 CDC updated it’s estimates of incidence of COVID-19 variants yesterday.  The most recent reading is that the latest one — BA.2.12.1 — accounted for around 37% of new cases, as of the week ending 4/30/2022.  That’s up from about 26% last week, so that fraction is now growing at slightly less than 50% per week.

Source:  CDC COVID data tracker, accessed 5/4/2022

That’s far slower than the rate at which Omicron took over from Delta.  That’s probably due to a) more immunity in the population, following the Omicron wave, and b) only modestly higher infectiousness of BA.2.12.1 compared to Omicron (BA.2).

That said, as these new-case rates rise week after week, eventually states are returning to levels that we had hoped we’d left behind us.  As of today, rounding the estimates up just a bit (because the trend is up, and there’s no indication that will change any time soon),

  • Vermont is pushing 60 new cases / 100K.
  • Rhode Island, Maine are at or above 50 / 100K.
  • New York, Massachusetts, and Washington are around 40 / 100K.

That said, hospitalizations continue to rise less rapidly than new cases, with hospital admissions for (with) COVID up just 15% in the past seven days.  Deaths have not yet started to rise.

Post #1499: W&M COVID uptick continues

 

 

Source:  Calculated from W&M COVID-19 dashboard, accessed 5/2/2022.

The most recent count of new cases from W&M works out to just under 140 new COVID-19 cases per 100K population per day.   There has been no corresponding uptick in cases in the Virginia 18-24 population as a whole.

We’re now about two weeks away from graduation.  It will be interesting to see how the current outbreak evolves.  Even if this isn’t particularly dangerous for the young, you’re about to have the campus flooded with crowds of their parents, some of whom are likely to be in higher-risk categories.  In that context, this is an unfortunate turn of events.

Booster or not?

Separately, I’ve been strategizing over when to get my second booster.  I’m thinking, in light of this, maybe now wouldn’t be too bad a time.  It’s tough to say, particularly given that a lot of the W&M graduation events will be held outdoors, where risks of disease spread are inherently low.

The first issue with a booster shot is that you only get one.  As of today, there’s no approved third booster shot. Best not to waste it.

The second issue is that protection against any infection is short-lived (but protection against severe infection remains quite long-lived).  You get maybe a couple of months of enhanced antibody levels that will reduce your likelihood of any infection.  Then those return to baseline.  That’s why the CDC currently shows that those with booster shots are about half as likely to have some COVID-19 infection, but only about 5% as likely to die from COVID, compared to the unvaccinated.

Source:  CDC COVID data tracker, accessed 5/2/2022.

Given the low risk of transmission in the community, I’ve been saving mine.  I figure it would be smarter to get one this fall, in anticipation of a likely winter flu-and-COVID season.

Now I’m looking at two days of various graduation ceremonies at William and Mary, hanging out with a maskless crowd of students who are in the middle of a COVID-19 outbreak.

Hmm. Vax up now, or save it for the winter?  The booster is free, harmless, and helpful, of course I’m going to get it.  It’s just a matter of when.

Well, whatever I do, I’d better to it soon.  It takes a couple of weeks for antibody levels to rise after those vaccine shots.