Post #1084: William and Mary brief COVID-19 update

I’ve added another day’s worth of testing information to my prior table.

The surprise here is that they added fewer than 200 new test results yesterday.  They still don’t have tests back from what appears to be about one-sixth of the students.

It’s not clear to me what that means.

On the one hand, they might just be waiting for the lab performing the tests to return results.

On the other hand, maybe a lot of students aren’t cooperating with the testing.  I looked on the William and Mary website and all I could find is the phrase “testing is required”.  I can’t see anything about (e.g.) penalties for non-compliance.

On yet a third hand, maybe the total count of students ever tested (on the W&M COVID-19 dashboard) is significantly larger than the count of persons required to be tested.  That seems unlikely, as W&M appears to make few exceptions to its testing requirement.   The make “limited exceptions for students enrolled in certain graduate programs“.  But there’s no public information on the number of such students exempt from the testing requirement.  They also exempt persons who have tested positive, for 90 days following a positive tess, due to the likelihood of a false positive test during that period.

So it’s not crystal clear, but it certainly looks like test results are still pending for more than 1000 students.

Post #1083: COVID-19 trend, fourth U.S. wave

I’ve rebased all the numbers to use 3/23/2021 as the starting point.  By eye, that’s the start of the U.S. fourth wave of COVID-19.  If we take that as the starting point, then daily new COVID-19 cases are up 20% so far, and are rising at the rate of about 24 percent per week.

Trying to look on the bright side, it gets boring having to blog about good news.  Bad news, by contrast, pretty much writes itself.

Here are the national tables, followed by the six regional tables. Continue reading Post #1083: COVID-19 trend, fourth U.S. wave

Post #1082: William and Mary update, still waiting for the other shoe to drop

Yesterday’s update of the William and Mary COVID-19 dashboard produced a few surprises.  To cut to the chase:

  • They still need to report test results for about 1300 more students.  So what’s up on the dashboard now is not the final total.
  • On Monday, they added the results of a few hundred tests with a very high positivity rate.  That suggests to me that this last batch was probably tests for students who were identified via contact tracing, or who came forward for testing because they had symptoms.
  • At present, it looks like about 2 percent of W&M students were infected with COVID during this outbreak.  That will probably fall somewhat as the last 1300 “mass testing” results are reported.

The bottom line is that this is a larger outbreak than I would have guessed, based on the data report as of last Friday.  That doesn’t mean it’s getting worse.  It just means that I under-estimated it, based on public information as of last Friday.

Details follow. Continue reading Post #1082: William and Mary update, still waiting for the other shoe to drop

Post #1081: Vaccines and diminishing marginal returns.

If you’ve been following current events, you probably saw that the CDC  now estimates that a single shot of the Pfizer or Moderna vaccines reduces your chance of getting COVID-19 by 80 percent.  That’s per this research.

Most of you probably through, hey, that’s great.

By contrast, I thought, if the CDC believes its own research, it should immediately ask the states to cease giving second shots.  Because, if this most recent research is true, it makes a compelling case for doing as they are doing in Great Britain, and getting one vaccine shot into as many people as possible, rather than providing complete (two-shot) vaccinations to anyone.

And the reason here is obvious:  It’s a case of diminishing marginal returns.  Based on this most recent study, the first shot gives you 80 percent effectiveness.  And the second shot adds a mere 10 percent more effectiveness.  Obviously, you get more bang for the buck by providing more people with just one shot, rather than fewer people with two shots. Continue reading Post #1081: Vaccines and diminishing marginal returns.

Post #1080: COVID-19 trends; vaccination, self-selection, and herd immunity

 

In terms of the trend in new COVID-19 cases, today is much the same as yesterday.  Looks like we’ve entered the U.S. fourth wave of COVID.  U.S. new case counts are now back to 25% of the U.S. third wave peak.  And now it looks like things are starting to accelerate.

 

Source:  Calculated from: The New York Times. (2021). Coronavirus (Covid-19) Data in the United States. Retrieved 3/29/2021 , from https://github.com/nytimes/covid-19-data.  The NY Times U.S. tracking page is located at https://www.nytimes.com/interactive/2020/us/coronavirus-us-cases.html.

Trends have turned upward in New York (really, all of the Northeast) and Florida.  Michigan is set to become the state with the highest rate of reported new infections.

I don’t think it’s worth creating the six regional graphs as they look pretty much as they did when I posted them yesterday.


Vaccination and self-selection, or why vaccination matters less than the simple count of persons would indicate.

Vaccination continues apace.  In the last two days, the U.S. delivered COVID-19 vaccine at the rate of 3.4 million doses per day.  And the fraction of the elderly who have been vaccinated continues to grow (below, more than 0.6 percentage points per day increase, over the last two days.)

Source:  U.S. CDC

But.

Back in February, I outlined the two reasons why vaccination didn’t much matter, at that time, for stopping the pandemic (Post #1035).  That was for two separate reasons.

First, the classes of individuals being vaccinated first were not, by and large, the individuals who were spreading the disease.  We set about vaccinating all the old people first, in what had become a young person’s pandemic.  Here’s how Virginia looked at the time.  This is infection rates by age (light blue) versus vaccination rates by age (dark blue) as of the end of February.

Source:  Virginia Department of Health COVID-19 dashboard accessed end-of-February 2021.

This was a conscious choice by public health officials, and we just have to live with it.  For some smaller subsets of the population (e.g., health care workers, first responders), vaccines were given to people at high risk of contracting the disease.  But the bulk of vaccine so far has gone to the elderly.  Persons age 65 and up account for about 16% of the population but more than half of the fully-vaccinated population.

But there’s a second reason, and I think that’s coming out in the data now:  Self-selection.  Vaccination is voluntary.  Within each eligibility class (e.g., the elderly), the people who are NOT vaccinated may by systematically different from those who are.

There’s a second factor, that you can’t see, but that probably plays an even greater role in reducing the effectiveness of vaccines at slowing the spread of COVID-19:  Self-selection.  And by that I mean that the people lining up to get vaccinated early are probably people who are both worried about COVID-19 and cautious about exposing themselves to infection.

In other words, the people pressing to get vaccinated first are probably the people who were less likely to spread disease in the first place.  They are probably mostly from the stay-at-home, employ-proper-COVID-hygiene group.  Or, to turn that around, it’s a fair bet that the anti-vaxxers overlap pretty strongly with the anti-maskers and others who fail to adopt simple measures to prevent spread of disease.

And, while I can’t say anything definite yet, it sure looks to me as if this is showing up in the data now.  Whether it’s due to a lack of COVID hygiene, or to frailty, or maybe to their living situation, I can’t say.  But based on some crude back-of-the-envelope analysis, infection rates in the elderly have not dropped in proportion to vaccination rates in the elderly. 

This is tough to say definitively, because a) there are scant timely U.S. data breaking out infection rates by age, and b) there are only scattershot data by state breaking out infection rates in the elderly over time.  But let me just take the CDC’s plot of weekly average infection rates per 100,000, by age:

Source:  U.S. CDC.  The ends of lines are omitted here because they reflect incomplete reporting.

Notice anything odd about the 80+ infection rate?  The gap between that purple line (age 80+) and (say) all the green lines (younger people) has hardly changed since January 1.  By the end of March, the purple line (80+) is a modestly lower fraction of those green lines (younger people).  So it dips.  Vaccination appears to have an effect.

But it only dips a little.

As of the end point of this graph, something like 45% of the 80+ population would have been fully vaccinated, and a further 30% would have had at least one shot.  When I do the math based on the effectiveness of the vaccine (45% x 90% effective + 30% x 55% effective), I estimate that, in effect, by the end of the time period above, the equivalent of 60% of that elderly (purple-line) population should have been immune.  And yet, there’s nothing approaching a 60% reduction in new cases, relative to (say) the nearly-unvaccinated younger population.

And you can spin that either way.  One way to say it is that the elderly who were eager to get vaccinated were the ones who were not spreading disease in the first place.  And so vaccinating a lot of them did very little to the ongoing spread of disease, because they were (e.g.) careful enough not to catch COVID in any case.  And the flip side of that is to say that the elderly who were out-and-about spreading disease are the same ones who won’t (or perhaps can’t?) get vaccinated.

The upshot is that both factors limit the effectiveness of the vaccines at reducing spread of COVID-19.  The selection of the populations given priority for vaccination, and then self-selection within those populations, both appear to limit the effectiveness of the vaccine at stopping the pandemic.


How does this relate to herd immunity?

All of these things — the simple-minded expected impact of vaccine, or the level of vaccination required to end the pandemic — they’re all based on really crude-bordering-on-dumb models of the population.  Effectively, every person is the same, and all persons interact at random.

In effect, the basic model of a herd immunity really and truly is a model of what you’d expect to see in a herd of cattle.  And while there are some more-sophisticated models, pretty much everything you hear about herd immunity is based on the simple “cattle herd” model.

And I’m beginning to think that the simple “cattle herd” model of a pandemic might be seriously misleading, as a model for an actual pandemic among people.

This is pure speculation, I have no hard evidence, but in some sense, the numbers just don’t add up.  When you’re doing the addition based on the simple-minded model of a pandemic.

The only thing I’m fairly certain of is that if we’re vaccinating people who, by and large, wouldn’t have gotten infected anyway, then the overall population level of vaccination required for herd immunity is going to be higher than the simple “cattle herd” model suggests.  The often quoted figure of 70% vaccination rate required for herd immunity assumes that’s a randomly-chosen 70%, and that individuals then interact at random.  That’s the only set of assumptions that results in 70% of the chains of infection being broken.  And, based on the infectiousness of the previously dominant strains, that’s the number you’d need to break to end the pandemic.

But suppose, by contrast, that the population consists of two subgroups.  One of which obeys all the COVID hygiene rules, has a low rate of infection, and is eager to be vaccinated.  And a second group that routinely ignores the COVID-19 hygiene rules, has a high rate of infections, and is reluctant to be vaccinated.

In a nutshell, the question is, can that second group — call them the rule breakers — keep the pandemic going despite a high overall average rate of vaccination?  And, just fuzzy-thinking through this, I think the answer is that under the right circumstances, yes they can.  In particular, if rule-abiders tend to interact with rule-abiders, and rule-breakers interact with rule-breakers, you can keep the pandemic going among the rule-breakers even though the average vaccination level in the population suggest that the pandemic should end.

This is tough to model explicitly.  But just take the simplest case where the two populations are completely separated, with no interaction.  In that case, the pandemic will continue until both halves of the population reach herd immunity.

Just to throw some numbers at that simple scenario, if

  1. the two populations (rule-abiders and rule-breakers) were of equal size,
  2. vaccination were the only way to achieve immunity, and
  3. you need 70% of a population vaccinated to achieve herd immunity, and
  4. the rule-breakers are only half as likely to accept the vaccine,

Then you’d actually need to get 85% of the total population vaccinated before the pandemic would end.  That would be 100% of the rule-abiding population, and 70% of the rule-breaking population.

In any case, here’s my take on this.  I’ve been expecting to see some states hit herd immunity for quite some time now.  And it’s just not happening.  At least, not yet.

At this point, we’ve got states that already had high infection rates in the U.S. third wave, and that now have one dose of vaccine given to nearly 40% of the population and full vaccination given to 25% of the population.  Some of these are states that the CDC says have few or none of the new more-infectious variants. And yet, new COVID-19 case rates are now rising in those states.

Somehow, something about the simple-minded “cattle herd” model really is not right, when applied to the actual U.S. population.  I can’t quite put my finger on it, but I now suspect that the actual path to ending this pandemic is a lot more complicated than just getting adequate average voluntary compliance with COVID hygiene rules and COVID vaccination.

Post G21-004: Low-effort three-season kitchen compost system

 

Edit 2024:  The approach I describe in this post worked well, but it looks bad in the kitchen.  In the end, I replaced my crude compost holder with the smallest kitchen compost holder I could find, the three-quart OXO model (Amazon reference).  That still forces me to empty it every few days, and as long as I rinse it (outside), there’s been no odor in the kitchen. 

This is a brief note on everybody’s favorite topic, rotting garbage.  I mean, composting kitchen waste.

Our household generates a fair amount of compostable kitchen waste  It’s nothing unusual:  Vegetable peels, coffee grounds, and the like.  But it’s enough volume that it’s well worth composting for the garden.

Over the years, I’ve tried a variety of methods for composting my kitchen waste.   All the ones I used to use were failures, to a greater or lesser degree.

Sometime the failure was due to the equipment.  But more often, it was operator error. Because, when you get right down to it, who in their right mind wants to deal with composting kitchen waste?  It’s way too easy to say “I’ll take the compost out tomorrow”, particularly if it’s a nasty job.  And if you ignore a composting system that needs some TLC, it’ll let you know about it.

It was only when I more-or-less gave up on the gizmos and the tricks that I stumbled across a system that works for me.  It was really a question of channeling my inner sloth.  So I thought I’d share what finally worked for me. Continue reading Post G21-004: Low-effort three-season kitchen compost system

Post #1079: The U.S. COVID-19 fourth wave has started, I guess.

 

The current COVID-19 story is that we have new, more-infectious variants of COVID-19 here in the U.S.  And so, in theory, we’re in a race between the spread of those more infectious variants, on the one hand, and vaccination, on the other.

Over the past few weeks I’ve been tracking the COVID-19 new case data, waiting for new-case rates in a handful of states to turn upward.  These are states that, based on CDC or other data, were reported to have a high fraction of at least one of those new variants.

And now, those new-case rates have turned upward.  Mostly.  And, yeah, rates appear to be turning upward at more-or-less the time you would expect, based on prevalence of the new variants.  (When about half of cases are the new variants.)

But new case rates have also turned up in a lot of states where the presumed prevalence of those new variants is far less.  At more-or-less the same time as the high-variant states.  And at more-or-less the same rate as those states.

You may find other people who are just rock-solid sure that they are looking at the impact of these new COVID-19 variants.  But I’m not so sure what I’m looking at.

Regardless of the reason, the data are what they are.  New case rates are rising.


National trend

Nationally, in three graphs:  1) We’re now back to 24% of the peak level, 2) the overall US trend is up, and 3) cases rose yesterday in the overwhelming majority of states.

Pace of vaccination and limits of vaccine acceptance.

That said, the pace of vaccination is picking up, and we have not yet reached the limits of vaccine acceptance in the elderly.  Here are my most recent snapshots of the CDC COVID data tracker, showing fraction of the elderly vaccinated.  That’s a rate of 0.5 percentage points per day, so this has not yet stalled out.

In Virginia, snapshots from 3/27/2021 (top) and 3/22/2021 (bottom) show about 0.4 percentage points per day, or roughly the same pace as the U.S. data.

The upshot of all of that is that vaccination of the elderly continues apace, and, contrary to what I guessed would happen, we have not yet hit the limit of vaccine acceptance in the elderly.

If I now update my “herd immunity” chart based on the recent record of more than 3M vaccine shots per day, then here’s where we stand, and where we would be projected to stand as of April 1 2021.

(I should say that this chart continues to assume that once you’ve had COVID-19, you are fully immune.  There’s now a pretty good body of evidence to say that some modest fraction of that population is subject to re-infection.  But my impression is that re-infections are not nearly as dangerous, on average, as the initial infection.  So, for consistency, I’m sticking with the (incorrect) assumption of 100% immunity of the already-infected population.)

Here’s the same chart, the last time I recalculated it, less than two weeks ago.

So, we are making slow progress.


State-level detail.

If you look at the state-level detail, it’s not crystal clear that this is being driven (or, driven only) by the more-infectious variants.  New case rates are turning upward all over, not just in the states presumed to have a high fraction of these new variants.

As you can see below, the majority of states are trending upwards now in the Northeast, South Atlantic, and Midwest regions.  The South Central, Mountain, and Pacific regions are more mixed.

And that’s what has me a little uncertain as to what’s going on.  Everybody noted that Florida had a high incidence of these new variants.  But nobody said that about (e.g.) West Virginia, New Hampshire, Vermont, or North Dakota.  But new case rates are rising as fast there as they are in (say) New York State.

So whatever is driving this, it doesn’t seem to be quite as simple as “new COVID-19 variants”.  Either that, or the distribution of those new variants managed to even itself out across all those states, in just a few weeks.

Post #1078: W&M St. Patrick’s Day outbreak, updated

 

William and Mary updated their COVID-19 dashboard at close-of-business yesterday (Friday, 3/26/2021).  They normally don’t update it over the weekend, so that should be the last count of COVID-19 cases we’ll have until Monday evening.

Yesterday’s update was in line with expectations.  Each new batch of tests results is showing that more-or-less a steady 1.4% of students test positive for COVID-19.  Assuming that holds, by the time all the test results are back, they’ll have had just under 250 known on-campus positives this semester.  Unless the lab they are using closes for the weekend, that’s about how things should stand on Monday. Continue reading Post #1078: W&M St. Patrick’s Day outbreak, updated

Post #1077: Michigan school-sports outbreak.

The Michigan outbreak is now being characterized in national news as being driven by school children, and in particular, by school sports.  That’s what showed up when I opened up the Google News website today.

Source:  Google news, accessed 9 AM 3/26/2021.

That’s not implausible.  If you look at college COVID-19 re-opening guidelines, student athletes have always been considered a high-risk class of individuals.  They are a “high contact” population, in the jargon.  (That’s not as in “contact sport”, but as in, they are going to have a lot of close contact with a lot of people.  Probably maskless and breathing hard.)  They are to be given particular attention in any college re-opening plan, including frequent testing.

Michigan was already reported as requiring weekly testing of student athletes.  It doesn’t look as if they would even consider suspending high school athletics.  So I guess they’ll just have to deal with it.  Their rate of reported new case growth is high enough that it’s driving up the average for the entire Midwest.

Source: Calculated from:  The New York Times. (2021). Coronavirus (Covid-19) Data in the United States. Retrieved 3/26/2021, https://github.com/nytimes/covid-19-data.  Their U.S. tracking page may be found at https://www.nytimes.com/interactive/2020/us/coronavirus-us-cases.html.

But there are couple of odd things about this Michigan outbreak.  Both in general, and in relation to school sports, which seems to have been chosen as the culprit. Continue reading Post #1077: Michigan school-sports outbreak.

Post #1076: Virginia’s COVID-19 hospitalization rate: Home alone?

This is about the rising hospitalization rate of diagnosed COVID-19 cases in Virginia.  It’s about new hospitalizations per newly diagnosed case.

This posting is long enough to require an executive summary.  Briefly.

  • Hospitalizations for COVID-19 are concentrated among the elderly.
  • The age of Virginia COVID-19 cases has been dropping.
  • That trend toward “a young person’s pandemic” sped up rapidly with the onset of COVID-19 vaccination, focused first on vaccinating the elderly.
  • And yet, the rate of COVID-19 hospitalization per new case has risen sharply.
  • How sharply?  Among the oldest old, half of those newly diagnosed with COVID-19 are now being hospitalized for it.

Why has the hospitalization rate per new COVID-19 case skyrocketed among the oldest old?  My guess is that the un-vaccinated geriatric population has a high fraction of individuals who had difficulty getting the vaccine.  And I’ll bet that’s because a lot of them are living alone, on the margins of living independently.  That population — elderly, living alone, no formal caregiver — is the population that physicians will choose to hospitalize, for safety’s sake, rather than let them try to ride out a moderate illness at home. Continue reading Post #1076: Virginia’s COVID-19 hospitalization rate: Home alone?