Category: COVID through 2022

 

I used to know what exercise was.  If I wasn’t out of breath and sweating, that wasn’t really exercise.

I completely lost sight of that in the pandemic.  As I aged another year and got ever fatter, I found myself counting more and more things as “mild exercise”.  Puttering around the garden, walking around the block, taking a bit of a bike ride, and so on.  Medically speaking, that’s all exercise. 

Yesterday I found out just how badly I was kidding myself. 

My wife and I went back to the gym for the first time in well over a year.  I don’t know if this event is of interest to anyone, but in this post, I’m going to walk through the odds, the logic, and the experience of getting back into the gym.

The odds in brief:  I figure that at our current community rate of COVID-19 incidence (1.6 new cases / 100,000/ day), going to our gym every other day, in a room with an average of 30 people, we’d end up sharing gym space with a COVID-19 infected individual about once per year.  But the likelihood that we’d end up spending considerable time close to an infected individual — the sort of situation that can easily lead to transmission of disease — works out to about once per 15 years.  And the likelihood that we’d end up in the same room as an infected “super-emitter” of COVID-19 — another situation that can easily lead to spread of infection — is also about once per 15 years.

The long and the short of it is that for me — fully vaccinated, age 62, and fat — the positive health impact of going to the gym vastly outweighs the COVID-19 risk at present.   Easily a 100-to-1 ratio of benefit to cost.  As with the average American, I’m far more likely to die from slowly degenerative diseases than from anything as swift and dramatic as COVID-19. Continue reading Post #1163: Returning to the gym

The overall trend of new COVID-19 cases continues downward for the U.S. Whatever impact the new Delta COVID-19 variant is having, it’s not large enough (yet) to offset the pre-existing trend.

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 6/18/2021, 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.

As I was updating my graphs, I noticed that one state stands out for having a strong upward trend in new cases:  Missouri.  That’s quite the outlier, given that every other state in that region shows a fairly consistent downward trend.  

That also rang a bell.  The last time the CDC published data on incidence of variants by state,Missouri stood at the top of the list for incidence of the Delta variant. 

Source:  CDC COVID data tracker.

There are a few caveats for the table above.  First, those data are based on a small sample and so likely have a lot of uncertainty in the estimated incidence rate.  Second, that’s ancient history.  The average date for those sequenced samples would be the first week of May.  Given the less-than-two-week doubling time of incidence of the Delta variant, the incidence now should be maybe 6 times higher than what is shown.

I then searched systematically for all the states with strong and consistent upward trends.  In particular, I looked for states that had both one-week and two-week trends in excess of a 20% increase in cases per week.  Only two other states met that criterion, other than Missouri.  And, again, somewhat oddly, they were geographically clustered.  A handful of other states had smaller or less consistent upward trends.  But only these three had a strong and consistent upward trend for both of the past two weeks:

Then I read the news, and found that there’s a COVID-19 outbreak in Southwest Missouri that is being attributed to the Delta variant.

The reporting is not quite deja vu all over again.  Sure, hospitals are filling up, emergency departments are overloaded, and so on.  That’s familiar.  But this time, we have a vaccine, the patients are almost entirely un-vaccinated individuals.  In the words of a local hospital administrator in that area, what you you waiting for?

“Bed capacity is strained. ED waits are long. COVID patients are younger, sicker and unvaccinated. Vaccines are free, available and effective. What are you waiting for? 82? 102? 152? What about 1? 1 person you care about? You?”

Source:  Saint Louis Post Dispatch., emphasis mine.

Based on that reporting, Delta is now my far the most prevalent variant of the virus in Southwest Missouri.  The virus doesn’t respect state boundaries.  It doesn’t take much of an imagination to connect Southwest Missouri to states south and west of Missouri, per the map above.

Maybe this will be an isolated outbreak.  Or maybe its a harbinger for the U.S. fifth wave of COVID-19.

Before this U.S. outbreak, the only information to guide a prediction came from Great Britain.  The recent uptick in cases in Great Britain has been attributed to the spread of Delta, despite an ongoing partial lockdown.

But now we have the example of southwest Missouri.  The high incidence of Delta in Missouri was known more than a month ago.  It’s now the dominant strain in southwest Missouri.  And there’s a fresh COVID-19 outbreak there attributed to that variant that is now straining the capacity of the local hospital system.

One thing we can be sure of:  If we have another COVID-19 wave of any consequence, we’ll owe it entirely to the dumbasses who won’t get vaccinated.  Right now, vaccinated individuals account for 53 percent of the U.S. population, but only one to two percent of the U.S. COVID-19 hospitalized population (reference 1, reference 2).  More-or-less, vaccination appears to confer a fifty-fold reduction in the odds of being hospitalized with COVID-19.  The vaccines are that effective at preventing severe illness.

Source:  CDC COVID data tracker.

The trend of vaccinations picked up a bit in the past two weeks.  We’re still vaccinating at a rate in excess of 1 million doses per day.

We can quantify the degree of vaccine slacking in the US by measuring the number of doses that could have been given, if we’d kept up the highest demonstrated pace.  As illustrated below, that works out to an average of 1.5 million doses not administered for the past 60 days, or another 90 million doses that could have been given, but weren’t due to lack of demand.

The 53 percent of the population vaccinated could have been, in theory, 80%, if we had merely kept up the pace.  Just something to bear in mind of we end up with a Delta-drive fifth wave.

 

With these reasonably effective vaccines, we’re no longer at the mercy of the virus.  Instead, we’re at the mercy of the intelligence and public-spiritedness of our fellow citizens.  You’d hope we’d be coming ahead for that change, wouldn’t you?

 

If you can’t beat ’em, rename ’em.

If you track trends in COVID-19, you’re probably well aware that a new variant has taken over Great Britain and is in the process of taking over the U.S.  This is the COVID-19 variant formerly known as “Indian”, B.1.617.2.  Henceforth to be called Delta.  The British variant is now Alpha.

In this post, I’m getting my thinking straight about the new Delta variant.  Best guess is that, as with Great Britain, we’re going to get another wave of increased daily new case counts from the spread of the Delta variant.

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Delta makes herd immunity effectively impossible with current vaccines alone.

I’m fairly sure this cheery bit of new is correct.  I’m almost equally sure you aren’t going to see anyone in our public health establishment saying it in public.  But math is math, and this new variant brings a double whammy.

• The virus is more contagious
• The vaccine is less effective

Practically speaking, those two factors put herd immunity via vaccination out of reach for the U.S.

Briefly recall how this works.  A pandemic will eventually collapse if each infected individual goes on to infect an average of less than one new individual.  If you can get that to happen, each round of newly-infected individuals is smaller than the last, and the pandemic shrinks away.

Now recall “R-nought” and the classical definition of herd immunity.  R-nought is the number of individuals each infected person would go on to infect, if there were no protection or immunity within the population.  For example, if each infected person would normally go on to infect three others (R-nought of 3.0), you need to interrupt at least two-thirds of those infections to bring the pandemic to a halt.  If R-nought is 10, you’d need to interrupt 90% of those infections to bring the pandemic under control.  And so on.

The more infectious the virus, the more people need to be immune to it before you achieve herd immunity.  Or the more COVID-19 hygiene protocols need to be enforced to cut off what would otherwise be chains of infection.

(I need to put a marker down here.  Epidemiologists always discuss this solely in terms of preventing new infections via vaccination.  But prior infections also confer immunity.  And good COVID-19 hygiene also prevents infections.  In reality, all of those factors work to interrupt would would otherwise be chains of disease transmission, and so all of those factors matter in a herd immunity calculation.  But for the rest of this section, I’m going to do what all the epidemiologists do, and pretend that the only way to interrupt chains of infection is via vaccination.)

The first key fact is that the Delta variant is more infectious than the Alpha variant which is more infectious than the original strain.  Rather than try to daisy-chain all those imprecise numbers, I’m just going to take somebody’s estimate.  Like so, from this seemingly-plausible reference, where R0 = “R-nought”:

Professor Cheng said last year's Wuhan strain had an R0 value of around 2.5, the Alpha strain was about 3.75 and the Delta strain was about 5.

That means if we were living life like we were in 2019, one person with the Delta strain would likely infect five other people, compared to just 2.5 last year.

I’m sure there’s considerable uncertainty around that estimated R-nought of 5.0 for the Delta variant, but I’m just going to accept it as a fact.  (You can find apparently legitimate sources suggesting a much higher value.)  And so, if each each infected individuals would natively infect 5 others, you have to interrupt four out of five of those infections to bring the pandemic under control.  In other words, with the estimated R-nought of 5.0 for the Delta variant, we now need to have 80% of the U.S. population immune to it before we have any hope of it going away.

The second key fact is that the vaccines are less effective against this strain of COVID-19.  The Pfizer vaccine is 88% effective against the Delta variant after two shots.  But, for the U.S., nobody knows how effective the Moderna or Johnson and Johnson vaccines will be.  Fauci guessed that Moderna will be about as effective as Pfizer, but that’s just a guess.  The AstraZeneca vaccine, commonly used in Great Britain, is only 60% effective against the Delta variant.  (The Pfizer and AstraZeneca numbers are based on this study.)

If vaccination were the only way to stop this, between those two factors, we would require at least 91% of the U.S. population to be vaccinated before we could achieve herd immunity.  (That is, .91 x .88 = .80, the level of immunity required for herd immunity against the Delta variant.   Re-stated, 91 percent of the population, vaccinated with an 88% effective vaccine, would stop 80 percent of the chains of infection.)

Short of vaccination-at-gunpoint, that’s not going to happen.

(There are some nuances here.  Probably, you are less likely to transmit the disease, if infected, if you are vaccinated.  And people will continue to achieve immunity by recovering from infection.  But in terms of your textbook herd immunity calculation, herd immunity is pretty clearly out of reach for the U.S. population.)

In practice, two things happen when you try to calculate where we stand on herd immunity with the Delta variant.  First, your estimate of the existing level of immunity falls, because the existing vaccinated population has less immunity to this new strain than it did to the existing strain.  And then, separately, the fraction of the population that needs to be immune goes up.

Again, between those two factors, there’s a world of difference between the way the U.S. looked against the Alpha (British) variant, and how it now looks against the rapidly-spreading Delta (Indian) variant.

Let me now redo my herd immunity chart.  This still assumes that you have complete immunity once you’ve recovered from infection.  I’m not changing that for now.  I’m only changing how effective one and two vaccine shots are.

Alpha variant (what we have now, the British variant).

• R-nought = 3.75
• Herd immunity goal = 73% immune
• Current estimate = 64% immune.
• Additional full vaccinations required = 9.5% @ 95% effectiveness

Delta variant (what is coming, Indian variant).

• R-nought = 5.0
• Herd immunity goal = 80% immune
• Current estimate = 59% immune.
• Additional full vaccinations required = 24% @ 88% effectiveness

As I said, double whammy.  We need more immunity to achieve herd immunity, and we instantly have less immunity, because the existing vaccinated population has less resistance to this new strain.

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Where do we stand on the Delta variant and its growth

Let me first quickly benchmark Great Britain’s latest outbreak.  Currently, the Delta variant accounts for almost all (90 to 94 percent) of new cases in Great Britain.  At about 7000 new cases per day in a population of 66 million, that’s about 10 new cases / 100,000/day, with a strong upward trend.  And that’s despite significant restrictions on public life and public gatherings in Great Britain.

That compares to the current U.S. rate of about 4 new cases/ 100,000 per day.  And a slight downward trend.  With, as far as I can see, roughly no restrictions on public life left in most U.S. states.

The vaccination situation in Great Britain is roughly comparable to that of the U.S.  Fully-vaccinated individuals in Great Britain account for about one percentage point more than in the U.S., and Great Britain has injected about 14% more total doses per capita.  But a) a large share of their vaccinations are the AstraZeneca vaccine, which is less effective than Pfizer against the Delta variant, and b) those with just a single shot of vaccine receive little protection against the Delta variant (one shot of vaccine is about 33% effective).

The U.S. has the edge in terms of total reported cases per capita so far.  Presumably, those individuals add to the pool of persons immune to COVID-19. In the U.S., over 10 percent of the population has been diagnosed with COVID-19, versus about 7 percent of the population of Great Britain.  For each diagnosed person, there is probably another 2 to 3 persons who had COVID-19 but were not diagnosed.  (All of those statistics would depend strongly on test availability and testing behavior.).  Thus, the U.S. plausibly has an additional 10 percent of the population immune via recovery from infection, compared to Great Britain.

(FWIW, I looked up all of those statistics, I’m just too lazy to provide citation as to source for every one of them, as they are just background.)

What fraction of new cases is accounted for by the Delta variant in the U.S.?  This is a number that is changing rapidly, so you need to pay strict attention to the dates.

As of the two-week period ending 6/5/2021, the CDC estimated that the Delta variant accounted for just under 10% of all new cases in the U.S.

Source:  CDC COVID data tracker.

The doubling time for these cases in the U.S. appears to be something less than two weeks.  (The last three sets of CDC two-week observations or projections were 1.2%, 2.5%, and 9.9% of new cases.  In each two-week period, the fraction of new cases attributed to Delta more than doubled.)

Without bothering to define it, the case-weighted midpoint date for that two-week period ending 6/5/2021 is about 5/31/2021.  (The 9.9% is the average for the entire period.  It was less than that early on, greater than that later.  The date of  5/31/2021 is my best guess for the day, over that period, when the fraction literally hit 9.9%.)  That was more than two weeks ago.  Hence, we should add just over two weeks’ growth to that estimate to project forward to the rate as of 6/15/2021.  So, something in excess of a  doubling of those cases.

Best guess, by that calculation, somewhere around one-quarter of new US COVID-19 cases on 6/15/2021 were the Delta variant.  At that rate, it should be the most common strain of the virus in the U.S. by the end of this month.

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Is it different this time?

The U.S. fourth wave was due to the growth of the British (now Alpha) variant, moderated by the rapid increase in vaccination.  It was a race, and back in early March (Post #1051), I used the best available data to project that vaccination would win.

I emphasize that to demonstrate that I’m not some nervous Nellie who cries “wolf” at any pretext.  The numbers reasonably clearly indicated that at the then-prevalent rate of new vaccinations, and the known efficacy of the vaccine, we’d be able to vaccinate enough individuals to stifle a major outbreak of the British (Alpha) variant.

But now?  Now we’re bringing in a variant that is yet-again as infections relative to Alpha, as Alpha was to the original COVID-19 variant.  But now,

a)  There’s no big build-up of vaccinations to offset that.  To the contrary, the U.S. vaccination rate is down to 1M per day.

Source:  CDC COVID data tracker.

b)  We’re dropped the greater portion of our COVID-19 hygiene at the CDC’s direction.

c) Good luck getting people to mask up again in case this gets ugly.  What are the odds that the CDC will be able to pull a timely about-face and tell us to put our masks back on, and then have Republican governors follow that advice, let along the U.S. population as a whole?

and finally,

d) The lower efficacy of the vaccine against this strain means that, from the outset, we lose ground as this variant spreads.  To be clear, not only is vaccination not rapidly increasing our collective immunity, instead, the lower efficacy of the vaccine means that we are, in effect, losing immunity.  That was the whole point of the charts in the second section above.

The way I see it, at this point, this time, whatever happens, happens.  Certainly no Republican states, and likely no states, are going to take action in the event that the Delta strain leads to a U.S. fifth wave.  So whatever is going to happen is going to happen.

Run that mix through the blender and my guess is that we’re going to have (some sort of) a fifth wave.  Not, as I initially expected, due to heavy use of air conditioning mid-summer, as was the case for the U.S. second wave.  But because we’re facing yet another round of substantial increase in the infectiousness of COVID-19, and far from taking offsetting measures, we’ve all let our guards down and are vaccinating at a casual pace.

On the plus side, at some point, the virus runs out of bodies.   We now have a fairly large chunk of the population that is immune.  So this can’t possibly be as bad as the U.S. third wave.   But my bet is, this pandemic isn’t over yet.   Just as it is not yet over in Great Britain.

Data dropouts

Well, this had to happen sooner or later.  More states are reporting less data, less frequently, regarding COVID-19.  You can read the full writeup at this link.

This less-than-daily report is not a completely new phenomenon.  It has always been true that some states — typically low-population rural states — did not report data on Sundays.  This added a harmless little “flat spot” in their seven-day-moving average curves, but did not meaningfully distort the overall picture.

But now Florida (of course, Florida) has decided to report information just once a week.  With some lag, as well.  This is the only state where the new-cases data are now, in effect, missing for an entire week at a time, driving the seven-day moving average down to zero on a real-time basis.  That began June 4.   And that puts a serious kink in any sort of data analysis.

Across the states, the data reporting situation is summarized in the table below.    Out of 51 states (including DC), about half continue to report every day.  Those tend to be the larger states, and they contain about 69% of the population.  The rest of the states skip reporting one or more days per week.  For those states, the daily new case count will show as zero for those days, followed by some larger number as multiple days’ worth of cases are reported on the next reporting day.

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 6/11/2021, 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.

For most of these states, the non-reporting remains a minor issue.  One or two days per week, their time-series will show a flat spot.  This will be followed by a jump as the time series corrects back to the true underlying level of new cases.  A trend line that ends on (say) a Thursday (such as today’s analysis) will show all those states at their true levels.

But Florida is a special case.  I can either drop it, or gap-fill it by using the prior week’s new-case rate as the gap-fill, until new data appear again.  When all is said and done, it’s probably smarter just to drop Florida, for now, at least.

These changes, along with ongoing reporting issues in (e.g.) Texas and elsewhere, make it hard to say much about ongoing trends.

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A leveling-off off of the new cases curve

With the data reporting caveats in mind, as far as I can tell, this past week, the downward trend of the U.S. COVID-19 fourth wave appears to have stopped.  In my last look at trends, I overstated the downward trend due to missing data from Florida.  But when I now drop Florida, and add the last few days’ worth of data, the new-cases curve appears to have flattened.

That may slightly overstate the flattening of the curve, due to some data reporting issues in Texas.  (Texas added then removed a considerable number of old cases to their data last week, but without enough information to allow me to correct the time-series.)

If I divide the states by (my estimate of) the fraction of the population already immune to COVID-19, it seems fairly clear that this is not merely the consequence of bad data reporting in a few states.  There’s still a slight downward trend in the states with the highest levels of immunity (black line), but a complete leveling-off in states with the lowest levels of immunity.

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Why?

Why has the downward trend in case cases now flattened out?

There has been a lot of talk about the new Delta variant of COVID-19 (formerly the Indian variant, still identifiable as B.1.617.2, now simply termed “Delta”).  But that’s still far too infrequent in the U.S. to have any material impact.  As of now, it accounts for about 6% of new cases.

Source:  CDC COVID-19 data tracker.

There are plenty of reasons to worry about this for the near future.

• • It’s about 40% more transmissible (infectious) than the British variant that is now the dominant strain in the U.S.
  • It causes much worse symptoms, particularly among younger people.
  • The current vaccines are not as effective against it as they are against other strains.

You can read all that good news by clicking the link to this WebMD article.  But, again, it’s not prevalent enough yet in the U.S. to be causing a flattening of the curve.

Seasonality is always a good guess.  COVID-19 appears to have a strong seasonality to it.  As we made the transition from winter to summer, disease transmission fell — just as it would for influenza, say.  But now were in summer, and should expect no more seasonality-related declines.

Memorial Day weekend is not really a plausible suspect for this leveling-off of new cases.  The main reason is that, despite the hype, there never was any post-holiday “surge” in the U.S., for any prior holidays (e.g., Post #922, Post #1029).  Given that, it’s hard to believe that, uniquely, there would be one for Memorial Day, when most social activities are in safe outdoor locations anyway.  The only thing that makes this even remotely plausible is the timing.  Infections acquired at the start of Memorial Day weekend would start showing up in the data at the end of this current week.  (June 9 is 12 days from the Saturday of Memorial Day weekend.  That 12-day figure is my best estimate for the typical lag between infection and reporting in the U.S.)

If I had to pick a cause, I’d say seasonality.  Part of the decline in new cases, after the peak of the U.S. fourth wave, was due to vaccination.  And part was just ongoing seasonal trend.  New vaccinations have slowed to a crawl.   And we’re now fully into summer, and should expect no more help from seasonality this year.  Absent those two drivers, it seems reasonable that the decline in cases would cease.

That said, it’s only been a week now.  It’s too soon to make any firm conclusions.  And the picture is muddled by data reporting issues from the Memorial Day holiday, and by changes in data reporting by the states.  Give it another week and it should be clear whether or not the U.S. fourth wave has ended.

 

I’ve analyzed enough health care data to know that this can’t be a real increase in cases.  It has to be a data reporting glitch.  I just have to work out what it is.

Here’s the answer:  This is a result of the Memorial Day.  And it will disappear tomorrow.  The reason is that today’s seven-day moving average actually has eight days’ worth of cases it in, for states that didn’t report data on Memorial Day.

A simple spreadsheet illustrates what’s happening.  Here I’ve represented a day’s worth of new cases with a “1”.  A lot of states didn’t report new cases on Memorial day, but instead reported two days’ worth of cases the next day.  With that reporting pattern, you’ll see a dip in the seven-day moving average reported on Memorial day, and an offsetting jump in the seven-day moving average seven days later.

 

If you are still following the trend in new COVID-19 cases, you would have noticed that today we finally seemed to have entered the end phase of the pandemic.  But that’s not so.

The sharp dip in today’s counts reflects the Memorial Day holiday.  A lot of states simply didn’t report data, resulting in zero new cases, and the sharp downturns in their trend lines.  That should get fixed tomorrow.

So, no quick end of this in sight.  Just a slow fizzling-out of the pandemic in the U.S. Continue reading Post #1152: COVID-19 trends, holiday artifact, and fizzling out.

I apologize to my readers for failing to post lately.  I hope to make it up to both of you by posting more in the next couple of days.

Otherwise, I’m probably going to stop posting as frequently about COVID-19, because there just isn’t much to say at the moment.  As far as most of America is concerned, the pandemic is more-or-less over.

The rate of new COVID-19 cases per day is now 61% below the peak of the U.S. fourth wave.  Every region is seeing weekly percentage declines in the double digits.  The rate of decline seems fairly steady.

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 5/21/2021, 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.

What was a chaotic mix of different rates and trends just a few weeks ago is now and orderly “regression toward the mean”.  The trend lines are all funneling down toward a narrow range of levels and trends.

The remaining problem is that while the rates are coming down, COVID-19 isn’t fully going away.  Not in even one state.  I’ve documented a few low-population rural counties that are plausibly COVID-19 free.  But in terms of the overall scope of the pandemic, we’re seeing states achieve low rates, but we not seeing any state actually get the virus out of circulation.  There’s still some air under the right-hand-side of the curve.

With the slowdown in infections, and the slowdown in vaccinations:

Source:  CDC

progress toward achieving herd immunity has slowed and is getting slower.

And so, I guess the next thing to look for is whether the formal advice from CDC to relax mask rules for the vaccinated had any impact on the rate of new infections.  I would guess not, given what I see in this area, which is that mask use pretty much continued as it has been before, maybe just a little sloppier.  In any case, given the lags involved, if there is an uptick as a result of the CDC guidance, that will only show up toward the end of the month.

After that, the next thing to look for will be a repeat of the U.S. second wave, wtih a peak of new cases in hot-climate states in July.  This was plausibly attributed to the large amount of time spent in air-conditioned spaces in those states.

And then we’ll see what the fall brings.  Maybe by that time, we’ll finally get enough people vaccinated to achieve herd immunity.  And maybe not.  Maybe either way, this virus will become a permanent part of the infectious landscape.

Too soon to tell.  But for sure, things are blessedly boring right now.  And that suggests that there’s no need to post obsessively about trends.  Maybe once a week, I’ll check back in and see how the trends are going, from now on.