[conspire] COVID at the beginning of 2022

[Rick Moen]

I wrote:

> I need to send something out before we run out of 2021.  So, this is
> being written quickly and without re-editing.  Also, things I say may
> look silly or obsolete in a week.

Other than typos, I didn't do _too_ badly, did I?

I appreciate several other folks contributing comments of substance,
including Deirdre fleshing out the "But what do I do individually?"
section.  (Thanks!)  I see at least one spot, maybe more, where I want
to elaborate:

> And, therefore, don't get surprised if, until there are fundamental
> advances or change to the disease outlook, we'll need 1-2 new boosters
> per year.
> https://www.theatlantic.com/science/archive/2021/12/how-many-covid-19-booster-shots/621132/

I'm seriously puzzled that I'm not yet hearing about Pfizer and Moderna
rushing out a revised-design booster to compensate for newer variants.
Part of the whole point of rRNA technology is gaining the ability to 
develop or revise a vaccine or other rRNA payload order of magnitude
more quickly than was previously possible.

The duration of clinical trials thereafter would be a political / public
health policy question -- but I'd be grateful if we had the problem of
deciding that rather than nothing.


[Framings as to scale of effect:]

> They're all important, but differ.  

It's not exactly a new point, but I keep noticing discussion of public
health keeps getting dragged back to how [thing X] affects you and your
interaction with others.  It's fine to discuss that; I mean, I want good
health for myself and my not adversely affecting others, too, but _most_
of the time, it's the wrong framing.  Effective public health policies 
have to concern population-level effects, trends, and mechanisms.

I noticed this when the Bay Area was threatened by measles outbreaks,
some years ago, and most attention was on "How do I make sure I don't
get measles."  I talked about that disease's high inherent-infectiveness
R-naught (12 to 18) and how because the MMR vaccine is highly effective
(93%) against that virus, any population with 94%+ population coverage
will on average have declining rather than expanding infection
(R-effective under 1.0).  I could tell that my audience was thinking
"But there's still a 7% chance I could get the disease?  That's bad."

Well, yes, that would suck as an infected individual.  But, seen with a
population-level framing, a vaccine good enough to haul R-eff to under
1.0, breakthrough infections or not, is a huge win, because then any
outbreak implodes and goes away over time.

Not all the "Vaccines don't work" people are deliberately spreading
misinformation.  Probably few of them are.  Many obviously just don't
_get_ that 70% effectiveness against symptomatic Omicron-based disease
(Pfizer- and AstroZenica-based stats from the UK) is _good_ (and Moderna
with a booster is better than that, still).
https://www.businessinsider.com/omicron-chart-protection-2-3-vaccine-booster-effectiveness-hospitalization-symptomatic-2022-1
https://www.cnet.com/health/moderna-booster-faq-covid-shot-side-effects-vaccine-effectiveness-what-to-know-about-third-dose/


Booster eligibility in the USA:  All adults 18 and older became eligible
to receive COVID-19 booster shots if it's been at least six months since
they've received a second dose of either the Moderna or Pfizer vaccine.
Those who received the Johnson & Johnson vaccine are eligible for a
booster dose after two months. Mixing and matching is fine, but Moderna
or Pfizer for the third shot is recommended.


> Some county stats:

Predictably, there are no _new_ stats, because of the holidays.
Next week, when reporting and collecting data is fully staffed again, I
wouldn't be surprised to see some revisions to existing reporting.


> New Year's Eve is likely to be a colossal superspreader event.

So, the next few weeks look to be pivotal, as the cascading effects of
New Year's Eve parties hit.  Last night, at 9:15pm, Deirdre and I drove
past Town & Country Village Shopping Center, Palo Alto, and the parking
lot was nearly full.  What was that about?  Obviously:  New Year's Eve
gatherings.  _Indoor_ New Year's Eve gatherings -- in the (numerous)
restaurants.  https://tandcvillage.com/shops-restaurants/

I'll be watching county stats with _particular_ interest starting
Monday, Jan. 10, as a result.


[R-eff:]

> o California: 1.59.  Spread of COVID-19 is likely increasing rapidly

Still rising.  Up to 1.61 overnight.

> San Mateo County:  1.63.  Spread of COVID-19 is likely increasing rapidly.

Risen to 1.84 overnight.

(However, R-eff modeling has some volatility, and is after all
predictive rather than measured.)


As the pandemic's worn on, I've had qualms about many of the metrics we
tend to use.  Take the concept of "case", for example.  A COVID "case" 
is the record of an individual being PCR-confirmed as having had a
detectable viral load of SARS-CoV-2, irrespective of whether the patient
currently is shedding virus and irrespective of whether he/she ever had
any symptoms, if any.  Many "cases" thus involve people unaware they
were ever ill.  Also, the count is an artifact of testing.  In
times/places where testing is rare, the case count is artificially low.

Additionally, the fact that "case" has no connection to severity means
using those numbers will be misleading in comparing, say, earlier waves
against the current Omicron/Delta one.  From an article today in 
_The Guardian_:

  The US on Thursday had more than 580,000 new Covid cases, the second
  time this week that the country has broken its record for daily Covid
  cases, according to New York Times data. But over the past two weeks,
  while the number of Covid cases in the United States has increased by
  181%, the number of hospitalizations has increased by 19% and the
  number of deaths has decreased by 5%.

https://www.theguardian.com/us-news/2022/jan/01/us-covid-case-counts-omicron

For that reason, many months ago, I concentrated mostly on
hospitalisation (acute care and ICU) occupied-beds numbers, such 
as I've quoted for San Mateo County -- because at least that tracks 
a real, important, exhaustible resource (treatment beds).  However,
even there, there's a hidden problem.  Consider the stats I quoted:

  ICU beds:
  Dec. 27:  4
  Dec. 28:  8
  Dec. 29:  9
  Dec. 30: 11

  Acute-care beds:
  Dec. 27: 15
  Dec. 28: 14
  Dec. 29: 12
  Dec. 30: 20

So, over that four-day period, _how many COVID patients_ did San Mateo
County hospitals treat?  40?  100?  An avalanche of patients being
admitted and then rapidly discharged?

You actually cannot tell, from the data provided -- because all we're
being told is how many beds were occupied at a certain time each day
used for as a checkpoint for reporting metrics.  The total number of
patients seen could be anywhere from 31 to a veritable conga line of
patients getting checked in, and fairly quickly discharged.  In other
words, turnover is untracked.

"Beds" is the right metric where the concern is making sure you don't
run out of beds -- but it's the wrong metric where the concern is "Are
we testing to destruction our medical personnel, through treating too
many patients?"

That reportedly isn't true in the Bay Area (yet), but spare a thought
for physicians and nurses in, say, Maryland, where six major hospitals
have been driven to shift to "crisis standards of care", which is a
delicate way of saying "Sorry about that appendicits.  You'll probably
die."

Deirdre follows (and participates in) the /r/Nursing subReddit, and has
seen things going quickly from bad to very bad, with astonishing speed.
Here's one nurse's comment from yesterday:

  I just quit on the spot and am not going back

  Tested positive for Covid. Feel like crap, but just a headache and
  fatigue. Called out and told them. Was told I could still come in if I
  wear a mask and I don’t have moderate to severe symptoms and I’d get
  penalized for calling out on a holiday.

  I kind of blacked out in anger and said “Ok. That’s fine. You can take
  me off the schedule because I am not coming back.” I’m so done. Signed a
  travel contract starting in January anyways.

Yes, _way_ too many medical establishments really are doing such things.
Doctors and nurses ill with symptomatic, active-phase COVID infections are 
being ordered to come back in and get right back to work.


Today, one of the people I quoted yesterday from Twitter, Myoung Cha,
President of Home-Based Care and Chief Strategy Officer for Carbon
Health in San Francisco, formerly Head of Health Strategic Initiatives
for Apple, risked a bit of prognosticating
(https://twitter.com/cha_myoung/status/1477422069251915777):

  1/ There are a lot of takes that this omicron wave will bring us
  closer to “normal” in 2022 when COVID will become endemic and be “just
  like the flu.” A comparison with historical flu seasons shows just how
  far away this really is and how much longer we may need to go.

  2/ The key societal question is what level of mortality & morbidity do
  we accept from COVID in the long run. If influenza is the right
  analogue, then this chart shows that COVID has broken well beyond the
  baseline and “epidemic” threshold of mortality of prior flu seasons.

  [RM: obviously, follow the link to see it, but suffice to say
  that COVID has greatly outstripped flu's mortality, in the US]

  3/ “Just like the flu,” you say?

  Let’s drill into some US data:
  * 11,707 weekly PIC (pneumo, influenza, COVID) deaths since Labor Day
  * At the peak of Delta, ~18,000 weekly PIC deaths 
  This is 3-5x our pre-COVID flu baseline (~3,500 weekly deaths).   
  https://t.co/NXtRoRpJn4

  4/ The mortality rate could be viewed as a proxy for all sorts of
  decisions that individuals, companies, policymakers make to gauge how
  dangerous COVID is and what structural changes we need to make to
  protect lives.

  5/ My heuristic is that things will feel “normal” when the mortality
  rate is <500 deaths per day (i.e., the pre-COVID flu baseline), which
  coincidentally was the rate last summer when we declared
  “independence” from COVID.

  [RM: another chart, this one of confirmed COVID deaths, daily, 2nd
  half 2021]

  6/ A “new normal” of 500 deaths/day from endemic COVID would be a
  non-trivial loss to bear “forever” — this loss of life implies a
  structural change in our healthcare system and economy (@$10 M “value
  per statistical life”, this equates to a $1.8 trillion annual loss for
  the US).

  7/ What will it take to reduce the mortality rate by >50-70%?
  * Omicron ends up being less severe than Delta (yes, but…)
  * The vax/booster rate increases materially (not happening fast enough)
  * Oral therapies live up to their promise in real world (jury’s out)

  8/ While omicron appears to be less severe on a per case basis, the
  sheer volume of new cases right now means the overall pool of people
  susceptible is much larger.  Net-net, a lot of people are still dying
  from a “milder” variant.

  [RM: graph of daily confirmed new COVID deaths per million, US vs. UK]

  9/ Omicron has not yet fully spread to the older, sicker segment of
  the population and the worst could be yet to come with more time.

  [RM: link to https://www.cnbc.com/2021/12/29/covid-who-says-omicron-has-not-spread-widely-among-vulnerable-severity-unclear.html ]

  10/ I already wrote about Paxlovid and why it may not be the silver
  bullet:  

  [RM: link to a tweet thread at
  https://twitter.com/cha_myoung/status/1476080634158219264 ]

  11/ And remember, we have already had remdesivir for a while now in
  our toolkit, which is comparable in efficacy to Paxlovid.

  [RM: link to
  https://twitter.com/antonioregalado/status/1477360207630114838 , 
  the point being that redesivir wasn't a silver bullet, so 
  Paxlovid cannot be expected to be, either]

  12/ Even if we manage to get the death rate down, the volatility of
  COVID surges must be lower for us to treat COVID as an endemic
  phenomenon. Each new variant has brought with it a surge in cases and
  hospitalizations that has stressed our healthcare system.

  13/ The omicron “flash flood” phenomenon compounds the volatility with
  the sheer number of people who are getting sick at the same time — even
  when they aren’t sick enough to be hospitalized — a “soft lockdown” in
  effect.

  [RM: Link to _The Altantic_'s "soft lockdown piece,
  https://www.theatlantic.com/health/archive/2021/12/omicron-soft-lockdown/621121/ ]

  14/ Estimates of 60% of people getting sick from omicron (140 M
  people) in the next few months would be 4-5x the number of people who
  get sick with flu in a “normal” year.

  [RM: Link to
https://www.usatoday.com/story/news/health/2021/12/22/covid-omicron-variant-ihme-models-predict-140-m-new-infections-winter/8967421002/ 
  that says the current wave may yield 140 million new US COVID 
  infections in the next two months .  Note that that's about
  _half the country_ predicted to get significantly ill over the
  next two months.]

  15/ The trillion-dollar question is whether the omicron wave will
  induce durable and strong immunity. After all of the data we have seen
  on waning immunity (both vaccine-based and natural), my bet is the
  immunity will be short-lived and/or weak.

  [RM: Link to https://twitter.com/Bob_Wachter/status/1477334568000651264 ]

  16/ There are even signs of waning immunity in those who have
  so-called “super-immunity”

  [RM: Link to https://www.nature.com/articles/d41586-021-03674-1 ,
  which is about the alarming rate at which both vaccine immunity
  and disease-conferred immunity decline, as shown by Israeli data]

  17/ None of the above takes into account the unknown morbidity that
  comes from a COVID infection (or repeated infections over time). It
  would radically change the game if the risk of long COVID from omicron
  was found to be material.

  18/ It is too late to impact this current wave, but we should be doing
  everything in our power over the next year to get ready for a similar
  (or more devastating) variant next fall.
 

> Who are the USA's vaccine holdouts?  No, surprise.  Not the people you
> thought.  It's young people.
> https://www.salon.com/2021/12/22/are-the-vaccine-holdouts-americas-real-divide-might-not-be-what-you-think/

...like those idiots last night at the Town and Country Village
restaurants, swapping germs and then going home and preparing to
do their part to spread those to others.



> Many businesses are experiencing "soft lockdowns" where they are obliged
> to shut down because of too many people ill.
> https://www.theatlantic.com/health/archive/2021/12/omicron-soft-lockdown/621121/

Expect a _lot_ of that to follow for (at least) the next couple of
months.  So, for example, 10% of the worldwide schedule of airline 
flights today, 4,200 flights, have been cancelled because of staffing 
problems, i.e., airline employees have been unable to work because
they're ill -- according to the Web site "FlightAware".  That site
says 11,000 flights have been cancelled since Christmas.

FAA has also warned of a rising tide of illness among its workers.  When
the air-traffic controllers can't work, nobody flies.

Point is:  I predict that's going to happen broadly around all of the
economy.


> If you do end up needing to isolate, California DPH's isolation
> recommendations are saner than the now-much-mocked new CDC ones:
> https://deadline.com/2021/12/california-covid-quarantine-isolation-guidelines-1234903013/

In particular, California's guidelines strongly recommend ending
isolation only after a negative rapid-test result.  CDC's guidance makes
no such recommendation -- and it is confidently predicted that persons
still infectious with Omicron (particularly the unvaxed) will follow
CDC's guidance and go infect many more people.