[conspire] COVID at the end of 2021

Fri Dec 31 23:50:56 PST 2021

I've been wanting to update the COVID-19 situatio.  The situation
keeps morphing and being difficult to describe simply, but 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.

Most important:  Get the damned booster.  Here's one reason:
https://twitter.com/deirdresm/status/1476986016250556416
https://twitter.com/deirdresm/status/1477004792861900803

And, to quote an S.F. Chronicle article mentioned below:

  Boosters increase protection from severe disease to roughly 90%, and
  raise protection against infection to about 50%.

  Indeed, boosters are so important that many health experts have pushed
  to redefine “fully vaccinated” as including the third dose for Pfizer or
  Moderna vaccine recipients, or the second dose for those who got Johnson
  & Johnson. California has mandated that all health care workers get
  boosters, and many counties have expanded that to include certain
  front-line staff who work with high-risk communities.

  In much of the Bay Area, just over half of those eligible for boosters
  have gotten them. Disease models suggest that number needs to climb, and
  fast, to more like 70% or 80% to prevent hospitals from becoming
  overwhelmed. But it also depends somewhat on who is getting boosted —
  it’s much more important for older adults and others at risk of severe
  illness get boosted than younger adults, though everyone should as soon
  as they are eligible, health officials said.

So, get the damned booster.  You need it.  Stat.

Note Deirdre's key point:  "There is no lifelong coronavirus vaccine 
_for any species_."  All those people bitching about the need for
boosters and claiming it shows "vaccines don't work"?  Ignore them.
They have no clue.

More on that:

  The mean viral shedding for unvaccinated individuals is 8.9 days with
  a standard deviation of 10 days. This is where the 10 day quarantine
  came from. Yes, you read that right, while most will no longer be
  infectious, many are still shedding long after, but they had to put the
  line somewhere. For vaccinated individuals the mean length of viral
  shedding is 2.7 days with a standard deviation of 3. This is just one of
  the many benefits of vaccination. 

https://www.facebook.com/story.php?story_fbid=10158660973225838&id=751020837

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/

The current COVID wave in the USA is CDC-estimated as 59% Omicron 
("new! improved!") and 41% Delta.  Nationwide, it's been skyrocketing
with brutal speed.  

I should distinguish between four perspectives:

1. Humanity.
2. The USA.
3. The Bay Area.
4. "That's nice, but what should I do for myself, my family, my friends?"

They're all important, but differ.  Let's start (mostly) with the Bay Area. 
Erin Allday @ S.F. Chronicle summed up the Bay Area's current status today:
https://www.sfchronicle.com/health/article/omicron-surge-Bay-Area-peak-16739561.php

o  We are in a dramatic surge in cases, _estimated_ to end in late Feb.
   Cases doubled this past _week_.
o  Hospitals are hit, and staggering.  Ability to handle anything is fraying.
o  Schools are going ahead with classroom teaching, which is going to 
   worsen things after the new year.
o  Test kits are in short supply.

Something I didn't know until a few days ago:  _Even though_ PCR tests
are the "gold standard" for accurate detection of viral infection,
there's a problem:  They're kind of useless for answering one of the 
most common questions ("Is it OK for me to end my isolation period?"),
because the test returns positive results for a long tiem after someone
is no longer contagious.  Here's that situation in a nutshell.  Look
at the curve on this graph carefully (which is for the current Omicron +
Delta mix), as it explains the typical timing of exposure to symptoms to
infectiousness to PCR-test-positive:
https://twitter.com/deirdresm/status/1477004792861900803

The "rapid tests" aka "lateral-flow tests" better answer the question
"Am I currently infectious _now_?" -- but are less accurate than is PCR.
https://www.nytimes.com/2021/12/28/health/covid-isolation-period-omicron.html

As it says on the graph, PCR testing can yield a positive result for up
to _83 days_ (average 17 days).  So, it's great for saying whether you
_were_ infected, but terrible at "_Am_ I infected?"

But things are currently so screwed that you may not be able to buy one.
And, even if tests were bountiful, the dramatically shorter incubation
period for Omicron makes it tougher to test:
https://www.theatlantic.com/science/archive/2021/12/omicron-incubation-period-testing/621066/

Some county stats:  A couple of days ago, I would have said "ICU beds
are low (four) with a totally flat curve.  Acute-care bed occupancy has
doubled from 7 to 15 in two weeks, but we have lots of spare capacity."
Thing is, with geometric growth, things can go bad in two days.

ICU beds have gone from four, mid-month, to 11 yesterday.  _Very_ fast,
like this:

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

Are you concerned, yet?  I am.

Acute-care beds have gone up from 7, mid-month, to 20 yesterday -- and
is also jumping dramatically:

Dec. 27: 15
Dec. 28: 14
Dec. 29: 12
Dec. 30: 20

That pattern is being observed in other Bay Area counties, too:
https://www.sfgate.com/coronavirus/article/charts-show-omicron-in-Bay-Area-16731977.php
(But note that the above article is too optimistic because it's from 
Dec. 28th, just before the sharp rise.)

San Mateo County has 3 remaining ICU beds in its regular supply (but has
67 "ICU surge beds" in reserve).  Likewise, the county's main supply of 
available acute-care beds is down to 15 (out of 363 total) -- again,
with 134 "surge beds" in reserve.  

What's ominous is the steep climb _and_ the fact that you cannot stop
Americans from gathering for the holidays
(https://www.theatlantic.com/health/archive/2021/12/omicron-covid-holiday-travel-cancel-plans/621078/).
New Year's Eve is likely to be a colossal superspreader event.

By the way, the county is now 78.2% vaccinated (on a full-popluation
basis).  To my knowledge, the county doesn't yet have stats on "also
boostered", and we need to watch that.  In fact, that'll need to be
the revised definition of "fully vaccinated".  Now, actually.
https://www.theatlantic.com/health/archive/2021/12/fully-vaccinated-cdc-boosters/621037/
https://www.theatlantic.com/health/archive/2021/12/omicron-covid-vaccine-booster/620936/

Next time you hear some idiot claim "vaccination makes little difference
against Omicron", point him/her to this stunning data from NYC's Dept.
of health:  https://twitter.com/cooperlund/status/1476612381153411077
(Here, as throughout this pandemic, the full picture is unavailable
because of a large number of unreported, unrecorded cases.  Also, many lab
people who do testing and data-reporting have been gone for the
holidays, so we're suffering data blindness.
https://www.theatlantic.com/ideas/archive/2021/12/were-about-to-lose-track-of-the-pandemic/621097/)

Here's a similar, night-and-day comparison of case rates for vaxed
vs. unvaxed, for Santa Clara County:
https://twitter.com/cpollock25/status/1476713193183465475

Quoting another _The Atlantic_ article:

  In the past month, we’ve learned that Omicron excels at breaking
  through the first layer of immunity, which is our neutralizing
  antibodies. But our next layer of protection, our T-cell response, seems
  to hold up much better against the variant. If you think of the vaccines
  as a castle-defense system, Omicron is like an invading army that can
  scale walls (i.e., bypass neutralizing-antibody protection) but not
  fight the knights within them (i.e., overcome T-cell protection).
  Boosted Americans are particularly well equipped against the Omicron
  variant, because the third shot increases the number and quality of our
  neutralizing antibodies, which effectively builds up our immunity wall.

https://www.theatlantic.com/ideas/archive/2021/12/omicron-mild-covid-variant-severity/621090/

I always consult the "Nowcast" graphas at
https://calcat.covid19.ca.gov/cacovidmodels/ for the county and state
extimates of R-effective.  Bear in mind that prediction may be more
difficult than usual, but we currently have:

California: 1.59.  Spread of COVID-19 is likely increasing rapidly
San Mateo County:  1.63.  Spread of COVID-19 is likely increasing rapidly.

That's dramatically different, in that California, and especially the
Bay Area, had R-eff well under 1.0 in the recent past.

USA-wide view:  A birds-eye view of how the USA as a _whole_ came to be
screwed, right now, can be read in this Twitter stream:
https://twitter.com/cha_myoung/status/1474293040659374082
In short:  The USA has at no point done the parts that actually work,
such as real contact-tracing and large-scale testing.  And, we may
remain screwed unless/until that happens.

America _has no plan_, other than "get everyone vaccinated", and isn't
even considering doing those things that are  actually necessary.
https://www.theatlantic.com/health/archive/2021/12/omicron-mistakes/621112/

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/

This Dec. 21st article prophetically predicts the meltdown of the
hospitals and urgent-care facilities that's starting to happen _now_:
https://www.theatlantic.com/ideas/archive/2021/12/our-emergency-rooms-arent-ready-for-omicron/621080/

  Omicron Will Overwhelm America’s Emergency Rooms
  Hospitals are already strained, and many health-care workers have little
  left to give.
  By Craig Spencer

Yeah, that.  That's _now occurring_.  Be grateful you're in the Bay Area
(well, most Conspire members are), as it's not _yet_ bad here, but at
least two major hospitals we've heard about, one in Scottsdale, AZ and
the other somewhere in Los Angeles, are out of _body bags_.

And we're about to burn out (and yes, you've heard this before)
essential medical personnel.
https://www.washingtonpost.com/health/2021/12/30/hospitals-staffing-shortages-omicron/

The sudden deluge of infection's difficult to get one's head around --
but look at these graphs of viral load in sewer wastewater in Boston:
https://twitter.com/pbleic/status/1476744765798502407

The societal effects may become severe.  We are entering new territory.

Schools:  They're dead-set on reopening after New Years Day.  Here's why
that's going to be a debacle:
https://www.tvo.org/article/you-cant-open-in-january-an-infection-control-epidemiologist-on-omicron-in-schools

I expect the USA will be in for a new round of wildfire infections after
the schools re-open.

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/

Individual view:  You're probably going to have a dance with Omicron.
Here's an excellent pragmatic guide, to how to handle that:
https://www.theatlantic.com/health/archive/2021/12/omicron-breakthrough-vaccine-testing/621014/
And here's how to distinguish mild-COVID from cold from flu:
https://whdh.com/news/do-you-have-a-cold-the-flu-or-covid-19-experts-explain-how-to-tell-the-difference/

And again, _The Atlantic_ has a sane perspective (from Dec. 22):

  What does all this mean for you? The tough thing about answering this
  question is that I don’t know who “you” are, what your T-cell protection
  is, or how you’re going to spend the holidays. The best way to think
  about total severity in the U.S. is to imagine four concentric circles,
  where the risk of illness increases as you fan outward.

  In the center ring are boosted non-seniors. This group seems quite safe
  from severe illness and well protected against infection. One ring out
  are doubly vaccinated Americans under 65 without immune-system
  complications. This group is more at risk for breakthrough Omicron
  cases—and could spread Omicron cases to more vulnerable people—but seems
  fairly protected against severe illness thanks to T-cell immunity. (As
  for these groups’ long-COVID risk from Omicron, I don’t think we have
  any good information yet. But previous strains have been associated with
  months of labored breathing and impaired lung function.)

  In the third ring are people who are vaccinated, or even boosted, but
  still at-risk. This group, which includes seniors and immune-compromised
  individuals, deserves special care. People in the center-most circles
  should be cautious about mixing households with seniors, because in the
  case of a breakthrough, we can’t be sure that older people’s T-cell
  protection will protect them against severe illness. Remember that,
  among boosted seniors, age still matters: According to the CDC, people
  older than 85 have a COVID fatality risk that is roughly five times
  higher than the typical 65-year-old.

  Finally, the fourth circle represents the broader unvaccinated
  population, both in the U.S. and throughout the world. Omicron seems so
  contagious that, even with an overall milder course of disease, we
  should expect a surge of hospitalizations among the unvaccinated.

Especially for the vaxed, an Omicron infection seems mostly to not be 
not nearly as damaging as prior strains, and a new lab study suggests this
is because Omicron cannot usually get into the lower longs, staying up 
in the bronchial passages, instead:
https://www.livescience.com/omicron-less-severe-disease-early-evidence

Also covered at 
https://www.theatlantic.com/science/archive/2021/12/t-cells-omicron-vaccine-immunity/620995/

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/

Worldwide perspective:

Oh dear.  The USA, Canada, and Europe keep acting as if they can just
ignore or wall off the rest of the world -- and that's a big reason why
we're not winning.  And a lot of humanity looks like it's about to get
creamed.

  WHO says omicron has not spread widely among the vulnerable yet, still
  too early to determine severity
  PUBLISHED WED, DEC 29 20218:14 PM EST

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

THat.  The world at large is much less well protected than we are.
Reliable stats are spotty for lesser-developed countries, but likely
their near future will be grim.

Which brings me to two of Indi Samarajiva's articles on medium.com,
which you should read:
https://gen.medium.com/i-lived-through-collapse-america-is-already-there-ba1e4b54c5fc
https://indica.medium.com/how-omicron-makes-a-mockery-of-herd-immunity-2c2f1cf1c601

Because of the paywall, you may want to browse using Chromium (or Google
Chrome, if you insist) and the Hover Bypass Paywalls extension --
recommended.
https://github.com/nathan-149/hover-paywalls-browser-extension

Samarajiva lists the ways the USA and Europe not only haven't dealt
effectively with the pandemic but has actively hindered humanity 
in doing so.  Read it and get annoyed at how badly we hurt both
ourselves and everyone else.

By the way, I haven't yet decided whether the in-person portion of CABAL
will occur on the upcoming Saturday, Jan. 8th date.  My hunch is that 
if dry weather's predicted, we'll go ahead, but if rain threatens, then
online only.  I'll make an announcement before then.