[conspire] Seeing the back of Omicron v. 1.0 (BA.1 lineage)

[Rick Moen]

I haven't done a COVID summary in a few weeks because, frankly, things
have been unsettled and a bit confusing.  I believe we're finally seeing
the back of the Omicron BA.1-strain "wave".  Here's what appears to be
going on:

1.  Hospital bed COVID occupancy (counted separately for ICU and acute care) 
had been elevated but is now falling.  See, for S.M. County:
https://www.smchealth.org/data-dashboard/hospital-data
News reports likewise say it's falling steeply in L.A. County.

2.  A truly genius metric for how much COVID viral infectious load is
currently active, checking for two SARS-CoV-2 RNA genes in sewage
wastewater, a knack pioneered by (among others) Santa Clara County, 
is also falling.  https://covid19.sccgov.org/dashboard-wastewater

3.  The community infectious-spread rate metric "R-effective", estimated
by https://calcat.covid19.ca.gov/cacovidmodels/ (go to Nowcast) for both
the state as a whole and for Bay Area counties has dropped reassuringly 
down _way_ below the 1.0 mark where infection is neither spreading nor 
dropping.  Therefore, the estimate predicts that rate of spread is
shrinking rapidly.  R-eff for the state is estimated at 0.65 ("Spread of
COVID-19 is likely decreasing").  San Mateo County weighs in at 0.61,
which is fantastic given relatively high pop. density.

4.  Then there's the concept of "case" counts.  Let's talk about that,
because there's a big problem.  What's a case?  A "case" comes into
existence when someone gets diagnosed for COVID and gets PCR-tested 
(or a similar type of molecular-amplification test).  Each such incident
is counted once on the date of test confirmation.  There is no effort
to make the "case" number accurately reflect how many ongoing cases
exist on a given day.  And:  The big problem is that very few people get
PCR-tested.  Also, unlike (say) Taiwan, the USA does a pitifully
ineffective, almost nonexistent job of contact-tracing to find community
infection.
https://www.smchealth.org/data-dashboard/county-data-dashboard says in
very small type:

  Because of limited testing capacity, the number of cases detected
  through testing represents only a small portion of the total number
  of the total number of likely cases in the County. [...]

(That typing brought to you by LASIK.)



I've typically ignored the county's (and CDC's) statistics of "case" 
numbers, both locally and elsewhere, because any number cited is
going to almost laughably underreport _real_ new infections.  A rather 
large fraction of real, in-the-field new infections never get PCR-tested
at all, both symptomatic and asymptomatic.  Additionally, the degree of
underreporting is inevitably going to differ from place to place -- 
if only because wealthy-leaning, medical-facility-rich places like the
Bay Area have greater access to, and use of, PCR test kits than other
places.  ("Rapid" aka "lateral flow" tests aren't very available,
either, have some reliability and accuracy problems, and are appropriate
at a different time from PCR test kits, something I'll not cover
further, here.)

S.M. County says on
https://www.smchealth.org/data-dashboard/criteria-lifting-indoor-mask-mandate
that we should visit CDC's Web site for the most recent county case rate
stats.  Following the link, and picking our county at
https://covid.cdc.gov/covid-data-tracker/#county-view , 
we see

   Community Transmission: High (red)
   Case Rate per 100k:  256.47

CDC defined "high" as anywhere that new daily case rates are greater
than or equal to 100 cases per 100k population -- or if 10% or more of
PCR & similar tests have returned positive over the prior 7 days.  So,
we're 2.5x higher than the "high" boundary, as to case rate per 100k.

CDC claims the corresponding daily-new-cases number for the USA as a
whole, for most recent reporting (most recent 7 days) is a daily average
of 614.6 cases per 100k population -- much worse than locally.

What does that really mean, though?  One complication is that this is an
average over a week's worth of daily numbers.  It's a smeared metric
blending the recent with the old.  Also, there's a weird time
progression.  With the current Omicron strain, host humans typically get
a high level of viral load in their upper respiratory tract and start
being extremely infectious to others long before they develop symptoms
(if ever), and then for a while the infection becomes PCR-detectable,
and then further on, the infection itself fades away, and as it fades
away, symptoms start showing up (if they ever will) and most symptoms
are "sequelae" -- effects that occur because your immune system has
belatedly started freaking out even though the viral presence is mostly
or entirely gone.

It follows that hospitalisation tends to be a _trailing_ indicator of
community infection.  So, S.M. County's hospitalisation rates staring to
fall suggests the actual infection peaked a while (weeks) further back.

Anyway, "cases":  Pick San Mateo County on
https://covid.cdc.gov/covid-data-tracker/#county-view?list_select_county=06081
and look at the graph of "Daily Cases - 7-Day Moving Average", currently 
showing Tue, Jan 21st 2020 - Sun, Feb 6th 2022.  Look at that gigantic,
astonishingly steep vertical spike, rising up into the sky like Olympus
Mons.  Use the slider to adjust horizontal scale:  The spike is
basically December 19th to the present.  That's Omicron going through
people (mostly the unvaxed) like friggin' wildfire.  The peak was about
Jan 15th (a week after January's CABAL day); rapid falloff in the 3
weeks since then.  Again, that tracks with my inference about the
hospital stats.


81.3% of my county, counting all ages, is now fully vaccinated.  ("All ages"
means it includes children not qualified yet to receive the vaccine.)
About 60% are boostered.  Comparable figure for the USA as a whole is
63% fully vaxed, 41% boostered.  

Boosters make a hefty difference for level of protection against serious
disease and hospitalisation.  If you haven't gotten a booster, do it
_now_.  It's already paid for by us taxpayers.  You're welcome.


There are all sorts of reasons for vaccination _and_ getting your
antibodies topped off by a booster.  For one thing, we _may_ be starting
to see the end of this, but that's nothing like a safe bet.  Just
because we're tired of SARS-CoV-2 doesn't mean it's tired of us.
For one thing, an Omnicron Mark II variant, the BA.2 lineage, 
recently started ravaging Denmark and is now showing up in the UK and
maybe soon on these shores.  It's a bit further mutated, and similar in
many ways but even-faster spreading (about 30% more transmissible).
https://www.washingtonpost.com/business/what-we-knowabout-fast-spreading-omicron-subvariant-ba2/2022/02/02/5b578148-8425-11ec-951c-1e0cc3723e53_story.html
https://www.bbc.com/news/health-60233899
As the WashPo article covers, many questions of interest don't yet have
clear answers, as it's early days, for "BA.2".  

It _is_ clear that vaccinated persons, even if they are infected and
show symptoms, are much less likely to infect others.
https://www.cnbc.com/2022/01/31/the-new-omicron-subvariant-is-more-contagious-but-vaccinated-people-are-less-likely-to-spread-it-study-finds.html
It appears that the underlying reason is that infected vaccinated
people tend to carry much lower viral loads.

Questions for not just BA.2 but all earlier (and future) variants
include "How common is repeated reinfection?" (probably pretty common,
despite claims of disease-conferred and/or vaccine-conferred immunity)
and "What are the possible or likely long-term health consequences of
infection?" (a very worrying unknown).


What I'm leading up to is:  We'll be on for in-person (hybrid) CABAL,
this coming Saturday.  As always, full vaccination will be checked.
Boosters are recommended, but will not be required.  Meeting
announcement will follow.