NCHS estimates of #LongCovid—based on Household Pulse Survey.

HTOPS has yet to publish data, despite having avowedly collected data Oct & Dec:

https://hcommons.social/@beadsland/113728679706939484

Hospital capacity data was ended under prior administration. Only Federal Reserve disability data continues to update.

#ThisIsOurPolio #CountLongCovid #CovidIsNotOver #MassDisablingEvent

[This is first toot of periodically refreshed thread, providing various dataviz of ongoing #pandemic.]

Last period:
https://hcommons.social/@beadsland/113870662111085905

sport of sacred spherical cows (@[email protected])

Attached: 2 images Middle or late last week, Census Bureau updated landing page for the Household Pulse Survey, adding two paragraphs to the introduction [first screencap below]. According to this update, the HPS has not been dormant since last update in October; rather they've been converting over to a new format. The Census Blog (under the category "Random Samplings"), linked to, was apparently published on Sept 16, though there was no obvious link calling it out on various HPS pages before last week. According to said blog, data collection continued in October and December, reflecting an every-other-month sampling strategy, with release of that data to occur with the January re-launch. Unstated is whether the changes will include revision of the underlying questionnaire. A longitudinal design suggests that they will be sampling the same respondents on a repeated basis, rather than an entirely random sample each round. If so, we might anticipate questions being dropped to reduce respondent burden.

hcommons.social

A FLuQE wavelet opened September, cresting as KP.3.1.1 / MC wave into November. FDA's second-guess vaccine target, KP.2, dropped out in December. Updated #CDC estimates indicate we've been in a JN.1.11 soup pretty much since then.

No new variants broken out by CDC, as KP.1.1.3 / LP descendant LP.8.1 approaches majority.

No recent GISAID data—as Raj's dashboard hasn't updated in near a month.

#ThisIsOurPolio #Covid #Covid19 #SARS2 #variants #CovidIsNotOver #CovidIsAirborne #dataviz #datavis

Second time #CDC has reported estimates for more than two regions at a time since October.

To be clear, national data used for chart above are modeled on regional data collection.

LP.8.1 now estimated at majority in Great Lakes, nearing majority in NY/NJ and Mid-Atlantic.

XEC (incl. XEC.4) still around a quarter share in all three regions.

[For color key, see: https://covid.cdc.gov/covid-data-tracker/#variant-proportions]

#ThisIsOurPolio #Covid #Covid19 #SARS2 #variants #CovidIsNotOver #CovidIsAirborne #WearAMask #BetterMasks

COVID Data Tracker

CDC’s home for COVID-19 data. Visualizations, graphs, and data in one easy-to-use website.

Centers for Disease Control and Prevention

In other news, it appears #CDC is investing more energy in the subtle art of sending subliminal semaphore messages via their charts than with collecting data.

LP.8.1 is the first variant to appear poised for dominance since November, so okay, fine.

But when the next dozen or so variants after XEC—many of which were only broken out recently, none of which are terribly successful at the moment—are all some shade or cousin of blue, it does seem rather a bit too on the olfactory-compromised nose.

Updated #CDC estimates show we've pretty much been in a JN.1.11 soup since Dec, until late March, when LP.8.1 took majority.

Data collection continues to be a low priority nationally, as only one region (NY/NJ) has enough data for CDC to plot.

No new variants broken out, yet CDC seems to have resources to tailor their color key: https://hcommons.social/@beadsland/114163320179234281

Raj's dashboard was updated on Sunday.

#ThisIsOurPolio #Covid #Covid19 #SARS2 #variants #CovidIsNotOver #CovidIsAirborne #dataviz #datavis

sport of sacred spherical cows (@[email protected])

Attached: 1 image In other news, it appears #CDC is investing more energy in the subtle art of sending subliminal semaphore messages via their charts than with collecting data. LP.8.1 is the first variant to appear poised for dominance since November, so okay, fine. But when the next dozen or so variants after XEC—many of which were only broken out recently, none of which are terribly successful at the moment—are all some shade or cousin of blue, it does seem rather a bit too on the olfactory-compromised nose.

hcommons.social

Updated #CDC estimates show we've pretty much been in a JN.1.11 soup since Dec, until late March, when LP.8.1 took majority.

Data collection continues to be a low priority nationally, as exactly zero regions have enough data for CDC to plot.

No new variants broken out, yet CDC seems to have resources to tailor their color key: https://hcommons.social/@beadsland/114163320179234281

Raj's dashboard was updated on today.

#ThisIsOurPolio #Covid #Covid19 #SARS2 #variants #CovidIsNotOver #CovidIsAirborne #dataviz #datavis

sport of sacred spherical cows (@[email protected])

Attached: 1 image In other news, it appears #CDC is investing more energy in the subtle art of sending subliminal semaphore messages via their charts than with collecting data. LP.8.1 is the first variant to appear poised for dominance since November, so okay, fine. But when the next dozen or so variants after XEC—many of which were only broken out recently, none of which are terribly successful at the moment—are all some shade or cousin of blue, it does seem rather a bit too on the olfactory-compromised nose.

hcommons.social

Updated #CDC estimates show we'd pretty much been in a JN.1.11 soup since Dec, until late March, when LP.8.1 took majority.

Data collection continues to be a low priority nationally, as exactly zero regions have enough data for CDC to plot.

Two children of LF.7.7, dot1 and dot2, broken out by CDC, together with PA.1, a grandchild of MC.10.

Raj's dashboard was last updated a week ago today.

#ThisIsOurPolio #Covid #Covid19 #SARS2 #variants #CovidIsNotOver #CovidIsAirborne #dataviz #datavis

#CDC continues with motif of painting covid blue:

https://hcommons.social/@beadsland/114163320179234281

Newest variants added have been assigned light royal blue (PA.1), ultramarine blue (LF.7.7.1) and periwinkle lavender blue (LF.7.7.2).

They're going so hard on Variant Blue No Matter Which, they've exhausted the palette, LF.7.7.2's color key being visually indistinguishable from that of LF.7.2.1 (crocus lavender blue).

The difference is only evident in the hex codes. LF.7.7.2 is # 8686FF, where LF.7.2.1 is # 8480FF.

sport of sacred spherical cows (@[email protected])

Attached: 1 image In other news, it appears #CDC is investing more energy in the subtle art of sending subliminal semaphore messages via their charts than with collecting data. LP.8.1 is the first variant to appear poised for dominance since November, so okay, fine. But when the next dozen or so variants after XEC—many of which were only broken out recently, none of which are terribly successful at the moment—are all some shade or cousin of blue, it does seem rather a bit too on the olfactory-compromised nose.

hcommons.social

Another hundred lines for #AnnoPlot #dataviz project in March:

https://hcommons.social/@beadsland/113977456216970296

Work in March included:

• accommodating less frequent updates to GISAID data
• debug flattening in preparation for tilt
• mixin for checking orientation and helper class for rotation and mirroring
• rework and refactor tilt calculations for inline bubble charts
• refactor degrees str method to helper class and consolidate older asdegrees util method

Updated #CDC estimates show we'd pretty much been in a JN.1.11 soup since Dec, until late March, when LP.8.1 took majority.

Data collection continues to be low priority nationally—as exactly zero regions have enough data for CDC to plot.

CDC breaks out recombinant XFC from FLiRT parent LF.7 . (Our dataviz now identifies parentage for each recombinant.) Raj's dashboard was last updated today.

#ThisIsOurPolio #Covid #Covid19 #SARS2 #variants #CovidIsNotOver #CovidIsAirborne #dataviz #datavis

With newest, quickly ascending recombinant—XFC—#CDC finally drops motif of painting covid blue:

https://hcommons.social/@beadsland/114410540100025447

Color chosen for most recently broken out variant? Brown. Which is to say, dark orange.

They'd been going so hard on Variant Blue No Matter Which, they'd exhausted the palette, LF.7.7.2's color key being visually indistinguishable from that of LF.7.2.1 (crocus lavender blue).

The difference is only evident in the hex codes. LF.7.7.2 is # 8686FF, where LF.7.2.1 is # 8480FF.

sport of sacred spherical cows (@[email protected])

Attached: 1 image #CDC continues with motif of painting covid blue: https://hcommons.social/@beadsland/114163320179234281 Newest variants added have been assigned light royal blue (PA.1), ultramarine blue (LF.7.7.1) and periwinkle lavender blue (LF.7.7.2). They're going so hard on Variant Blue No Matter Which, they've exhausted the palette, LF.7.7.2's color key being visually indistinguishable from that of LF.7.2.1 (crocus lavender blue). The difference is only evident in the hex codes. LF.7.7.2 is # 8686FF, where LF.7.2.1 is # 8480FF.

hcommons.social

Since March, LP.8.1 has been dominant. FDA designates same as vaccine target, on very week its share has plateaued.

Data collection continues to be low priority nationally—as exactly zero regions have enough data for CDC to plot.

No new variants broken out by #CDC, although the "razor blade throat" variant, NB.1.8.1, remains significant in GISAID.

Raj's dashboard was last updated yesterday.

#ThisIsOurPolio #Covid #Covid19 #SARS2 #variants #CovidIsNotOver #CovidIsAirborne #dataviz #datavis

Oh, dear.

It seems that my move to assign a name to a variant that wanted a name but (apparently at the time) didn't have any has gotten some traction.

This despite, unbenownst to me, the variant already having been given a name the same day as my chart dropped.

Not even half a dozen sources, apparently all carrying the same syndicated article, mentioned the symptom "razor blade throat" (which am given to understand was old Chinese idiom for severe sore throat well before covid).

Myself said "Well, that's evocative. Am gonna use it to hang a lantern on this new variant in my chart, given that it's otherwise hidden at the bottom of a legend, what with CDC not having broken it out & having only GISAID data to show its significance in the U.S."

Now folk are talking about the appellation as authoritative.

Gawsh.

My apologies to T. Ryan Gregory and the rest of the WHN folk who came up with the apt, if not as exciting, "Nimbus" for the same strain.

Surprised anyone even saw my chart.

Another four hundred lines for #AnnoPlot #dataviz project since last round of work in March:

https://hcommons.social/@beadsland/114475406737012154

Work in May/early June included:

• tweaks to this pie chart, chirp logging, annoplot legend classes and newspaper columns orphan control;

• tweaks to variants #datavis: tree constructor process, alt-text pruning internals, legend subclass, tree constructor methods, name collisions and recombinant lineage assignments, family groupings and legend headers, variant mocking, title overhang, tile embossing, growth calculation, and captions, all including significant refactoring;

• migration of bug to legend footer, and build out of prioritized legend footnotes for prominent lineages and recombinants, including recombinant chains, with calculation and approximation of historical peaks, and pruning for space constraints of both alt-text and footer proper.

Just dropping this here for reference.

Essentially, today's fortnightly variant proportions data has been indefinitely postponed.

Not by a three-day weekend (as per two weeks ago) but by a "software issue".

In other news, the "razor-blade throat" XDV scion #Nimbus NB.1.8.1 was near 14% of GISAID data for the fortnight two weeks prior, per Raj's dashboard dropped today.

Nimbus had not been broken out by CDC as of the last data drop.

#CDC #covid-19 #XFG #XFC #PublicHealth

Since March, LP.8.1 has been dominant. FDA designated same as vaccine target, on very week its share had plateaued.

Data collection continued to be low priority nationally—as exactly zero regions had enough data for CDC to plot.

#CDC released no new data this week, due to "software issue". This after data was delayed two weeks ago by holiday weekend.

The "razor-blade throat" XDV scion, Nimbus NB.1.8.1, near doubled its share in GISAID from two weeks prior, per Raj's dashboard, updated today.

#ThisIsOurPolio #Covid #Covid19 #SARS2 #variants #CovidIsNotOver #CovidIsAirborne #dataviz #datavis

You don't say, #CDC?

Notably, CDC has added Nimbus NB.1.8.1, scion of "razor-blade throat" XDV, as of chart published today, due last Friday. Banner advising of a "software" error impacting assignment of some recombinants remains at the top of page.

Over the past three fortnights, CDC's estimate for NB.1.8.1 climbs form 5% share (4/27-5/10) to 15% share (5/11-5/24) to 37% share (5/25-6/7).

But lets move to "longer reporting periods…to provide reliable estimates."

#CDC #Covid #PublicHealth

To be clear, this ain't about federal shenanigans.

The "low number of sequences being reported to" #CDC is reflected by March being last time regional Nowcast map for then current period displayed for any of ten HHS regions. (NY/NJ on its lonesome.)

Last time even half of HHS regions had estimates available was October.

Last time all ten regions reported, July 2023.

CDC moved from weekly to fortnightly reporting in April 2023.

Low numbers of sequences being reported for well over two years.

FDA vaccine target LP.8.1, dominant since March, plateaued in April. June sees Nimbus NB.1.8.1, scion of "razor-blade throat" XDV, push LP.8.1 out of majority.

#CDC adds NB.1.8.1 only in latest, late-published public dataset. "Software error" that heralded data delay remains unresolved. Hatching for "less reliable" data reflects "low numbers of sequences being reported".

Raj's dashboard, updated Sunday, shows Nimbus diversifying in May.

#ThisIsOurPolio #Covid #Covid19 #SARS2 #variants #CovidIsNotOver #CovidIsAirborne #dataviz #datavis

All those dot-hatched tiles, where there's not even space for the name of variants to be listed? That indicates the data has been flagged as "less reliable".

That's not federal government.

That's 50 state health agencies not reporting sufficiently to give the #CDC anything more reliable to base an estimate on.

The process of disassembling #PublicHealth has accelerated, yes.

It was already careening off a cliff years ago.

Two weeks ago, Mike Honey noted that there are three recombinants that have arrived on Doppelgänger spike proteins, namely XFJ, XFM, and XFP:

https://aus.social/@mike_honey_/114611686572899925

Last week, Xu Zhu (HT D. Focosi) identified a superset of recombinants that have all arrived at a pairing of LF.7's NTD with RBD from elsewhere, namely: XFC, XFG, XFH, XFJ, XFM, XFN and XFP:

https://x.com/dfocosi/status/1931351676880879856

Above variants chart #AnnoPlot script is now updated to favor grouping by such emerging clusters preferentially over grouping by legacy ancestors.

As a reminder, recombinants happen when more than one virus strain is actively replicating in the same organism.

Here, that means two simultaneous infections, from different sources, finding a home in the same person.

When #PublicHealth is a priority, this should be a rare occurrence.

There are seven unique recombinants identified in this new cluster, alone.

#ThisIsOurPolio #Covid #Covid19 #SARS2 #variants #CovidIsNotOver #CovidIsAirborne #dataviz #datavis