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

Have been holding off refreshing this thread, as Census was due to relaunch HPS as HTOPS in January:

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

Word of a moratorium on government communications, makes this seem unlikely:

https://zeroes.ca/@maleve/113869675383946385

Nonetheless HPS reporting was suspended, despite ongoing data collection, in October of the prior administration.

#ThisIsOurPolio #CountLongCovid #CovidIsNotOver #MassDisablingEvent

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

Last period:
https://hcommons.social/@beadsland/113608415072830510

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, becoming MC wave into November. December saw both FLiRT clans and JN.1.11 vie for dominance, only for JN.1 FLiRT to win out.

After skipping update two weeks prior, #CDC broke out XEC.4, as FLiRT KS.1.1 / FLuQE KP.3.3 hybrid XEC family—never having reached majority—being pressed by FLiRT LP.8.1.

New dashboard from Raj givs us more recent GISAID data.

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

Updated GISAID data entering January has FluQE31 KP.3.1.1 / MC and children down to just over a third of all sequences.

FLiRT KS.1.1 / FLuQE KP.3.3 hybrid XEC now approaching two fifths.

JN.1 FLiRT descendant LF.7 is diversifying, while KP.1.1.3 / LP scion LP.8.1, and recombinant XEL—child of JN.1 and FLiRT KS.1.1.2—both stand out.

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

Oh, me?

Just sitting here, wondering how much GISAID data for the U.S. there will be from late January forward. (Raj's dashboard last shows data through the 17th.)

Aware that #CDC long ago would have preferred to stop publishing #covid variants estimates, am expecting to not see same updated this Friday.

They stopped publishing all other related data long before now, and still weren't publishing anything useful wrt #BirdFlu, as of close of last administration.

So now we wait to see how much compliance in advance impacts academic researchers submitting data to a global non-profit. (Let alone how much of U.S. GISAID data may be typically provided by gov't researchers.)

Yes, GISAID was founded in opposition to WHO's proprietary data practices. But also, GISAID's public domain ethos is close enough in spirit to F/OSS that it might just as readily be a target of isolationist fervor.

So, it's wait in see.

#CovidIsNotOver #BirdFluBegins

Welp, so much for that.

Will note that the Census Bureau page for Household Pulse Survey changed to link to the promised relaunched HTOPS some time after the 26th. (This was the last date archive.org managed to crawl the page.)

So they seem to have achieved the relaunch, only for it to now be down. Archive.org never got to crawl the newly launched site.

A FLuQE wavelet opened September, becoming MC wave into November. December saw both FLiRT clans and JN.1.11 vie for dominance, only for JN.1 FLiRT to win out.

Although #CDC did update metadata today, data remains unchanged from two weeks ago.

At that time, FLiRT KS.1.1 / FLuQE KP.3.3 hybrid XEC family—never having reached majority—was being pressed by FLiRT LP.8.1.

New GISAID data from Raj.

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

Updated GISAID data early-mid January has FluQE31 KP.3.1.1 / MC and children down to under a third of all sequences.

FLiRT KS.1.1 / FLuQE KP.3.3 hybrid XEC now over two fifths.

JN.1 FLiRT descendant LF.7 is diversifying, while LP.8.1.1 / NY, MC.8.1, and XEQ (recombinant of FLiRT KS.1.1.2 and KP.3) all stand out.

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

And now data.cdc.gov is offline.

At least the #CDC, unlike the Census Bureau, aren't being coy about why.

Still, an awful lot of compliance happening. They even use the word.

So, about this:

https://hcommons.social/@beadsland/113904501178492408

Raj's dashboard for U.S. hasn't been updated since Jan 31, reflecting submitted data for samples through Jan 24.

Global dashboard was updated this morning, reflecting submitted data through Feb 4.

For North America, Ontario seems to be only division actively submitting data, with over a hundred sequences Jan 25 forward.

Followed by Nebraska (30 sequences), Iowa (21), New Brunswick (13), Colorado (13), Alberta (9), Utah (9), Virginia (5), Nevada (5)…

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

Oh, me? Just sitting here, wondering how much GISAID data for the U.S. there will be from late January forward. (Raj's dashboard last shows data through the 17th.) Aware that #CDC long ago would have preferred to stop publishing #covid variants estimates, am expecting to not see same updated this Friday. They stopped publishing all other related data long before now, and still weren't publishing anything useful wrt #BirdFlu, as of close of last administration. So now we wait to see how much compliance in advance impacts academic researchers submitting data to a global non-profit. (Let alone how much of U.S. GISAID data may be typically provided by gov't researchers.) Yes, GISAID was founded in opposition to WHO's proprietary data practices. But also, GISAID's public domain ethos is close enough in spirit to F/OSS that it might just as readily be a target of isolationist fervor. So, it's wait in see. #CovidIsNotOver #BirdFluBegins

hcommons.social

Holiday programming ticked over another hundred lines for #AnnoPlot #dataviz project since last update:

https://hcommons.social/@beadsland/113842033121034976

Variants was last #datavis being updated. May be the end.

Work in last month includes:

• auto-generated alt-text for variants chart
• rework of markdown utility module
• runtime-option aware captions
• prelim devpie alt-text generation
• tweaks to variant bundling, cluster ancestry & recombinant assignment; also emboss hemming, GISAID import, and footnote plumbing.

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

Attached: 1 image Gave myself some programming time as a holiday treat. Added ~300 lines to #AnnoPlot #dataviz project since last update: https://hcommons.social/@beadsland/113711696418854256 In our post-data era, only variants #datavis is still actively being updated. Work in last month includes: • tweaks to variant bundling, family grouping, cluster ancestry & recombinant assignment • footnote on legend • auto-generated alt-text for variants chart • rework of markdown utility module • tweaks to GISAID imports, bubbles & tile embossing

hcommons.social

After no data two weeks ago, #CDC updates variant estimates.

After January's FLiRT soup (JN.1 and JN.1.11 lineages vying for dominance), we've returned to JN.1.11 soup (FLiRT and FLuQE clusters competing), that began when FLuQE majority ended in November.

There's been insufficient GISAID data for Raj to update U.S. dashboard. Might assume LP.8.1.1 / NY continues to drive growth of LP.8.1 fam.

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

To put recent news—of #influenza deaths exceeding #covid deaths—in context, #CDC now has preliminary #flu burden estimates for season ended Sept 2024.

#PublicHealth surveillance systems have never been adequate for tracking flu, so CDC uses models to arrive at estimates.

By comparison, covid mortality reflects actual deaths reported as due to covid. There's no comparable covid burden modeling being done, so covid deaths believed misreported—as "natural causes" or otherwise—don't show up in this figure.

End of last flu season, annualized covid mortality was more than double estimated influenza burden deaths.

Covid death reporting began sharp deceleration in December, after spike in July/August. Such drop-off in reporting must be taken into account when comparing mortality stats.

Won't likely see flu burden estimates for this new season until early next year. But we know non-#BirdFlu flu is stressing hospitals, and #H5N1 cases have gone unrecognized.

#CovidIsNotOver #BirdFluBegins