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hometown - Link to source

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

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

hcommons.social/@beadsland/113…

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:
hcommons.social/@beadsland/113…

Chart: Estimates of Long Covid: Extrapolated to Entire U.S. Population Data: Census Bureau, Nat'l Cntr for Health Stats, Dept of Health & Human Svcs, Bureau of Labor Stats (via FRED), CDC [ beadsland on Ko-fi ] Line chart, from Apr 2022 to date, of: • Ever Experienced Long Covid for 3+ Months (60.3M as of Sep 16) • Reported Staffed Hospital Beds (2.1K per Million) [Was 2.3K Apr '22] • Population 16+ With a Disability — Labor Stats (34.3M) [Apr '22: 32.7M] • Now Living with LC (17.9M) • Current Activity Limitations from LC (14.8M) • Significant Limitations (4.4M) Caption (in part): Household Pulse Survey (HPS)…an Internet questionnaire…by…Census Bureau…includes questions regarding “any symptoms lasting 3 months or longer that you did not have prior to having coronavirus or COVID-19.” [Note] that the list of long-term symptoms, provided for this question, may not reflect all sequelae of covid infection, e.g., systemic organ damage or increased susceptibility to subsequent infections and other adverse health outcomes. NCHS uses HPS responses to estimate incidence of [LC] in adult population. With [retraction & new studies] now assume U.S. under 18 population (22% of total) meet criteria for [LC] at same rate as adults. Census…was due to relaunch Household Pulse Survey (HPS) as Household Trends and Outlook Pulse Survey (HTOPS)…January 2025….had been no relaunch as of [Jan 20].…now is word of a general moratorium on…executive branch agencies communicating with the public….

sport of sacred spherical cows (@beadsland@hcommons.social)

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].
hcommons.social
This entry was edited (4 months ago)
in reply to sport of sacred spherical cows

hometown - Link to source

sport of sacred spherical cows

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

Chart: Estimated U.S. Variant Proportions by Common Name Sources: Centers for Disease Control, CoV-Lineages, NYITCOM Research, Daniele Focosi, World Health Network, others [ beadsland on Ko-fi ] Reskin of CDC's Variants Nowcast, and any significant variants in GISAID not broken out by CDC. Five bar-style tree-charts, for fortnights through March 2–15. Legend of last fortnight, organized by subheadings of color-grouped families and convergent clusters. Percentages overlay each color key, reflecting share as of most recent tree-chart. Essentially all WHO-Vaccine-Target JN.1. JN.1.11 accounts for over three fifths; JN.1.11 + FLiRT for near half. For fortnight of 1/19–2/1, packed bubble charts fill single-variant tiles, indicating diversification of those variants (per GISAID) that wouldn't otherwise be apparent from CDC's Nowcast. Legend: LP.8.1 [purple]: 47% - LP.8.1.1 / NY† & other LP.8.1 JN.1 + FLiRT-KS [browns]: 26% - XEC.2†, XEC.8† & other XEC 2% - XEC.4 2% - XEQ ⅒% - other KS.1 JN.1.11 [greens]: ¾% - KP.3 15% - MC.10.1, MC.28.1, MC.19, MC.1 & other KP.3.1.1 / MC JN.1 + FLiRT [reds]: 4% - LF.7 3% - LB.1.3.1 / NL 0% - LB.1 JN.1.11 + FLiRT [blues]: ½% - XEK 0% - KP.2.3 & KP.1.1.3 / LP Other [greys]: ½% - JN.1.16 ⅐% - other WHO-Vaccine-Target JN.1 ⅒% - Other (not specified) † Dagger variants are not broken out by CDC, yet represent a significant share of recent GISAID sequences.
in reply to sport of sacred spherical cows

hometown - Link to source

sport of sacred spherical cows

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: covid.cdc.gov/covid-data-track…]

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

Map: Nowcast Estimates for 3/2/2025 - 3/15/2025 by HHS Region Source: Centers for Disease Control Map shows pie charts for three of ten regions, reflecting regional estimated proportions for specimens collected for the most recent biweekly reporting period. Bold text over Canada portion of map reads: "Nowcast estimates are only available for HHS regions having at least 300 sequences in the two weeks ending 02/15/2025". Dominant strains by tracked region: NY/NJ: LP.8.1 (orange) 47%, XEC (clover) 22%, LF.7 (dirty blue) 5%, LB.1.3.1 (fountain blue) 5%. Mid-Atlantic: LP.8.1 (orange) 42%, XEC (clover) 25%, MC.28.1 (flat blue) 8%, KP.3.1.1 (sea bluish cyan) 5%. Great Lakes: LP.8.1 (orange) 60%, XEC (clover) 24%, KP.3.1.1 (sea bluish cyan) 4%. Of ten regions, seven regions are blank. ALT-text by beadsland at ko-fi.

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 reply to sport of sacred spherical cows

hometown - Link to source

sport of sacred spherical cows

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.

Cropped screen-capture of CDC Nowcast, showing bar charts for fortnights ending 3/1/25 and 3/15/25, together with a legend showing lineage estimates for the USA region. LP.8.1, at 47% share, has been assigned bright carrot orange. XEC, at 26% share, is a muted pastel green. The next few variants, all 5% or less, are assigned the following colors: sea bluish cyan (a/k/a eastern blue), science blue, dirty wedgewood blue, flat muted blue, fountain moonstone blue, green teal, medium slate blue, mid blue. [All color names derived from ArtyClick's Color Name Finder tool.]
in reply to sport of sacred spherical cows

hometown - Link to source

sport of sacred spherical cows

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: hcommons.social/@beadsland/114…

Raj's dashboard was updated on Sunday.

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

Chart: Estimated U.S. Variant Proportions by Common Name Sources: Centers for Disease Control, CoV-Lineages, NYITCOM Research, Daniele Focosi, World Health Network, others [ beadsland on Ko-fi ] Reskin of CDC's Variants Nowcast, and any significant variants in GISAID not broken out by CDC. Five bar-style tree-charts, for fortnights through March 16–29. Legend of last fortnight, organized by subheadings of color-grouped families and convergent clusters. Percentages overlay each color key, reflecting share as of most recent tree-chart. Essentially all WHO-Vaccine-Target JN.1. LP.8.1 accounts for well over half; JN.1 + FLiRT for over a quarter. For fortnight of 3/2–3/15, packed bubble charts fill single-variant tiles, indicating diversification of those variants (per GISAID) that wouldn't otherwise be apparent from CDC's Nowcast. Legend: LP.8.1 [purple]: 55% - LP.8.1.1 / NY† & other LP.8.1 XEC [browns]: 21% - XEC.2† & other XEC 2% - XEC.4 JN.1.11 + FLuQE [greens]: 6% - MC.10.1 & MC.19 3% - MC.28.1 2% - XEQ 4% - MC.1 & other KP.3.1.1 / MC ⅘% - other KP.3 JN.1 + FLiRT [reds]: 4% - LF.7 2% - LB.1.3.1 / NL JN.1.11 + FLiRT [blues]: ½% - XEK 0% - KP.2.3 & KP.1.1.3 / LP Other [greys]: ⅖% - JN.1.16 ⅙% - other WHO-Vaccine-Target JN.1 0% - Other (not specified) † Dagger variants are not broken out by CDC, yet represent a significant share of recent GISAID sequences.

sport of sacred spherical cows

2025-03-14 23:13:41

hometown - Link to source

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.

Cropped screen-capture of CDC Nowcast, showing bar charts for fortnights ending 3/1/25 and 3/15/25, together with a legend showing lineage estimates for the USA region. LP.8.1, at 47% share, has been assigned bright carrot orange. XEC, at 26% share, is a muted pastel green. The next few variants, all 5% or less, are assigned the following colors: sea bluish cyan (a/k/a eastern blue), science blue, dirty wedgewood blue, flat muted blue, fountain moonstone blue, green teal, medium slate blue, mid blue. [All color names derived from ArtyClick's Color Name Finder tool.]

This entry was edited (3 months ago)
in reply to sport of sacred spherical cows

hometown - Link to source

sport of sacred spherical cows

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: hcommons.social/@beadsland/114…

Raj's dashboard was updated on today.

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

Chart: Estimated U.S. Variant Proportions by Common Name Sources: Centers for Disease Control, CoV-Lineages, NYITCOM Research, Daniele Focosi, World Health Network, others [ beadsland on Ko-fi ] Reskin of CDC's Variants Nowcast, and any significant variants in GISAID not broken out by CDC. Five bar-style tree-charts, for fortnights through Mar 30–Apr 12. Legend of last fortnight, organized by subheadings of color-grouped families and convergent clusters. Percentages overlay each color key, reflecting share as of most recent tree-chart. Essentially all WHO-Vaccine-Target JN.1. LP.8.1 accounts for over three fifths; JN.1 + FLiRT for near a quarter. For fortnight of 3/16–3/29, packed bubble charts fill single-variant tiles, indicating diversification of those variants (per GISAID) that wouldn't otherwise be apparent from CDC's Nowcast. Legend: LP.8.1 [purple]: 64% - LP.8.1.1 / NY† & other LP.8.1 XEC [browns]: 2% - XEC.4 15% - other XEC JN.1.11 + FLuQE [greens]: 5% - MC.10.1 & MC.19 1% - MC.28.1 2% - XEQ & other KP.3 3% - MC.1 & other KP.3.1.1 / MC JN.1 + FLiRT [reds]: 4% - LF.7 2% - LB.1.3.1 / NL ¾% - LF.7.2.1 / PC JN.1.11 + FLiRT [blues]: ½% - XEK 0% - KP.2.3 Other [greys]: ⅓% - JN.1.16 ⅒% - other WHO-Vaccine-Target JN.1 0% - Other (not specified) † Dagger variant is not broken out by CDC, yet represent a significant share of recent GISAID sequences.

sport of sacred spherical cows

2025-03-14 23:13:41

hometown - Link to source

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.

Cropped screen-capture of CDC Nowcast, showing bar charts for fortnights ending 3/1/25 and 3/15/25, together with a legend showing lineage estimates for the USA region. LP.8.1, at 47% share, has been assigned bright carrot orange. XEC, at 26% share, is a muted pastel green. The next few variants, all 5% or less, are assigned the following colors: sea bluish cyan (a/k/a eastern blue), science blue, dirty wedgewood blue, flat muted blue, fountain moonstone blue, green teal, medium slate blue, mid blue. [All color names derived from ArtyClick's Color Name Finder tool.]

in reply to sport of sacred spherical cows

hometown - Link to source

sport of sacred spherical cows

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

Chart: Estimated U.S. Variant Proportions by Common Name Sources: Centers for Disease Control, CoV-Lineages, NYITCOM Research, Daniele Focosi, World Health Network, others [ beadsland on Ko-fi ] Reskin of CDC's Variants Nowcast, and any significant variants in GISAID not broken out by CDC. Five bar-style tree-charts, for fortnights through April 13–26. Legend of last fortnight, organized by subheadings of color-grouped families and convergent clusters. Percentages overlay each color key, reflecting share as of most recent tree-chart. Essentially all WHO-Vaccine-Target JN.1. LP.8.1 accounts for over two thirds; JN.1 + FLiRT for near a quarter. For fortnight of 3/30–4/12, packed bubble charts fill single-variant tiles, indicating diversification of those variants (per GISAID) that wouldn't otherwise be apparent from CDC's Nowcast. Legend: LP.8.1 [purple]: 69% - LP.8.1.1 / NY† & other LP.8.1 JN.1 + FLiRT-KS [browns]: 1% - XEC.4 ¾% - XEQ 10% - other XEC JN.1 + FLiRT [reds]: 6% - LF.7.7.2 4% - LF.7.7.1, LF.7 & LF.7.2.1 / PC 2% - LB.1.3.1 / NL JN.1.11 [greens]: 3% - MC.10.1, MC.28.1 & MC.19 2% - PA.1 ½% - KP.3 2% - MC.1 & other KP.3.1.1 / MC XEK [blue]: ⅜% - XEK Other [greys]: ⅙% - JN.1.16 ⅒% - NB.1† & other WHO-Vaccine-Target JN.1 ¼% - Other (not specified) † Dagger variants are not broken out by CDC, yet represent a significant share of recent GISAID sequences.
This entry was edited (2 months ago)
in reply to sport of sacred spherical cows

hometown - Link to source

sport of sacred spherical cows

#CDC continues with motif of painting covid blue:

hcommons.social/@beadsland/114…

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.

Screencrop of legend from CDC's latest variant proportions dataviz, showing top 14 variants (all those estimated with at least 1% share) with their respective color keys. With the exception of LP.8.1 (orange), XEC (clover), XEC.4 (green teal) and KP.3 (Turkish rose) all of the variants displayed have been assigned various shades of blue. Legend keys, from top to bottom: orange, clover green, periwinkle lavender blue, fountain blue, science blue, ultramarine blue, light royal blue, green teal, dirty blue, sea blue, flat blue, medium slate blue, Turkish rose, crocus lavender blue. All color names sourced ArtyClick's color name finder.

sport of sacred spherical cows

2025-03-14 23:13:41

hometown - Link to source

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.

Cropped screen-capture of CDC Nowcast, showing bar charts for fortnights ending 3/1/25 and 3/15/25, together with a legend showing lineage estimates for the USA region. LP.8.1, at 47% share, has been assigned bright carrot orange. XEC, at 26% share, is a muted pastel green. The next few variants, all 5% or less, are assigned the following colors: sea bluish cyan (a/k/a eastern blue), science blue, dirty wedgewood blue, flat muted blue, fountain moonstone blue, green teal, medium slate blue, mid blue. [All color names derived from ArtyClick's Color Name Finder tool.]

in reply to sport of sacred spherical cows

hometown - Link to source

sport of sacred spherical cows

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

hcommons.social/@beadsland/113…

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

Chart: Annoplot Dataviz Library*: Project Profile Subtitle: 10.9K lines† across component modules and significant submodules. Multi-level pie chart organized into six major categories by color. Each outer wedge shows a tally of number of lines for that sub-component. Green wedge for variants/rajdash/suds exploded; also, slightly, blue util wedge. A legend is split across both sides of the chart. Each key mirrors one of the wedges on the dual pie chart, along with a sentence or two description of each (sub)component thereby represented. Caption: * Pre-release development version 2025-03-31. † Python, Markdown, C, and Elixir source files. Blank lines omitted form tallies. Exploded wedges reflect proportions of lines changed in prior 30 days. Dotted areas represent non-blank comment lines and Markdown. Wedges: 🔴 levels 🧀 [blank wedge] - 460, 🧀 hospitals - 282 🟣 chirp 🧀 [blank] - 290, 🧀 audio - 241 🔵 annoplot 🧀 [blank] - 549, 🧀 artists - 351, 🧀 artists/deco - 503, 🧀 artists/legend - 145, 🧀 …/legend/deco - 234, 🧀 artists/pie - 287, 🧀 artists/text - 324, 🧀 coord - 583, 🧀 coord/base - 259, 🧀 margin - 255, 🧀 util - 535 🟢 tiop 🧀 [blank] - 244, 🧀 bullseye - 321, 🧀 capacity - 455, 🧀 devpie - 433, 🧀 devpie/slice - 234, 🧀 variants - 582, 🧀 variants/orchard - 416, 🧀 variants/rajdash - 168, 🧀 variants/rajdash/suds - 289,🧀 variants/tree - 414, 🧀 …/tree/branch - 266 🟤 bots 🧀 [blank] - 181, 🧀 talky - 75, 🧀 talky/talky - 746 ⚫ . [period by itself] 🧀 [blank] - 427, 🧀 TODO.md - 348

sport of sacred spherical cows (@beadsland@hcommons.social)

Attached: 1 image 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.
hcommons.social
This entry was edited (1 month ago)
in reply to sport of sacred spherical cows

hometown - Link to source

sport of sacred spherical cows

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

Chart: Estimated U.S. Variant Proportions by Common Name Sources: CDC, Cov-Lineages, NYITCOM, D. Focosi, WHN, others [ beadsland on Ko-fi ] Reskin of CDC's Variants Nowcast, and any significant variants in GISAID not broken out by CDC. Five bar-style tree-charts, for fortnights through 4/27–5/10. Legend of last fortnight, organized by subheadings of color-grouped families and convergent clusters. Percentages overlay each color key, reflecting share as of most recent tree-chart. LP.8.1 accounts for over two thirds. For 4/13–4/26, packed bubble charts fill single-variant tiles, reflecting GISAID detail not shown by CDC's Nowcast. Legend: JN.1.11 + FLiRT31 [purple]: 70% - LP.8.1.1 / NY†, LP.8.1.8† & other LP.8.1 JN.1 + FLiRT-LF [browns]: 9% - XFC 3% - LF.7.7.2 2% - XFG† & other LF.7 2% - LF.7.7.1 & LF.7.2.1 / PC JN.1 + FLiRT [reds]: 2% - LB.1.3.1 / NL 1% - XEC.4 ½% - XEQ 6% - other XEC JN.1.11 [greens]: 3% - MC.10.1 & PA.1 ⅓% - KP.3 2% - MC.1, MC.19 & other KP.3.1.1 / MC JN.1.11 + FLiRT31 [blue]: ⅓% - XEK Other [greys]: ⅐% - NB.1.8.1†, JN.1.16 & other WHO-Vaccine-Target JN.1 ⅒% - Other (not specified) _____ XEC is a child of FLiRT cluster KS.1.1 and FLuQE cluster KP.3.3. XEK is a child of FLiRT31 cluster KP.2.3 and recombinant XEC. XEQ is a child of FLiRT cluster KS.1.1.2 and FLuQE cluster KP.3. XFC is a child of FLiRT31 cluster LP.8.1.1 and FLiRT cluster LF.7. XFG is a child of FLiRT31 cluster LP.8.1.2 and FLiRT cluster LF.7. [Add'l footnotes omitted.]
This entry was edited (2 months ago)
in reply to sport of sacred spherical cows

hometown - Link to source

sport of sacred spherical cows

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

hcommons.social/@beadsland/114…

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.

Screencrop of legend from CDC's latest variant proportions dataviz, showing all variants broken out in their dataviz, each with their respective color key. With the exception of LP.8.1 (orange), XFC (light brown), XEC (clover), XEC.4 (green teal) and KP.3 (Turkish rose) all of the top thirteen variants displayed have been assigned various shades of blue. First thirteen legend keys, from top to bottom: orange, light brown, clover green, periwinkle lavender blue, dirty blue, science blue, fountain blue, sea blue, green teal, light royal blue, ultramarine blue, medium slate blue, crocus lavender blue. All color names sourced ArtyClick's color name finder.

sport of sacred spherical cows

2025-04-27 15:04:57

hometown - Link to source

#CDC continues with motif of painting covid blue:

hcommons.social/@beadsland/114…

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.

Screencrop of legend from CDC's latest variant proportions dataviz, showing top 14 variants (all those estimated with at least 1% share) with their respective color keys. With the exception of LP.8.1 (orange), XEC (clover), XEC.4 (green teal) and KP.3 (Turkish rose) all of the variants displayed have been assigned various shades of blue. Legend keys, from top to bottom: orange, clover green, periwinkle lavender blue, fountain blue, science blue, ultramarine blue, light royal blue, green teal, dirty blue, sea blue, flat blue, medium slate blue, Turkish rose, crocus lavender blue. All color names sourced ArtyClick's color name finder.

in reply to sport of sacred spherical cows

hometown - Link to source

sport of sacred spherical cows

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

Chart: Est. U.S. Variant Proportions by Common Name Sources: CDC, Cov-Lineages, NYITCOM, others [ beadsland on Ko-fi ] Reskin of CDC's Variants Nowcast, and any significant variants in GISAID not broken out by CDC. Five bar-style tree-charts, for fortnights through 5/11–5/24. Legend of last fortnight, organized by subheadings of color-grouped families and convergent clusters. Percentages overlay each color key, reflecting share as of most recent tree-chart. For 4/27–5/10, packed bubble charts fill single-variant tiles, reflecting GISAID detail not shown by CDC's Nowcast. Legend: JN.1.11 + FLiRT31 [purple]: 73% - LP.8.1.1 / NY† & other FDA-Vaccine-Target LP.8.1 JN.1 + FLiRT-LF [browns]: 10% - XFC 3% - LF.7.7.2 2% - XFG.2†, XFG†, LF.7.9† & other LF.7 1% - LF.7.7.1 & LF.7.2.1 / PC WHO-Vaccine-Target JN.1 [red]: 6% - XEC, LB.1.3.1 / NL, XEC.4, XEC.4.1† & XFJ† JN.1.11 [greens]: 3% - MC.10.1 & PA.1 ¾% - KP.3 & XEQ ⅞% - MC.1, MC.19 & other KP.3.1.1 / MC JN.1.11 + FLiRT31 [blue]: ¼% - XEK Other [greys]: 0% - Razor-Blade-Throat NB.1.8.1 / PQ† & other WHO-Vaccine-Target JN.1 0% - Other (not specified) _____ XEC is a child of FLiRT cluster KS.1.1 and FLuQE cluster KP.3.3. XEK is a child of FLiRT31 cluster KP.2.3 and recombinant XEC. XEQ is a child of FLiRT cluster KS.1.1.2 and FLuQE cluster KP.3. XFC is a child of FLiRT31 cluster LP.8.1.1 and JN.1.16.1 scion LF.7. XFG is a child of FLiRT31 cluster LP.8.1.2 and JN.1.16.1 scion LF.7. [Add'l footnotes omitted.]
This entry was edited (1 month ago)
in reply to sport of sacred spherical cows

hometown - Link to source

sport of sacred spherical cows

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.

in reply to sport of sacred spherical cows

hometown - Link to source

sport of sacred spherical cows

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

hcommons.social/@beadsland/114…

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.

Chart: Annoplot Dataviz Library*: Project Profile Subtitle: 11.3K lines† across component modules and significant submodules. Multi-level pie chart organized into six major categories by color. Each outer wedge shows a tally of number of lines for that sub-component. Green variants wedges all variously exploded out; also, less so, blue artists/legend wedges. A legend is split across both sides of the chart. Each key mirrors one of the wedges on the dual pie chart, along with a sentence or two description of each (sub)component thereby represented. Caption: * Pre-release development version 2025-06-05. † Python, Markdown, C, and Elixir source files. Blank lines omitted form tallies. Exploded wedges reflect proportions of lines changed in prior 30 days. Dotted areas represent non-blank comment lines and Markdown. Wedges: 🔴 levels 🧀 [blank wedge] - 460, 🧀 hospitals - 282 🟣 chirp 🧀 [blank] - 535 🔵 annoplot 🧀 [blank] - 549, 🧀 artists - 374, 🧀 artists/deco - 503, 🧀 artists/legend - 161, 🧀 …/legend/deco - 258, 🧀 artists/pie - 287, 🧀 artists/text - 326, 🧀 coord - 583, 🧀 coord/base - 259, 🧀 margin - 255, 🧀 util - 535 🟢 tiop 🧀 [blank] - 235, 🧀 bullseye - 321, 🧀 capacity - 455, 🧀 devpie - 673, 🧀 variants - 518, 🧀 variants/legend - 348, 🧀 variants/orchard - 421, 🧀 variants/rajdash - 168, 🧀 variants/rajdash/suds - 280,🧀 variants/tree - 417, 🧀 …/tree/branch - 352 🟤 bots 🧀 [blank] - 181, 🧀 talky - 75, 🧀 talky/talky - 746 ⚫ . [period by itself] 🧀 [blank] - 427, 🧀 TODO.md - 348

sport of sacred spherical cows

2025-05-09 02:01:24

hometown - Link to source

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

hcommons.social/@beadsland/113…

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

Chart: Annoplot Dataviz Library*: Project Profile Subtitle: 10.9K lines† across component modules and significant submodules. Multi-level pie chart organized into six major categories by color. Each outer wedge shows a tally of number of lines for that sub-component. Green wedge for variants/rajdash/suds exploded; also, slightly, blue util wedge. A legend is split across both sides of the chart. Each key mirrors one of the wedges on the dual pie chart, along with a sentence or two description of each (sub)component thereby represented. Caption: * Pre-release development version 2025-03-31. † Python, Markdown, C, and Elixir source files. Blank lines omitted form tallies. Exploded wedges reflect proportions of lines changed in prior 30 days. Dotted areas represent non-blank comment lines and Markdown. Wedges: 🔴 levels 🧀 [blank wedge] - 460, 🧀 hospitals - 282 🟣 chirp 🧀 [blank] - 290, 🧀 audio - 241 🔵 annoplot 🧀 [blank] - 549, 🧀 artists - 351, 🧀 artists/deco - 503, 🧀 artists/legend - 145, 🧀 …/legend/deco - 234, 🧀 artists/pie - 287, 🧀 artists/text - 324, 🧀 coord - 583, 🧀 coord/base - 259, 🧀 margin - 255, 🧀 util - 535 🟢 tiop 🧀 [blank] - 244, 🧀 bullseye - 321, 🧀 capacity - 455, 🧀 devpie - 433, 🧀 devpie/slice - 234, 🧀 variants - 582, 🧀 variants/orchard - 416, 🧀 variants/rajdash - 168, 🧀 variants/rajdash/suds - 289,🧀 variants/tree - 414, 🧀 …/tree/branch - 266 🟤 bots 🧀 [blank] - 181, 🧀 talky - 75, 🧀 talky/talky - 746 ⚫ . [period by itself] 🧀 [blank] - 427, 🧀 TODO.md - 348

sport of sacred spherical cows (@beadsland@hcommons.social)

Attached: 1 image 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.
hcommons.social

in reply to sport of sacred spherical cows

hometown - Link to source

sport of sacred spherical cows

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

Screencap of banner from top of CDC web page: ⚠ CDC is aware of an issue with the software that is used to classify lineages of SARS-CoV-2. This issue affects the accuracy of classifications of XFG and XFC variants. While we resolve the issue, data for these variants may be inaccurate. CDC will post updated data once resolved.
This entry was edited (1 month ago)
in reply to sport of sacred spherical cows

hometown - Link to source

sport of sacred spherical cows

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

Chart: Est. U.S. Variant Proportions by Common Name Sources: CDC, Cov-Lineages, NYITCOM, others [ beadsland on Ko-fi ] Reskin of CDC's Variants Nowcast, and any significant variants in GISAID not broken out by CDC. Five bar-style tree-charts, for fortnights through 5/11–5/24. Legend of last fortnight, organized by subheadings of color-grouped families and convergent clusters. Percentages overlay each color key, reflecting share as of most recent tree-chart. For 5/11–5/24, packed bubble charts fill single-variant tiles, reflecting GISAID detail not shown by CDC's Nowcast. Legend: JN.1.11 + FLiRT31 [purple]: 73% - LP.8.1.1 / NY† & other FDA-Vaccine-Target LP.8.1 JN.1 + FLiRT-LF [browns]: 10% - XFC 3% - LF.7.7.2 2% - XFG.2†, XFG†, LF.7.9.1 / PY† & other LF.7 1% - LF.7.7.1 / PV & LF.7.2.1 / PC WHO-Vaccine-Target JN.1 [red]: 6% - XEC, LB.1.3.1 / NL & XEC.4 JN.1.11 [greens]: 3% - MC.10.1 & PA.1 ¾% - KP.3 & XEQ ⅞% - MC.1, MC.19 & other KP.3.1.1 / MC JN.1.11 + FLiRT31 [blue]: ¼% - XEK Other [greys]: 0% - XFP† & other WHO-Vaccine-Target JN.1 0% - Nimbus NB.1.8.1 / PQ† & Other (not specified) _____ XFC is a child of April's JN.1.16.1 kid LF.7 and newish FLiRT31 cluster LP.8.1.1. XFG is a child of April's JN.1.16.1 kid LF.7 and newish FLiRT31 cluster LP.8.1.2. XFP is a child of April's JN.1.16.1 kid LF.7 and left-field FLiRT cluster LS.2.1.1. [Some footnotes omitted, due to too many recombinants.]
This entry was edited (1 month ago)
in reply to sport of sacred spherical cows

hometown - Link to source

sport of sacred spherical cows

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

Screencap of modal pop-up message that obscures the CDC variant proportions dataviz until dismissed: Due to low numbers of sequences being reported to the CDC, precision in the most recent reporting period is low. CDC is moving to longer reporting periods to gather the number of sequences required to provide reliable Nowcast estimates.
This entry was edited (1 month ago)
in reply to sport of sacred spherical cows

hometown - Link to source

sport of sacred spherical cows

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.

Chart: Nowcast Estimates for 2/16/2025 - 3/1/2025 by HHS Region. One region out of ten is shown with a pie chart depicting variant shares, that being the NY/NJ region. All other regions are a swath of uninterrupted grey without any information displayed. A note at the top reads: Nowcast estimates are only available for HHS regions having about 300 sequences in the two weeks ending 02/01/2025
Chart: Nowcast Estimates for 10/13/2024 - 10/26/2024 by HHS Region. Five region out of ten is shown, each with a pie chart depicting variant shares, these being: NY/NJ, Mid-Atlantic, Great Lakes, Mtn/Dakotas, and Southwest. All other regions are a swath of uninterrupted grey without any information displayed. A note at the top reads: Nowcast estimates are only available for HHS regions having about 300 sequences in the two weeks ending 09/14/2024
Chart: Nowcast Estimates for 7/9/2023 - 7/22/2023 by HHS Region. All ten regions out of ten is shown, each with a pie chart depicting variant shares.
Chart: Weekly and Nowcast Estimates in United States for Weeks of 1/1/2023 - 4/8/2023 Stacked bar chart depicting share of variants estimated for each of 14 weeks, the first 11 of which are designated "Weighted Estimates: Variant proportions based on reported genomic sequencing results", and the last three of which are designated "Nowcast: model based projected estimates of variant proportions." By comparison, current Nowcast dataviz shows eight fortnights, the first six of which are Weighted Estimates; the last two Nowcast.
in reply to sport of sacred spherical cows

hometown - Link to source

sport of sacred spherical cows

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

Chart: Est. U.S. Variant Proportions by Common Name Sources: CDC, Cov-Lineages, NYITCOM, others [ beadsland on Ko-fi ] Reskin of CDC's Variants Nowcast, and any significant variants in GISAID not broken out by CDC. Five bar-style tree-charts, for fortnights through 5/25–6/7. Legend of last fortnight, organized by subheadings of color-grouped families and convergent clusters. Percentages overlay each color key, reflecting share as of most recent tree-chart. For 5/11–5/24, packed bubble charts fill single-variant tiles, reflecting GISAID detail not shown by CDC's Nowcast. Legend: JN.1.11 + FLiRT31 [purples]: 38% - LP.8.1.1 / NY† & other FDA-Vaccine-Target LP.8.1 ⅛% - XEK Omicron-2 BA.2 [red]: 37% - Nimbus NB.1.8.1 / PQ JN.1 + FLiRT-LF [browns]: 8% - XFG.2† & other XFG 7% - XFC 4% - LF.7.9.1 / PY† & other LF.7.9 1% - LF.7.7.2 & LF.7.7.1 / PV ⁹⁄₁₀% - other LF.7 WHO-Vaccine-Target JN.1 [green]: 2% - XEC, LB.1.3.1 / NL & XEC.4 JN.1.11 [blues]: ⅜% - KP.3 & XEQ 1% - PA.1, MC.10.1, MC.1 & other KP.3.1.1 / MC Other [grey]: 0% - Other (not specified) _____ Nimbus NB.1.8.1 / PQ is a scion of left-field Razor-Blade-Throat XDV. Razor-Blade-Throat XDV was a child of Winter 2024's WHO-Vaccine-Target JN.1 and left-field recombinant XDE. XDE was a child of left-field Hyperion grandkid FL.13.4 and left-field Hippogryph scion GW.5.1. XFG is a child of April's JN.1.16.1 kid LF.7 and newish FLiRT31 cluster LP.8.1.2. [Some footnotes omitted, due to too many recombinants.]
This entry was edited (1 month ago)
in reply to sport of sacred spherical cows

hometown - Link to source

sport of sacred spherical cows

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.

Cropped portion of orchard chart from last toot, showing tree chart columns for each of three fortnights: March 30-April 12, April 13-16, and April 27-May 10. On the first column, the purple "LP.8.1.1 / NY & other FDA-Vaccine-Target LP.8.1" tile has an emboss label identifying it. Blue "MC.10.1, et al." and green "XEC, LB.1.3.1 / NL & XEC.4" also have emboss labels, although both also have dot hatching at their bottoms, indicating that at least some of the variants included in those two tiles are flagged as having "less reliable" estimates. On the second column, only purple LP.8.1.1 / NY tile has a label. All the other over half dozen tiles are full top to bottom with dot hatching. All variants in each of those tiles are flagged as "less reliable". The last column is dot hatched to the very brim. Even LP.8.1.1 is flagged as "less reliable".
This entry was edited (1 month ago)
in reply to sport of sacred spherical cows

hometown - Link to source

sport of sacred spherical cows

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

aus.social/@mike_honey_/114611…

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:

x.com/dfocosi/status/193135167…

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

Chart: Est. U.S. Variant Proportions by Common Name Sources: CDC, Cov-Lineages, NYITCOM, others [ beadsland on Ko-fi ] Reskin of CDC's Variants Nowcast, and any significant variants in GISAID not broken out by CDC. Five bar-style tree-charts, for fortnights through 5/25–6/7. Legend of last fortnight, organized by subheadings of color-grouped families and convergent clusters. Percentages overlay each color key, reflecting share as of most recent tree-chart. WHO-Vaccine-Target JN.1 accounts for over three fifths. JN.1.11 for over two fifths. For 5/11–5/24, packed bubble charts fill single-variant tiles, reflecting GISAID detail not shown by CDC's Nowcast. Legend: JN.1.11 + FLiRT31 [blues]: 38% - LP.8.1.1 / NY† & other FDA-Vaccine-Target LP.8.1 ⅛% - XEK Omicron-2 BA.2 [purple]: 37% - Nimbus NB.1.8.1 / PQ LF.7 + NTD-meets-RBD [browns]: 8% - XFG.2† & other XFG 7% - XFC JN.1 + FLiRT-LF-7 [reds]: 5% - LF.7.7.2, LF.7.9.1 / PY† & other LF.7.9 1% - LF.7.7.1 / PV & other LF.7 JN.1.11 [greens]: ⅜% - KP.3 & XEQ 1% - PA.1, MC.10.1, MC.1 & other KP.3.1.1 / MC Other [greys]: ½% - LB.1.3.1 / NL 2% - XEC.4 & other XEC 0% - Other (not specified) _____ Nimbus NB.1.8.1 / PQ is a scion of left-field Razor-Blade-Throat XDV. Razor-Blade-Throat XDV was a child of Winter 2024's WHO-Vaccine-Target JN.1 and left-field recombinant XDE. XDE was a child of left-field Hyperion grandkid FL.13.4 and left-field Hippogryph scion GW.5.1. [Some footnotes omitted, due to too many recombinants.]

Mike Honey (@mike_honey_@aus.social)

Attached: 1 image XFP is the latest recombinant variant to be classified and incredibly it is the third of a recent set of recombinants with identical spike mutations. The earlier ones were XFJ and XFM. I think of them as the "Doppelgängers".
Aus.Social
This entry was edited (1 month ago)
in reply to sport of sacred spherical cows

hometown - Link to source

sport of sacred spherical cows

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 added NB.1.8.1 only in latest, late-published public dataset. Notice of "software error" that heralded data delay… has been removed. Hatching for "less reliable" data reflects "low numbers of sequences being reported".

Raj's dashboard, updated this morning, shows Nimbus diversifying in May. Also, XFJ significant, even if CDC hasn't broken out.

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

Chart: Est. U.S. Variant Proportions by Common Name Sources: CDC, Cov-Lineages, NYITCOM, others [ beadsland on Ko-fi ] Reskin of CDC's Variants Nowcast, and any significant variants in GISAID not broken out by CDC. Five bar-style tree-charts, for fortnights through 5/25–6/7. Legend of last fortnight, organized by subheadings of color-grouped families and convergent clusters. Percentages overlay each color key, reflecting share as of most recent tree-chart. WHO-Vaccine-Target JN.1 accounts for over three fifths. JN.1.11 for over two fifths. For 5/11–5/24, packed bubble charts fill single-variant tiles, reflecting GISAID detail not shown by CDC's Nowcast. Legend: JN.1.11 + FLiRT31 [blues]: 38% - LP.8.1.1 / NY† & other FDA-Vaccine-Target LP.8.1 ⅛% - XEK Omicron-2 BA.2 [purple]: 37% - Nimbus NB.1.8.1 / PQ LF.7 + NTD-meets-RBD [browns]: 8% - XFG.2† & other Stratus XFG 7% - XFC 0% - XFJ† JN.1 + FLiRT-LF-7 [reds]: 5% - LF.7.9 & LF.7.7.2 1% - LF.7.7.1 / PV & other LF.7 JN.1.11 [greens]: ⅜% - KP.3 & XEQ 1% - PA.1, MC.10.1, MC.1 & other KP.3.1.1 / MC Other [greys]: ½% - LB.1.3.1 / NL 2% - XEC.4 & other XEC 0% - Other (not specified) _____ Nimbus NB.1.8.1 / PQ is a scion of left-field Razor-Blade-Throat XDV. Razor-Blade-Throat XDV was a child of Winter 2024's WHO-Vaccine-Target JN.1 and left-field recombinant XDE. XDE was a child of left-field Hyperion grandkid FL.13.4 and left-field Hippogryph scion GW.5.1. [Some footnotes omitted, due to too many recombinants.]
This entry was edited (1 month ago)
in reply to sport of sacred spherical cows

hometown - Link to source

sport of sacred spherical cows

Just corrected major bug by changing one assignment.

Purpose of including inline bubble #datavis of GISAID data was to demonstrate how major subvariants, not broken out by the CDC, were being obscured by CDC bundling those subvariants into ancestor for reporting purposes.

Which is what these #dataviz would have been doing, if only they'd been using the actual share of the given ancestor to set the size of its bubble. Instead, of, well (*clears throat with embarrassment*) the total sum of shares of the root variant and its descendants.

Would say that this was down to my focusing so much attention on dynamic legend and family grouping logic, but that ignores time spent adjusting how bubbles were aligned within tiles.

So, really, it was just that never bothered to consistency check the bubbles as drawn against data as given, assuming without validating that everything was correct.

Anyway, charts going forward now work as intended, reflecting when #CDC data hides more than it reveals.

Chart: Est. U.S. Variant Proportions by Common Name Sources: CDC, Cov-Lineages, NYITCOM, others [ beadsland on Ko-fi ] Reskin of CDC's Variants Nowcast, and any significant variants in GISAID not broken out by CDC. Five bar-style tree-charts, for fortnights through 5/25–6/7. Legend of last fortnight, organized by subheadings of color-grouped families and convergent clusters. Percentages overlay each color key, reflecting share as of most recent tree-chart. WHO-Vaccine-Target JN.1 accounts for over three fifths. JN.1.11 for over two fifths. For 5/11–5/24, packed bubble charts fill single-variant tiles, reflecting GISAID detail not shown by CDC's Nowcast. Legend: JN.1.11 + FLiRT31 [blues]: 38% - LP.8.1.1 / NY† & other FDA-Vaccine-Target LP.8.1 ⅛% - XEK Omicron-2 BA.2 [purple]: 37% - Nimbus NB.1.8.1 / PQ LF.7 + NTD-meets-RBD [browns]: 8% - XFG.2† & other Stratus XFG 7% - XFC 0% - XFJ† JN.1 + FLiRT-LF-7 [reds]: 5% - LF.7.9 & LF.7.7.2 1% - LF.7.7.1 / PV & other LF.7 JN.1.11 [greens]: ⅜% - KP.3 & XEQ 1% - PA.1, MC.10.1, MC.1 & other KP.3.1.1 / MC Other [greys]: ½% - LB.1.3.1 / NL 2% - XEC.4 & other XEC 0% - Other (not specified) _____ Nimbus NB.1.8.1 / PQ is a scion of left-field Razor-Blade-Throat XDV. Razor-Blade-Throat XDV was a child of Winter 2024's WHO-Vaccine-Target JN.1 and left-field recombinant XDE. XDE is a child of left-field Hyperion grandkid FL.13.4 and left-field Hippogryph scion GW.5.1. [Some footnotes omitted, due to too many recombinants.]
This entry was edited (1 month ago)
in reply to sport of sacred spherical cows

hometown - Link to source

sport of sacred spherical cows

The trials of a passion project where one has no team to help vet one's work and identify when one has gotten shit completely FUBAR with respect to intended goals.

But yeah, compare the above chart to the one immediately prior. The difference may seem subtle (and the newer chart is using a data set from Raj that's a day fresher than the prior chart), but the difference can't be unseen once one recognizes what has changed.

This entry was edited (1 month ago)
in reply to sport of sacred spherical cows

hometown - Link to source

sport of sacred spherical cows

Per announcement two weeks ago:

hcommons.social/@beadsland/114…

We didn't get a covid variant proportions update from #CDC today.

Anyone wanna give odds on whether they're gonna go to a three week reporting period for a four week reporting period?

sport of sacred spherical cows

2025-06-11 01:30:43

hometown - Link to source

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

Screencap of modal pop-up message that obscures the CDC variant proportions dataviz until dismissed: Due to low numbers of sequences being reported to the CDC, precision in the most recent reporting period is low. CDC is moving to longer reporting periods to gather the number of sequences required to provide reliable Nowcast estimates.

in reply to sport of sacred spherical cows

hometown - Link to source

sport of sacred spherical cows

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

Due to "low numbers of sequences being reported" (as evidenced by "less reliable" dot hatching on below chart), #CDC did not publish data this week, having advised only of "moving to longer reporting periods":

hcommons.social/@beadsland/114…

Raj's dashboard, updated this morning, shows PQ.2 as standout child of Nimbus NB.1.8.1 / PQ; Stratus XFG in competition with kids XFG.2 and XFG.3; and LP.8.1 long ago overshadowed by LP.8.1.1/ NY.

❖ #ThisIsOurPolio #variants #CovidIsNotOver #dataviz #datavis

Chart: Est. U.S. Variant Proportions by Common Name Sources: CDC, Cov-Lineages, NYITCOM, others [ beadsland on Ko-fi ] Reskin of CDC's Variants Nowcast, and any significant variants in GISAID not broken out by CDC. Five bar-style tree-charts, for fortnights through 5/25–6/7. Legend of last fortnight, organized by subheadings of color-grouped families and convergent clusters. Percentages overlay each color key, reflecting share as of most recent tree-chart. WHO-Vaccine-Target JN.1 accounts for over three fifths. JN.1.11 for over two fifths. For 5/25–6/7, packed bubble charts fill single-variant tiles, reflecting GISAID detail not shown by CDC's Nowcast. Legend: JN.1.11 + FLiRT31 [blues]: 38% - LP.8.1.1 / NY†, NW.1† & other FDA-Vaccine-Target LP.8.1 ⅛% - XEK Omicron-2 BA.2 [purple]: 37% - Nimbus NB.1.8.1 / PQ LF.7 + NTD-meets-RBD [browns]: 8% - XFG.2†, XFG.3† & other Stratus XFG 7% - XFC JN.1 + FLiRT-LF-7 [reds]: 5% - LF.7.9 & LF.7.7.2 1% - LF.7.7.1 / PV & other LF.7 JN.1.11 [greens]: ⅜% - KP.3 & XEQ 1% - PA.1, MC.10.1, MC.1 & other KP.3.1.1 / MC Other [greys]: ½% - LB.1.3.1 / NL 2% - XEC.4 & other XEC 0% - Other (not specified) _____ Nimbus NB.1.8.1 / PQ is a scion of left-field Razor-Blade-Throat XDV. Razor-Blade-Throat XDV was a child of Winter 2024's WHO-Vaccine-Target JN.1 and left-field recombinant XDE. XDE was a child of left-field Hyperion grandkid FL.13.4 and left-field Hippogryph scion GW.5.1. [Some footnotes omitted, due to too many recombinants.]

sport of sacred spherical cows

2025-06-11 01:30:43

hometown - Link to source

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

Screencap of modal pop-up message that obscures the CDC variant proportions dataviz until dismissed: Due to low numbers of sequences being reported to the CDC, precision in the most recent reporting period is low. CDC is moving to longer reporting periods to gather the number of sequences required to provide reliable Nowcast estimates.

This entry was edited (3 weeks ago)
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