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Mastodon: AboutGet the appKeyboard shortcutsView source codev4.4.0-nightly.2025-03-25

#variants

1 post1 participant1 post today
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Public
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.
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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.
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Eric's Risk Assessment

Frequency, kinetics and determinants of viable #SARSCoV2 in #bioaerosols from ambulatory #COVID19 patients infected with the Beta, Delta or Omicron #variants

nature.com/articles/s41467-024

> Half of Covid-19 patients emitted infectious virus in respiratory particles smaller than 5 microns (>30 min to settle out). Culturability of aerosols was associated with lower neutralizing antibody titers, so immune response matters for transmission potential.

#COVIDisAirborne#sars2
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sport of sacred spherical cows

#CDC has long time now been piloting the craft of #PublicHealth sans navigational equipment.

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

Given little data we do have, LP.8.1 now estimated as nearing majority status in NY/NJ, with XEC (incl. XEC.4) still near a third share.

As for other regions?

[For color key, see: covid.cdc.gov/covid-data-track]

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

Map: Nowcast Estimates for 2/16/2025 - 3/1/2025 by HHS Region Source: Centers for Disease Control Map shows pie charts for one 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 02/01/2025". Dominant strains by tracked region: NY/NJ: LP.8.1 (orange) 44%, XEC (clover) 26%, KP.3.1.1 (sea bluish cyan) 6%, XEC.4 (mint green) 6%. Of ten regions, nine regions are blank. ALT-text by beadsland at ko-fi.
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sport of sacred spherical cows

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.

#CDC breaks out a new FLuQE variant, MC.28.1, even as being squeezed by LP.8.1 fam.

Raj updated global dashboard Sunday, incl. hundreds of U.S. samples early Feb. Still await updated U.S. dashboard.

❖ #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 Feb 16–Mar 1. 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 over two fifths. 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]: 42% - LP.8.1.1 / NY† & other LP.8.1 XEC [browns]: 31% - XEC.2†, XEC.8† & other XEC 3% - XEC.4 JN.1.11 + FLuQE [greens]: 5% - MC.10.1 & MC.19 3% - MC.28.1 2% - XEQ 8% - MC.1 & other KP.3.1.1 / MC ½% - other KP.3 JN.1 + FLiRT [reds]: 3% - LF.7 2% - LB.1.3.1 / NL ⅛% - LB.1 & KS.1 JN.1.11 + FLiRT [blues]: ⅘% - XEK 0% - KP.2.3 & KP.1.1.3 / LP Other [greys]: ⅕% - other Pirola BA.2.86 ⅒% - Other (not specified) † Dagger variants are not broken out by CDC, yet represent a significant share of recent GISAID sequences.
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sport of sacred spherical cows

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

FLiRT KS.1.1 / FLuQE KP.3.3 hybrid XEC down near two fifths.

LP.8.1 and child LP.8.1.1 / NY together already another fifth.

Meanwhile, in remaining fifth:
• JN.1 FLiRT descendant LF.7 remains diverse despite pressure; and
• XEQ (recombinant of FLiRT KS.1.1.2 and KP.3) continues to stand out.

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

Chart: SARSCoV2 Variant Dashboard - USA | 30-DAY TRENDS Source: NYITCOM Research Report (Raj Rajnarayanan) Caption (in part): Circulating Variants in…following US States: All - Specimen Collected in…last 30 days | Updated on 2/16/2025 4:45:09 AM [GMT?] | Source (sequences): GISAID Packed-bubble chart showing tallies of each identified variant for each state, for collection dates 1/19/2025 to 2/1/2025. Top subvariants: XEC (24.06%), LP.8.1 (11.11%), LP.8.1.1 (9.8%), MC.10.1 (5.34%), MC.1 (4.23%), XEC.2 (4.09%). Raj has standardized bubbles to violet (BA.2.86.*), aqua green (XBB.1.16.*), forest green (XEC, a recombinant of two B.2.86 strains), and yellow (LP.8.*). although some newer Pango aliases may still be getting unique colors assigned by Tableau. Bubbles largest and most prominent for: XEC (forest) for New York (59), Colorado (53), Minnesota (25), New Jersey, California, Illinois, Nebraska, Iowa, Pennsylvania, Virginia, Delaware, Rhode Island; LP.8.1 (yellow) for New York (43), California, Iowa, Colorado, Delaware; LP.8.1.1 (yellow) for New York (36), Illinois (33), Minnesota, California; XEC.8 (forest) for Nebraska (24); XEQ (aqua) for Colorado (23). Many dozens of bubbles of varying sizes representing near a hundred variants across various states. ALT-text by beadsland at ko-fi.
Chart: Variants by Pango-Designated Lineage: U.S. Jan 19 to Feb 1 Source: GISAID (via Raj Rajnarayanan's COVID-19 Variant Dashboard, updated Feb 16) [ beadsland on Ko-fi ] Pie chart of major lineages, with lesser lineages bundled together by common alphanumeric initial character. Call-outs for each pie slice list number of variants counted and provide a percentage of pie. Percentage is in a dull grey font, to which a dark backing has been applied to aid legibility. Color key of pie slices aligns to that of latest "Estimated Variant Proportions by Common Name" (earlier in this thread), namely: • Browns: JN.1.11 + FLiRT • Greens: JN.1.11 + FLuQE • Reds: XEC • Purple: JN.1 + FLiRT-KS • Blues: JN.1 + FLiRT • Greys: Other Reading clockwise from top: - Multiple unlabeled slivers of grey and tan brown. 4.0% - KP.3.1.1 / MC [green] - Unlabeled slice green. 1.9% - LB.1.3.1 (1 variant) [green] - Unlbl. sliver of grey. 4.8% - LF.7 (8 variants) [blue] 9.8% - LP.8.1.1 (1 variant) [brown] 11.7% - LP.8.1 (2 variants) [brown] - Unlbl. sliver tan. 5.7% - MC.1 (4 variants) [green] Unlbl. sliver green. 5.3% - MC.10.1 (1 variant) [green] - Two unlbl. slices green. 4.3% - other MC (17 variants) [green] - Unlbl. slice grey. 2.3% - NL (4 variants) [blue] 1.2% - NC, NF, NB, NA, … [grey] 6.1% - XEC.2 (4 variants) [red] 1.8% - XEC.4 (1 variant) [pink red] 3.1% - XEC.8 (1 variant) [red] 28.9% - other XEC (12 variants) [red] - Unlbl. slice tan. 2.4% - XEQ (1 variant) [grey] - Unlbl. sliver grey.
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sport of sacred spherical cows

#CDC has long time now been piloting the craft of #PublicHealth sans navigational equipment.

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

Given little data we do have, LP.8.1 has gained plurality status in NY/NJ and Great Lakes regions, XEC still majority in Mtn/Dakotas, with cousin XEQ prominent.

[For color key, see: covid.cdc.gov/covid-data-track]

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

Map: Nowcast Estimates for 2/2/2025 - 2/15/2025 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 01/18/2025". Dominant strains by tracked region: NY/NJ: LP.8.1 (orange) 34%, XEC (clover) 33%, KP.3.1.1 (sea bluish cyan) 9%, XEC.4 (mint green) 7%. Great Lakes: LP.8.1 (orange) 38%, XEC (clover) 37%, KP.3.1.1 (sea) 6%. Mtn/Dakotas: XEC (clover) 44%, LP.8.1 (orange) 16%, XEQ (slate blue) 14%, MC.10.1 (sapphire blue) 7%, KP.3.1.1 (sea) 6%. Of ten regions, seven regions are blank. ALT-text by beadsland at ko-fi.
Continued thread
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sport of sacred spherical cows

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.

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

Raj has updated dashboard Sunday with new GISAID sequences. As of data two weeks ago, XEC.8 joins XEC.2 and LP.8.1.1 / NY as significant.

❖ #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 February 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 half; JN.1 + 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: XEC [reds]: 37% - XEC.2†, XEC.8† & other XEC 4% - XEC.4 JN.1.11 + FLiRT [browns]: 31% - LP.8.1.1 / NY† & other LP.8.1 1% - XEK ⅒% - KP.2.3, FDA-Vaccine-Target KP.2 & KP.1.1.3 / LP JN.1.11 + FLuQE [greens]: 3% - XEQ 17% - MC.10.1, MC.1, MC.19 & other KP.3.1.1 / MC ⅗% - other KP.3 JN.1 + FLiRT [blues]: 3% - LF.7 2% - LB.1.3.1 / NL 0% - LB.1 JN.1 + FLiRT-KS [purple]: ⅒% - other KS.1 Other [greys]: ½% - JN.1.16 ⅓% - other Pirola BA.2.86 ⅒% - Other (not specified) † Dagger variants are not broken out by CDC, yet represent a significant share of recent GISAID sequences.
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