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
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.](https://spaces.hcommons.social/media_attachments/files/114/163/035/799/833/179/original/9a1523ae932eddff.jpg "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.")
#XBB.1.5 monovalent #vaccine induces lasting cross-reactive responses to #SARS-CoV-2 #variants such as HV.1 and #JN1, as well as SARS-CoV-1, but elicits limited XBB.1.5 specific #antibodies, https://etidiohnew.blogspot.com/2025/03/xbb15-monovalent-vaccine-induces.html
Evolutionary Studies on the #Coxsackievirus A24 #Variants Causing Acute #Hemorrhagic #Conjunctivitis with Emphasis on the Recent #Outbreak of 2023 in #India, https://etidiohnew.blogspot.com/2025/03/evolutionary-studies-on-coxsackievirus.html
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
![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 1/5–1/18, 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† & 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]:
17% - MC.10.1, MC.1, MC.19, MC.8.1† & other KP.3.1.1 / MC
3% - XEQ
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.](https://spaces.hcommons.social/media_attachments/files/114/004/692/397/171/374/original/12689f349ea5c8c6.jpg "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 1/5–1/18, 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† & 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]:
17% - MC.10.1, MC.1, MC.19, MC.8.1† & other KP.3.1.1 / MC
3% - XEQ
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.")
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
![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 1/31/2025 6:43:47 AM [GMT?] | Source (sequences): GISAID
Packed-bubble chart showing tallies of each identified variant for each state, for collection dates 1/5/2025 to 1/18/2025. Top subvariants: XEC (26.32%), KP.3.1.1 (8.61%), LP.8.1 (5.74%), XEC.2 (4.23%), MC.10.1 (4.18%).
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) in Ohio (171), New York (85), Colorado (58), Minnesota (46), New Jersey, Iowa, Utah; KP.3.1.1 (violet) for Ohio (58), Minnesota, New York; MC.8.1 (violet) for Ohio (51); XEQ (aqua) for Colorado (34); LP.8.1 (yellow) for New York, Ohio.
Many dozens of bubbles of varying sizes representing over a hundred variants across various states.
ALT-text by beadsland at ko-fi.](https://spaces.hcommons.social/media_attachments/files/113/925/598/052/682/439/original/4b72cd6231c464fe.png "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 1/31/2025 6:43:47 AM [GMT?] | Source (sequences): GISAID
Packed-bubble chart showing tallies of each identified variant for each state, for collection dates 1/5/2025 to 1/18/2025. Top subvariants: XEC (26.32%), KP.3.1.1 (8.61%), LP.8.1 (5.74%), XEC.2 (4.23%), MC.10.1 (4.18%).
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) in Ohio (171), New York (85), Colorado (58), Minnesota (46), New Jersey, Iowa, Utah; KP.3.1.1 (violet) for Ohio (58), Minnesota, New York; MC.8.1 (violet) for Ohio (51); XEQ (aqua) for Colorado (34); LP.8.1 (yellow) for New York, Ohio.
Many dozens of bubbles of varying sizes representing over a hundred variants across various states.
ALT-text by beadsland at ko-fi.")
![Chart: Variants by Pango-Designated Lineage: U.S. Jan 5 to 18
Source: GISAID (via Raj Rajnarayanan's COVID-19 Variant Dashboard, updated Jan 31)
[ 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:
• Purples: JN.1.11
• Reds/Pinks: JN.1.11 + FLiRT
• Browns: JN.1.11 + FLiRT-LP
• Blues: XEC
• Greens: JN.1 + FLiRT
• Greys: Other
Reading clockwise from top:
- Multiple unlabeled slivers of grey and pink.
8.6% - KP.3.1.1 / MC [purple]
- Unlabeled purple sliver & grey sliver
2.2% - LB.1.3.1 (1 var) [green]
- Unlabeled green sliver
3.4% - LF.7 (10 variants) [green]
3.9% - LP.8.1.1 (1 var) [brown]
5.9% - LP.8.1 (2 variants) [brown]
- Unlabeled brown and grey silvers
5.2% - MC.1 (5 variants) [purple]
3.4% - MC.8.1 (2 variants) [purple]
4.2% - MC.10.1 (1 var) [purple]
- Two unlabeled purple slices
8.5% - other MC (22 variants) [purple]
- Unlabeled grey slice
1.4% - NL (4 variants) [green]
- Unlabeled grey slice
5.7% - XEC.2 (5 variants) [blue]
2.0% - XEC.2 (1 var) [blue]
34% - other XEC (10 variants) [blue]
1.6% - XEK (4 variants) [red orange]
3.0% - XEQ (1 var) [grey]
- Unlabeled grey slice](https://spaces.hcommons.social/media_attachments/files/113/925/598/461/876/410/original/409a1e8fa79e0fd6.png "Chart: Variants by Pango-Designated Lineage: U.S. Jan 5 to 18
Source: GISAID (via Raj Rajnarayanan's COVID-19 Variant Dashboard, updated Jan 31)
[ 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:
• Purples: JN.1.11
• Reds/Pinks: JN.1.11 + FLiRT
• Browns: JN.1.11 + FLiRT-LP
• Blues: XEC
• Greens: JN.1 + FLiRT
• Greys: Other
Reading clockwise from top:
- Multiple unlabeled slivers of grey and pink.
8.6% - KP.3.1.1 / MC [purple]
- Unlabeled purple sliver & grey sliver
2.2% - LB.1.3.1 (1 var) [green]
- Unlabeled green sliver
3.4% - LF.7 (10 variants) [green]
3.9% - LP.8.1.1 (1 var) [brown]
5.9% - LP.8.1 (2 variants) [brown]
- Unlabeled brown and grey silvers
5.2% - MC.1 (5 variants) [purple]
3.4% - MC.8.1 (2 variants) [purple]
4.2% - MC.10.1 (1 var) [purple]
- Two unlabeled purple slices
8.5% - other MC (22 variants) [purple]
- Unlabeled grey slice
1.4% - NL (4 variants) [green]
- Unlabeled grey slice
5.7% - XEC.2 (5 variants) [blue]
2.0% - XEC.2 (1 var) [blue]
34% - other XEC (10 variants) [blue]
1.6% - XEK (4 variants) [red orange]
3.0% - XEQ (1 var) [grey]
- Unlabeled grey slice")
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
![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 January 5–18. 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 + FLiRT accounts for well over half; XEC for near half.
For fortnight of 1/5–1/18, 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 [blues]:
47% - XEC.2† & other XEC
3% - XEC.4
JN.1.11 [purples]:
23% - MC.10.1, MC.1, MC.19, MC.8.1† & other KP.3.1.1 / MC
1% - KP.3 & XEQ†
JN.1.11 + FLiRT-LP [browns]:
15% - LP.8.1.1 / NY† & other LP.8.1
⅛% - LP.1 & other KP.1.1.3 / LP
JN.1 + FLiRT [greens]:
4% - LF.7
2% - LB.1.3.1 / NL
1% - JN.1.18.6 / LY
⅒% - LB.1
JN.1.11 + FLiRT [reds]:
4% - XEK
⅒% - FDA-Vaccine-Target KP.2
⅑% - other KP.2.3
Other [greys]:
⅒% - 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.](https://spaces.hcommons.social/media_attachments/files/113/925/353/197/745/222/original/94093d6ec2405a9c.jpg "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 January 5–18. 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 + FLiRT accounts for well over half; XEC for near half.
For fortnight of 1/5–1/18, 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 [blues]:
47% - XEC.2† & other XEC
3% - XEC.4
JN.1.11 [purples]:
23% - MC.10.1, MC.1, MC.19, MC.8.1† & other KP.3.1.1 / MC
1% - KP.3 & XEQ†
JN.1.11 + FLiRT-LP [browns]:
15% - LP.8.1.1 / NY† & other LP.8.1
⅛% - LP.1 & other KP.1.1.3 / LP
JN.1 + FLiRT [greens]:
4% - LF.7
2% - LB.1.3.1 / NL
1% - JN.1.18.6 / LY
⅒% - LB.1
JN.1.11 + FLiRT [reds]:
4% - XEK
⅒% - FDA-Vaccine-Target KP.2
⅑% - other KP.2.3
Other [greys]:
⅒% - 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.")
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
![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 1/20/2025 6:14:21 AM [GMT?] | Source (sequences): GISAID
Packed-bubble chart showing tallies of each identified variant for each state, for collection dates 12/22/2024 to 1/4/2025. Top subvariants: XEC (30.71%), KP.3.1.1 (16.45%), LP.8.1 (8.11%), XEC.2 (4.60%), MC.10.1 (4.08%).
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) in Minnesota (83), Colorado (66), Ohio (65), New York (53), Utah (40), New Jersey (35), Nebraska (30), Pennsylvania, California, Arizona, Iowa, Illinois; KP.3.1.1 (violet) for Minnesota (52), Ohio (35), Colorado (29), California, New York, Iowa, Nebraska; LP.8.1 (yellow) for Minnesota, New York, California; XEC.2 (forest) for New York.
Dozens of bubbles of varying sizes representing a many dozens of variants across various states.
ALT-text by beadsland at ko-fi.](https://spaces.hcommons.social/media_attachments/files/113/871/405/556/703/116/original/9f948a436f03b135.png "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 1/20/2025 6:14:21 AM [GMT?] | Source (sequences): GISAID
Packed-bubble chart showing tallies of each identified variant for each state, for collection dates 12/22/2024 to 1/4/2025. Top subvariants: XEC (30.71%), KP.3.1.1 (16.45%), LP.8.1 (8.11%), XEC.2 (4.60%), MC.10.1 (4.08%).
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) in Minnesota (83), Colorado (66), Ohio (65), New York (53), Utah (40), New Jersey (35), Nebraska (30), Pennsylvania, California, Arizona, Iowa, Illinois; KP.3.1.1 (violet) for Minnesota (52), Ohio (35), Colorado (29), California, New York, Iowa, Nebraska; LP.8.1 (yellow) for Minnesota, New York, California; XEC.2 (forest) for New York.
Dozens of bubbles of varying sizes representing a many dozens of variants across various states.
ALT-text by beadsland at ko-fi.")
![Chart: Variants by Pango-Designated Lineage: U.S. Dec 22 to Jan 4
Source: GISAID (via Raj Rajnarayanan's COVID-19 Variant Dashboard, updated January 20)
[ 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:
• Purples: JN.1.11
• Reds/Pinks: JN.1.11 + FLiRT
• Browns: JN.1.11 + FLiRT-LP
• Blues: XEC
• Greens: JN.1 + FLiRT
• Greys: Other
Reading clockwise from top:
- Mult. unlabeled slivers of grey & pink.
16.4% - KP.3.1.1 / MC [purple]
3.0% - other KP.3 (9 variants) [pink]
- Unlabeled sliver of grey.
2.2% - LB.1.3.1 (1 var.) [green]
- Unlabeled sliver of green.
4.0% - LF.7 (7 variants) [green]
8.1% - LP.8.1 (1 var.) [brown]
- Unlabeled slivers of brown, green, grey.
3.5% - MC.1 (2 variants) [purple]
4.1% - MC.10.1 (1 var.) [purple]
- Unlabeled sliver of purple.
1.4% - MC.19 (1 var.) [purple]
7.5% - other MC (19 variants) [purple]
- Unlabeled slice of grey.
2.4% - NL (6 variants) [green]
- Unlabeled slice of grey.
4.6% - XEC.2 (1 var.) [blue]
- Unlabeled slice of blue.
32.2% - other XEC (5 variants) [blue]
- Unlabeled slice of pink.
2.2% - XEL (1 var.) [grey]
- Unlabeled slice of grey](https://spaces.hcommons.social/media_attachments/files/113/871/406/386/336/746/original/68c398d78fe1b42a.png "Chart: Variants by Pango-Designated Lineage: U.S. Dec 22 to Jan 4
Source: GISAID (via Raj Rajnarayanan's COVID-19 Variant Dashboard, updated January 20)
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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:
• Purples: JN.1.11
• Reds/Pinks: JN.1.11 + FLiRT
• Browns: JN.1.11 + FLiRT-LP
• Blues: XEC
• Greens: JN.1 + FLiRT
• Greys: Other
Reading clockwise from top:
- Mult. unlabeled slivers of grey & pink.
16.4% - KP.3.1.1 / MC [purple]
3.0% - other KP.3 (9 variants) [pink]
- Unlabeled sliver of grey.
2.2% - LB.1.3.1 (1 var.) [green]
- Unlabeled sliver of green.
4.0% - LF.7 (7 variants) [green]
8.1% - LP.8.1 (1 var.) [brown]
- Unlabeled slivers of brown, green, grey.
3.5% - MC.1 (2 variants) [purple]
4.1% - MC.10.1 (1 var.) [purple]
- Unlabeled sliver of purple.
1.4% - MC.19 (1 var.) [purple]
7.5% - other MC (19 variants) [purple]
- Unlabeled slice of grey.
2.4% - NL (6 variants) [green]
- Unlabeled slice of grey.
4.6% - XEC.2 (1 var.) [blue]
- Unlabeled slice of blue.
32.2% - other XEC (5 variants) [blue]
- Unlabeled slice of pink.
2.2% - XEL (1 var.) [grey]
- Unlabeled slice of grey")
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
![Chart: Estimated U.S. Variant Proportions by Common Name
Sources: Centers for Disease Control, CoV-Lineages, NYITCOM Research, Daniele Focosi, World Health Network, others
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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 January 5–18. 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 + FLiRT accounts for well over half; XEC for near half.
For fortnight of 12/22–1/4, 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 [blues]:
47% - XEC.2† & other XEC
3% - XEC.4
JN.1.11 [purples]:
1% - KP.3
23% - MC.10.1, MC.1, MC.19 & other KP.3.1.1 / MC
JN.1.11 + FLiRT-LP [browns]:
15% - LP.8.1
⅛% - LP.1 & other KP.1.1.3 / LP
JN.1 + FLiRT [greens]:
4% - LF.7
2% - LB.1.3.1 / NL
1% - JN.1.18.6 / LY
⅒% - LB.1
JN.1.11 + FLiRT [reds]:
4% - XEK
⅒% - FDA-Vaccine-Target KP.2
⅑% - other KP.2.3
Other [greys]:
⅒% - other WHO-Vaccine-Target JN.1
⅒% - Other (not specified)
† Dagger variant is not broken out by CDC, yet represent a significant share of recent GISAID sequences.](https://spaces.hcommons.social/media_attachments/files/113/871/149/086/456/148/original/ab960ae7a01a0789.jpg "Chart: Estimated U.S. Variant Proportions by Common Name
Sources: Centers for Disease Control, CoV-Lineages, NYITCOM Research, Daniele Focosi, World Health Network, others
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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 January 5–18. 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 + FLiRT accounts for well over half; XEC for near half.
For fortnight of 12/22–1/4, 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 [blues]:
47% - XEC.2† & other XEC
3% - XEC.4
JN.1.11 [purples]:
1% - KP.3
23% - MC.10.1, MC.1, MC.19 & other KP.3.1.1 / MC
JN.1.11 + FLiRT-LP [browns]:
15% - LP.8.1
⅛% - LP.1 & other KP.1.1.3 / LP
JN.1 + FLiRT [greens]:
4% - LF.7
2% - LB.1.3.1 / NL
1% - JN.1.18.6 / LY
⅒% - LB.1
JN.1.11 + FLiRT [reds]:
4% - XEK
⅒% - FDA-Vaccine-Target KP.2
⅑% - other KP.2.3
Other [greys]:
⅒% - other WHO-Vaccine-Target JN.1
⅒% - Other (not specified)
† Dagger variant is not broken out by CDC, yet represent a significant share of recent GISAID sequences.")
In August, summer FLiRT wave receded into S:F546L soup. September FLuQE wavelet matured into MC wave into November. Now #CDC breaks out two new MC variants, as that family is pushed aside by FLiRT KS.1.1 / FLuQE KP.3.3 hybrid XEC.
CDC also breaks out LP.8.1, previously significant in GISAID, along with XEK, child of XEC and FLiRT KP.2.3.
With Raj's Mon update, a new recombinant apparent: XEL.
❖ #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, D. Focosi, WHN, others
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A reskin of CDC's Variants Nowcast, emphasizing significant variants, incl. those in GISAID yet not broken out by CDC.
Five rectangular tree-charts, side by side, for fortnights through December 8–11. Legend 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 JN.1. XEC accounts for near half total, with JN.1.11 + FLuQE a bit more than a third.
For week of 11/24–12/7, packed bubble charts fill many single-variant tiles, indicating diversification of those variants—per GISAID—that wouldn't otherwise be apparent given CDC's choices of what to break out or not.
Legend:
XEC [red]:
45% - XEC.2† and other XEC
JN.1.11 + FLuQE [browns]:
9% - MC.1, MC.10.1, MC.19
2% - KP.3
24% - other KP.3.1.1 / MC
JN.1.11 + FLiRT [blues]:
8% - LP.8.1
4% - XEK, KP.2.3, FDA-Vaccine-Target KP.2, KP.4.1 & KP.2.15
¼% - LP.1 & other KP.1.1.3 / LP
0% - other KP.1.1
JN.1 + FLiRT [green]:
7% - LF.7, LB.1.3.1 / NL, LB.1, JN.1.18.6 / LY, LF.3.1 & JN.1.16.1 / LF
JN.1 + FLiRT-KS [purple]:
⅒% - other KS.1
Other [greys]:
¼% - JN.1.16, JN.1.18, XEL† & four tracked variants at <⅒%
0% - HV.1
⅓% - other WHO-Vaccine-Target JN.1
0% - other Omicron-2 BA.2
0% - other Omicron B.1.1.529 / BA
⅜% - Other (not specified)](https://spaces.hcommons.social/media_attachments/files/113/711/214/282/560/700/original/ab4c26a8a627dc34.jpg "Chart: Estimated U.S. Variant Proportions by Common Name
Sources: Centers for Disease Control, CoV-Lineages, NYITCOM, D. Focosi, WHN, others
[ beadsland on Ko-fi ]
A reskin of CDC's Variants Nowcast, emphasizing significant variants, incl. those in GISAID yet not broken out by CDC.
Five rectangular tree-charts, side by side, for fortnights through December 8–11. Legend 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 JN.1. XEC accounts for near half total, with JN.1.11 + FLuQE a bit more than a third.
For week of 11/24–12/7, packed bubble charts fill many single-variant tiles, indicating diversification of those variants—per GISAID—that wouldn't otherwise be apparent given CDC's choices of what to break out or not.
Legend:
XEC [red]:
45% - XEC.2† and other XEC
JN.1.11 + FLuQE [browns]:
9% - MC.1, MC.10.1, MC.19
2% - KP.3
24% - other KP.3.1.1 / MC
JN.1.11 + FLiRT [blues]:
8% - LP.8.1
4% - XEK, KP.2.3, FDA-Vaccine-Target KP.2, KP.4.1 & KP.2.15
¼% - LP.1 & other KP.1.1.3 / LP
0% - other KP.1.1
JN.1 + FLiRT [green]:
7% - LF.7, LB.1.3.1 / NL, LB.1, JN.1.18.6 / LY, LF.3.1 & JN.1.16.1 / LF
JN.1 + FLiRT-KS [purple]:
⅒% - other KS.1
Other [greys]:
¼% - JN.1.16, JN.1.18, XEL† & four tracked variants at <⅒%
0% - HV.1
⅓% - other WHO-Vaccine-Target JN.1
0% - other Omicron-2 BA.2
0% - other Omicron B.1.1.529 / BA
⅜% - Other (not specified)")
#CDC now piloting the craft that is #PublicHealth sans navigational equipment. The problem is, they seem to like it that way.
To be clear, national Nowcast data used for chart above are modeled on regional data collection.
Given paucity of data reflected here, expect national Nowcast estimates for late 2024 to be revised significantly.
[For color key, see: https://covid.cdc.gov/covid-data-tracker/#variant-proportions]
❖ #ThisIsOurPolio #Covid #Covid19 #SARS2 #CDC #variants #CovidIsNotOver #CovidIsAirborne #WearAMask #BetterMasks
In August, summer FLiRT wave receded into S:F546L soup. Sept FLuQE wavelet became MC wave, sustained into Nov.
Now #CDC breaks out two new MC variants—as that family pushed into soup by FLiRT KS.1.1 / FLuQE KP.3.3 hybrid XEC.
CDC also breaks out LP.8.1, previously significant in GISAID, along with XEK, child of XEC and FLiRT KP.2.3.
Latest GISAID data sparse, even after Raj's update 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, D. Focosi, WHN, others
[ beadsland on Ko-fi ]
A reskin of CDC's Variants Nowcast, emphasizing significant variants, incl. those in GISAID yet not broken out by CDC.
Five rectangular tree-charts, side by side, for fortnights through December 8–11. Legend 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 JN.1. XEC accounts for near half total, with JN.1.11 + FLuQE a bit more than a third.
For week of 11/24–12/7, packed bubble charts fill many single-variant tiles, indicating diversification of those variants—per GISAID—that wouldn't otherwise be apparent given CDC's choices of what to break out or not.
Legend:
XEC [red]:
45% - XEC
JN.1.11 + FLuQE [browns]:
9% - MC.1, MC.10.1, MC.19
3% - KP.3
24% - other KP.3.1.1 / MC
JN.1.11 + FLiRT [blues]:
8% - LP.8.1
4% - XEK, KP.2.3, FDA-Vaccine-Target KP.2, KP.4.1 & KP.2.15
¼% - LP.1 & other KP.1.1.3 / LP
0% - other KP.1.1
JN.1 + FLiRT [green]:
7% - LF.7, LB.1.3.1 / NL, LB.1, JN.1.18.6 / LY, LF.3.1 & JN.1.16.1 / LF
JN.1 + FLiRT-KS [purple]:
⅒% - other KS.1
Other [greys]:
¼% - JN.1.16, JN.1.18 & four tracked variants at <⅒%
0% - HV.1
⅓% - other WHO-Vaccine-Target JN.1
0% - other Omicron-2 BA.2
0% - other Omicron B.1.1.529 / BA
⅜% - Other (not specified)](https://spaces.hcommons.social/media_attachments/files/113/688/708/912/059/681/original/f4db11a583edb72b.jpg "Chart: Estimated U.S. Variant Proportions by Common Name
Sources: Centers for Disease Control, CoV-Lineages, NYITCOM, D. Focosi, WHN, others
[ beadsland on Ko-fi ]
A reskin of CDC's Variants Nowcast, emphasizing significant variants, incl. those in GISAID yet not broken out by CDC.
Five rectangular tree-charts, side by side, for fortnights through December 8–11. Legend 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 JN.1. XEC accounts for near half total, with JN.1.11 + FLuQE a bit more than a third.
For week of 11/24–12/7, packed bubble charts fill many single-variant tiles, indicating diversification of those variants—per GISAID—that wouldn't otherwise be apparent given CDC's choices of what to break out or not.
Legend:
XEC [red]:
45% - XEC
JN.1.11 + FLuQE [browns]:
9% - MC.1, MC.10.1, MC.19
3% - KP.3
24% - other KP.3.1.1 / MC
JN.1.11 + FLiRT [blues]:
8% - LP.8.1
4% - XEK, KP.2.3, FDA-Vaccine-Target KP.2, KP.4.1 & KP.2.15
¼% - LP.1 & other KP.1.1.3 / LP
0% - other KP.1.1
JN.1 + FLiRT [green]:
7% - LF.7, LB.1.3.1 / NL, LB.1, JN.1.18.6 / LY, LF.3.1 & JN.1.16.1 / LF
JN.1 + FLiRT-KS [purple]:
⅒% - other KS.1
Other [greys]:
¼% - JN.1.16, JN.1.18 & four tracked variants at <⅒%
0% - HV.1
⅓% - other WHO-Vaccine-Target JN.1
0% - other Omicron-2 BA.2
0% - other Omicron B.1.1.529 / BA
⅜% - Other (not specified)")
