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Raj Rajnarayanan Profile picture
@RajlabN
Feb 1, 2023 • 16 tweets • 16 min read • Read on X
Scrolly
#COVID19 #VariantDashboard - #UnitedStates

TOP lineages (#15DAYTRENDS):

44.6% XBB.1.5
17.2% BQ.1.1
3.7% BQ.1
2.9% XBB.1
1.7% BQ.1.1.4
1.2% BQ.1.2
1.2% BQ.1.3
1.1% BQ.1.1.18

Tracker: tinyurl.com/mryj4uu7
Updated: 01/31/2023

1/n Image
Sequence count by US State

#NorthCarolina, #NewYork, #California and #Washington have submitted a big share of sequences

XBB.1.5 stays strong at the top spot and is establishing a clear foot print outside NE USA!

2/n Image
USA Airport surveillance update #15DayTrends

97 sequences from 6 US States (#California, #NewYork, #Washington, #NewJersey, #Georgia and #Virginia)

3/n Image
Granular details -#VariantDashboard #USA #15DayTrends

XBB.1.5 is surging ahead, leaving the rest of the swarm behind!

4/n Image
.@CDCgov updated variant proportions estimates on 01/27/2023 (updated every Friday)

CH.1.1 makes an entry @ 1.5% in the CDC Variant Dashboard

XBB.1.5 is leading at the top!



5/n
Top circulating #SARSCOV2 lineages around the world 01/11 to 01/31/23 (#20DayTrends):

BQ.1.1 (18.4%)
XBB.1.5 (13.5%)
CH.1.1 (6.1%)
BQ.1 (3.7%)
XBF (2.4%)
XBB.1 (2.3%)
BA.5.2.48 (2.3%)
BF.7 (2.0%)
BQ.1.9 (1.9%)
CH.1.1.1 (1.7%)
BQ.1.1.20 (1.3%)
BQ.1.1.13 (1.2%)

6/n
Predicted Immune Escape and ACE2 binding of top lineages in USA (relative to BA.2)

Bivalent boosters (OG/Omicron.BA.5) will potentially protect the boosted from getting severe disease/hospitalizations.

Please get #boosted ASAP!

public.tableau.com/app/profile/ra…

7/n
#Hospital #Capacity - (by State/Division)

All hospitalizations not just COVID-19

public.tableau.com/app/profile/ra…

8/n
#COVID19 #Hospitalizations in the #UnitedStates

Please get #boosted (especially > 50 yr old and immune compromised) and #MaskUP!

Hospital Tracker (by States, by age group): public.tableau.com/app/profile/ra…

9/n
Status of the latest #COVID19 Wave in #NewYork

XBB.1.5 is still the top circulating lineage in NY

10/n ImageImage
Circulating recombinant lineages - USA #15DayTrends

XBB.1.5 is still the top recombinant in circulation!

11/n ImageImage
Tracking circulating #SARSCoV2 lineages, Cases, #COVID19 #hospitalizations 👀 in #California

XBB.1.5 is the top circulating lineage in CA

Top circulating lineages

XBB.1.5 (30.6%)👀
BQ.1.1 (15.7%)
BQ.1 (4.2%)
BQ.1.1.32 (4.2%)
BQ.1.28 (2.8%)
BQ.1.25.1 (2.3%)
XBB (2.3%)

12/n ImageImage
Weekly Trends in Number of COVID-19 Deaths and Weekly Case Rate in The United States Reported to CDC, per 100,000 population.

covid.cdc.gov/covid-data-tra…

13/n Image
Tracking circulating #SARSCoV2 lineages, Cases, #COVID19 #hospitalizations 👀 in #Arizona

Only 5 sequences with sample collection dates in the last 15 days (1 XBB.1.5 & 4 BQ.1.1*)

14/n Image
Tracking circulating #SARSCoV2 lineages, Cases, #COVID19 #hospitalizations in #Texas

XBB.1.5 is the top circulating lineage in TX

Top circulating lineages

XBB.1.5 (34.3%)👀
BQ.1.1 (20.6%)
XBB.1 (12.3%)

15/n ImageImage
Tracking circulating #SARSCoV2 lineages, Cases, #COVID19 #hospitalizations in #NorthCarolina

XBB.1.5 is the top circulating lineage in NC

Top circulating lineages

XBB.1.5 (41.1%)👀
BQ.1.1 (20.0%)
BQ.1 (6.3%)
XBB.1 (3.7%)

16/n ImageImage

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More from @RajlabN

Raj Rajnarayanan Profile picture
May 6
#COVID19 #VariantDashboard - #USA | 05/05/24

#SARSCoV2 #Lineages #30DAYTRENDS

JN.1.7 (12%)
JN.1 (11.5%)
KP.2 (8.9%)
JN.1.4 (8.4%)
JN.1.13.1 (5.6%)
JN.1.8.1 (4.5%)
JN.1.18 (3.9%)
JN.1.16 (3.6%)
KQ.1 (2.8%)
JN.1.16.1 (2.7%)
KP.3 (2.2%)

||
1/ntinyurl.com/mryj4uu7
Sequence count by US States

A total of 1886 sequences were submitted with specimen collection dates on or after 04/04/2024 (of which 373 (~19.8%) were collected via airport surveillance)

2/n Image
Predicted #ImmuneEscape vs ACE2 Binding Scores (Relative to BA.2)



3/n public.tableau.com/app/profile/ra…
Image
Read 6 tweets
Raj Rajnarayanan Profile picture
Apr 28
#H5N1 #LessonLearned - Domestic and Farm cats!

Common theme among H5N1 clade 2.3.4.4b infected Cats:
- Present multiple symptoms almost immediately
- Neurologic, Respiratory, rapid decline leading to death
(or compassionate euthanasia)
- Pick PB2 mammalian adaptations

1/n Image
French Cat (2022)

Phylogenetic analysis linked the infection closely to virus circulating in the neighboring duck farm, with minor genetic differences.

Key mutations: PB2 E627K & NS: E26G

Again, rapid selection of mammalian adaptation mutation

2/n
Polish Cats (2023)

First widespread H5N1 clade 2.3.4.4b infection across a wide geographic area within a country

Outbreak affected both indoor/outdoor cats

Cat food/ Stork investigated as a likely sources

Mammalian adaptations: PB2 E627K & K526R



3/n
Read 6 tweets
Raj Rajnarayanan Profile picture
Apr 16
#COVID19 #VariantDashboard - #USA | 04/16/24

#SARSCoV2 #Lineages #30DAYTRENDS

JN.1 (24.7%)
JN.1.4 (13.3%)
JN.1.7 (9.8%)
JN.1.8.1 (5.6%)
KP.2 (4.6%)
JN.1.18 (3.5%)
KQ.1 (3%)
JN.1.13.1 (2.6%)
JN.1.4.5 (2.6%)
JN.1.32 (2.3%)

Tracker:
1/ntinyurl.com/mryj4uu7
Sequence count by US States

A total of 1509 sequences were submitted with specimen collection dates on or after 03/16/2024 (of which 69 (~4.6%) were collected via airport surveillance)

2/n Image
It's getting difficult to separate GBW airport vs baseline screening

#30DayTrends GBW uploaded 275 sequences
out of which 69 airport seqs & 206 baseline surveillance seqs

Here is a detailed account of their surveillance efforts



3/n public.tableau.com/app/profile/ra…
Image
Read 4 tweets
Raj Rajnarayanan Profile picture
Apr 14
Tracking #SARSCoV2 #Lineages - Globally |04/13/24

Top lineages -#30DayTrends (#G30):

JN.1 (27.7%)
JN.1.4 (15%)
JN.1.7 (9%)
JN.1.18 (4.3%)
KP.2 (3.4%)
JN.1.8.1 (3.3%)
JN.1.32 (3.1%)
JN.1.16 (2.8%)
JN.1.4.3 (2.7%)
JN.1.11.1 (2%)

Track:

1/n public.tableau.com/app/profile/ra…
Image
Granular details #Global #30DayTrends

JN.1* is still the dominant group of lineages in the world.

This analysis includes #SARSCoV2 sequences submitted to @GISAID with sample collection dates on or after 03/14/2024 (6,157 sequences)

2/n Image
@GISAID Predicted Immune Escape vs ACE2 Binding Scores of circulating SARSCoV2 lineages (Relative to BA.2)

Closely looking at JN.1* with #FLiRT mutations (S:R346T & S:F456L) & #FLiRTTI ( #FLiRT + T572I)!


3/n public.tableau.com/app/profile/ra…
Image
Read 6 tweets
Raj Rajnarayanan Profile picture
Apr 12
#SARSCoV2 #VariantProportions - #USA |04/12/24

@CDCgov #Nowcast 2-Week estimates

JN.1* is still the dominant circulating group of lineages

Expected JN.1.11.1* sub-lineages (KP*) and others with #FLiRT mutations to feature in the dashboard



1/n covid.cdc.gov/covid-data-tra…
Image
#FLiRT lineages are growing 👀

Nearly 20% of JN.1.13 (listed in CDC dashboard) is KS.1 (JN.1.13.1.1; not separated from the parent lineage yet)

and 55% of JN.1.16 is JN.1.16.1

Both KS.1 and JN.1.16.1 are #FLiRT lineages

2/n
Consistent with #VariantDashboard #30DayTrends #USA



3/n
Read 4 tweets
Raj Rajnarayanan Profile picture
Apr 7
Tracking #SARSCoV2 #Lineages - Globally |04/06/24

Top lineages -#30DayTrends (#G30):

JN.1 (31%)
JN.1.4 (16.6%)
JN.1.7 (8%)
JN.1.18 (4%)
JN.1.32 (3.3%)
JN.1.8.1 (3.1%)
KP.2 (2.4%)
JN.1.4.3 (2.3%)
JN.1.1 (2%)
JN.1.39 (1.9%)

Track:

1/npublic.tableau.com/app/profile/ra…
Granular details #Global #30DayTrends

JN.1* is still the dominant group of lineages in the world.

This analysis includes #SARSCoV2 sequences submitted to @GISAID with sample collection dates on or after 03/07/2024 (6,619 sequences)

2/n Image
@GISAID Predicted Immune Escape vs ACE2 Binding Scores of circulating SARSCoV2 lineages (Relative to BA.2)

Closely looking at JN.1* with #FLiRT mutations (S:R346T & S:F456L) & #FLiRTTI ( #FLiRT + T572I)!


3/n public.tableau.com/app/profile/ra…
Image
Read 6 tweets

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