Raj Rajnarayanan Profile picture
Sep 28, 2022 18 tweets 17 min read Read on X
#COVID19 #VariantDashboard - #UnitedStates

TOP lineages (15-DAY TRENDS):

22.18% BA.5.2.1
12.64% BA.5.2
10.88% BA.4.6
10.02% BA.5.1
4.19% BA.5
3.63% BA.5.5
3.23% BA.5.6
3.04% BF.10
2.32% BA.5.2.9

Tracker: tinyurl.com/mryj4uu7
#OmicronUpdates 09/27/22
1/n
Top circulating lineages:

82.4% BA.5*
10.9% BA.4.6*
2.7% BA.4*
1.4% BF.7*
0.8% BA.2.75*
0.7% BQ.1* 👀
0.2% BQ.1.1*👀
0.3% BA.2.75.2*
0.05% BA.2.3.20*
0.02% BJ.1*

2/n
.@CDCgov updated variant proportions estimates on 9/23/2022



3/n
#NewYork, #NorthCarolina and #Massachusetts 👀 are BA.4.6* (Spike R346T) hotspots

#15DayTrends

4/n
Status of BF.7* is USA - #15DayTrends

5/n
Tracking BA.2.75* (#Centaurus) over time in #USA

Closely following several newly designated BA.2.75* sub-lineages

USA Tracker: public.tableau.com/app/profile/ra…

6/n
BA.2.75.2* is the top circulating BA.2.75* lineage in the USA (#15DayTrends)

7/n
#LineageWatchTeam's @GenSpectrum #Collection24 maintained by @siamosolocani/@Asinickle1

>> All eyes on BQ.1*/BQ.1.1*, BA.2.3.20 and BA.2.75* lineages <<

Collection24: cov-spectrum.org/collections/24…

Tracker: public.tableau.com/shared/QFBZWNX…

(#15DayTrends - #USA)

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

All hospitalizations not just COVID-19

public.tableau.com/app/profile/ra…

9/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…

10/n
Closely watching #COVID19 #Hospitalizations in > 50 years old in #USA

11/n
Closely watching #Pediatric #COVID19 #Hospitalizations in #USA

11/n
#COVID19 #Cases and #Deaths - US States
-
@CDCgov data

Tracker: public.tableau.com/app/profile/ra…

13/n
Status of the latest #COVID19 Wave in #NewYork #BellwetherState

Top circulating variants - BA.5.2.1 (20.4%), BA.5.2 (13.6%), BA.4.6 (13.2%)

Other key lineages
BQ.1* (1.06%)
BQ.1.1* (0.53%)
BA.2.75.1* (1.48%)

Don't let your guard down!

14/n
Status of the latest #COVID19 Wave in #Massachusetts

Top circulating variants - BA.5.2.1, BA.4.6 (16.74%), BA.5.2

Other:
BE.1.1 (2.51%)
BQ.1 (1.05%)
BA.2.75.2 (0.4%)

Closely watching hospitalizations.. Don't let your guard down!
15/n
Status of the latest #COVID19 Wave in #NorthEast #USA (MD, PA, DE, NY, MA, VT, CT, NJ, ME, NH, RI)

Top circulating variants - BA.5.2.1, BA.4.6 (13.7%), BA.5.2

Other:
BF.7 (2.23%)
BQ.1 (1.3%)
BQ.1.1 (0.4%)

Closely watching hospitalizations.. Don't let your guard down!
15/n
#WasteWater analytics from @BiobotAnalytics

All eyes on "Northeast USA" | (States: MD, PA, DE, NY, MA, VT, CT, NJ, ME, NH, RI)

16/n
.@IHME_UW projections: #COVID19 cases will trend down for a few weeks and then start surging again!

Please get #boosted ASAP!

16/n

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More from @RajlabN

May 18
Tracking #SARSCoV2 #Lineages - Globally |05/18/24

Top lineages -#30DayTrends (#G30)

KP.2 (12.7%)
KP.3 (11.6%)👀
JN.1.7 (6.9%)
JN.1 (6.8%)
JN.1.16 (5%)
JN.1.4 (4.9%)
JN.1.16.1 (4.6%)
KP.1.1 (3.6%)
KS.1 (2.8%)
JN.1.32 (2.7%)
LB.1 (2.7%)


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

KP* is the dominant group of lineages in the world.

This analysis includes #SARSCoV2 sequences submitted to @GISAID with sample collection dates on or after 04/18/2024 (6,469 sequences)

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



3/n public.tableau.com/app/profile/ra…
Image
Read 7 tweets
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
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
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
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
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

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