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Raj Rajnarayanan Profile picture
@RajlabN
Jun 27, 2022 • 13 tweets • 18 min read • Read on X
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#COVID19 #VariantDashboard - #UnitedStates

TOP lineages (15-DAY TRENDS):

46.66% BA.2.12.1**,
23.33% BA.5^^,
12.15% BA.4^^,
7.64% BA.2,
4.24% BA.5.1^^,
1.29% BA.2.9 and
1.17% unassigned

**S:L452Q; ^^S:L452R/F486V

Tracker: tinyurl.com/mryj4uu7
#OmicronUpdates 6/27/22
#OmicronVariantUpdates #UnitedStates 06/27/22

Top 5 lineages:
BA.2.12.1, ⬇️ (Spike: L452Q)
BA.5, ⬆️ (Spike: L452R)
BA.4 ⬆️ (Spike: L452R)
BA.2 ⬇️
BA.5.1 ⬆️👀 (Lineage prevalent in #Portugal)

* includes recently designated BA.2.x.y and undesignated BA.2s
#SARSCoV2 lineages in USA (#15DayTrends)

Circulating #BA5*/#BA4* sub-lineages:
BA.5, BA.4.1, BA.5.2.1, BA.5.1, BA.4, BA.5.2, BA.5.3.1, BE.1, BF.1, BA.5.3

Assignments via: #Nextclade #PANGO - clades.nextclade.org
BA.5*/BA.4* hotspots - #UnitedStates #15DayTrends

All eyes on #NewYork!
#Hospital #Capacity - (by State/Division)

All hospitalizations not just COVID-19

public.tableau.com/app/profile/ra…
#COVID19 #Hospitalizations in the #UnitedStates (filtered to last 90 days)

Hospital Tracker (by States, by age group): public.tableau.com/app/profile/ra…
#COVID19 #Cases and #Deaths - US States (@CDCgov data) #15DayTrends

Tracker: public.tableau.com/app/profile/ra…
Tracking #circulating #variants in New York (#Bellwether state) #15DayTrends

BA.2.12.1 is still the top circulating variant in NY..
>>Spike L452R > L452Q

Top circulating lineages:
42.83% BA.2.12.1
26.46% BA.5 <<<
13.26% BA.4 <<<
6.40% BA.5.1 👀<<
5.67% BA.2

#MaskUP #NewYork
#COVID19 #Hospitalizations in #NewYork

Do not let your guard down! #MaskUP!!

Closely monitoring hospitalizations in #NY!

BA.2.12.1* (L452Q)⬇️
BA.5*⬆️
BA.4* ⬆️
Status of #COVID19 wave in #Florida

Looks like BA.2.12.1 wave in FL may have peaked, don't let your guard down!

Get #Boosted and #MaskUP!
Status of #COVID19 wave in #Texas
Status of #COVID19 in #California
Status of #COVID19 in the #DeltaRegion (#Alabama, #Arkansas, #Illinois, #Kentucky, #Louisiana, #Missouri, #Mississippi, #Tennessee)

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More from @RajlabN

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
Raj Rajnarayanan Profile picture
Apr 5
#H5N1 Clade 2.3.2.1c - #Vietnam

New sequence from Khanh Hoa has intriguing #avianflu reassortment and PB2-E627K mammalian adaptation signature.

PB2-E627K was absent in previously submitted avian sequences.

Case description: fao.org/vietnam/news/d…
Image
more information on H5N1 Clade 2.3.2.1c from @WHO

who.int/emergencies/di…
Case description Image
Read 5 tweets

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