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Raj Rajnarayanan

Jun 29, 2022 • 12 tweets • 16 min read • Read on X

#COVID19 #VariantDashboard - #UnitedStates

TOP lineages (15-DAY TRENDS):

43.89% BA.2.12.1**,
23.48% BA.5^^,
12.63% BA.4^^,
7.82% BA.2,
5.22% BA.5.1^^,
2.54% unassigned and
1.18% BA.2.9

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

Tracker: tinyurl.com/mryj4uu7
#OmicronUpdates 6/28/22

#OmicronVariantUpdates #UnitedStates 06/28/22

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

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…

@CDCgov

#COVID19 #Cases and #Deaths - US States (
@CDCgov data)

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

Tracking #circulating #variants in New York (#Bellwether state) #15DayTrends

Spike L452R > L452Q

Top circulating lineages:
41.74% BA.2.12.1
27.23% BA.5 <<<
13.68% BA.4 <<<
6.65% BA.5.1 👀<<
5.45% 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

BA.2.12.1 wave in FL has 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

@RajlabN

Aug 11

Tracking #SARSCoV2 #Lineages - Globally |08/10/24

Top lineages -#30DayTrends

KP.3.1.1 (24.2%)👀
KP.2.3 (9.5%)
KP.3.3 (8.4%)
KP.3.1 (5.9%)
LB.1 (2.5%)
KP.2.2 (2.4%)
KP.2 (2.4%)
KP.3 (2.3%)
LB.1.7 (2.3%)
KP.3.2.3 (2.2%)

Track #G30 :

1/n public.tableau.com/app/profile/ra…

Granular details #Global #30DayTrends

KP.3.1.1 is the top circulating lineage in the world. This analysis includes #SARSCoV2 sequences submitted to @GISAID with sample collection dates on or after 07/11/2024 (15,325 sequences)

2/n

@GISAID Thanks to all the countries that are still supporting #SARSCoV2 testing and rapidly submitting sequences to @GISAID

Top submitters: #USA #Canada #UK #Japan #Spain
#France #China #Netherlands #Israel #Ireland
#Australia #Singapore #Denmark #Italy #Sweden #Germany #Guatemala

Read 21 tweets

Raj Rajnarayanan

@RajlabN

Jul 28

Tracking #SARSCoV2 #Lineages - Globally |07/27/24

Top lineages -#30DayTrends

KP.3.1.1 (17.4%)👀
KP.2.3 (8.1%)
KP.3.3 (8%)
KP.3.1 (7.2%)
KP.3 (3.3%)
KP.2 (3.1%)
KP.3.1.4 (3.1%)
KP.3.2 (3%)
LB.1 (2.5%)
KP.3.2.3 (2.5%)

Track #G30 :

1/n public.tableau.com/app/profile/ra…

Granular details #Global #30DayTrends KP.3* is the dominant group of lineages in the world.

This analysis includes #SARSCoV2 sequences submitted to @GISAID with sample collection dates on or after 06/27/2024 (12,753 sequences)

2/n

Thanks to all the countries that are still supporting #SARSCoV2 testing and rapidly submitting sequences to @GISAID

Top submitters: #USA #UK #Canada #Spain #Japan #Israel #Australia #Ireland #France #Denmark #Singapore #NewZealand #Germany #Netherlands #Sweden #Taiwan

3/n

Read 15 tweets

Raj Rajnarayanan

@RajlabN

Jul 26

#H5N1 Updates #AvianInfluenza

@USDA #APHIS #NVSL has submitted 211 sequences on 7/24/24 with collection dates in 01 to 06/2024

12 #cow milk seqs from #Minnesota with **PB2 Q591R** in addition to the cattle outbreak signature M631L [isolate ID 24-016288-001 to 015!]

1/n

PB2 Q591R: A basic amino acid at position 591 of PB2 can compensate for the lack of lysine at position 627 and confers efficient viral replication to pandemic H1N1 viruses in mammals.

ie., Q591R ~ E627K! 👀

2/n pubmed.ncbi.nlm.nih.gov/20700447/

https://twitter.com/0bFuSc8/status/1811720044205756419

Some of the seqs are already in the tableau mutational profile of WGS data from USDA-NVSL

as highlighted by @0bFuSc8

3/n

https://twitter.com/0bFuSc8/status/1811720044205756419

Read 6 tweets

Raj Rajnarayanan

@RajlabN

Jul 20

Tracking #SARSCoV2 #Lineages - Globally |07/20/24

Top lineages -#30DayTrends

KP.3.1.1 (14.2%)👀
KP.2.3 (7.9%)
KP.3.1 (7.8%)
KP.3.3 (7.7%)
KP.3.2 (3.8%)
KP.3 (3.4%)
KP.3.1.4 (3.4%)
KP.2 (3.4%)
LB.1 (2.7%)
KP.2.2 (2.7%)

Track #G30 :

1/n public.tableau.com/app/profile/ra…

Granular details #Global #30DayTrends KP.3* & KP.2* are the dominant group of lineages in the world.

This analysis includes #SARSCoV2 sequences submitted to @GISAID with sample collection dates on or after 06/20/2024 (12,854 sequences)

2/n

@GISAID Thanks to all the countries that are still supporting #SARSCoV2 testing and rapidly submitting sequences to @GISAID

Top submitters: #USA #UK #Canada #Spain #Japan #Israel #France #Singapore #Netherlands #Australia #Ireland #Iceland #China #Sweden #Portugal #Italy

3/n

Read 19 tweets

Raj Rajnarayanan

@RajlabN

Jun 19

#COVID19 #VariantDashboard - #USA | 06/18/24
#SARSCoV2 #Lineages #30DAYTRENDS

KP.2.3 (7.7%)
KP.2 (7.4%)
KP.3.1 (5%)
KP.3.3 (4.8%)
JN.1.16.1 (4.2%)
LB.1.7 (4%)
JN.1.16 (3.4%)
KP.1.1.1 (3.4%)
LB.1.3 (3.3%)
KP.2.2 (3.1%)
--
KP.3.1.1 (1.5%)👀

1/ntinyurl.com/mryj4uu7

You can filter spike mutations S31del, R346T, L455S, F456L, T572I (Top convergent mutations) to display #SLip, #FLiRT, #TiRT, #FLiRTTI, #DeFLiRT combo mutations; (Note: retired #FLip as of now)

Also, by state, lineage, collection date

2/n

#AirportSurveillance data - @CDCgov

Traveler Based Genomic Surveillance Program ( )

New: included "Travel history: Mediterranean Norwegian escape" use sampling strategy menu to display (a KP.5 and KP.2 is reported from WY)

3/n wwwnc.cdc.gov/travel/page/tr…

Read 7 tweets

Raj Rajnarayanan

@RajlabN

Jun 9

Tracking #SARSCoV2 #Lineages - Globally |06/08/24

Top lineages -#30DayTrends (#G30)

KP.2.3 (8.7%)
KP.2 (8.7%)
KP.3.1 (7.7%)
KP.3 (6.2%)
KP.3.2 (5.1%)
LB.1 (5%)
KP.1.1 (4.9%)

Track:

1/n public.tableau.com/app/profile/ra…

Granular details #Global #30DayTrends

KP.3* & KP.2* are the dominant group of lineages in the world.

This analysis includes #SARSCoV2 sequences submitted to @GISAID with sample collection dates on or after 05/09/2024 (8,025 sequences)

2/n

@GISAID You can filter spike mutations S31del, R346T, L455S, F456L, T572I (Top convergent mutations) to display #SLip, #FLiRT, #TiRT, #FLiRTTI, #DeFLiRT combo mutations; (Note: retired #FLip as of now)

4/n

Read 15 tweets

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