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Raj Rajnarayanan

@RajlabN

Jul 28 • 15 tweets • 5 min read • Read on X

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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

@GISAID KP.3* lineages 👀

4/n

@GISAID Variant landscape #30DayTrends - #USA

KP.2.3, KP.3.1.1 and KP.3.1 are the top circulating lineages

5/n

@GISAID Variant landscape #30DayTrends - #UnitedKingdom

KP.3.1.1, KP.3.1 and KP.3.3 are the top circulating lineages

6/n

@GISAID Variant landscape #30DayTrends - #Canada

KP.3.1.1, KP.3.2.3 and KP.3 are the top circulating lineages

7/n

@GISAID Variant landscape #30DayTrends - #Spain

KP.3.1.1 is the dominant circulating lineage in Spain

8/n

@GISAID Variant landscape #30DayTrends - #Japan

KP.3.3 is the dominant circulating lineage in Japan

9/n

@GISAID Variant landscape #30DayTrends - #Israel

KP.3.1.4 is the dominant circulating lineage in Israel

10/n

@GISAID Variant landscape #30DayTrends - #Australia

KP.3.1, KP.3.2, KP.3 and KP.3.3 are the top circulating lineages

[low sequence count]

11/n

@GISAID Variant landscape #30DayTrends - #Ireland

KP.3.1.1 and KP.3.1 are the top circulating lineages

[low sequence count]

12/n

@GISAID Variant landscape #30DayTrends - #France

KP.3.1.1 is the top circulating lineage in France

[low sequence count]

13/n

@GISAID Variant landscape #30DayTrends - #Denmark

KP.3.1.1 is the top circulating lineage in Denmark

[low sequence count]

14/n

@GISAID Variant landscape #30DayTrends - #Singapore

KP.2.3 is the top circulating lineage in Singapore

[low sequence count]

15/n

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More from @RajlabN

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

Raj Rajnarayanan

@RajlabN

Jun 5

#SARSCoV2 #VaccineAntigen Updates

Question before @US_FDA #VRBPAC committee:

For the 2024-2025 Formula of #COVID19 vaccines in the U.S., does the committee recommend a monovalent JN.1-lineage vaccine composition?

Watch:

1/n youtube.com/live/weaKQiFk_…

Mutations of Interest on JN.1 background

JN.1 + F456L (FL) |JN.1.16 • JN.1.11.1
JN.1 + R346T (RT) |•JN.1.18 •JN.1.13.1 • KQ.1
JN.1 + R346T + F456L (#FLiRT) |•KP.2 • KP.1.1
JN.1 + R346T + F456L + T572I (#FLiRTTI) |• KZ.1.1.1
JN.1 + F456L + Q493E (#FLuQE) |• KP.3

2/n

from @Novavax presentation

JN.1 Vaccine Induces Broad Neutralizing Responses to All Subvariants Tested

3/n

Read 4 tweets

Raj Rajnarayanan

@RajlabN

Jun 5

#SARSCoV2 Updates

KP.3 group of lineages (as of 6/4/2024)

KP.2 (JN.1.11.1 w/ S:R346T) group of lineages (as of 6/4/2024)

JN.1* group swells to 266 (not counting recombinants)

Read 4 tweets

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