Raj Rajnarayanan Profile picture
Oct 7, 2022 12 tweets 14 min read Read on X
Tracking #SARSCoV2 #Convergent #Lineages ( aka #VariantSoup) over time - Globally | #30DayTrends

BQ.1 (#Typhon)/BQ.1.1(#Cerberus) are currently at the top & BA.2.75.2* (#Chiron) is not far behind!

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

Updated 10/6/2022
Granular details - #VariantSoup with Convergent Mutations #30DayTrends

BQ.1/BQ.1.1 and BA.2.75.2 are heading the charts!

2/n
Tracked #Convergent #lineages are predicted to be immune evasive and bind to host ACE2 receptor better than Omicron.BA2

XBB is most immune evasive
Most BA.2.75* binds better to ACE2 receptors

Closely watched lineages - XBB, CA.1, BQ.1.1, BN.1, BR.3

3/n
#Singapore is a #XBB* hotspot (#30DayTrends)

4/n
#UnitedKingdom, #USA, #Denmark, #France, and #Belgium are BQ.1.1* hotspots (#30DayTrends)

5/n
#USA, #Singapore, #Denmark, #Austria, #Australia, #Canada are emerging BA.2.3.20* hotspots (#30DayTrends)

6/n
#Singapore is an emerging BM.1.1.1 (#Mimas) hotspot (#30DayTrends)

9/n
List of "unofficial" variant nicknames for easy social media communication

H/T @TRyanGregory

Why are we watching these lineages?



11/n
Live tracking of convergent lineages with the
@GenSpectrum #Collection54 by @CorneliusRoemer

cov-spectrum.org/collections/54

12/n

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More from @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…
Image
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 Image
@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 Image
Read 21 tweets
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…
Image
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 Image
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 Image
Read 15 tweets
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 Image
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/
Image
Some of the seqs are already in the tableau mutational profile of WGS data from USDA-NVSL

as highlighted by @0bFuSc8



3/n
Image
Read 6 tweets
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…
Image
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 Image
@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 Image
Read 19 tweets
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 Image
#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…
Image
Read 7 tweets
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…
Image
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 Image
@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 Image
Read 15 tweets

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