Tracking #SARSCoV2 #Lineages - Globally |09/07/24

Top lineages -#30DayTrends

KP.3.1.1 (37.1%)
KP.2.3 (9%)
KP.3.3 (5.7%)
KP.3.1 (2.9%)
XDV.1 (2.9%)
KP.1.1.3 (2.7%)
LB.1 (2.3%)
LB.1.3 (2.1%)
KP.2.2 (2%)
---
XEC (1.4%)👀

Track #G30 :

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

KP.3.1.1* is still the top circulating group of lineages in the world.

This analysis includes #SARSCoV2 sequences submitted to @GISAID with sample collection dates on or after 08/08/2024 (12,884 sequences)

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What the XEC!

Recombinant #SARSCoV2 lineage #XEC (recombinant of KS.1.1/KP.3.3) has the potential to outcompete other circulating lineages in #USA (and other countries)

More data is needed to provide a reliable growth advantage estimates

https://twitter.com/RajlabN/status/1827585876437647729

#VariantHunters are closely monitoring XEC.1 with signature mutations Spike K182R & ORF1a:L4182F

Tracking #SARSCoV2 #Lineages - Globally |08/25/24

Top lineages -#30DayTrends

KP.3.1.1 (30.1%)👀
KP.2.3 (11%)
KP.3.3 (7.1%)
KP.3.1 (4.2%)
LB.1.7 (2.7%)
KP.2 (2.5%)
LB.1 (2.5%)
KP.1.1.3 (2.5%)
KP.2.2 (2.2%)
---
XEC (0.4%)

Track #G30 :

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

KP.3.1.1* is the top circulating group of lineages in the world. This analysis includes #SARSCoV2 sequences submitted to @GISAID with sample collection dates on or after 07/25/2024 (14,688 sequences)

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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)

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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)

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#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/

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

#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

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

#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

#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)

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

#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)

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#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 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

#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

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…
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

#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…
#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

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

#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…
more information on H5N1 Clade 2.3.2.1c from @WHO

who.int/emergencies/di…

H5N1 Update | Avian Flu Clade 2.3.4.4b

Looked at the newly uploaded Human Sequence (ID: 19027114) from Texas

- PB2 contains 👀E627K 👀

in addition to the mutations found in the dairy cattle and wild bird sequences uploaded earlier (used #Fluserver for mutational analysis)

https://twitter.com/RajlabN/status/1773769597881073814

Thanks to the labs that are testing, rapidly sequencing and submitting data to public databases (GISAID and others)!

#SARSCoV2 #VariantProportions - #USA |03/29/24

@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…
In the next few weeks expect to see an increase in lineages containing Spike mutations R436T and/or F456L

Closely watching lineages with #FLiRT mutations (high immune escape)

2/n