Raj Rajnarayanan Profile picture
Feb 3, 2023 8 tweets 8 min read Read on X
Tracking #SARSCoV2 #Lineages - Globally

Top lineages -#20DayTrends (#G20):

BQ.1.1 (18.9%)
XBB.1.5 (18.7%)👀^
CH.1.1 (5.3%)👀
BQ.1 (3.7%)
XBB.1 (2.7%)
BA.5.2.48 (2.3%)
XBF (1.7%)

^more sequences from USA in this period

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

Updated 02/02/2023
Granular details #Global #20DayTrends

This analysis includes all designated #SARSCoV2 sequences submitted to GISAID with sample collection dates on or after 01/12/2023
USA has submitted a lion's share of sequences with sample collection dates on or after 01/12/2023 ...followed by #Canada, #UnitedKingdom, #Austria, #Japan, #Denmark, #Germany, #France, #China, #Australia, #Italy
In Silico Immune escape and ACE2 receptor binding scores (relative to BA.2)*

Data is intended to prioritize select lineages to generate rapid laboratory experiments to gauge immune escape and ACE2 binding affinity.

[Credits in the legend]

* Only Spike RBD mutations considered
#SARSCoV2 lineages DS.1^^ (BN.1.3.1.1), XBB.1.5*, XBF, BN.1*, DN.1.1^^, XBB.6.1^^, XBB.1.9.1^^, CJ.1^^, CP.1.3^^, XBL^^, XBK^^ are in the zone of concern (red box) - Predicted to have high immune escape and tight ACE2 binding affinity!

DS.1* stands out!

^^ low sequence count
What to expect in the next few weeks?

github.com/neherlab/SARS-…

Excellent SARSCoV2 Variant report
H/T @richardneher, @CorneliusRoemer
Global variant landscape without sequences from USA (for context)
Top circulating lineages in #UnitedKingdom #20DayTrends

18% CH.1.1,
15.4% BQ.1.1,
11.6% XBB.1.5
7.6% CH.1.1.1
4% BQ.1.1.2
2.2% CH.1.1.2
2.1% XBF

public.tableau.com/app/profile/ra…

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More from @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…
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
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_…
Image
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 Image
from @Novavax presentation

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

3/n Image
Read 4 tweets
Jun 5
#SARSCoV2 Updates

KP.3 group of lineages (as of 6/4/2024) Image
KP.2 (JN.1.11.1 w/ S:R346T) group of lineages (as of 6/4/2024) Image
JN.1* group swells to 266 (not counting recombinants)
Read 4 tweets
May 18
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 Image
@GISAID Predicted Immune Escape vs ACE2 Binding Scores of circulating SARSCoV2 lineages (Relative to BA.2)



3/n public.tableau.com/app/profile/ra…
Image
Read 7 tweets
May 6
#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)

2/n Image
Predicted #ImmuneEscape vs ACE2 Binding Scores (Relative to BA.2)



3/n public.tableau.com/app/profile/ra…
Image
Read 6 tweets
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

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