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Raj Rajnarayanan Profile picture
@RajlabN
Feb 2 • 4 tweets • 2 min read • Read on X
#COVID19 #VariantDashboard - #USA

#SARSCoV2 #Lineages #30DAYTRENDS

JN.1 (43.8%)
JN.1.4 (21.7%)
JN.1.1 (5.1%)
HV.1 (5.1%)
JN.1.8.1 (2.1%)
JN.1.7 (1.7%)
JN.1.2 (1.6%)
JN.1.9 (1.1%)
JD.1.1 (1.1%)

Tracker: | 02/02/24
1/n tinyurl.com/mryj4uu7
Image
Sequence count by US States

A total of 8993 sequences were submitted with specimen collection dates on or after 01/02/2024 (of which 374 (~4.2%) were collected via airport surveillance)

2/n Image
Sequences from @CDCgov Traveler Based Surveillance Program*

*Currently at six airports from 5 US States (#California, #NewYork, #Washington, #NewJersey and #Virginia)

3/n Image
@CDCgov .@CDCgov updated variant proportions estimates on 1/19/2024 (updated biweekly)

JN.1* is the dominant SARSCOV2 lineage group now!



4/n

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More from @RajlabN

Raj Rajnarayanan Profile picture
Feb 1
Closely following the new BA.2.X SARS-CoV-2 lineage with with > 100 mutations (>30 mutations in Spike) from South Africa

H/T @Tuliodna
#NewLineageAlert #OmicronSaltation

This just got designated as BA.2.87.1 (Alias of B.1.1.529.2.87.1) | BA.2.87 with 15+ Spike mutations

H/T @CorneliusRoemer

more info: github.com/cov-lineages/p…
Preliminary in silico analysis

BA.2.87.1 (based on sequences submitted; mostly bad QC)

less predicted immune escape compared to JN.1
less predicted ACE2 binding affinity compared to JN.1

It has to pick additional mutations to stay relevant in the competition Image
Read 4 tweets
Raj Rajnarayanan Profile picture
Feb 1
#COVID19 #VariantDashboard - #USA

#SARSCoV2 #Lineages #30DAYTRENDS

JN.1 (42.8%)
JN.1.4 (22.5%)
HV.1 (5.3%)
JN.1.1 (5.2%)
JN.1.8.1 (2.1%)
JN.1.7 (1.7%)
JN.1.2 (1.6%)
JD.1.1 (1.2%)
JN.1.9 (1.1%)

Tracker: | 02/01/24
1/n tinyurl.com/mryj4uu7
Image
Sequence count by US States

A total of 9844 sequences were submitted with specimen collection dates on or after 01/01/2024 (of which 404 (~4.1%) were collected via airport surveillance)

2/n Image
Sequences from @CDCgov Traveler Based Surveillance Program*

*Currently at six airports from 5 US States (#California, #NewYork, #Washington, #NewJersey and #Virginia)

3/n Image
Read 4 tweets
Raj Rajnarayanan Profile picture
Jan 27
#COVID19 #VariantDashboard - #USA

#SARSCoV2 #Lineages #30DAYTRENDS

JN.1 (41.5%)👁️
JN.1.4 (19.7%)👁️
HV.1 (6.9%)
JN.1.1 (5.5%)
JN.1.8.1 (1.8%)👁️
JN.1.2 (1.6%)
JN.1.7 (1.4%)
JD.1.1 (1.3%)
HK.3 (1%)
BA.2.86.1 (1%)

Tracker: | 01/26/24
1/n tinyurl.com/mryj4uu7
Image
Sequence count by US States

A total of 9880 sequences were submitted with specimen collection dates on or after 12/25/2023 (of which 474 (~4.8%) were collected via airport surveillance)

2/n Image
Sequences from @CDCgov Traveler Based Surveillance Program*

*Currently at six airports from 5 US States (#California, #NewYork, #Washington, #NewJersey and #Virginia)

3/n Image
Read 8 tweets
Raj Rajnarayanan Profile picture
Jan 24
#COVID19 #VariantDashboard - #USA

#SARSCoV2 #Lineages #30DAYTRENDS

JN.1 (38.7%)👁️
JN.1.4 (18.2%)⬆️👀
HV.1 (8.2%)
JN.1.1 (5.7%)
JN.1.8.1 (1.4%)
JD.1.1 (1.4%)
JN.1.2 (1.4%)
BA.2.86.1 (1.2%)
HK.3 (1.1%)
JN.1.7 (1.1%)

Tracker: | 01/23/24
1/n tinyurl.com/mryj4uu7
Image
Sequence count by US States

A total of 6647 sequences were submitted with specimen collection dates on or after 12/24/2023 (of which 508 (~7.6%) were collected via airport surveillance)

2/n Image
Sequences from @CDCgov Traveler Based Surveillance Program*

*Currently at six airports from 5 US States (#California, #NewYork, #Washington, #NewJersey and #Virginia)

3/n Image
Read 5 tweets
Raj Rajnarayanan Profile picture
Jan 19
#SARSCoV2 #VariantProportions - #USA |01/19/23

@CDCgov #Nowcast 2-Week estimates

JN.1 (BA.2.86.1.1 w/ S:L455S)^^ is the dominant circulating lineage🚀👀

^^Still doesn't separate JN.1.4* (likely the top lineage) and 22 JN.1* sub-lineages



1/n covid.cdc.gov/covid-data-tra…
Image
JN.1* sub-lineages^^ not yet separated from JN.1 in CDC variant dashboard

Source: @PangoNetwork

2/n Image
@PangoNetwork JN.1 hotspots per CDC Nowcast

3/n Image
Read 5 tweets
Raj Rajnarayanan Profile picture
Jan 15
Tracking #SARSCoV2 #Lineages - Globally |01/15/24

Top lineages -#30DayTrends (#G30):

JN.1 (34.9%)👁️
JN.1.4 (12.4%)👀⬆️
JN.1.1 (7.5%)
HV.1 (7.1%)
BA.2.86.1 (3.1%)
HK.3 (2.4)
JD.1.1 (2.2%)
JG.3 (2%)
JN.2 (1.5%)
JN.1.2 (1.3%)

Tracker:

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

JN.1* establishes firm footing as the dominant group of lineages in the world.

This analysis includes #SARSCoV2 sequences submitted to @GISAID with sample collection dates on or after 12/15/2023 (24,060 sequences)

2/n Image
@GISAID Global BA.2.86* hotspots (#Pirola) #30DayTrends (included recombinants XDD: EG.5.1.1*/JN.1* and XDK: JN.1.1.1*/XBB.1.16.11* recombinant)

3/n Image
Read 6 tweets

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