Raj Rajnarayanan Profile picture
Apr 30 8 tweets 10 min read Twitter logo Read on Twitter
Tracking #SARSCoV2 #Lineages - Globally

Top lineages -#20DayTrends (#G20):

XBB.1.5 (36.6%)⬇️
XBB.1.9.1 (11.5%)⬆️
EG.1 (4.7%)⬆️
XBB.1.16 (4.4%)⬆️
XBB.1.9.2 (3.1%)
XBB.2.3 (1.8%)
XBB.1.5.13 (1.6%)
XBB.1.16.1 (1.5%)

public.tableau.com/app/profile/ra…

Updated 04/29/23 Image
Granular details #Global #20DayTrends

This analysis includes all designated #SARSCoV2 sequences submitted to @GISAID with sample collection dates on or after 04/09/2023 (14,137 sequences) Image
#USA, #Austria, #France & #Canada have submitted a lion's share of sequences with sample collection dates on or after 04/09/2023 ...followed by #UnitedKingdom, #Australia, #Germany, #Sweden, #SouthKorea, #Singapore, #China, #Spain Image
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 Image
#SARSCoV2 lineages in the zone of concern (red box) - Predicted to have high immune escape and tight ACE2 binding activity - A Closer look

XBB.1.16* family (XBB.1.16.1, FU.1, FU.2, XBB.1.16.2, XBB.1.16.3) cluster together

Chart: public.tableau.com/app/profile/ra… Image
What to expect in the next few weeks?

github.com/neherlab/SARS-…

Excellent SARSCoV2 Variant report
by @richardneher @CorneliusRoemer
“Currently, XBB.1.16 is the big dog” ... “It’s picking up mutations that are common in other variants that will increase its advantage further.”

H/T @ErinMPrater @WellatFortune
@FortuneMagazine
fortune.com/well/2023/03/3…
A closer look at #Arctrus (XBB.1.16*), #Hyperion (XBB.1.9*) and #Acrux (XBB.2.3*) constellations

more on common names from @TRyanGregory
Image

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More from @RajlabN

May 2
#COVID19 #VariantDashboard - #UnitedStates

TOP lineages (#15DAYTRENDS):

56.2% XBB.1.5
6.1% XBB.1.9.1
4.5% XBB.1.16
2.2% XBB.1.5.1
2.1% XBB.1.9.2
1.4% XBB.1.5.13
1.4% XBB.1.5.15
1.4% XBB.1.5.17

#SARSCoV2 Tracker: tinyurl.com/mryj4uu7 Updated: 05/01/23

1/n Image
#COVID19 #VariantDashboard - #USA
[without sequences from "Airport Surveillance"]

Top lineages (#15DayTrends):

XBB.1.5 (61.7%)
XBB.1.9.1 (5.5%)
XBB.1.16 (2.4%)
XBB.1.5.1 (2.3%)
XBB.1.5.13 (1.6%)
XBB.1.5.17 (1.6%)
XBB.1.9.2 (1.6%)
XBB.1.5.15 (1.3%)
FD.2 (1%)

2/n Image
Airport sequences constitute ~12.4% of sequences with sample collection dates in the last 15 days (#15DayTrends)

Its going to be a three way race to outcompete XBB.1.5*: XBB.1.9* vs XBB.1.16* vs XBB.2.3*

As of now, XBB.1.16* family looks to over take everything else!

3/n Image
Read 17 tweets
May 1
Tracking #SARSCoV2 lineage XBB.1.16* (#Arcturus) over time - Globally

Total Sequences : 8,182 (circulating in 43 countries)

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

Note: Recent Epi weeks are incomplete; Includes seqs from targeted & Airport surveillance

Updated:05/01/23 Image
Tracker now includes all the designated XBB.1.16* sub-lineages

Tracking #SARSCoV2 lineage XBB.1.16* (#Arcturus) over time - Globally Image
Read 4 tweets
May 1
#COVID19 #VariantDashboard - #UnitedStates

TOP lineages (#15DAYTRENDS):

49.7% XBB.1.5
8.3% XBB.1.16
8.3% XBB.1.9.1
2.3% XBB.1.9.2
2.1% XBB.1.16.1
1.6% XBB.1.5.1
1.4% XBB.2.3

>> Low Sequence Count <<
#SARSCoV2 Tracker: tinyurl.com/mryj4uu7 Updated: 04/30/23

1/n
#COVID19 #VariantDashboard - #USA
[without sequences from "Airport Surveillance"]

Top lineages (#15DayTrends):

XBB.1.5 (61.1%)
XBB.1.9.1 (8.0%)
XBB.1.16 (3.5%)
FL.2 (1.7%)
XBB.1.5.1 (1.7%)
XBB.1.5.17 (1.7%)
XBB.1.9.2 (1.4%)
XBB.1.5.15 (1.2%)

2/n Image
Airport sequences constitute a significant proportion of sequences (~27%; #15DayTrends)

Its going to be a three way race to outcompete XBB.1.5*: XBB.1.9* vs XBB.1.16* vs XBB.2.3*

As of now, XBB.1.16* family looks to over take everything else!

3/n Image
Read 18 tweets
Apr 21
#SARSCoV2 #VariantProportions - #USA |04/21/23

New @CDCgov #Nowcast estimates:

Top circulating lineages:

XBB.1.5 (73.6%)⬇️
XBB.1.16 (9.6%) ⬆️
XBB.1.9.1 (7.9%)
XBB.1.9.2 (2.9%)
XBB.1.5.1 (2.2%)
FD.2 (1.6%)
XBB (1%)

covid.cdc.gov/covid-data-tra…

1/n Image
Over all trends are consistent with #15DayTrends (based on sequences uploaded in the public databases)

XBB.1.5 is still at the top; followed by XBB.1.16 & XBB.1.9.1

Expect XBB.2.3 to feature in the @CDCgov dashboard soon!



2/n
XBB.1.16* hotspots per CDC #Nowcast

>5% spread in almost all regions

Region 6 estimate reads 14.4% (looks more reasonable than the previous week's estimate of 21.3% spread which looked suspect; )

3/n Image
Read 4 tweets
Apr 21
#COVID19 #VariantDashboard - #UnitedStates

TOP lineages (#15DAYTRENDS):

52.8% XBB.1.5
9.5% XBB.1.16👀
4.7% XBB.1.9.1
2.6% XBB.1.16.1👀
2.3% XBB.1.9.2
1.3% EG.1
1.2% XBB.2.3
1.2% XBB.1.5.15

#SARSCoV2 Tracker: tinyurl.com/mryj4uu7 Updated: 04/20/23

1/n Image
Use "Airport Surveillance" (AS) pull-down menu to easily track variant proportions Nationally or by State with or without AS sequences

Top lineages (#15DayTrends w/o AS seqs):

XBB.1.5 (64%),
XBB.1.9.1 (3.8%),
XBB.1.16 (3%),
XBB.1.5.19 (1.6%),
XBB.1.9.2 (1.4%)

2/n Image
Sequence count by US States

#NewYork & #California have submitted a big share of sequences with specimen collection dates on or after 04/05/2023

XBB.1.5 is still at the top spot; followed by XBB.1.9.1 and XBB.1.16

3/n Image
Read 17 tweets
Apr 20
Tracking #SARSCoV2 lineage XBB.1.16* (#Arcturus) over time - Globally

Total Sequences : 4,837 (circulating in 37 countries)

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

Note: Recent Epi weeks are incomplete; Includes seqs from targeted & Airport surveillance
Updated:04/20/23 Image
New entrant: #Bulgaria Image
Tracking #SARSCoV2 lineage XBB.1.16.1 over time - Globally

Total Sequences : 1003

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

Note: Recent Epi weeks are incomplete; Includes seqs from targeted & Airport surveillance

Updated: 04/20/23 Image
Read 4 tweets

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