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Raj Rajnarayanan Profile picture
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Apr 19 • 6 tweets • 5 min read
First sequence of BA.2.12.1, the #BA2 #Subvariant with #Spike #L452Q mutation is uploaded in @gisaid from #Arkasnas

This #Omicron #Sublineage has significant growth advantage over BA.2 and BA.1.1

Please get #Boosted!

Get #tested if you have any #COVID19 symptoms
@brandonhicks @arkepi2020 @roarkka @jamesgraham714 @ADHPIO
Publication highlighting Spike L452Q (image credits for the previous tweet): biorxiv.org/content/10.110…
Have to wait and see if there is an uptick in cases/hospitalizations.

I am worried because of a significant decrease in reportable tests and sporadic sequencing efforts.

Thanks to the sequencing labs and their rapid reporting, we now know what to expect 👀

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More from @RajlabN

Raj Rajnarayanan Profile picture
Apr 20
#COVID19 #VariantDashboard - #UnitedStates

TOP lineages (15-DAY TRENDS):
27.06% BA.2,
15.80% BA.2.9,
13.04% BA.2.12.1, <---Spike #L452Q
12.27% BA.2.12,
8.97% BA.2.3,
8.13% BA.1.1, and
8.06% BA.2.10

Tracker (by State): tinyurl.com/mryj4uu7

#OmicronUpdates 04/18/22 Image
#OmicronVariantUpdates #UnitedStates 04/19/22

Top circulating #sublineages: BA.2*, BA.2.9, BA.2.12.1, BA.2.12, BA.2.3, BA.1.1, and BA.2.10

* includes recently designated BA.2.x.y Image
Sequence count by Division - #UnitedStates 04/19/22

#NewYork, #California, ##Texas, #Illinois, #NewJersey and #Washington have submitted >200 sequences with sample collection dates between April 04 to April 19, 2022. Image
Read 5 tweets
Raj Rajnarayanan Profile picture
Apr 19
#OmicronUpdates #NewLineagesAlert

BA.1.22 -Prevalent in #Peru
BA.2.17 - #Vietnam and others
BA.2.18 - #UK/#Ireland
BA.2.19 -#Germany
XU - BA.1*/BA.2 recombinant - #Japan/#Canada/#India

(BA -alias of B.1.1.529)

#PANGO issues: #520, #522, #528, #529, #535 Image
These are new PANGO designations

Key mutations:

BA.2.17 - ORF3a:D173Y
BA.2.18 - S:K417T
BA.2.19 - ORF1a:T333M

more to follow ..... will update key mutational differences and transmission advantage (if any)

Other designations are in 🧵:
#OmicronUpdates #NewLineagesAlert

BA.2.22 prevalent in #UnitedKingdom
BA.2.21 prevalent in #USA/#Canada
BA.2.20 prevalent in #Canada

(BA alias of B.1.1.529)

PANGO issues: #547 #562 #544 Image
Read 5 tweets
Raj Rajnarayanan Profile picture
Apr 19
#COVID19 #VariantDashboard - #UnitedStates

TOP lineages (15-DAY TRENDS):
27.06% BA.2,
15.54% BA.2.9,
12.50% BA.2.12.1, <-- Spike L452Q!
11.73% BA.2.12,
9.49% BA.2.3,
8.43% BA.1.1, and
8.43% BA.2.10

Tracker (by State): tinyurl.com/mryj4uu7

#OmicronUpdates 04/18/22
#OmicronVariantUpdates #UnitedStates 04/18/22

Top circulating #sublineages: BA.2*, BA.2.9, BA.2.12.1, BA.2.12, BA.2.3, BA.1.1, and BA.2.10

* includes recently designated BA.2.x.y
Sequence count by Division - #UnitedStates 04/18/22

#NewYork, #California, ##Texas, #Illinois, #Washington, #NewJersey and #Florida have submitted >200 sequences with sample collection dates between April 03 to April 18, 2022.
Read 5 tweets
Raj Rajnarayanan Profile picture
Apr 18
#COVID19 #VariantDashboard - #UnitedStates

TOP lineages (15-DAY TRENDS):
23.33% BA.2,
16.87% BA.2.9,
12.70% BA.2.10,
10.87% BA.2.3,
9.68% BA.2.12,
9.56% BA.2.12.1,
8.58% BA.1.1, and
1.72% BA.2.5

Tracker (by State): tinyurl.com/mryj4uu7

#OmicronUpdates 04/17/22 Image
#OmicronVariantUpdates #UnitedStates 04/17/22

Top circulating #sublineages: BA.2*, BA.2.9, BA.2.10, BA.2.3, BA.2.12, BA.2.12.1, and BA.1.1

* includes recently designated BA.2.x.y Image
Sequence count by Division - #UnitedStates 04/17/22

#NewYork, #California, #Washington, #NewJersey, #Colorado and #WashingtonDC have submitted >100 sequences with sample collection dates between April 2st to April 17, 2022. Image
Read 5 tweets
Raj Rajnarayanan Profile picture
Apr 12
Closely monitoring new #omicron sub-lineages - BA.4 & BA.5 (first identified in #SouthAfrica)

No BA.4/BA.5 sequences identified in the #UnitedStates yet. But the key signature mutation Spike L452 is found in >400 BA.2 sequences in the past 3 months.

express.co.uk/news/science/1…
Key Mutations to follow

-Spike L452(R/M/Q)
-Spike L452R* and L452Q is prevalent in #Wastewater samples (will update in a separate thread)

*currently unassigned/unclassified/undesignated sequences and some of them are tagged "ML" by @GISAID

cov-spectrum.org/explore/United…
A quick look at the tree generated from the nextclade tool that @CorneliusRoemer point to earlier -- clades.nextstrain.org
Read 6 tweets
Raj Rajnarayanan Profile picture
Apr 10
#CoronavirusUpdates #HospitalCapacity #UnitedStates

Are we ready to handle another #COVID #WAVE?

In-patients beds are >75% full in 25 States + DC
ICU beds are >75% full in 16 States + DC

public.tableau.com/app/profile/ra… ImageImage
These represent all hospitalizations not just COVID

Data Source: protect-public.hhs.gov/pages/hospital…
Monitoring all hospitalizations because #COVID #hospitalizations reporting and definitions keep changing!
Read 5 tweets

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