Discover and read the best of Twitter Threads about #OmicronUpdates

Most recents (22)

#COVID19 #VariantDashboard - #UnitedStates

TOP lineages (15-DAY TRENDS):

46.66% BA.2.12.1**,
23.33% BA.5^^,
12.15% BA.4^^,
7.64% BA.2,
4.24% BA.5.1^^,
1.29% BA.2.9 and
1.17% unassigned

**S:L452Q; ^^S:L452R/F486V

Tracker: tinyurl.com/mryj4uu7
#OmicronUpdates 6/27/22
#OmicronVariantUpdates #UnitedStates 06/27/22

Top 5 lineages:
BA.2.12.1, ⬇️ (Spike: L452Q)
BA.5, ⬆️ (Spike: L452R)
BA.4 ⬆️ (Spike: L452R)
BA.2 ⬇️
BA.5.1 ⬆️👀 (Lineage prevalent in #Portugal)

* includes recently designated BA.2.x.y and undesignated BA.2s
#SARSCoV2 lineages in USA (#15DayTrends)

Circulating #BA5*/#BA4* sub-lineages:
BA.5, BA.4.1, BA.5.2.1, BA.5.1, BA.4, BA.5.2, BA.5.3.1, BE.1, BF.1, BA.5.3

Assignments via: #Nextclade #PANGO - clades.nextclade.org
Read 13 tweets
#COVID19 #VariantDashboard - #UnitedStates

TOP lineages (15-DAY TRENDS):

50.65% BA.2.12.1**,
19.90% BA.5^^,
10.46% BA.4^^,
9.83% BA.2,
3.30% BA.5.1^^,
1.21% BA.2.3 and
1.09% BA.2.9

**S:L452Q; ^^S:L452R/F486V

Tracker: tinyurl.com/mryj4uu7
#OmicronUpdates 06/26/22
#OmicronVariantUpdates #UnitedStates 06/26/22

Top 5 lineages:
BA.2.12.1, ⬆️ (Spike: L452Q)
BA.5, ⬆️ (Spike: L452R)
BA.4 ⬆️ (Spike: L452R)
BA.2 ⬇️
BA.5.1 ⬆️👀 (Lineage prevalent in #Portugal)

* includes recently designated BA.2.x.y and undesignated BA.2s
#SARSCoV2 lineages in USA (#15DayTrends)

Circulating #BA5*/#BA4* sublineages:
BA.5, BA.4.1, BA.5.2.1, BA.5.1, BA.4, BA.5.3.1, BA.5.2, BE.1, BA.5.3, BF.1
Read 14 tweets
#COVID19 #VariantDashboard - #UnitedStates

TOP lineages (15-DAY TRENDS):

47.60% BA.2.12.1**
22.33% BA.5^^
11.44% BA.2,
10.48% BA.4^^
3.61% BA.2.12,
1.08% BA.2.9 and
1.05% BA.2.3

**S:L452Q; ^^S:L452R/F486V

Tracker: tinyurl.com/mryj4uu7
#OmicronUpdates 06/25/22 Image
#OmicronVariantUpdates #UnitedStates 06/25/22

Top 5 lineages:
BA.2.12.1, ↔️ (Spike: L452Q)
BA.5, ⬆️ (Spike: L452R)
BA.2 ⬇️
BA.4 ⬆️ (Spike: L452R)
BA.2.12

* includes recently designated BA.2.x.y and undesignated BA.2s Image
Read 12 tweets
#COVID19 #VariantDashboard - #UnitedStates

TOP lineages (15-DAY TRENDS):

57.01% BA.2.12.1**,
22.06% BA.2,
4.07% BA.5^^,
3.19% BA.2.12,
3.06% BA.4^^,
2.73% BA.2.9 and
2.65% BA.2.3

**S:L452Q; ^^S:L452R/F486V

Tracker: tinyurl.com/mryj4uu7
#OmicronUpdates 06/07/22
#OmicronVariantUpdates #UnitedStates 06/07/22

Top circulating lineages: BA.2.12.1, BA.2*, BA.5, BA.2.12, BA.4, BA.2.9, BA.2.3

Proportion of BA.5/BA.4 is increasing

* includes recently designated BA.2.x.y
BA.2.12.1 hotspots - #UnitedStates (#15DayTrends)

Top 5 Hotspots: #NewYork, #Florida, #Texas, #California, #Arizona
Read 12 tweets
#COVID19 #VariantDashboard - #UnitedStates

TOP lineages (15-DAY TRENDS):

58.39% BA.2.12.1**,
21.76% BA.2,
3.88% BA.5^^,
3.14% BA.2.9,
2.97% BA.2.3,
2.95% BA.4^^ and
2.73% BA.2.12

**S:L452Q; ^^S:L452R/F486V

Tracker: tinyurl.com/mryj4uu7
#OmicronUpdates 06/06/22
#OmicronVariantUpdates #UnitedStates 06/06/22

Top circulating lineages: BA.2.12.1, BA.2*, BA.5, BA.2.9, BA.2.3, BA.4 and BA.2.12

Proportion of BA.5/BA.4 is increasing

* includes recently designated BA.2.x.y
BA.2.12.1 hotspots - #UnitedStates (#15DayTrends)

Top 5 Hotspots: #NewYork, #Florida, #California, #Arizona, #Pennsylvania
Read 10 tweets
#COVID19 #VariantDashboard - #UnitedStates

TOP lineages (15-DAY TRENDS):

56.27% BA.2.12.1**,
22.94% BA.2,
3.74% BA.5^^,
3.69% BA.2.3,
3.50% BA.2.12,
2.92% BA.4^^ and
2.72% BA.2.9

**S:L452Q; ^^S:L452R/F486V

Tracker: tinyurl.com/mryj4uu7

#OmicronUpdates 06/05/22
#OmicronVariantUpdates #UnitedStates 06/05/22

Top circulating lineages: BA.2.12.1, BA.2*, BA.5, BA.2.3, BA.2.12, BA.4 and BA.2.9

Proportion of BA.5/BA.4 is increasing

* includes recently designated BA.2.x.y
Read 11 tweets
#COVID19 #VariantDashboard - #UnitedStates

TOP lineages (15-DAY TRENDS):

55.63% BA.2.12.1**,
23.43% BA.2,
4.02% BA.2.12,
3.88% BA.2.3,
3.44% BA.5^^,
2.89% BA.2.9, and
2.58% BA.4^^

**S:L452Q; ^^S:L452R/F486V

Tracker: tinyurl.com/mryj4uu7
#OmicronUpdates 06/04/22 Image
#OmicronVariantUpdates #UnitedStates 06/04/22

Top circulating lineages: BA.2.12.1, BA.2*, BA.2.12, BA.2.3,, BA.5 BA.2.9, and BA.4

Proportion of BA.5/BA.4 is increasing

* includes recently designated BA.2.x.y Image
BA.2.12.1 hotspots - #UnitedStates (#15DayTrends) Image
Read 10 tweets
Potential BA.5.2.1 sub-lineage!

Key mutations: ORF3a [NS3] - V244I
97 sequences in total (56 from #UK, 17 from #Spain)

Earliest Sequence: 4/15/22

#OmicronUpdates #BA5 Image
Too early to compute growth advantages..
Cov-spectrum GA prediction: cov-spectrum.org/explore/World/…

Cov-Spectrum Query to follow this potential new sub-lineage: cov-spectrum.org/explore/World/…
Read 4 tweets
#COVID19 #VariantDashboard - #UnitedStates

TOP lineages (15-DAY TRENDS):

55.27% BA.2.12.1**,
24.07% BA.2,
3.90% BA.2.12,
3.90% BA.2.3,
3.23% BA.2.9,
3.10% BA.5^^ and
2.51% BA.4^^

**S:L452Q; ^^S:L452R/F486V

Tracker: tinyurl.com/mryj4uu7
#OmicronUpdates 06/03/22 Image
#OmicronVariantUpdates #UnitedStates 06/03/22

Top circulating lineages: BA.2.12.1, BA.2*, BA.2.12, BA.2.3, BA.2.9, BA.5 and BA.4

Proportion of BA.5/BA.4 is increasing

* includes recently designated BA.2.x.y Image
BA.2.12.1 hotspots - #UnitedStates (#15DayTrends) Image
Read 7 tweets
#COVID19 #VariantDashboard - #UnitedStates

TOP lineages (15-DAY TRENDS):

38.23% BA.2,
35.84% BA.2.12.1**,
8.82% BA.2.12,
5.85% BA.2.3,
4.03% BA.2.9,
1.55% BA.5/BA.4^^

** S:L452Q;
^^ S:L452R/F486V

Tracker (by location): tinyurl.com/mryj4uu7
#OmicronUpdates 05/22/22
#OmicronVariantUpdates #UnitedStates 05/22/22

Top circulating lineages: BA.2*, BA.2.12.1, BA.2.12#, BA.2.3, BA.2.9, BA.5 and BA.4

Proportion of BA.5/BA.4 is increasing

* includes recently designated BA.2.x.y
# potential misassignments
BA.2.12 and BA.2.12.1 hotspots (#15DayTrends)
Read 5 tweets
#COVID19 #VariantDashboard - #UnitedStates

TOP lineages (15-DAY TRENDS):

38.18% BA.2,
35.67% BA.2.12.1**,
7.95% BA.2.12,
6.35% BA.2.3,
4.22% BA.2.9,
0.79% BA.5 and
0.68% BA.2.18

** S:L452Q

Tracker (by location): tinyurl.com/mryj4uu7
#OmicronUpdates 05/21/22
#OmicronVariantUpdates #UnitedStates 05/21/22

Top 10 circulating lineages: BA.2*, BA.2.12.1, BA.2.12#, BA.2.3, BA.2.9, BA.5, BA.2.18, BA.2.10, BA.2.23, BA.2.7 and BA.4

* includes recently designated BA.2.x.y
# potential misassignments
BA.2.12 and BA.2.12.1 hotspots
Read 5 tweets
#COVID19 #VariantDashboard - #UnitedStates

TOP lineages (15-DAY TRENDS):

37.66% BA.2,
37.16% BA.2.12.1**,
6.76% BA.2.12,
6.41% BA.2.3,
4.96% BA.2.9,
0.85% BA.2.7 &
0.70% BA.5

** S:L452Q

Tracker (by location): tinyurl.com/mryj4uu7
#OmicronUpdates 05/20/22 Image
#OmicronVariantUpdates #UnitedStates 05/20/22

Top 10 circulating lineages: BA.2*, BA.2.12.1, BA.2.12#, BA.2.3, BA.2.9, BA.2.7, BA.5, BA.2.10, BA.2.18, BA.2.23 and BA.4

* includes recently designated BA.2.x.y
# potential misassignments Image
BA.2.12 and BA.2.12.1 hotspots ImageImage
Read 5 tweets
#COVID19 #VariantDashboard - #UnitedStates

TOP lineages (15-DAY TRENDS):

24.63% BA.2.12.1, <- Spike:L452Q
17.54% BA.2,
14.93% BA.2.9,
12.00% BA.2.12,
11.38% BA.2.10,
9.55% BA.2.3, and
2.35% BA.1.1

Tracker (by State): tinyurl.com/mryj4uu7

#OmicronUpdates 05/01/22
#OmicronVariantUpdates #UnitedStates 05/01/22

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

* includes recently designated BA.2.x.y
Read 5 tweets
#COVID19 #VariantDashboard - #UnitedStates

TOP lineages (15-DAY TRENDS):

23.39% BA.2.12.1, <- Spike:L452Q
19.16% BA.2,
14.85% BA.2.9,
12.25% BA.2.10,
10.79% BA.2.12,
9.43% BA.2.3 and
2.33% BA.1.1

Tracker (by State): tinyurl.com/mryj4uu7

#OmicronUpdates 04/30/22
#OmicronVariantUpdates #UnitedStates 04/30/22

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

* includes recently designated BA.2.x.y
Sequence count by Division - #UnitedStates 04/30/22

#NewYork, #NorthCarolina, #Arizona, #California and #Connecticut have submitted >125 sequences with sample collection dates between April 15 to April 30, 2022.
Read 8 tweets
#COVID19 #VariantDashboard - #UnitedStates

BA.2.12.1 is the top circulating lineage in the USA

Its not the dominating strain yet by looks like it will get there in 2-3 weeks!

Tracker (by State): tinyurl.com/mryj4uu7

#OmicronUpdates 04/29/22
#COVID19 #VariantDashboard

TOP lineages (15-DAY TRENDS) - #UnitedStates:

23.76% BA.2.12.1, <-S:L452Q
19.22% BA.2,
15.47% BA.2.9,
11.81% BA.2.10,
10.45% BA.2.12,
9.31% BA.2.3 and
2.64% BA.1.1

Tracker (by State): tinyurl.com/mryj4uu7

#OmicronUpdates 04/28/22 Image
*Typo corrected: Its not the dominating strain yet *but* looks like it will get there in 2-3 weeks!
Read 13 tweets
#OmicronUpdates #NewLineagesAlert

BA.2.35 alias of B.1.1.529.2.35 | Prevalent in #Portugal

Key mutations: S:L452R & N:221F

PANGO issues: #554 | github.com/cov-lineages/p… Image
Cov-spectrum prediction: BA.2.35 has 39% growth advantage over BA.2 and ~95% over BA.1.1 in #Portugal (in the recent 3 month period)

Currently spotted in #Portugal, #UnitedKingdom, #USA, #Austria, #France, #Denmark and #Spain Image
Cov-spectrum link to follow this lineage: cov-spectrum.org/explore/Portug…
Read 4 tweets
#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
#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
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.
Read 5 tweets
#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
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
Read 5 tweets
#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
#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
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
New #PANGO designations - BA.2.*

BA.2.4Alias of B.1.1.529.2.4, #Singapore lineage

BA.2.5Alias of B.1.1.529.2.5, lineage in #Portugal and other countries

BA.2.6Alias of B.1.1.529.2.6, lineage in #France and other countries

BA.2.7Alias of B.1.1.529.2.7, #USA lineage ImageImage
These are new designations - branching from the BA.2 subvariant

more to follow ..... will update key mutational differences and transmission advantage (if any)
BA.2.4 (aka B.1.1.529.2.4) | prevalent in Singapore

Key mutation: ORF6:M58K

COV-spectrum predicts a growth advantage of 14% over BA.2 and 46% over BA.1.1 in #Singapore

BA.2 and BA.1.1 are currently the dominant lineages in circulation in Singapore Image
Read 29 tweets

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