Raj Rajnarayanan Profile picture
Oct 12 β€’ 16 tweets β€’ 14 min read
#COVID19 #VariantDashboard - #UnitedStates

TOP lineages (15-DAY TRENDS):

17.0% BA.5.2.1
15.1% BA.5.2
12.5% BA.4.6
9.0% BA.5.1
3.6% BQ.1πŸ‘€
2.9% BA.5
2.7% BF.10
2.6% BA.5.6
2.3% BF.7
2.0% BF.5.2.9

Tracker: tinyurl.com/mryj4uu7

#OmicronUpdates 10/11/22
1/n Image
Sequence count by US State

#NewYork has uploaded a lion's share of sequences with sample collection dates in the last 15 days.

2/n Image
29 of the 2626 sequences are from opt-in airport screening with sample collections dates in the last 15 days

3 BQ.1.1 (2-NY, 1-CA airport)
1 XBB (CA)
1 BA.2.3.20 (GA)
1 BN.1 (CA)
1 BY.1 (NJ)
1 BA.2.75.2 (NJ)

#MaskUp inβœˆοΈπŸ›³οΈπŸšπŸš‰etc

3/n
Top circulating lineages (#15DayTrends)

75.3% BA.5*
12.5% BA.4.6*
3.6% BQ.1*
2.3% BF.7*
2.3% BQ.1.1*
1.6% BA.2.75*
1.5% BA.4*
0.2% XBB*
0.2% BA.2.3.30*

4/n Image
. @CDCgov updated variant proportions estimates on 10/7/2022



5/n
The Great Convergence!

Key #Spike amino acids tracked: 346, 356, 444-446, 450, 452, 460, 486, 490, 493-494



6/n
Immune Escape and ACE2 binding of top lineages in USA (relative to BA.2)

Bivalent boosters (OG/Omicron.BA.5) will potentially protect the boosted from getting severe disease/hospitalizations.

Please get #boosted ASAP!

public.tableau.com/app/profile/ra…

8/n
#Hospital #Capacity - (by State/Division)

All hospitalizations not just COVID-19

(looks like hospital bed data error in DE and VI -will check and update)

public.tableau.com/app/profile/ra…

9/n
#COVID19 #Hospitalizations in the #UnitedStates

Please get #boosted (especially > 50 yr old and immune compromised) and #MaskUP!

Hospital Tracker (by States, by age group): public.tableau.com/app/profile/ra…

10/n
Closely following >50 yr old age group #COVID19 #Hospitalizations data

11/n Image
Status of the latest #COVID19 Wave in #NewYork #BellwetherState

Top Circulating Lineages (#15DAYTrends):

BA.5.2.1 (15.1%) ⬇️
BA.4.6 (12.4%)
BA.5.2 (10.8%)
BQ.1 (9.1%) πŸ‘€πŸš€
BA.5.1 (7.7%)
BF.7 (5.2%)
BQ.1.1 (3.9%)πŸ‘€

Please get #Boosted, #Ventilate and #MaskUp!

13/n ImageImage
Granular details - #VariantSoup #NewYork Image
Rise of BQ.1*/BQ.1.1* is concerning

fortune.com/well/2022/09/2…
WasteWater analytics from @BiobotAnalytics

Wastewater SARSCoV2 content from Northeast USA is stuck on a high plateau! Image

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More from @RajlabN

Oct 14
Tracking #SARSCoV2 #Convergent #Lineages ( aka #VariantSoup) over time - Globally | #30DayTrends

BQ.1.1(#Cerberus) is currently leading the charts!
BQ.1 (#Typhon) & BA.2.75.2* (#Chiron) are not far behind!

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

Updated 10/13/2022 Image
Note: Tracker includes Preselected (PS) or Airport Screening (AS) from the following countries

BA.2.3.20*:
108 Austria (PS)
11 Japan (AS)

XBB*
17 Austria (PS)
10 Japan (AS)

BQ*
6 Austria (PS)
7 Japan (AS)
7 USA (AS)

BA.2.75*
269 Austria (PS)
21 Japan (AS)
10 USA (AS)

2/n
Granular details - #VariantSoup with Convergent Mutations #30DayTrends

Top Lineages with Convergent Mutations-

BQ.1.1*
BQ.1*
BA.2.75.2*
BM.1.1*
XBB.1*
BN.1*
BA.2.3.20*
BA.2.75.5*
BL.1*
BA.2.75.1*
BY.1*

3/n Image
Read 7 tweets
Oct 13
Tracking BQ* lineages (BQ.1* & BQ.1.1-17*) over time

Total BQ* Sequences: 2,970
Total BQ.1.1*: 1,218πŸ‘€

Tracker now includes BQ.1, BQ.1.1 to BQ.1.17!

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

[Nick names - BQ.1*: #Typhon BQ.1.1*: #Cerberus]

10/13/22 2 pm
Tracking BQ* lineages over time in the #UnitedKingdom

#England is a BQ* hotspot Image
Closely following BQ.1.1* and BQ.1.9* over time in #USA

Both are BQ* lineages with Spike: R346T mutation

BQ.1.9 is defined by ORF1a:V2604I and has picked up Spike:R346T later (independent from BQ.1.1) Image
Read 4 tweets
Oct 13
#COVID19 #VariantDashboard - #UnitedStates

TOP lineages (15-DAY TRENDS):

19.0% BA.5.2.1
14.4% BA.5.2
11.8% BA.4.6
9.2% BA.5.1
3.9% BQ.1πŸ‘€
3.0% BA.5
2.9% BF.7
2.6% BF.10
2.5% BQ.1.1πŸ‘€

Tracker: tinyurl.com/mryj4uu7

#OmicronUpdates 10/12/22
1/n Image
Sequence count by US State

#NewYork has uploaded a lion's share of sequences with sample collection dates in the last 15 days.

2/n Image
32 of the 1820 sequences are from opt-in voluntary airport screening with sample collections dates in the last 15 days

4 BQ.1.1 (3-NY, 1-CA airport)
1 BQ.1 (NY)
1 BN.1 (CA)
1 BM.1.1 (NJ)
1 BA.2.75.2 (NJ)

#MaskUp inβœˆοΈπŸ›³οΈπŸšπŸš‰etc

3/n
Read 15 tweets
Oct 12
#NewLineagesAlert #OmicronUpdates

CN.1 (BA.5.2.21 with S:N450D) from #1108

BR.4 (BA.2.75.4 + S:K444T, S:S446G) from #1179

CM.1 (BA.2.3.20 with S:N17S) from #1129

CJ.1 (BM.1.1.1 with S:S486P) from #1171

CH.2 (BM.4.1.1.2 with S:Q183H)

CH.1 (BM.4.1.1 + S:K444T), #1113

1/n
#NewLineagesAlert #OmicronUpdates

BQ.1.9 (ORF1a:V2604I, S:346T)

BQ.1.8 (ORF1a:S505F)

BQ.1.7 (S:L54F)

BQ.1.6 (ORF1a:G94C)

BQ.1.5 (ORF1b:T1076I)

BQ.1.4 (S:R190T)

XBB.1 (S:G252V)

2/n
#NewLineagesAlert #OmicronUpdates

CG.1 (BA.5.2.26.1 with S:K444M) from #1126

CL.1 (BA.5.1.29 with S:460K) from #1187

CK.1 (BA.5.2.24 + S:460K) from #1120

BA.4.6.3 (S:444N, S:460K, S:144-)

BE.4.2 (S:K444N & S:N460K) from #1114

BA.4.6.2 (S:V445A) from #1198

3/n
Read 5 tweets
Oct 11
#COVID19 #VariantDashboard - #UnitedStates

TOP lineages (15-DAY TRENDS):

18.7% BA.5.2.1
14.3% BA.4.6⬆️
13.1% BA.5.2
8.8% BA.5.1
4.1% BQ.1πŸ‘€
3.1% BF.7
2.7% BA.5.6
2.3% BQ.1.1πŸ‘€
2.2% BF.10

Tracker: tinyurl.com/mryj4uu7

#OmicronUpdates 10/10/22

1/n Image
Sequence count by US State

#NewYork has uploaded a lion's share of sequences with sample collection dates in the last 15 days.

2/n Image
37 of the 2144 sequences are from opt-in airport screening with sample collections dates in the last 15 days

3 BQ.1.1 (2-NY, 1-CA airport)
2 XBB (NJ, CA)
1 BA.2.3.20 (GA)
1 BN.1 (CA)
1 BY.1 (NJ)
1 BM.1.1.1 (NJ)
1 BA.2.75.2 (NJ)

#MaskUp inβœˆοΈπŸ›³οΈπŸšπŸš‰etc

3/n
Read 13 tweets
Oct 10
#COVID19 #VariantDashboard - #UnitedStates

TOP lineages (15-DAY TRENDS):

20.0% BA.5.2.1
12.7% BA.5.2
12.7% BA.4.6
8.6% BA.5.1
4.8% BQ.1πŸ‘€
3.6% BF.7
2.6% BQ.1.1πŸ‘€
2.1% BA.5.6
2.1% BF.10
1.8% BA.5

Tracker: tinyurl.com/mryj4uu7
#OmicronUpdates 10/09/22
1/n
Charts represent #15DayTrends

~50% of sequences are from #NewYorkCity!

919 sequences out of 1825 total sequences uploaded in @GISAID from #USA with sample collection dates in the last 15 days!

2/n
44 of the 1825 sequences are from opt-in airport screening

Mostly Asymptomatic

5 BQ.1.1 (2-NJ, 2-NY, 1-CA)
2 XBB (NJ, CA airport)
1 BA.2.3.20 (GA)
1 BN.1 (CA)
1 BY.1 (NJ)
1 BM.1.1.1 (NJ)
1 BA.2.75.2 (NJ)

Time to bring back Universal Masking in the Transportation Sector!

3/n
Read 13 tweets

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