Raj Rajnarayanan Profile picture
Dec 29 18 tweets 16 min read
#COVID19 #VariantDashboard - #UnitedStates

Interesting tug of war between BQ.1.1 & XBB.1.5

TOP lineages (15-DAY TRENDS):

16.3% BQ.1.1
13.5% XBB.1.5
10.7% BQ.1
6.7% BQ.1.22
3.3% XBB.1
2.6% BQ.1.1.4

Tracker: tinyurl.com/mryj4uu7

#OmicronUpdates 12/28/22
1/n
Sequence count by US State

New York, California and Texas have submitted a huge share of sequences with specimen collection dates in the last 15 days.

[It appears like a tug of war between XBB.1.5 and BQ.1.1 mainly because of no. of sequences uploaded from West and South]

2/n
Granular details -#VariantDashboard #USA #15DayTrends

3/n
.@CDCgov updated variant proportions estimates on 12/23/2022 (CDC updates nowcast estimates every Friday)

Several BQ* are circulating at >1% & XBB.1.5* are good candidates to be included in CDC's Nowcast estimates next week!



4/n
#Global #VariantSoup

Top lineages with at least 5 key convergent #Spike mutations (#30DayTrends):

BQ.1.1 (23.01%)
BQ.1 (9.52%)
XBB.1 (4.24%)
BQ.1.22 (3.96%)
CH.1.1 (2.65%)👀
BQ.1.2 (2.31%)
XBB.1.5 (2.16%)👀
BQ.1.1.20 (2.00%)
BQ.1.1.4 (1.97%)

public.tableau.com/app/profile/ra…

5/n
Predicted 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…

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

All hospitalizations not just COVID-19

public.tableau.com/app/profile/ra…

7/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…

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

XBB.1.5 is the top circulating lineage in NY

Top Lineages (#15DAYTrends):

XBB.1.5 (43.3%)👀🚀
BQ.1.1 (12.8%)⬇️
XBB.1 (8.4%)
BQ.1 (7.3%)
BQ.1.1.4 (2.3%)
BQ.1.14 (1.8%)
BQ.1.3 (1.7%)

9/n
Rise of highly immune evasive XBB* family of lineages especially XBB.1.5 (Key mutation: Spike F486P) in NY is concerning

fortune.com/well/2022/11/0…

10/n
BQ* Hotspots - #USA #15DayTrends

11/n
Recombinant lineage hotspots - #USA #15DayTrends

12/n
Tracking the current #COVID19 wave, variant soup and #Hospitalizations in #California

BQ.1, BQ.1.22 and BQ.1.1 are the top circulating lineage in CA

13/n
Tracking the current #COVID19 wave, variant soup and #Hospitalizations in #Massachusetts

XBB.1.5 is the top circulating lineage in MA

[low sequence count]

14/n
Tracking the current #COVID19 wave, variant soup and #Hospitalizations in #Connecticut

XBB.1.5 is the top circulating lineage in CT

15/n
Tracking the current #COVID19 wave, variant soup and #Hospitalizations in #NewJersey

XBB.1.5 is the top circulating lineage in NJ

16/n
Tracking the current #COVID19 wave, variant soup and #Hospitalizations in #Pennsylvania

XBB.1.5 is the top circulating lineage in PA

[low sequence count]

17/n

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More from @RajlabN

Dec 30
#SARSCoV2 #VariantProportions - #USA |12/30/22

Top lineages (per @CDCgov #Nowcast estimates):

40.5% XBB.1.5🚀🚀🚀👀
26.9% BQ.1.1⬇️
18.3% BQ.1⬇️
3.7% BA.5⬇️
3.6% XBB
2.4% BN.1
2.1% BF.7
0.9% BA.2.75
and others

covid.cdc.gov/covid-data-tra…

1/n Image
BQ.1, BQ.1.1 hotspots per nowcast estimates

3/n Image
Read 6 tweets
Dec 30
Tracking XBB.1.5* lineage over time | 12/30/2022

Total Sequence Count - Global: 2,719
Total Sequence Count - USA: 2,426

Earliest sample collection date: 10/22/22 (NY, USA)*

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

* [excluding samples with date errors] Image
Tracking XBB.1.5* in Asia over time | 12/20/2022

3 new XBB.1.5^^ sequences uploaded from #Shanghai, #China [metadata indicates - baseline surveillance]

^^ will closely look at these sequences for some epi clues Image
Tracking XBB.1.5* in North America over time | 12/30/2022

#Ontario, #Canada is an emerging hotspot

New entrant: #PuertoRico Image
Read 4 tweets
Dec 30
#COVID19 #VariantDashboard - #UnitedStates

Interesting tug of war between BQ.1.1 & XBB.1.5

TOP lineages (15-DAY TRENDS):

14.7% BQ.1.1
11.4% XBB.1.5👀
10.7% BQ.1
9.2% BQ.1.22
3.1% XBB.1
2.3% BQ.1.1.3

Tracker: tinyurl.com/mryj4uu7

#OmicronUpdates 12/29/22

1/n Image
Sequence count by US State

California, New York and Texas have submitted a huge share of sequences with specimen collection dates in the last 15 days.

[It appears like a tug of war between XBB.1.5 and BQ.1.1 mainly because of no. of sequences uploaded from West and South]

2/n Image
Granular details -#VariantDashboard #USA #15DayTrends

3/n Image
Read 18 tweets
Dec 28
#COVID19 #VariantDashboard - #UnitedStates

TOP lineages (15-DAY TRENDS):

16.6% XBB.1.5👀
16.5% BQ.1.1
10.4% BQ.1
5.2% BQ.1.22
4.0% XBB.1
2.0% BQ.1.1.4
1.9% BQ.1.1.3
1.8% BQ.1.2
1.8% BQ.1.3

Tracker: tinyurl.com/mryj4uu7

#OmicronUpdates 12/27/22
1/n
Sequence count by US State

New York has submitted a huge share of sequences with specimen collection dates in the last 15 days.

2/n Image
Granular details -#VariantDashboard #USA #15DayTrends

3/n Image
Read 16 tweets
Dec 27
#Omicron family swells to 653+ #sublineages!

Currently, we are watching "Omicron" Great-Great-Great grand kids.. especially the recombinant family members

Expected to outcompete other circulating Omicrons including Omicron-BQ*

XBB.1.5* poised to take over North America soon! Image
BQ* family swells to 73
New members CZ.1, DN.1, DN.1.1, DK.1, DP.1, CW.1, DM.1, among others

Source: @PangoNetwork Image
Recombinant lineage watch list Image
Read 5 tweets
Dec 26
#COVID19updates #China 12/25/2022

BF.7 seems to be the top circulating lineage in #China based on #SARSCoV2 sequences uploaded in GISAID
25 sequences were uploaded from #Beijing, #InnerMongolia and #Guangdong
BF.7's from China have a unique mutations Spike:C1243F & ORF1a:V274L
Read 4 tweets

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