Raj Rajnarayanan Profile picture
Jan 7 24 tweets 20 min read
#COVID19 #VariantDashboard - #UnitedStates

Interesting tug or war between BQ.1.1 vs XBB.1.5

TOP lineages (#15DAYTRENDS):

23.3% BQ.1.1
15.5% XBB.1.5
10.8% BQ.1
2.9% BQ.1.1.4
2.8% XBB.1
2.1% BQ.1.1.3

Tracker: tinyurl.com/mryj4uu7
#OmicronUpdates 01/06/2023

1/n
Sequence count by US State

Large share of sequences from outside NE States with specimen collection dates in the last 15 days.

The proportion of BQ.1*/BQ.1.1* >> XBB.1.5 outside NE states.

XBB.1.5 is expected to outcompete all other circulating lineages soon.

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

3/n
.@CDCgov updated variant proportions estimates on 01/06/2023 (updated every Friday)

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



4/n
#Global #VariantSoup 01/06/2023

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

BQ.1.1 (28.94%)
BQ.1 (8.32%)
XBB.1 (4.02%)
CH.1.1 (3.06%)
XBB.1.5 (2.99%)
BN.1.3 (2.12%)
BQ.1.1.20 (2.07%)

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 dominant #SARSCoV2 lineage in NY

Top Lineages (#15DAYTrends):

XBB.1.5 (59.5%)👀🚀
BQ.1.1 (10.1%)
XBB.1 (7.1%)
CQ.2 (2.4%)
BQ.1.1.4 (1.8%)
BQ.1.1.3 (1.8%)
BQ.1 (1.2%)
XBB.2 (1.2%)

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
The ‘Kraken’ COVID variant has competition at the top—‘Cerberus’ is running neck-and-neck in the U.S.

Nicknames: Kraken - XBB.1.5 & Cerberus - BQ.1.1

fortune.com/well/2023/01/0…

11/n
BQ.1*/BQ.1.1* lineage hotspots - #USA #15DayTrends

BQ.1.1 is still the top circulating lineage in several states outside NE USA

12/n
BN*, CJ* and CH* lineage hotspots - #USA #15DayTrends

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

Uptick of XBB.1.5 in several states outside NE USA

14/n
Why the new COVID variant XBB.1.5 is taking over the U.S. so quickly

salon.com/2023/01/04/why…

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

4 sequences with sample collection dates in the last 15 days (1 each of BQ.1, BQ.1.1.18, CK.1 & XBB.1.5).

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

XBB.1.5 is the top circulating lineage in CT

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

XBB.1.5 is the top circulating lineage in NJ

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

BQ.1.1, BQ.1 & XBB.1.5 are the top circulating lineages in CA

20/n
Tracking the current #COVID19 wave, variant soup and #Hospitalizations in #Texas

BQ.1.1, BQ.1 & XBB.1.5 are the top circulating lineages in TX

21/n
Tracking the current #COVID19 wave, variant soup and #Hospitalizations in #Florida

BQ.1.1, XBB.1.5 & XBB.1 are the top circulating lineages in FL

22/n
XBB.1.5* still maintains a strong growth advantage over BQ.1*/BQ.1.1* lineages in USA

23/n
Special thanks to the specimen collection, sequencing and submitting labs, @CDCgov, @NIH/@NCBI, @GISAID Initiative, @PangoNetwork, Variant Trackers and Science enthusiasts!

24/n

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More from @RajlabN

Jan 6
#SARSCoV2 #VariantProportions - #USA |01/06/23

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

As expected new @CDCgov #Nowcast estimates
BQ.1.1 (34.4%) > XBB.1.5* (27.6%)

covid.cdc.gov/covid-data-tra…

1/n
Use the "nowcast off" button in the CDC Variant Proportions dashboard to get a clear picture of the variant spread

covid.cdc.gov/covid-data-tra…

3/n
Read 7 tweets
Jan 6
Tracking XBB.1.5* lineage over time | 01/06/2023

Total Sequence Count
- Global: 4,269
- USA: 3,722

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

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

* [excluding samples with date errors]
Tracking XBB.1.5* lineage over time in North America | 01/06/2023

Northeast USA is a major hotspot (mainly NY & NE USA)

Emerging hotspot outside USA: Ontario, Canada
A closer look at XBB.1.5 in USA over time

Not many sequences were submitted with collection dates after Dec 25, 2022.

Check other Divisions/Countries/Regions here at public.tableau.com/app/profile/ra…
Read 5 tweets
Jan 6
#COVID19 #VariantDashboard - #UnitedStates

Interesting tug or war between BQ.1.1 vs XBB.1.5

TOP lineages (#15DAYTRENDS):

19.4% BQ.1.1
17.0% XBB.1.5
10.8% BQ.1
3.3% XBB.1
2.8% BQ.1.1.4
2.4% BQ.1.1.3

Tracker: tinyurl.com/mryj4uu7
#OmicronUpdates 01/05/2023

1/n
Note: Thanks to Emily Smith (tweet below), misassigned BQ.1.22s were reassigned now to BQ.1.1 or BQ.1.x.y (will check them again and update if there are any additional changes)



2/n
Sequence count by US State

Large share of sequences from outside NE States with specimen collection dates in the last 15 days. The proportion of BQ.1*/BQ.1.1* >> XBB.1.5 outside NE states. XBB.1.5 is expected to outcompete all other circulating lineages soon.

2/n
Read 19 tweets
Jan 5
Tracking XBB.1.5* lineage over time | 01/05/2023

Total Sequence Count
- Global: 4,064
- USA: 3,597

Earliest sample collection date: 10/22/22 (NY, USA)*
Now circulating in 33 countries

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

* [excluding samples with date errors]
Tracking XBB.1.5* lineage over time in North America | 01/05/2023

Northeast USA is a major hotspot (mainly NY & NE USA)

Emerging hotspot outside USA: Ontario, Canada
Tracking XBB.1.5* lineage over time in Europe | 01/05/2023

Emerging hotspots #UnitedKingdom, #Denmark, #Germany, #Austria
Read 4 tweets
Jan 5
#COVID19 #VariantDashboard - #UnitedStates

TOP lineages (#15DAYTRENDS):

18.9% XBB.1.5
14.5% BQ.1.1
9.6% BQ.1
6.6% BQ.1.22
3.2% XBB.1
2.4% BQ.1.1.4
2.3% BQ.1.3
2.1% BQ.1.12
2.0% BQ.1.1.3

Tracker: tinyurl.com/mryj4uu7
#OmicronUpdates 01/04/2023

1/n
Sequence count by US State

New York, California, North Carolina, Washington, Virginia and Florida have submitted a large share of sequences with specimen collection dates in the last 15 days.

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

3/n
Read 21 tweets
Jan 4
Tracking XBB.1.5* lineage over time | 01/04/2023

Total Sequence Count
- Global: 3,582
- USA: 3,161

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* lineage over time in North America | 01/04/2023

Northeast USA is a major hotspot (mainly NY) Image
Tracking XBB.1.5* lineage over time in Europe | 01/04/2023

Emerging hotspots #UnitedKingdom, #Denmark, #Germany, #Austria Image
Read 4 tweets

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