Raj Rajnarayanan Profile picture
Jan 2 β€’ 19 tweets β€’ 17 min read
#COVID19 #VariantDashboard - #UnitedStates

Wish everyone a Healthy New Year 2023!

TOP lineages (#15DAYTRENDS):

32.7% XBB.1.5 πŸ‘€
14.6% BQ.1.1
8.9% BQ.1
4.1% XBB.1
2.5% BQ.1.1.4
2.2% XBB

Tracker: tinyurl.com/mryj4uu7

#OmicronUpdates 01/01/2023

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
Granular details -#VariantDashboard #USA #15DayTrends

3/n
.@CDCgov updated variant proportions estimates on 12/30/2022 (updated every Friday)

Several BQ* are circulating at >1% especially BQ.1.22 is a good candidate to be included in CDC's Nowcast estimates next week!



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

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

BQ.1.1 (24.45%)
BQ.1 (9.38%)
BQ.1.22 (4.14%)
XBB.1 (4.09%)
CH.1.1 (2.71%)πŸ‘€
BQ.1.2 (2.29%)
XBB.1.5 (2.26%)πŸ‘€
BQ.1.1.4 (2.04%)
BN.1.3 (1.81%)

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 (54.6%)πŸ‘€πŸš€
BQ.1.1 (10%)⬇️
XBB.1 (6.1%)
BQ.1 (5.7%)
BQ.1.1.4 (2.5%)
XBB.2 (1.8%)
BQ.1.3 (1.5%)
BQ.1.1.3 (1.5%)
CQ.2 (1.4%)

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

[low sequence count]

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

Only three sequences with sample collection dates in the last 15 days (XBB.1.5, BQ.1 & BU.1)

[low sequence count]

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

XBB.1.5 is the top circulating lineage in CT

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

XBB.1.5 is the top circulating lineage in NJ

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

XBB.1.5 and BQ.1.1 are the top circulating lineages in PA

[low sequence count]

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

[low sequence count]

19/n

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More from @RajlabN

Jan 3
#VariantDashboard #India - #30DayTrends

>> Low Sequence Count (n=79) <<

Top circulating lineages:

XBB.1 (14.5%)
BQ.1.1 (9.6%)
XBB.1.5 (9.6%)
XBB (8.4%)
XBB.2 (7.2%)
BQ.1 (6.0%)
BY.1 (6.0%)
BA.5.2 (3.6%)

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

Updated: 01/02/2023
Granular details - #VariantProportions #India 1/2/23

XBB* is still the dominant circulating group of lineages in India

XBB.1.5* has entered the conversation in #Maharashtra, #Gujarat and #Telangana Image
Variant landscape in Indian States with reported XBB.1.5* sequences #30DayTrends (#Maharashtra, #Gujarat and #Telangana) ImageImageImage
Read 4 tweets
Jan 3
#COVID19 #VariantDashboard - #UnitedStates

Holiday season - Low seq count this 15day period!

TOP lineages (#15DAYTRENDS):

35.7% XBB.1.5
13.4% BQ.1.1
8.5% BQ.1
4.1% XBB.1
2.8% BQ.1.1.4
2.6% BQ.1.1.3

Tracker: tinyurl.com/mryj4uu7
#OmicronUpdates 01/02/2023

1/n Image
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 18 tweets
Jan 1
#COVID19 #VariantDashboard - #UnitedStates

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

TOP lineages (#15DAYTRENDS):

27.0% XBB.1.5 πŸ‘€
14.7% BQ.1.1
8.4% BQ.1
4.1% BQ.1.22
3.9% XBB.1
2.2% BQ.1.1.4

Tracker: tinyurl.com/mryj4uu7

#OmicronUpdates 12/31/22

1/n Image
Sequence count by US State

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

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

3/n Image
Read 20 tweets
Dec 31, 2022
#COVID19 #VariantDashboard - #UnitedStates

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

TOP lineages (15-DAY TRENDS):

14.8% BQ.1.1
12.8% XBB.1.5πŸ‘€
10.2% BQ.1
8.2% BQ.1.22
3.0% XBB.1
2.4% BQ.1.1.4

Tracker: tinyurl.com/mryj4uu7

#OmicronUpdates 12/30/22

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

3/n
Read 19 tweets
Dec 30, 2022
#SARSCoV2 #VariantProportions - #USA |12/30/22

Top lineages (per @CDCgov #Nowcast estimates):

40.5% XBB.1.5πŸš€πŸš€πŸš€πŸ‘€
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
BQ.1, BQ.1.1 hotspots per nowcast estimates

3/n
Read 6 tweets
Dec 30, 2022
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]
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
Tracking XBB.1.5* in North America over time | 12/30/2022

#Ontario, #Canada is an emerging hotspot

New entrant: #PuertoRico
Read 4 tweets

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