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Mar 24 • 8 tweets • 6 min read
#SARSCoV2 #VariantProportions - #USA |03/24/23

New @CDCgov #Nowcast estimates

XBB.1.9.1 (#Hyperion) makes an entry

Top circulating lineages:

XBB.1.5 (90.2%)
XBB.1.9.1 (2.5%)
BQ.1.1 (2.5%)
XBB.1.5.1 (2.4%)
XBB (1.2%)
CH.1.1 (0.4%)

covid.cdc.gov/covid-data-tra…

1/n Image
A closer look at nowcast estimates (modeled projections)

2/n Image
Over all trends are consistent with #15DayTrends (based on sequences uploaded in the public databases)

XBB.1.5 is still at the top; XBB.1.9.1 makes an entry

Expected XBB.1.5.13 and XBB.1.16 to feature in the CDC dashboard variant line up today..



3/n
XBB.1.9.1 hotspots per CDC Nowcast

HHS region 7 and 8 are XBB.1.9.1 hotspots

4/n Image
Tracking XBB.1.9* lineages in #USA - #15DayTrends

XBB.1.9.1, XBB.1.9.2 & EG.1

public.tableau.com/app/profile/ra…

5/n Image
#Wastewater #SARSCoV2 content from @BiobotAnalytics

Midwest #SARSCoV2 content is higher than the other regions.

6/n Image
XBB.1.5 hotspots per CDC Nowcast

XBB.1.5 is the top circulating lineage in all HHS regions

7/n Image
Circulating recombinant #SARSCoV2 lineages in #USA - #15DayTrends



8/n

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More from @RajlabN

Raj Rajnarayanan Profile picture
Mar 26
Tracking #SARSCoV2 #Lineages - Globally

Top lineages -#20DayTrends (#G20):

XBB.1.5 (48.1%)⬆️
XBB.1.9.1 (6.5%)⬆️
CH.1.1 (3.6%)
BQ.1.1 (2.6%)
EG.1 (2.4%)⬆️
CH.1.1.1 (2.1%)
..
XBB.1.16 (1.6%)👀

** includes Spike only seqs

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

Updt 03/26/23 Image
Granular details #Global #20DayTrends

This analysis includes all designated #SARSCoV2 sequences submitted to GISAID with sample collection dates on or after 03/06/2023 (25,590 sequences)

Contains many spike sequences from Austria Image
#USA, #UnitedKingdom & #Austria have submitted a lion's share of sequences with sample collection dates on or after 03/06/2023 ...followed by #Canada, #Germany, #Denmark, #Australia, #Italy, #France, #Nertherlands, #India, #Poland Image
Read 7 tweets
Raj Rajnarayanan Profile picture
Mar 26
#COVID19 #VariantDashboard - #UnitedStates

TOP lineages (#15DAYTRENDS):

69.3% XBB.1.5
4.0% XBB.1.5.15
2.6% XBB.1.9.1
1.6% XBB.1.5.13
1.4% BQ.1.1
1.3% XBB.1.5.1
1.3% XBB.1.5.17
1.2% XBB.1.16

#SARSCoV2 Tracker: tinyurl.com/mryj4uu7
Updated: 03/25/2023

1/n Image
Sequence count by US State

#California and #NewYork have submitted a big share of sequences with specimen collection dates on or after 03/10/2023

XBB.1.5 is still at the top spot;
followed by XBB.1.5.15 & XBB.1.9.1

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

XBB.1.5* (VOI - @WHO) is still ahead of the other lineages!

3/n Image
Read 12 tweets
Raj Rajnarayanan Profile picture
Mar 25
#COVID19 #VariantDashboard - #UnitedStates

TOP lineages (#15DAYTRENDS):

71.1% XBB.1.5
3.0% XBB.1.5.15
2.8% XBB.1.9.1
1.5% XBB.1.5.13
1.4% XBB.1.5.17
1.4% BQ.1.1
1.3% XBB.1.5.1
1.1% XBB.1.16

Tracker: tinyurl.com/mryj4uu7
Updated: 03/24/2023

1/n Image
Sequence count by US State

#California has submitted a big share of sequences with specimen collection dates on or after 03/09/2023

XBB.1.5 is still at the top spot;
followed by XBB.1.9.1 & XBB.1.5.15

XBB.1.16.1 is 1.1% and its child XBB.1.16.1 is circulating around 0.5%
2/n Image
Granular details -#VariantDashboard #USA #15DayTrends

XBB.1.5* (VOI - @WHO) is still ahead of the other lineages!

3/n Image
Read 12 tweets
Raj Rajnarayanan Profile picture
Mar 24
#SARSCoV2 #Omicron family quickly swells to 900+ #sublineages!

Add another 203+ recombinant lineages (w/ Omicron partner)

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

Recombinants have outcompeted others globally! Image
Expanding XBB family

Welcome to XBB.1.5 grand/great-grand kids

EM.1 (XBB.1.5.7.1)
EK.1 (XBB.1.5.13.1)
EK.2(XBB.1.5.13.2)
EK.2.1(XBB.1.5.13.2.1)
EK.3(XBB.1.5.13.3)
EL.1(XBB.1.5.14.1)
FD.1(XBB.1.5.15.1)
FD.1.1(XBB.1.5.15.1.1)
EU.1(XBB.1.5.26.1)
EU.1.1(XBB.1.5.26.1.1)
Simplified Phylogenetic tree from @CiscoRucinski to visualize XBB family (and other Lineages)

observablehq.com/@ciscorucinski…
Read 7 tweets
Raj Rajnarayanan Profile picture
Mar 24
Updated #Booster (#Bivalent) uptake in #USA

Who's boosted so far

~16% of total population (54.6 Million)

~42% of population 65 years or older (~23 Million)

@CDCgov recommends everyone stay up to date with #COVID19 vaccines for their age group

cdc.gov/coronavirus/20… Image
Percent of the Population 65 Years of Older with an Updated (Bivalent) Booster Dose (Source: @CDCgov) Image
Percent of the Population 18 Years of Age and Older with an Updated (Bivalent) Booster Dose (Source: @CDCgov) Image
Read 4 tweets
Raj Rajnarayanan Profile picture
Mar 24
#COVID19 #VariantDashboard - #UnitedStates

TOP lineages (#15DAYTRENDS):

72.7% XBB.1.5
3.0% XBB.1.9.1
2.3% XBB.1.5.15
1.4% BQ.1.1
1.2% XBB.1.16
1.2% XBB.1.5.1
1.2% XBB.1.5.13
1.2% XBB.1.5.17

Tracker: tinyurl.com/mryj4uu7
Updated: 03/23/2023

1/n Image
Sequence count by US State

#California has submitted a big share of sequences with specimen collection dates on or after 03/08/2023

XBB.1.5 is still at the top spot;
followed by XBB.1.9.1 & XBB.1.5.15

XBB.1.16.1 is 1.2% and its child XBB.1.16.1 is circulating around 0.5%
2/n Image
Granular details -#VariantDashboard #USA #15DayTrends

XBB.1.5* (VOI - @WHO) is still ahead of the other lineages!

3/n Image
Read 11 tweets

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