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Raj Rajnarayanan Profile picture
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Mar 16 • 7 tweets • 5 min read
Glad to see @WHO cares and will continue its #VariantTracking efforts!

These decisions generate a domino-type effect often ending up impacting the funds allocated for robust global surveillance efforts

#VariantTrackers have their task cut out...
Important resources to keep you updated with what's happening in the variant world

1. Cov-Spectrum Collection 24 for effective tracking- cov-spectrum.org/collections/24 (@siamosolocani @Asinickle1 @wolfeagle1989)
2. Nick names for effective communication- whn.global/common-names-f… (@TRyanGregory )
3. Variant Reports by @CorneliusRoemer @richardneher

github.com/neherlab/SARS-…
4. Pay close attention to lineages in the "Zone of Concern" - High ACE2 binding/ High immune escape

a. public.tableau.com/app/profile/ra…

b. public.tableau.com/app/profile/ra…
5. @CDCgov's #NowCast #Variant #Proportions dashboard

6. @CiscoRucinski's simplified phylogenetic trees
observablehq.com/@ciscorucinski…

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More from @RajlabN

Raj Rajnarayanan Profile picture
Mar 18
#COVID19 #VariantDashboard - #UnitedStates

TOP lineages (#15DAYTRENDS):

79.4% XBB.1.5
1.9% XBB.1.9.1
1.6% XBB.1.5.13
1.3% XBB.1.5.4
1.1% BQ.1.1
1.0% XBB.1.5.1
1.0% XBB.1.16👀
0.8% CH.1.1
0.8% XBB.1.5.2

Tracker: tinyurl.com/mryj4uu7
Uptd: 03/17/2023

1/n Image
Sequence count by US State

#California has submitted a big share of sequences with specimen collection dates on or after 03/02/2023

XBB.1.5 is still occupying the top spot; XBB.1.9.1 moves to #2 spot!

2/n Image
USA Airport surveillance update #15DayTrends

104 sequences from 6 US States (#California, #NewYork, #Washington, #NewJersey, #Georgia and #Virginia)

*Includes pooled swabs; Many bad QC seqs

3/n
Read 10 tweets
Raj Rajnarayanan Profile picture
Mar 17
#SARSCoV2 #VariantProportions - #USA |03/17/23

New @CDCgov #Nowcast estimates

Top circulating lineages:

XBB.1.5 (90.2%)
BQ.1.1 (3.5%)⬇️
XBB (2.5%)
XBB.1.5.1 (2.2%)
BQ.1 (0.7%)⬇️
CH.1.1 (0.5%)

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 the dominant lineage

Expected XBB.1.9.1 and XBB.1.5.13 to feature in the CDC dashboard variant line up today..



3/n
Read 6 tweets
Raj Rajnarayanan Profile picture
Mar 17
#COVID19 #VariantDashboard - #UnitedStates

TOP lineages (#15DAYTRENDS):

77.6% XBB.1.5
1.9% XBB.1.9.1
1.8% XBB.1.5.13
1.4% XBB.1.5.4
1.2% BQ.1.1
1.1% XBB.1.5.2
1.1% CH.1.1
1.0% XBB.1.5.1
0.5% XBB.1.16

Tracker: tinyurl.com/mryj4uu7
Updated: 03/16/2023
1/n Image
Sequence count by US State

#California, #Illinois, #Washington, #Massachusetts, #Texas, #Nebraska & #NewYork have submitted a big share of sequences with specimen collection dates on or after 03/01/2023

XBB.1.5 is still occupying the top spot; XBB.1.9.1 moves to #2 spot!

2/n Image
USA Airport surveillance update #15DayTrends

61 sequences from 6 US States (#California, #NewYork, #Washington, #NewJersey, #Georgia and #Virginia)

>50% XBB.1.16 seqs via airport surveillance (15 out of 26 seqs till date)

*Includes pooled swabs; Many bad QC seqs

3/n
Read 10 tweets
Raj Rajnarayanan Profile picture
Feb 3
#COVID19 #VariantDashboard - #UnitedStates

TOP lineages (#15DAYTRENDS):

48.0% XBB.1.5⬆️👀
14.2% BQ.1.1
5.5% XBB.1
4.1% BQ.1
1.4% BQ.1.1.4
1.4% CH.1.1
1.2% BQ.1.3
1.1% BQ.1.1.5

Tracker: tinyurl.com/mryj4uu7
Updated: 02/02/2023

1/n
Sequence count by US State

#California, #NorthCarolina, #NewYork, #NewJersey and #Massachusetts have submitted a big share of sequences

XBB.1.5 stays strong at the top spot and is establishing a clear foot print outside NE USA!

2/n
USA Airport surveillance update #15DayTrends

125 sequences from 6 US States (#California, #NewYork, #Washington, #NewJersey, #Georgia and #Virginia)

A good amount of XBB.1.5 detected via airport surveillance

3/n
Read 15 tweets
Raj Rajnarayanan Profile picture
Feb 3
Tracking #SARSCoV2 #Lineages - Globally

Top lineages -#20DayTrends (#G20):

BQ.1.1 (18.9%)
XBB.1.5 (18.7%)👀^
CH.1.1 (5.3%)👀
BQ.1 (3.7%)
XBB.1 (2.7%)
BA.5.2.48 (2.3%)
XBF (1.7%)

^more sequences from USA in this period

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

Updated 02/02/2023
Granular details #Global #20DayTrends

This analysis includes all designated #SARSCoV2 sequences submitted to GISAID with sample collection dates on or after 01/12/2023
USA has submitted a lion's share of sequences with sample collection dates on or after 01/12/2023 ...followed by #Canada, #UnitedKingdom, #Austria, #Japan, #Denmark, #Germany, #France, #China, #Australia, #Italy
Read 8 tweets
Raj Rajnarayanan Profile picture
Feb 2
#COVID19 #UglyPeak update

#SARSCoV2 Test Positivity Rate: 33.5% (slight very high and early signs of trending up again)

Source: @Walgreens Image
Treat this like an election exit poll - includes tests performed at Walgreens sites nationwide

1) We are still riding the #UglyPeak
2) Potentially many missed and unreported cases
3) Pandemic is far from over!
Walgreen's Variant proportions data (variants as of 01/23/2023) is consistent with #COVID19 Variant Dashboard #15DayTrends - Image
Read 5 tweets

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