Thread by @RajlabN

#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!

https://twitter.com/RajlabN/status/1611412725279690753

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

more on #Massachusetts's XBB.1.5 wave

bostonglobe.com/2022/12/28/met…

17/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