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Raj Rajnarayanan Profile picture
@RajlabN
Apr 30, 2023 • 8 tweets • 10 min read • Read on X
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Tracking #SARSCoV2 #Lineages - Globally

Top lineages -#20DayTrends (#G20):

XBB.1.5 (36.6%)⬇️
XBB.1.9.1 (11.5%)⬆️
EG.1 (4.7%)⬆️
XBB.1.16 (4.4%)⬆️
XBB.1.9.2 (3.1%)
XBB.2.3 (1.8%)
XBB.1.5.13 (1.6%)
XBB.1.16.1 (1.5%)

public.tableau.com/app/profile/ra…

Updated 04/29/23 Image
Granular details #Global #20DayTrends

This analysis includes all designated #SARSCoV2 sequences submitted to @GISAID with sample collection dates on or after 04/09/2023 (14,137 sequences) Image
#USA, #Austria, #France & #Canada have submitted a lion's share of sequences with sample collection dates on or after 04/09/2023 ...followed by #UnitedKingdom, #Australia, #Germany, #Sweden, #SouthKorea, #Singapore, #China, #Spain Image
In Silico Immune escape and ACE2 receptor binding scores (relative to BA.2)*

Data is intended to prioritize select lineages to generate rapid laboratory experiments to gauge immune escape and ACE2 binding affinity.

[Credits in the legend] * Only Spike RBD mutations considered Image
#SARSCoV2 lineages in the zone of concern (red box) - Predicted to have high immune escape and tight ACE2 binding activity - A Closer look

XBB.1.16* family (XBB.1.16.1, FU.1, FU.2, XBB.1.16.2, XBB.1.16.3) cluster together

Chart: public.tableau.com/app/profile/ra… Image
What to expect in the next few weeks?

github.com/neherlab/SARS-…

Excellent SARSCoV2 Variant report
by @richardneher @CorneliusRoemer
“Currently, XBB.1.16 is the big dog” ... “It’s picking up mutations that are common in other variants that will increase its advantage further.”

H/T @ErinMPrater @WellatFortune
@FortuneMagazine
fortune.com/well/2023/03/3…
A closer look at #Arctrus (XBB.1.16*), #Hyperion (XBB.1.9*) and #Acrux (XBB.2.3*) constellations

more on common names from @TRyanGregory
Image

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More from @RajlabN

Raj Rajnarayanan Profile picture
Jan 6
The Louisiana Department of Health reports the patient who had been hospitalized with the first human case of highly pathogenic avian influenza (HPAI), or H5N1, in Louisiana and the U.S. has died.

katc.com/news/covering-…Image
official report: ldh.la.gov/news/H5N1-death
Note: This is H5N1 Avian Influenza A #WildBird -D1.1 genotype and not #DairyCattle B3.13 genotype related
Read 4 tweets
Raj Rajnarayanan Profile picture
Jan 1
#H5N1 #AvianInfluenza updates

New @NEJM case report describing severe human illness caused by highly pathogenic avian influenza A -H5N1 in #BritishColumbia (#Canada) teenager with evidence of potential viral adaptation to humans.



1/n nejm.org/doi/full/10.10…Image
A 13-year-old girl with mild asthma and obesity (BMI >35) presented with conjunctivitis, fever, respiratory distress, and multi-organ complications was hospitalized on 11/7/24, and required intensive care, including ECMO and continuous renal therapy

2/n
RT-PCR confirmed A/H5N1 infection, and the virus was linked to wild birds in British Columbia.

Genetic analysis revealed mutations in the HA protein (E186D, Q222H), associated with increased binding to human airway receptors, facilitating viral entry and replication.

3/n
Read 6 tweets
Raj Rajnarayanan Profile picture
Dec 22, 2024
#H5N1 #AvianInfluenza updates

Quick analysis of the 7 sequences from NIAID experimental study of #Macaques infected w/ H5N1 2.3.4.4b (B3.13 type)

PB2 mutations: T58A, V109I, V139I, E362G, K389R, D441N, V478I, V495I, M631L, V649I, M676A, E677K

Ref: A/Duck/Guangdong/E1/2012

1/n
HA mutations: L120M, L131Q, T211I, V226A, I526V

Ref: A/Astrakhan/3212_cell/2020

2/n
NA mutations: V67I, D259E, L269M, V321I, S339P

Ref: A/AmericanWigeon/SouthCarolina/22-000345-001/2021

3/n
Read 4 tweets
Raj Rajnarayanan Profile picture
Oct 20, 2024
Tracking #SARSCoV2 #Lineages - Globally |10/19/24

Top lineages -#30DayTrends #G30

KP.3.1.1 (41.9%)
XEC (10.5%)👀
KP.2.3 (3.1%)
MC.13 (3.1%)
MC.16 (2.6%)
MC.1 (2.5%)
KP.3.3 (2.3%)
LB.1.3.1 (1.9%)
MC.10 (1.7%)
MC.11 (1.4%)
XEC.2 (1.3%)👀



1/n public.tableau.com/app/profile/ra…Image
Granular details #Global #30DayTrends

KP.3.1.1* is still the top circulating group of lineages in the world.

This analysis includes #SARSCoV2 sequences submitted to @GISAID with sample collection dates on or after 09/19/2024 (11,851sequences)

2/n Image
@GISAID Thanks to all the countries that are supporting #SARSCoV2 testing and rapidly submitting sequences to @GISAID

Top submitters #Canada #USA #France #UK #Netherlands #Sweden #Spain #Japan #Italy
#Denmark #Australia #Ireland #Singapore
#China #NewZealand #Slovenia #Germany

3/n Image
Read 4 tweets
Raj Rajnarayanan Profile picture
Sep 27, 2024
#SARSCoV2 #VariantProportions - #USA |09/27/24

@CDCgov #Nowcast 2-Week estimates

KP.3.1.1 (JN.1.11.1.3.1.1) is still the top circulating lineage in the USA

🚨XEC makes an entry @ 5.7%



1/n covid.cdc.gov/covid-data-tra…
Image
Reliable nowcast estimates are available only for HHS regions 2, 3, 4, 5, 7 and 9

Other regions did not sequence enough

2/n Image
KP.3.1.1* group of lineages

In the @CDCgov nowcast chart....
KP.3.1.1* is not further separated in to MC.1-MC.16 sub-lineages

3/n Image
Read 6 tweets
Raj Rajnarayanan Profile picture
Sep 8, 2024
Tracking #SARSCoV2 #Lineages - Globally |09/07/24

Top lineages -#30DayTrends

KP.3.1.1 (37.1%)
KP.2.3 (9%)
KP.3.3 (5.7%)
KP.3.1 (2.9%)
XDV.1 (2.9%)
KP.1.1.3 (2.7%)
LB.1 (2.3%)
LB.1.3 (2.1%)
KP.2.2 (2%)
---
XEC (1.4%)👀

Track #G30 :

1/n public.tableau.com/app/profile/ra…
Image
Granular details #Global #30DayTrends

KP.3.1.1* is still the top circulating group of lineages in the world.

This analysis includes #SARSCoV2 sequences submitted to @GISAID with sample collection dates on or after 08/08/2024 (12,884 sequences)

2/n Image
@GISAID Thanks to all the countries that are supporting #SARSCoV2 testing and rapidly submitting sequences to @GISAID

Top submitters #USA #Canada #UK #Sweden #Japan
#China #Spain #Australia #Germany #Denmark #SouthKorea #France #Singapore #NewZealand #Ireland #Italy #Netherlands Image
Read 16 tweets

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