Raj Rajnarayanan Profile picture
Assistant Dean of Research and Associate Professor, NYITCOM at Arkansas State University | My Tweets are my own
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Jan 6 4 tweets 2 min read
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
Jan 1 6 tweets 2 min read
#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

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Dec 22, 2024 4 tweets 1 min read
#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

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HA mutations: L120M, L131Q, T211I, V226A, I526V

Ref: A/Astrakhan/3212_cell/2020

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Oct 20, 2024 4 tweets 2 min read
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
Sep 27, 2024 6 tweets 2 min read
#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
Sep 8, 2024 16 tweets 5 min read
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
Sep 1, 2024 5 tweets 2 min read
What the XEC!

Recombinant #SARSCoV2 lineage #XEC (recombinant of KS.1.1/KP.3.3) has the potential to outcompete other circulating lineages in #USA (and other countries)

More data is needed to provide a reliable growth advantage estimates
Image #VariantHunters are closely monitoring XEC.1 with signature mutations Spike K182R & ORF1a:L4182F
Aug 25, 2024 17 tweets 5 min read
Tracking #SARSCoV2 #Lineages - Globally |08/25/24

Top lineages -#30DayTrends

KP.3.1.1 (30.1%)👀
KP.2.3 (11%)
KP.3.3 (7.1%)
KP.3.1 (4.2%)
LB.1.7 (2.7%)
KP.2 (2.5%)
LB.1 (2.5%)
KP.1.1.3 (2.5%)
KP.2.2 (2.2%)
---
XEC (0.4%)

Track #G30 :

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

KP.3.1.1* is the top circulating group of lineages in the world. This analysis includes #SARSCoV2 sequences submitted to @GISAID with sample collection dates on or after 07/25/2024 (14,688 sequences)

2/n Image
Aug 11, 2024 21 tweets 6 min read
Tracking #SARSCoV2 #Lineages - Globally |08/10/24

Top lineages -#30DayTrends

KP.3.1.1 (24.2%)👀
KP.2.3 (9.5%)
KP.3.3 (8.4%)
KP.3.1 (5.9%)
LB.1 (2.5%)
KP.2.2 (2.4%)
KP.2 (2.4%)
KP.3 (2.3%)
LB.1.7 (2.3%)
KP.3.2.3 (2.2%)

Track #G30 :

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

KP.3.1.1 is the top circulating lineage in the world. This analysis includes #SARSCoV2 sequences submitted to @GISAID with sample collection dates on or after 07/11/2024 (15,325 sequences)

2/n Image
Jul 28, 2024 15 tweets 5 min read
Tracking #SARSCoV2 #Lineages - Globally |07/27/24

Top lineages -#30DayTrends

KP.3.1.1 (17.4%)👀
KP.2.3 (8.1%)
KP.3.3 (8%)
KP.3.1 (7.2%)
KP.3 (3.3%)
KP.2 (3.1%)
KP.3.1.4 (3.1%)
KP.3.2 (3%)
LB.1 (2.5%)
KP.3.2.3 (2.5%)

Track #G30 :

1/n public.tableau.com/app/profile/ra…
Image Granular details #Global #30DayTrends KP.3* is the dominant group of lineages in the world.

This analysis includes #SARSCoV2 sequences submitted to @GISAID with sample collection dates on or after 06/27/2024 (12,753 sequences)

2/n Image
Jul 26, 2024 6 tweets 3 min read
#H5N1 Updates #AvianInfluenza

@USDA #APHIS #NVSL has submitted 211 sequences on 7/24/24 with collection dates in 01 to 06/2024

12 #cow milk seqs from #Minnesota with **PB2 Q591R** in addition to the cattle outbreak signature M631L [isolate ID 24-016288-001 to 015!]

1/n Image PB2 Q591R: A basic amino acid at position 591 of PB2 can compensate for the lack of lysine at position 627 and confers efficient viral replication to pandemic H1N1 viruses in mammals.

ie., Q591R ~ E627K! 👀



2/n pubmed.ncbi.nlm.nih.gov/20700447/
Image
Jul 20, 2024 19 tweets 6 min read
Tracking #SARSCoV2 #Lineages - Globally |07/20/24

Top lineages -#30DayTrends

KP.3.1.1 (14.2%)👀
KP.2.3 (7.9%)
KP.3.1 (7.8%)
KP.3.3 (7.7%)
KP.3.2 (3.8%)
KP.3 (3.4%)
KP.3.1.4 (3.4%)
KP.2 (3.4%)
LB.1 (2.7%)
KP.2.2 (2.7%)

Track #G30 :

1/n public.tableau.com/app/profile/ra…
Image Granular details #Global #30DayTrends KP.3* & KP.2* are the dominant group of lineages in the world.

This analysis includes #SARSCoV2 sequences submitted to @GISAID with sample collection dates on or after 06/20/2024 (12,854 sequences)

2/n Image
Jun 19, 2024 7 tweets 4 min read
#COVID19 #VariantDashboard - #USA | 06/18/24
#SARSCoV2 #Lineages #30DAYTRENDS

KP.2.3 (7.7%)
KP.2 (7.4%)
KP.3.1 (5%)
KP.3.3 (4.8%)
JN.1.16.1 (4.2%)
LB.1.7 (4%)
JN.1.16 (3.4%)
KP.1.1.1 (3.4%)
LB.1.3 (3.3%)
KP.2.2 (3.1%)
--
KP.3.1.1 (1.5%)👀


1/ntinyurl.com/mryj4uu7 You can filter spike mutations S31del, R346T, L455S, F456L, T572I (Top convergent mutations) to display #SLip, #FLiRT, #TiRT, #FLiRTTI, #DeFLiRT combo mutations; (Note: retired #FLip as of now)

Also, by state, lineage, collection date

2/n Image
Jun 9, 2024 15 tweets 5 min read
Tracking #SARSCoV2 #Lineages - Globally |06/08/24

Top lineages -#30DayTrends (#G30)

KP.2.3 (8.7%)
KP.2 (8.7%)
KP.3.1 (7.7%)
KP.3 (6.2%)
KP.3.2 (5.1%)
LB.1 (5%)
KP.1.1 (4.9%)

Track:

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

KP.3* & KP.2* are the dominant group of lineages in the world.

This analysis includes #SARSCoV2 sequences submitted to @GISAID with sample collection dates on or after 05/09/2024 (8,025 sequences)

2/n Image
Jun 5, 2024 4 tweets 2 min read
#SARSCoV2 #VaccineAntigen Updates

Question before @US_FDA #VRBPAC committee:

For the 2024-2025 Formula of #COVID19 vaccines in the U.S., does the committee recommend a monovalent JN.1-lineage vaccine composition?

Watch:

1/n youtube.com/live/weaKQiFk_…
Image Mutations of Interest on JN.1 background

JN.1 + F456L (FL) |JN.1.16 • JN.1.11.1
JN.1 + R346T (RT) |•JN.1.18 •JN.1.13.1 • KQ.1
JN.1 + R346T + F456L (#FLiRT) |•KP.2 • KP.1.1
JN.1 + R346T + F456L + T572I (#FLiRTTI) |• KZ.1.1.1
JN.1 + F456L + Q493E (#FLuQE) |• KP.3

2/n Image
Jun 5, 2024 4 tweets 1 min read
#SARSCoV2 Updates

KP.3 group of lineages (as of 6/4/2024) Image KP.2 (JN.1.11.1 w/ S:R346T) group of lineages (as of 6/4/2024) Image
May 18, 2024 7 tweets 3 min read
Tracking #SARSCoV2 #Lineages - Globally |05/18/24

Top lineages -#30DayTrends (#G30)

KP.2 (12.7%)
KP.3 (11.6%)👀
JN.1.7 (6.9%)
JN.1 (6.8%)
JN.1.16 (5%)
JN.1.4 (4.9%)
JN.1.16.1 (4.6%)
KP.1.1 (3.6%)
KS.1 (2.8%)
JN.1.32 (2.7%)
LB.1 (2.7%)


1/npublic.tableau.com/app/profile/ra… Granular details #Global #30DayTrends

KP* is the dominant group of lineages in the world.

This analysis includes #SARSCoV2 sequences submitted to @GISAID with sample collection dates on or after 04/18/2024 (6,469 sequences)

2/n Image
May 6, 2024 6 tweets 2 min read
#COVID19 #VariantDashboard - #USA | 05/05/24

#SARSCoV2 #Lineages #30DAYTRENDS

JN.1.7 (12%)
JN.1 (11.5%)
KP.2 (8.9%)
JN.1.4 (8.4%)
JN.1.13.1 (5.6%)
JN.1.8.1 (4.5%)
JN.1.18 (3.9%)
JN.1.16 (3.6%)
KQ.1 (2.8%)
JN.1.16.1 (2.7%)
KP.3 (2.2%)

||
1/ntinyurl.com/mryj4uu7 Sequence count by US States

A total of 1886 sequences were submitted with specimen collection dates on or after 04/04/2024 (of which 373 (~19.8%) were collected via airport surveillance)

2/n Image
Apr 28, 2024 6 tweets 2 min read
#H5N1 #LessonLearned - Domestic and Farm cats!

Common theme among H5N1 clade 2.3.4.4b infected Cats:
- Present multiple symptoms almost immediately
- Neurologic, Respiratory, rapid decline leading to death
(or compassionate euthanasia)
- Pick PB2 mammalian adaptations

1/n Image French Cat (2022)

Phylogenetic analysis linked the infection closely to virus circulating in the neighboring duck farm, with minor genetic differences.

Key mutations: PB2 E627K & NS: E26G

Again, rapid selection of mammalian adaptation mutation

2/n
Apr 16, 2024 4 tweets 2 min read
#COVID19 #VariantDashboard - #USA | 04/16/24

#SARSCoV2 #Lineages #30DAYTRENDS

JN.1 (24.7%)
JN.1.4 (13.3%)
JN.1.7 (9.8%)
JN.1.8.1 (5.6%)
KP.2 (4.6%)
JN.1.18 (3.5%)
KQ.1 (3%)
JN.1.13.1 (2.6%)
JN.1.4.5 (2.6%)
JN.1.32 (2.3%)

Tracker:
1/ntinyurl.com/mryj4uu7 Sequence count by US States

A total of 1509 sequences were submitted with specimen collection dates on or after 03/16/2024 (of which 69 (~4.6%) were collected via airport surveillance)

2/n Image
Apr 14, 2024 6 tweets 3 min read
Tracking #SARSCoV2 #Lineages - Globally |04/13/24

Top lineages -#30DayTrends (#G30):

JN.1 (27.7%)
JN.1.4 (15%)
JN.1.7 (9%)
JN.1.18 (4.3%)
KP.2 (3.4%)
JN.1.8.1 (3.3%)
JN.1.32 (3.1%)
JN.1.16 (2.8%)
JN.1.4.3 (2.7%)
JN.1.11.1 (2%)

Track:

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

JN.1* is still the dominant group of lineages in the world.

This analysis includes #SARSCoV2 sequences submitted to @GISAID with sample collection dates on or after 03/14/2024 (6,157 sequences)

2/n Image