Raj Rajnarayanan

BA.3.2* got its own nickname today: #Cicada

H/T @tryangregory.bsky.social

bsky.app/profile/trya...

Tracking SARSCoV2 Lineage BA.3.2* ( #Cicada) over time | 12/05/25

Total BA.3.2* seqs: 118 (+1)

Countries reporting BA.3.2*: #Australia, #SouthAfrica, #Netherlands, #USA (traveler seq), #Germany, #Mozambique, #Slovenia, #UK, #Denmark, #Ireland

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

Tracking SARSCoV2 Lineage BA.3.2* over time | 11/19/2025 update

Total BA.3.2* sequences: 91

Countries reporting BA.3.2*: #Australia, #SouthAfrica, #Netherlands, #USA (traveler seq), #Germany, #Mozambique, #Slovenia, #UK, #Denmark

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

Graph showing the change in number of directly submitted sequences to Pathoplexus since August 2024. 0 in Aug 2024 to almost 9000 today.

1/ 🚀 Big thanks to our community - since August we’ve added thousands of new sequences, rolled out major new features, and welcomed fresh faces into the #Pathoplexus world. Let’s dive into what’s new.👇🏻

Read the full update: pathoplexus.org/news/2025-11...

Canada could face ‘worst kind’ of flu season as experts warn evolving strain may be mismatch for vaccine | CBC News With flu cases now rising in Canada, medical experts are bracing for a difficult influenza season linked to the global spread of an evolving H3N2 strain that could be a mismatch for this year’s vaccin...

Canada could face ‘worst kind’ of flu season as experts warn evolving strain may be mismatch for vaccine

H/T @laurenpelley.bsky.social

www.cbc.ca/news/health/...

#H3N2 #FluUpdates 11/12/2025

Quick analysis of #H3N2 sequences (Subclade: K) uploaded from #Canada (#NewBrunswick)

Key mutations:
HA: T135K, S144N, N145S, N158D, I160K, A186D

Reference: A/Croatia/10136RV/2023(H3N2)

Collection dates: 20-31 Oct 2025

Note: My initial dashboard missed a few sequences with missing nucleotides. Thanks to @josetteschoenma.bsky.social and @siamosolocani.bsky.social for nucleotide queries which pick up all BA.3.2* as of now.

Pango issue, spotting & designation history:
github.com/cov-lineages...

Excellent thread on BA.3 from @ryanhisner.bsky.social bsky.app/profile/ryan...

BA.3.2 exhibits robust antibody evasion + low ACE2-binding capability (Guo et al, 2025; thelancet.com/journals/lan...

Tracking SARSCoV2 Lineage BA.3.2* over time

Total BA.3.2* - Globally: 63

Countries reporting BA.3.2*: #Australia, #SouthAfrica, #Netherlands, #USA (traveler seq), #Germany, #Mozambique, #Slovenia, #UK, #Denmark

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

Status of #COVID19 in #NewYork (#Bellwether State)

XFG.2, XFG.14.1, XFG.3.4.1, XFG.3 and XFG.4.2 are the top circulating #SARSCoV2 lineages in NY

#COVID19 hospitalizations - trending down| #WasteWater #SARSCoV2 -no recent update |
@HealthNYGov

2/n

#COVID19 #VariantDashboard - #USA| 11/07/25

#SARSCoV2 #Lineages #30DAYTRENDS

XFG.2 (10.9%)
XFG.3.4.1 (4.7%)
XFG.3 (4.7%)
XFG.14.1 (4.3%)
XFG.4.1 (3.8%)
XFG.5.1 (3.8%)
XFG.5.2 (2.8%)
XFG.3.4.3 (2.6%)
XFG.6 (2.6%)
XFG.3.4 (2.4%)

Tracker tinyurl.com/mryj4uu7

1/n

Thanks to all the countries that are supporting #SARSCoV2 testing & rapidly submitting sequences to @GISAID

Top submitters (> 100 Seqs w/ collection dates in the last 30 days): #UnitedKingdom #Canada #USA #France #Spain #Germany #Netherlands #Australia #Slovenia

3/n

This analysis includes #SARSCoV2 sequences submitted to
@GISAID with sample collection dates on or after 10/04/2025 (3,862 sequences)

Note: 171,095 SARSCoV2 seqs w/ collection dates on or after 01/01/2025 are available in GISAID/NCBI

2/n

Tracking #SARSCoV2 #Lineages - Globally |11/04/25

Top lineages -#30DayTrends #G30

XFG.3 (9.1%)
XFG.3.4.1 (6.1%)
XFG.2 (4.7%)
XFG.5.1 (4.4%)
NB.1.8.1 (3.5%)
XFG (2.8%)
XFG.4.1 (2.7%)
XFG.6 (2.7%)
XFG.8 (2.4%)
XFG.5.2 (2.4%)

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

1/n

Thanks to all the countries that are supporting #SARSCoV2 testing & rapidly submitting sequences to @GISAID

Top submitters (> 100 Seqs w/ collection dates in the last 30 days): #UnitedKingdom #USA #France #Canada #Spain #Netherlands #Australia #Germany #Italy

3/n

This analysis includes #SARSCoV2 sequences submitted to @GISAID with sample collection dates on or after 09/25/2025 (4,684 sequences)

Note: 164,341 SARSCoV2 seqs w/ collection dates on or after 01/01/2025 are available in GISAID/NCBI

2/n

Tracking #SARSCoV2 #Lineages - Globally |10/26/25

Top lineages -#30DayTrends #G30

XFG.3 (8.4%)
XFG.3.4.1 (6.7%)
XFG.5.1 (4.5%)
NB.1.8.1 (4.4%)
XFG.2 (3.6%)
XFG (3.4%)
XFG.4.1 (2.8%)
XFG.8 (2.6%)
XFG.6 (2.6%)
XFG.3.4 (2.5%)

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

1/n

These are sequences with sample collection dates in the last 30 days - I can check if this is missing some seqs

Following BA.3.2.2* in #WesternAustralia closely

4/n

Thanks to all the countries that are supporting #SARSCoV2 testing & rapidly submitting sequences to @GISAID

Top submitters (> 100 Seqs w/ collection dates in the last 30 days): #Canada #USA #UnitedKingdom #Spain #France #Australia #Netherlands #Italy #Germany

3/n

This analysis includes #SARSCoV2 sequences submitted to
@GISAID with sample collection dates on or after 09/16/2025 (5,714 sequences)

Note: 157,144 SARSCoV2 seqs w/ collection dates on or after 01/01/2025 are available in GISAID/NCBI

2/n

Tracking #SARSCoV2 #Lineages - Globally |10/16/25

Top lineages -#30DayTrends #G30

XFG.3 (9.2%)
NB.1.8.1 (5.3%)
XFG.2 (5.3%)
XFG.3.4.1 (4.8%)
XFG.5.1 (3.8%)
XFG.8 (3.2%)
XFG.4.1 (2.9%)
XFG (2.6%)
XFG.6 (2.1%)
PQ.17 (2%)

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

1/n

This analysis includes #SARSCoV2 sequences submitted to @GISAID with sample collection dates on or after 08/29/2025 (4,212 sequences)

Note: 146,261 seqs w/ collection dates on or after 01/01/2025 are available in GISAID/NCBI

2/n

XFG* mutations under watch

Spike K529T is worth watching (its one of the signature mutations of XFG.14 lineage)

Status of #COVID19 in #California

XFG.3, XFG, XFG.2 and PQ.2 are the top circulating #SARSCoV2 lineages in CA |[🚨Low sequence count]

#COVID19 hospitalizations -low | #WasteWater #SARSCoV2 - Very High | @capublichealth.bsky.social

Status of #COVID19 in #NewYork (#Bellwether State)

XFG and XFG.3 are the top circulating #SARSCoV2 lineages in NY [🚨low sequence count]

#COVID19 hospitalizations - trending up| #WasteWater #SARSCoV2 -low | @HealthNYGov

2/n

#COVID19 #VariantDashboard - #USA| 09/14/25

#SARSCoV2 #Lineages #30DAYTRENDS

XFG (35.9%)
XFG.3 (24.8%)
XFG.2 (14.2%)
NB.1.8.1 (6.3%)
PQ.2 (3.4%)
XFG.3.1 (2.2%)
LP.8.1.1 (1.4%)
NW.1.2 (1.4%)
NW.1 (1.1%)
XFC (1.1%)
PY.1 (0.8%)

Tracker: tinyurl.com/mryj4uu7

1/n

XFG.3* is the top circulating variant group in the world!

Top XFG sub-lineages in circulation (>=1%)

XFG.3, XFG, XFG.5, XFG.2, XFG.3.4.1, XFG.4.1,
XFG.9, XFG.8, XFG.3.1, XFG.3.4, XFG.6, XFG.3.4.3,
XFG.14.1, XFG.3.4.2, XFG.22, XFG.10, XFG.4, XFG.3.1.2,
XFG.21

102 XFG sub-lineages:

3/n