Stefan Pöhlmann
@snpoehlm.bsky.social
Viruses & Proteases, Head of Infection Biology Unit, Deutsches Primatenzentrum, @primatenzentrum.bsky.social, Decoding viral entry, Tracking SARS-CoV-2 variants, https://linktr.ee/snpoehlm, Views are my own
Pinned
Stefan Pöhlmann
@snpoehlm.bsky.social
· Oct 28
SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor
The emerging SARS-coronavirus 2 (SARS-CoV-2) threatens public health. Hoffmann and
coworkers show that SARS-CoV-2 infection depends on the host cell factors ACE2 and
TMPRSS2 and can be blocked by a cl...
www.cell.com
Our starting point
SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor: Cell www.cell.com/cell/fulltex...
SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor: Cell www.cell.com/cell/fulltex...
Reposted by Stefan Pöhlmann
Already two more BA.3.2.2 from Ireland today, both closely related to the first (and both with the ORF1a:∆141-143 deletion also found in most European BA.3.2.1).
Only real change was N:T271S in one of the two. (A29086T was inherited, but C->G muts like this are very rare.)
Only real change was N:T271S in one of the two. (A29086T was inherited, but C->G muts like this are very rare.)
November 28, 2025 at 7:58 PM
Already two more BA.3.2.2 from Ireland today, both closely related to the first (and both with the ORF1a:∆141-143 deletion also found in most European BA.3.2.1).
Only real change was N:T271S in one of the two. (A29086T was inherited, but C->G muts like this are very rare.)
Only real change was N:T271S in one of the two. (A29086T was inherited, but C->G muts like this are very rare.)
/1 The large deletion removing ORF7/8 together with Δ141–143 in Nsp1 in BA.3.2 likely reduce its capacity to counter the interferon (IFN) system and to interfere with host cell translation, respectively.
Primary difference is that BA.3.2.1 has H681R + P1162R while BA.3.2.2 has K356T and A575S.
Actually, I think there's one other important difference. The BA.3.2.1 sequences from the past 6 months all have ORF1a:∆141-143. That's almost certainly a deleterious mutation....
Actually, I think there's one other important difference. The BA.3.2.1 sequences from the past 6 months all have ORF1a:∆141-143. That's almost certainly a deleterious mutation....
November 27, 2025 at 1:02 PM
/1 The large deletion removing ORF7/8 together with Δ141–143 in Nsp1 in BA.3.2 likely reduce its capacity to counter the interferon (IFN) system and to interfere with host cell translation, respectively.
BA.3.2 still active in New Zealand.
🎃
🎃
Wastewater variants for week ended 9 Nov 2025:
💠NB.1.8.1 (Nimbus) 41.9%
💠XFG (Stratus) 23.0%
💠PE.1.4 17.2%
💠MC.10.2.1 9.6%
💠BA.3.2 3.7%
45% of NZ covered by testing:
💠Auckland
💠Rotorua
💠Wellington
💠Christchurch
💠Dunedin
💠Queenstown
poops.nz
2/
💠NB.1.8.1 (Nimbus) 41.9%
💠XFG (Stratus) 23.0%
💠PE.1.4 17.2%
💠MC.10.2.1 9.6%
💠BA.3.2 3.7%
45% of NZ covered by testing:
💠Auckland
💠Rotorua
💠Wellington
💠Christchurch
💠Dunedin
💠Queenstown
poops.nz
2/
ESR Wastewater Surveillance
poops.nz
November 27, 2025 at 12:02 PM
BA.3.2 still active in New Zealand.
🎃
🎃
Reposted by Stefan Pöhlmann
Another US BA.3.2 wastewater detection.
This time from Bristol County, RI on Nov 11. It was about a third of the seqs.
I wonder if it was someone who flew back from Australia through SF?
@ryanhisner.bsky.social @snpoehlm.bsky.social @rajlabn.bsky.social
This time from Bristol County, RI on Nov 11. It was about a third of the seqs.
I wonder if it was someone who flew back from Australia through SF?
@ryanhisner.bsky.social @snpoehlm.bsky.social @rajlabn.bsky.social
November 26, 2025 at 11:01 PM
Another US BA.3.2 wastewater detection.
This time from Bristol County, RI on Nov 11. It was about a third of the seqs.
I wonder if it was someone who flew back from Australia through SF?
@ryanhisner.bsky.social @snpoehlm.bsky.social @rajlabn.bsky.social
This time from Bristol County, RI on Nov 11. It was about a third of the seqs.
I wonder if it was someone who flew back from Australia through SF?
@ryanhisner.bsky.social @snpoehlm.bsky.social @rajlabn.bsky.social
BA.3.2.2 arrived in Ireland - EPI_ISL_20259113
🎃
🎃
November 26, 2025 at 7:00 PM
BA.3.2.2 arrived in Ireland - EPI_ISL_20259113
🎃
🎃
4 new BA.3.2.2 sequences from South Africa submitted to GISAID today - 4.5% of total sequences from South Africa.
4 new BA.3.2.2 sequences from New South Wales submitted on 24.11., 4.5% of total sequences from Australia.
Now waiting for new sequences from Germany… 👀
4 new BA.3.2.2 sequences from New South Wales submitted on 24.11., 4.5% of total sequences from Australia.
Now waiting for new sequences from Germany… 👀
November 26, 2025 at 2:45 PM
4 new BA.3.2.2 sequences from South Africa submitted to GISAID today - 4.5% of total sequences from South Africa.
4 new BA.3.2.2 sequences from New South Wales submitted on 24.11., 4.5% of total sequences from Australia.
Now waiting for new sequences from Germany… 👀
4 new BA.3.2.2 sequences from New South Wales submitted on 24.11., 4.5% of total sequences from Australia.
Now waiting for new sequences from Germany… 👀
Reposted by Stefan Pöhlmann
This is a very sad day for public health and evidence-based science in general.
November 20, 2025 at 3:17 PM
This is a very sad day for public health and evidence-based science in general.
Info on the 8 new BA.3.2 sequences from Germany:
➡️All are BA.3.2.2, deposited in GISAID.
➡️3 were collected in late October, 5 in November.
➡️Samples originate from Rhineland-Palatinate, North Rhine-Westphalia, and Berlin.
#BA32
➡️All are BA.3.2.2, deposited in GISAID.
➡️3 were collected in late October, 5 in November.
➡️Samples originate from Rhineland-Palatinate, North Rhine-Westphalia, and Berlin.
#BA32
November 20, 2025 at 1:49 PM
Info on the 8 new BA.3.2 sequences from Germany:
➡️All are BA.3.2.2, deposited in GISAID.
➡️3 were collected in late October, 5 in November.
➡️Samples originate from Rhineland-Palatinate, North Rhine-Westphalia, and Berlin.
#BA32
➡️All are BA.3.2.2, deposited in GISAID.
➡️3 were collected in late October, 5 in November.
➡️Samples originate from Rhineland-Palatinate, North Rhine-Westphalia, and Berlin.
#BA32
Overview of global BA.3.2 sequences, plus reference to 8 new sequences from Germany
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/...
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/...
November 20, 2025 at 1:48 PM
Overview of global BA.3.2 sequences, plus reference to 8 new sequences from Germany
BA.3.2 has been detected again in the USA.
Oh crap. There was a BA.3.2 in California last week.
It's GBW and 'environmental', so presumably from plane waste.
@ryanhisner.bsky.social
Had you heard about it? Did they miss it? It was only 5% of the sample, but very clear.
It's GBW and 'environmental', so presumably from plane waste.
@ryanhisner.bsky.social
Had you heard about it? Did they miss it? It was only 5% of the sample, but very clear.
November 19, 2025 at 11:11 PM
BA.3.2 has been detected again in the USA.
Our recent study on BA.3.2 is now available. Thanks to Markus Hoffmann, Lu Zhang and Georg Behrens for the great collaboration. Here’s a brief summary of our findings:
November 17, 2025 at 10:55 AM
Our recent study on BA.3.2 is now available. Thanks to Markus Hoffmann, Lu Zhang and Georg Behrens for the great collaboration. Here’s a brief summary of our findings:
two new BA.3.2.2 from NSW clustering with previous samples from there, likely local circualtion has started:
nextstrain.org/fetch/genome...
nextstrain.org/fetch/genome...
nextstrain.org
November 17, 2025 at 10:31 AM
Germany will invest in research on Long COVID and related conditions — great news!
Karl Lauterbach: Forschung gegen ME/CFS wird ausgeweitet: Union und SPD wollen mehr Geld in die Erforschung postinfektiöser Erkrankungen wie Long Covid stecken. Deutschland könne damit zum weltweiten Vorreiter werden, sagt Ex-Gesundheitsminister Lauterbach.
Karl Lauterbach: Forschung gegen ME/CFS wird ausgeweitet
Union und SPD wollen mehr Geld in die Erforschung postinfektiöser Erkrankungen wie Long Covid stecken. Deutschland könne damit zum weltweiten Vorreiter werden, sagt Ex-Gesundheitsminister Lauterbach.
www.spiegel.de
November 15, 2025 at 10:36 AM
Germany will invest in research on Long COVID and related conditions — great news!
Proud that Markus Hoffmann and I made the 2025 Clarivate Highly Cited Researchers list.
Huge thanks to everyone in the Infection Biology Unit at the German Primate Center - honoured and grateful. @primatenzentrum.bsky.social
clarivate.com/highly-cited...
Huge thanks to everyone in the Infection Biology Unit at the German Primate Center - honoured and grateful. @primatenzentrum.bsky.social
clarivate.com/highly-cited...
Clarivate Highly Cited Researchers 2025
The Highly Cited Researchers 2025 list identifies and celebrates individuals who have demonstrated significant and broad influence in their fields of research. Through rigorous selection criteria and ...
clarivate.com
November 15, 2025 at 9:07 AM
Proud that Markus Hoffmann and I made the 2025 Clarivate Highly Cited Researchers list.
Huge thanks to everyone in the Infection Biology Unit at the German Primate Center - honoured and grateful. @primatenzentrum.bsky.social
clarivate.com/highly-cited...
Huge thanks to everyone in the Infection Biology Unit at the German Primate Center - honoured and grateful. @primatenzentrum.bsky.social
clarivate.com/highly-cited...
BA.3.2 was first detected in Germany in April 2025, with a second detection in September - both single sequences (BA.3.2.2). Now 4 new sequences: EPI_ISL_20243694, EPI_ISL_20243686, EPI_ISL_20243677, and EPI_ISL_20243675.
+4 From Germany two regions BA.3.2.2 different branch from WA found by HynnSpylor github
New batch from WA AUS 9/22 are BA.3.2.2
In November 8/20 samples there have been BA.3.2.2
nextstrain.org/fetch/genome...
In November 8/20 samples there have been BA.3.2.2
nextstrain.org/fetch/genome...
November 12, 2025 at 5:58 PM
BA.3.2 was first detected in Germany in April 2025, with a second detection in September - both single sequences (BA.3.2.2). Now 4 new sequences: EPI_ISL_20243694, EPI_ISL_20243686, EPI_ISL_20243677, and EPI_ISL_20243675.
BA.3.2 on the road to dominance in Western Australia? The Great Pumpkin is getting serious.
🎃🎃🎃
🎃🎃🎃
New batch from WA AUS 9/22 are BA.3.2.2
In November 8/20 samples there have been BA.3.2.2
nextstrain.org/fetch/genome...
In November 8/20 samples there have been BA.3.2.2
nextstrain.org/fetch/genome...
nextstrain.org
November 12, 2025 at 1:57 PM
BA.3.2 on the road to dominance in Western Australia? The Great Pumpkin is getting serious.
🎃🎃🎃
🎃🎃🎃
Concerning.
#Canada could face ‘worst kind’ of flu season as experts warn evolving strain may be mismatch for vaccine
Alarm bells abroad, spread of a new form of H3N2 provide warnings as influenza cases start ticking up
/1 thread
www.cbc.ca/news/health/...
Alarm bells abroad, spread of a new form of H3N2 provide warnings as influenza cases start ticking up
/1 thread
www.cbc.ca/news/health/...
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...
www.cbc.ca
November 11, 2025 at 4:11 PM
Concerning.
Reposted by Stefan Pöhlmann
Can't emphasize how damaging this is. A single non-scientist—Peter Bogner—holds all power & makes all decisions at GISAID & provides no justifications for any of them, except blatantly false ones.
He has that power because he conned rich & powerful people into giving it to him. Enough.
He has that power because he conned rich & powerful people into giving it to him. Enough.
I want to spell this out in case the implications aren't clear:
This means all public tools/webapps of GISAID data (all the ones you've been used to seeing thru the pandemic, as far as we can tell) are prohibited.
The file allowed this. Cut that - cut off all tools the public & others were using.
This means all public tools/webapps of GISAID data (all the ones you've been used to seeing thru the pandemic, as far as we can tell) are prohibited.
The file allowed this. Cut that - cut off all tools the public & others were using.
On Oct 1, 2025, GISAID informed us that they had ended updates to the flat file of SARS-CoV-2 genomic sequences and associated metadata that we had used to update Nextstrain analyses since Feb 2020. GISAID's stated rationale was that their "resources are limited". 1/5
November 10, 2025 at 2:46 AM
Can't emphasize how damaging this is. A single non-scientist—Peter Bogner—holds all power & makes all decisions at GISAID & provides no justifications for any of them, except blatantly false ones.
He has that power because he conned rich & powerful people into giving it to him. Enough.
He has that power because he conned rich & powerful people into giving it to him. Enough.
Reposted by Stefan Pöhlmann
BA.3.2 update:
here the four (slighty) different BA.3.2 circulating branches:
github.com/sars-cov-2-v...
here the four (slighty) different BA.3.2 circulating branches:
github.com/sars-cov-2-v...
Multiple BA.3.2.1 and BA.3.2.2 circulating branches · Issue #3093 · sars-cov-2-variants/lineage-proposals
BA.3.2.1 Branch 1 BA.3.2.1 > A10978G > C4582T, A8755G, C12073T, N:T296I (C29160T) Query for this branch : A8755G, C12073T, C29160T Samples: 3 First 2025-08-13 Netherlands Zuid-Holland Last 2025-10-...
github.com
November 9, 2025 at 2:10 PM
BA.3.2 update:
here the four (slighty) different BA.3.2 circulating branches:
github.com/sars-cov-2-v...
here the four (slighty) different BA.3.2 circulating branches:
github.com/sars-cov-2-v...
US to demand countries share data on ‘pathogens with epidemic potential’ in return for health aid
US to demand countries share data on ‘pathogens with epidemic potential’ in return for health aid
Draft template seen by the Guardian has no reference to countries receiving benefits for sharing information, such as guaranteed access to medicines developed as a result
www.theguardian.com
November 9, 2025 at 1:38 PM
It was a great pleasure presenting @vigilant-eu.bsky.social at the @defender-project.bsky.social International Symposium! 🌟 Inspiring talks, fantastic collab opportunities - grateful for the experience! #EUResearch
🌍 Join us at the @defender-project.bsky.social International Symposium for a keynote by our #combineMARV coordinator @christian-7.bsky.social!
🎟️ Register free of charge for a day of insights, collaboration & global exchange 🔗 lnkd.in/eY9JwzXY
#PandemicPreparedness #Collaboration #EUfunded
🎟️ Register free of charge for a day of insights, collaboration & global exchange 🔗 lnkd.in/eY9JwzXY
#PandemicPreparedness #Collaboration #EUfunded
November 9, 2025 at 11:47 AM
It was a great pleasure presenting @vigilant-eu.bsky.social at the @defender-project.bsky.social International Symposium! 🌟 Inspiring talks, fantastic collab opportunities - grateful for the experience! #EUResearch
BA.3.2, the great pumpkin, is touring Europe. 🎃🎃
BA.3.2 has arrived in the UK. One BA.3.2.2, collected October 5, was uploaded from Scotland today.
Same branch as recent BA.3.2.2 from Germany & Slovenia.
It has a few errors (S:ins214:ASDT is misread & ORF1a:E4388K is an artifact). Ignoring those, the one notable new mutation is N:N126K.
Same branch as recent BA.3.2.2 from Germany & Slovenia.
It has a few errors (S:ins214:ASDT is misread & ORF1a:E4388K is an artifact). Ignoring those, the one notable new mutation is N:N126K.
November 7, 2025 at 6:20 PM
BA.3.2, the great pumpkin, is touring Europe. 🎃🎃
Reposted by Stefan Pöhlmann
🚨 NEW: The majority holder of the world's genetic sequence data is a bad actor who can cut off access to critics and competing services. We've tolerated this for years, and now it threatens the pandemic treaty. Time for WHO to step in. With @ctrlalttim.com: www.thinkglobalhealth.org/article/to-f...
To Finish the Pandemic Agreement, WHO Needs a Trustworthy Viral Database | Think Global Health
Online platforms for sharing virus sequences are in disarray. The World Health Organization has a chance to build something new
www.thinkglobalhealth.org
November 5, 2025 at 3:31 PM
🚨 NEW: The majority holder of the world's genetic sequence data is a bad actor who can cut off access to critics and competing services. We've tolerated this for years, and now it threatens the pandemic treaty. Time for WHO to step in. With @ctrlalttim.com: www.thinkglobalhealth.org/article/to-f...
Reposted by Stefan Pöhlmann
Nextstrain's daily-updated tree of SARS-CoV-2 genomes was my gateway into the world of viral phylogenetics in early 2020, and Nextstrain's beautiful interactive tree display is crucial to making usher.bio results usable. GISAID cutting off data harms global surveillance efforts. 🧵👇
On Oct 1, 2025, GISAID informed us that they had ended updates to the flat file of SARS-CoV-2 genomic sequences and associated metadata that we had used to update Nextstrain analyses since Feb 2020. GISAID's stated rationale was that their "resources are limited". 1/5
November 7, 2025 at 5:03 AM
Nextstrain's daily-updated tree of SARS-CoV-2 genomes was my gateway into the world of viral phylogenetics in early 2020, and Nextstrain's beautiful interactive tree display is crucial to making usher.bio results usable. GISAID cutting off data harms global surveillance efforts. 🧵👇
Continued surveillance and variant analysis is important, as highlighted by the emergence and spread of BA.3.2. Lack of data sharing by GISAID is bad news.
GISAID on providing data to @Nextstrain.org: "After consulting with our staff and advisors on the feasibility of keeping your global tree up-to-date, there was a clear consensus that continuing to generate, zip and move big files back and forth is not sustainable and a waste of resources."
🙃
🙃
Nextstrain: Interruption to GISAID-based SARS-CoV-2 sequence analyses
Nextstrain blog post from 2025-11-06; author(s): Trevor Bedford, Richard Neher and the Nextstrain team
next.nextstrain.org
November 6, 2025 at 10:14 PM
Continued surveillance and variant analysis is important, as highlighted by the emergence and spread of BA.3.2. Lack of data sharing by GISAID is bad news.