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
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...
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.
A new BA.3.2 sequence. This time from the Netherlands, collected October 25. BA.3.2.1, EPI_ISL_20237246
🎃🎃🎃
🎃🎃🎃
November 6, 2025 at 2:01 PM
A new BA.3.2 sequence. This time from the Netherlands, collected October 25. BA.3.2.1, EPI_ISL_20237246
🎃🎃🎃
🎃🎃🎃
And a new BA.3.2.2 sequence from Slovenia (EPI_ISL_20236520, collected on November 2) - a first for the country.
The Great Pumpkin remains active in different parts of the world...🎃
The Great Pumpkin remains active in different parts of the world...🎃
November 5, 2025 at 9:13 AM
And a new BA.3.2.2 sequence from Slovenia (EPI_ISL_20236520, collected on November 2) - a first for the country.
The Great Pumpkin remains active in different parts of the world...🎃
The Great Pumpkin remains active in different parts of the world...🎃
COVID-19 remains a significant public health issue - continued surveillance is important.
www.nature.com/articles/d41...
www.nature.com/articles/d41...
COVID-19 is spreading again — how serious is it and what are the symptoms?
Limited COVID-19 surveillance data are hampering vaccination and health strategies, researchers say.
www.nature.com
November 5, 2025 at 9:06 AM
COVID-19 remains a significant public health issue - continued surveillance is important.
www.nature.com/articles/d41...
www.nature.com/articles/d41...
The Great Pumpkin, BA.3.2, is back. Two new BA.3.2.2 sequences from Western Australia, collected on October 17: EPI_ISL_20236455 and EPI_ISL_20236456.
November 5, 2025 at 9:05 AM
The Great Pumpkin, BA.3.2, is back. Two new BA.3.2.2 sequences from Western Australia, collected on October 17: EPI_ISL_20236455 and EPI_ISL_20236456.
Reposted by Stefan Pöhlmann
arxiv.org/abs/2510.23833
@zachhensel.bsky.social has revisited Bruttel et al’s preprint and shows why the analysis of RE sites in SARS2 was deeply flawed. Spoiler: the sites are natural, the pattern explicable by recombination & the authors stacked the deck omitting some seqs and duplicating others.
@zachhensel.bsky.social has revisited Bruttel et al’s preprint and shows why the analysis of RE sites in SARS2 was deeply flawed. Spoiler: the sites are natural, the pattern explicable by recombination & the authors stacked the deck omitting some seqs and duplicating others.
On the distributions of restriction sites in human and pangolin sarbecoviruses
Since early 2020, several theories have suggested that a distribution of restriction endonuclease recognition sites in the SARS-CoV-2 genome indicates a synthetic origin. The most influential of these...
arxiv.org
November 3, 2025 at 2:47 PM
arxiv.org/abs/2510.23833
@zachhensel.bsky.social has revisited Bruttel et al’s preprint and shows why the analysis of RE sites in SARS2 was deeply flawed. Spoiler: the sites are natural, the pattern explicable by recombination & the authors stacked the deck omitting some seqs and duplicating others.
@zachhensel.bsky.social has revisited Bruttel et al’s preprint and shows why the analysis of RE sites in SARS2 was deeply flawed. Spoiler: the sites are natural, the pattern explicable by recombination & the authors stacked the deck omitting some seqs and duplicating others.
Reposted by Stefan Pöhlmann
So we have four branches of BA.3.2 circulating now
two BA.3.2.1 related each other but distinct and two BA.3.2.2 related but distinct.
My take about this is that both lineages are enough tuned to not disappear , with BA.3.2.2 having the potential of expand further.
two BA.3.2.1 related each other but distinct and two BA.3.2.2 related but distinct.
My take about this is that both lineages are enough tuned to not disappear , with BA.3.2.2 having the potential of expand further.
November 1, 2025 at 1:10 PM
So we have four branches of BA.3.2 circulating now
two BA.3.2.1 related each other but distinct and two BA.3.2.2 related but distinct.
My take about this is that both lineages are enough tuned to not disappear , with BA.3.2.2 having the potential of expand further.
two BA.3.2.1 related each other but distinct and two BA.3.2.2 related but distinct.
My take about this is that both lineages are enough tuned to not disappear , with BA.3.2.2 having the potential of expand further.
Reposted by Stefan Pöhlmann
Maybe an even more inside baseball in these documents -- but it's key:
No mention of furin cleavage site in the slides...
which matches a remark made by Peter Daszak in an email to David Morens in May 2021, made public by FOIA ▫️1/8
#CovidOrigin
www.hsgac.senate.gov/wp-content/u...
No mention of furin cleavage site in the slides...
which matches a remark made by Peter Daszak in an email to David Morens in May 2021, made public by FOIA ▫️1/8
#CovidOrigin
www.hsgac.senate.gov/wp-content/u...
October 31, 2025 at 8:50 PM
Maybe an even more inside baseball in these documents -- but it's key:
No mention of furin cleavage site in the slides...
which matches a remark made by Peter Daszak in an email to David Morens in May 2021, made public by FOIA ▫️1/8
#CovidOrigin
www.hsgac.senate.gov/wp-content/u...
No mention of furin cleavage site in the slides...
which matches a remark made by Peter Daszak in an email to David Morens in May 2021, made public by FOIA ▫️1/8
#CovidOrigin
www.hsgac.senate.gov/wp-content/u...
This study (preprint) looks at authentic BA.3.2.
October 31, 2025 at 9:21 PM
This study (preprint) looks at authentic BA.3.2.
It appears we have a premiere: the first BA.3.2 sequence from Denmark — EPI_ISL_20232495.
@ryanhisner.bsky.social @josetteschoenma.bsky.social @siamosolocani.bsky.social @siamosolocani.bsky.social
@ryanhisner.bsky.social @josetteschoenma.bsky.social @siamosolocani.bsky.social @siamosolocani.bsky.social
October 31, 2025 at 4:01 PM
It appears we have a premiere: the first BA.3.2 sequence from Denmark — EPI_ISL_20232495.
@ryanhisner.bsky.social @josetteschoenma.bsky.social @siamosolocani.bsky.social @siamosolocani.bsky.social
@ryanhisner.bsky.social @josetteschoenma.bsky.social @siamosolocani.bsky.social @siamosolocani.bsky.social
Reposted by Stefan Pöhlmann
That would have been big news a few years ago, unfortunately the great science that gives important understanding in coronaviruses is now back to the small circle of scientists. Anyway: A fully functional furin cleavage site in a bat betacorarnavirus! Congrats to the authors!
We’ve identified a highly divergent betacoronavirus from South American bat that encodes a functional furin cleavage site.
Another fascinating reminder of how diverse coronavirus evolution is in wildlife reservoirs.
#Virology #VirusEvolution #Bats #Coronavirus
www.biorxiv.org/content/10.1...
Another fascinating reminder of how diverse coronavirus evolution is in wildlife reservoirs.
#Virology #VirusEvolution #Bats #Coronavirus
www.biorxiv.org/content/10.1...
A divergent betacoronavirus with a functional furin cleavage site in South American bats
Bats are natural reservoirs for a wide range of RNA viruses. Members of the genus Betacoronavirus, including Severe Acute Respiratory Syndrome virus 2 (SARS-CoV-2) and Middle East Respiratory Syndrome...
www.biorxiv.org
October 29, 2025 at 9:56 PM
That would have been big news a few years ago, unfortunately the great science that gives important understanding in coronaviruses is now back to the small circle of scientists. Anyway: A fully functional furin cleavage site in a bat betacorarnavirus! Congrats to the authors!
BA.3.2 made it to New Zealand 👀
🦠Heads up. BA.3.2 has arrived in NZ
BA.3.2 detected in Aotearoa New Zealand wastewater
3.2% for the week to 5 October
BA.3.2 is not shown in the fortnight to 19 Oct. However, variants with a national percentage of < 1% are not included so BA.3.2 is likely to still be circulating
BA.3.2 detected in Aotearoa New Zealand wastewater
3.2% for the week to 5 October
BA.3.2 is not shown in the fortnight to 19 Oct. However, variants with a national percentage of < 1% are not included so BA.3.2 is likely to still be circulating
October 30, 2025 at 9:57 AM
BA.3.2 made it to New Zealand 👀
Reposted by Stefan Pöhlmann
🧵Remember the preprint claiming SARS-CoV-2 has a "synthetic fingerprint"?
It said a restriction map was "extremely unlikely to have arisen by random evolution.”
I took its claims seriously.
The "synthetic fingerprint" hypothesis collapses. My new preprint explains why.
arxiv.org/abs/2510.23833
It said a restriction map was "extremely unlikely to have arisen by random evolution.”
I took its claims seriously.
The "synthetic fingerprint" hypothesis collapses. My new preprint explains why.
arxiv.org/abs/2510.23833
October 29, 2025 at 7:32 AM
🧵Remember the preprint claiming SARS-CoV-2 has a "synthetic fingerprint"?
It said a restriction map was "extremely unlikely to have arisen by random evolution.”
I took its claims seriously.
The "synthetic fingerprint" hypothesis collapses. My new preprint explains why.
arxiv.org/abs/2510.23833
It said a restriction map was "extremely unlikely to have arisen by random evolution.”
I took its claims seriously.
The "synthetic fingerprint" hypothesis collapses. My new preprint explains why.
arxiv.org/abs/2510.23833
1/4 New BA.3.2 sequences from South Africa and a fresh one from Western Australia (EPI_ISL_20228241) suggest this variant isn’t fading away just yet.
October 29, 2025 at 1:57 PM
1/4 New BA.3.2 sequences from South Africa and a fresh one from Western Australia (EPI_ISL_20228241) suggest this variant isn’t fading away just yet.
Reposted by Stefan Pöhlmann
Study: Gut infection and dysbiosis are hallmarks of severe SARS-CoV-2 variants
Published: 24 October 2025
www.nature.com/articles/s44...
Published: 24 October 2025
www.nature.com/articles/s44...
Gut infection and dysbiosis are hallmarks of severe SARS-CoV-2 variants - npj Viruses
npj Viruses - Gut infection and dysbiosis are hallmarks of severe SARS-CoV-2 variants
www.nature.com
October 28, 2025 at 11:23 PM
Study: Gut infection and dysbiosis are hallmarks of severe SARS-CoV-2 variants
Published: 24 October 2025
www.nature.com/articles/s44...
Published: 24 October 2025
www.nature.com/articles/s44...