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

🚨 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...

"BlueSky" Indeed.

Some charts for those who don't know the extent of the US public (and private) investment in research (particularly in biomedical research) compared to other countries and institutions. The destruction of the US' scientific institutions has global implications.

The US funds the bulk of biomedical research globally by far. It's not like other countries can simply take up the slack. The more likely: people leave research, new people don't become researchers. There is no happy ending. www.pbs.org/newshour/sho...

“Furin cleavage site”, that is. Just casually, and naturally, sitting there in one of the most evolutionarily active parts of the genome. Mystery solved.

The key thing re. Moderna and other companies in the same situation - when the next pandemic hits, which it will, they won't be there to save us. The same will be true for scientists and other responders who immediately stood up in the face of a devastating pandemic - they too will be gone.

Bottom line of systematic assessment of studies on Covid vaccinations/boosters: ~50% reduction of hospitalization, across all adults (not just older) who are not immunocompromised Real data on vaccine-induced myocarditis: occurred in 1-3 per 100,000 male adolescents www.nejm.org/doi/full/10....

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...

This is 💯 Origin inside baseball, but I've always been perplexed by Baric's claim that our "market" studies could not be correct because, according to him, the molecular timing of the pandemic in in October, not later. That was always wrong, but where did he get this October date from? Well... 🧵👇

I am going to be that annoying friend. Get your #COVID & #flu shots. There is little downside to getting immunized and it will spare you from being out sick, having to go to the doctor's office, hospitalization and yes, death. Too many people aren't stepping up to get the shots. Do it this weekend.

This is heartbreaking 💔 to read. Thank you 🙏 for sharing this with us. I want to apologize to you on behalf of real Americans. It’s a painful reminder that we must keep resisting these harmful policies so we don’t lose more people like @wwenneuro.bsky.social, whom we spent over a decade training.

As expected, unfortunately. If ever you needed a reason for never using GISAID ever again (as a data producer or data user - we're both), look no further. Time to move on to more trusted and transparent solutions.

For 61 years the #BBCWorldService has been broadcasting the latest in science via its weekly Science in Action programme. That dies in the next half hour, with this final edition, reflecting on the fall in trust in expertise driven by malign interests over recent years.

Exactly this. Reading all the headlines this morning, none of them mention this very key point - in fact, it’s the *only* point that matters.

🧵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

I am genuinely impressed by large language models - they can absorb disparate components of text into some consolidated view, they can produce extremely good language and - with the right model - translate pretty well between languages and they are an excellent text based UI for humans to use. But..

There is a very good reply to that OpEd by @philippmarkolin.bsky.social in today's Letters to the Editor in STAT www.statnews.com/2025/10/25/s...

Assistant Professor Alejandra Mendoza (@thepenkpanther.bsky.social) is building a lab culture where discovery—and people—can thrive. 🔬🌟 Honored with this year’s Outstanding Mentor Award, she shares her mentorship style, advice for young scientists, and love of antiques in Scripps Research Magazine.

I have enjoyed a number of Howtown's YouTube videos and I thought this one was particularly poignant. Yes, unfreezing super bugs from deep in the permafrost is a concern, however, compared to existing forces driving pandemic risk, it's miniscule. Also, think "lab leak"... youtu.be/zAfoNtADtoI?...

I really enjoyed this podcast with @cohenjon.bsky.social where he talks about his recent book and the broader, often strange, world of infectious diseases. With so many non-science journalists opining on topics they know little about, this is a breath of fresh air! www.kqed.org/forum/201010...

I beg to differ! If it's not a sequencing mistake—and it looks clean—one of these BA.3.2 has something completely novel in SARS-CoV-2 evolution: an FCS-adjacent deletion! One of the two QT repeats appears to have been deleted. I've never seen anything like this before. BA.3.2 is a different beast.

I am so tired of hearing the opinions on the origins of COVID-19 from people who have literally no germane expertise to opine on it. The authors claim not to have a strong opinion. Fine, but it’s clear that they favor lab leak over spillover and their focus on lab leakers as the real victims…

I got annoyed by this StatNews opinion piece 🔽 So I wrote about it: www.protagonist-science.com/p/teaching-t...

Had an entertaining discussion with Chris and Matt about my book, gurus, media manipulators and how it all fits with the current attacks on science and scientists by the MAGA movement and beyond. www.youtube.com/watch?v=zrsV...

Our paper on the phenomenon of persistence and latency in Ebola virus in an unobserved reservoir is finally out in preprint: www.biorxiv.org/content/10.1...

Happy to see this out finally -- my thanks to the brilliant team!

I am fascinated by how viruses evolve - and not just since #SARSCoV2 has shown us at the global stage how consequential virus evolution can be for us. In my new story in @science.org I got to explore how researchers are probing deeper into the past with old RNA virus genome. So a 🧪 thread…

And now NextStrain as well. Next up, will GISAID start charging open-source community tools to have access? That would completely shaft users who contributed to GISAID, where we never agreed to that and assumed GISAID would be good custodians of the data we contributed. They're not.

Expert here. The weird thing is I don't expect people to trust me (on my specialty) just because. Expertise is all about knowing the broader context of new results, what's clear & what's not, and most experts are happy to help people through this if they're interested in 'doing their own research'.

During these uncertain times, I’m very happy to see that my institution, @scripps.edu has an open tenure-track Assistant Professor position. Any field in Chemistry or Biology is welcome. I’d especially love to see fellow neuroscientists apply. Please repost! apply.interfolio.com/174756

There's a new BA.3.2.2 from South Africa today. For the most part, there's been little substantial change in BA.3.2 over the past few months—mostly synonymous mutations & very little happening in spike. But this new one has 3 spike mutations & looks quite interesting. 1/6

For more information about the Friday night massacre at CDC, I wrote up an analysis of who got terminated and what that means for public health. Grateful to @saveamericamvmt.bsky.social for supporting and amplifying. We are in really terrible trouble. rasmussenretorts.substack.com/p/the-death-...

I don’t know who needs to hear this but the CDC is being eviscerated right now. America is not going to have any kind of outbreak response capacity after tonight. Americans’ health data is no longer secure. Say goodbye to federal public health in any capacity. It’s a disaster. We won’t recover.

“Hey, Kristian, you should try a continuous glucose monitor” Puts on continuous glucose monitor Drinks beer “Stelo has detected a glucose spike” Rips off continuous glucose monitor. Such rubbish.

As we’re sending Mark off on his next adventure - after nine amazing years in the lab - I can also conclude that AI made our cakes go next level… Mark will be spending the next year(s?) biking through North, Central, and South America! Gipson in hand, I’m sure! 🚴‍♂️

“Anyone who does not have an autoimmune disease, that’s because of these regulatory T cells,” says Markus Feuerer, an immunologist at the Leibniz Institute for Immunotherapy. www.science.org/content/arti...

My PhD was on regulatory T cells (focused on elucidating their evolutionary history + exploiting Foxp3 for genetic therapeutic tricks), so happy to see work on them awarded the Nobel. Surprised not to see Sasha Rudensky + Fiona Powrie in place of a couple of others in this list...

“I fear for public health in our country.” Former CDC Chief Medical Officer @drdebhoury.bsky.social says that the national US public health system has been subjected to a “hostile takeover” and she’s right. We should all share her fears. Kennedy must go. www.theguardian.com/us-news/2025...

Interesting interview of @peterdaszak.bsky.social by @nicolascgrey.bsky.social on the personal consequences of having become a public villain in a set of conspiracy theories www.thisrobotdreaming.com/blog/intervi...

Dr. Jeanne Marrazzo, former Director of NIAID, is Fired by Health and Human Services Secretary Kennedy in Retaliation for Filing Whistleblower Complaint with the Office of Special Counsel bit.ly/4gRA3yx

Here’s an op-ed I wrote arguing to get back to a focus on the relevant facts when it comes to pandemic origins. I wrote it in response to a debate that’s played out over the last year in Norwegian media that rarely slows down to check what’s true and false.

organizing works 😎 It is the only thing that works in the moment. Admins won't work. Funders won't work. If you're in academia, get involved and support @aaup.org, support your scientific societies, and help them learn to fight and speak out. Collective organizing is the only approach that works.

#CDC is renaming #Mpox using the old misleading and stigmatizing term. #Mpox was set as global consensus by @who.int and there is no scientific or public health reason to go back to an outdated terminology. What we need is action: vaccination, awareness & equitable access, not backward naming.

Attenuation of the SARS-2 furin-cleavage site (FCS) continues apace. It's beginning to look as if some form of FCS-weakening mutation might well become fixed in the near future. Collectively, they are at ~12% globally—a totally unprecedented level—& rising quickly. 1/4

I'm not in any way trying to diminish this development—it's a very good thing!—but we should not be in a position where philanthropy is required to ensure people can access lifesaving medication.

When you made the deadline, but didn't quite stick the landing.

A bit like spiralling publication costs we need to start having a proper discussion around lab equipment servicing costs. These are often completely disproportionate to the cost of instrument and the service that is provided and seem to serve as a cash cow for vendors.

Immigrants, particularly on H1Bs, are the lifeblood of American innovation. If you wanted to hurt US competitiveness in the next century, I can think of few more effective ways than a move like this Even when found illegal, the mere intent will have irreparably harmed our future

Science: Gold standard science requires gold standard scholarship by Holden Thorp bit.ly/46K5A26