New preprint featuring CCDD authors Léa Cavalli, @bradfordptaylor.bsky.social, Beau Schaeffer, and @billhanage.bsky.social: SARS-CoV-2 Intra-host Variation Shows Evidence of Transmission and Convergent Evolution in a University Surveillance Cohort. Read it at bit.ly/4pLO4BO

Can't pass ACA extensions but don't worry. We're going to probe whether Lyme disease is a US bioweapon instead.

💾 Prokka 1.15.6 is released! This is the last major release of Prokka. But don't be sad, because @oschwengers.bsky.social already has an excellent replacement called Bakta you can migrate to. #bioinformatics #microbiology #genomics github.com/tseemann/pro...

And from what I’ve seen the inquiry has focused on early 2020. I’d also like to know more about decision making in November/december 2020 when the devastating alpha variant (B.1.1.7) emerged. Because that was a failed opportunity to implement the costly lessons from the spring

I’m curious about where this “too early” advice came from, and the evidence base for it www.theguardian.com/uk-news/live...

ICYMI: Last night @jeremyfaust.bsky.social revealed that Drs. Makary and Prasad of the FDA have lied to all of us with their claims that COVID19 vaccines “killed 10 children”. The scientists that did the work found that there were ZERO deaths that they could be certain were caused by the vaccines.

Vaccines cause adults

Given recent evidence free pronouncements from FDA it’s interesting to see this *evidence* for the effectiveness of Covid vaccines at preventing visits to the emergency room or urgent care *in children* Especially the 76% effectiveness in the 9mo-4yrs age group www.cdc.gov/mmwr/volumes...

A student just shared this with me and it is AWESOME hadley.github.io/genzplyr/

Yes. 💯 times yes www.statnews.com/2025/12/10/a...

New publication from CCDD’s Léa Cavalli, @billhanage.bsky.social, & collaborators: bit.ly/4rF0Rr3

This is fascinating. Note the large variance around terms like “likely” or “probable” and their antonyms

Photographer Martin Parr just passed. If you don't know his work, the Guardian has a really nice introduction here. h/t @wvschaik.bsky.social

Imagine you're overseeing the termination of clinical trials, the destruction of people's livelihoods, the dismantling of scientific research in the US, and you're complaining that Twitter didn't give you a blue check 4 years ago.

This is the fringiest of fringe theories and complete and utter nonsense. Lyme has been around a lot longer than there have been labs, and makary should have the common sense to do the tiniest amt of fact checking (if he actually believes this). It’s like a violation of both oath and conscience.

Friends, Yesterday and today, I watched many hours of the CDC’s meeting of the Advisory Committee on Immunization Practices (ACIP). It was painful. But we learned a lot. That bad news is that our kids are going to pay the price for RFK jr’s views. insidemedicine.substack.com/p/analysis-o...

This is astonishing. All AI bar one shot. www.nowness.com/series/nowne...

ICE raided a James Beard award winning restaurant & because the chef/owner was prepared, left emptyhanded:

The health of Americans is at risk as those in power abandon evidence and process, and elevate anecdote and rhetoric in their place. Excellent article (if sad to read) www.statnews.com/2025/12/03/a...

Essential reading if you care about the health of scientific inquiry in the US www.nytimes.com/interactive/...

Can you guess which of these quotes are about COVID, and which about the 1918 influenza pandemic? Answers here: kucharski.substack.com/p/how-will-h...

Predicting headlines tomorrow about how #Arsenal have lost their set piece mojo

More from the UK on Baroness Hallett’s report. And yes it was obvious what was coming

Superb take on the UK govt’s pandemic response and what it signifies for politics in an emergency. It chimes with a lot of my own recollections and knowledge of expert discussions at the time. But I did not realise @rory-stewart.bsky.social had been such an advocate for a more sensible policy

After Canada now the US is on course to lose measles elimination status. The TX outbreak that started in jan this year has spread to AZ and UT with evidence of multiple transmission chains, some of which have not been chased down so there may well be more. www.nytimes.com/2025/11/17/h...

This, from @maciekboni.bsky.social, is a sobering reminder of just how bad things were five years ago. But it’s also five years since we got the trial results which signposted a way out of the nightmare. Warp speed was a huge success and we should not forget maciekboni.substack.com/p/covids-lea...

I never bothered reading The Tipping Point because my BS detector was off the chart. Sounds like that was the right choice

Just think, this was only 2009… youtu.be/jIWj3tI-DXg

Willing to bet that the images made with AI now will in a few years look as convincing as the special effects in Star Trek (the original) If they’re lucky

I’m reading Moby Dick, and I keeps hearing Ishmael as laszlo from what we do in the shadows and a) can’t stop and b) wonder if this was always intended

open.substack.com/pub/pauloffi... In the midst of a measles epidemic that killed 3 people, RFK Jr. reminds us that vaccines don't save lives.

“It’s hard to explain how the Secretary can think that the President deserves the Nobel Peace Prize for this, while at the same time believing that these vaccines are the most harmful that have ever been made” Me on mRNA vaccines hsph.harvard.edu/news/slashin...

This is the official communication from the FDA to physicians on acetaminophen use in pregnancy. - They acknowledge the lack of a causal link with autism - Essentially tell physicians to keep doing what we've been doing anyway It's very different from the press conference. Pass it on.

My understanding is that the situation for H1B visa holders outside the US today is urgent: if a current H-1B holder seeks entry into the U.S. after 12:01 a.m. EDT on September 21, 2025, it is too late to avoid the fee—entry will be restricted without the newly-imposed $100,000 employer payment.

There have been some… extensive changes to this web page. This thread will include resources to help understand them cdc.gov/about/cdc/in... 1/2

Crikey atomic mass is a hard concept to explain

“If a new pandemic began today, mRNA vaccines are currently the only type of vaccine that could be developed quickly enough to disrupt its spread” www.cnn.com/2025/09/10/h...

Recently we published a report describing what I *think* is the longest known continuous case of Covid-19 to date. For some reason I've not found time to post about it. While I get around to doing so you can read a summary here 👇 www.contagionlive.com/view/persist...

This astonishing feat has been dismissed across the political spectrum Some are upset about things the administration did/did not do Warp speed still delivered and deserves recognition Others applaud things the administration did/did not do Warp speed still delivered and deserves recognition

Imagine doing something that saved quite literally millions of lives That’s a summary of Operation Warp Speed, started under the first Trump Administration. And everyone involved including the president should be proud Vaccines don’t care how you vote

Operation Warp Speed was arguably one of the most successful policy initiatives in recent history, accelerating vaccine delivery that saved millions of lives. It’s remarkable to see some now urging the leaders who backed it to disown the achievement.

Well who’da thunk it?

Discussions grounded in science and clear that pandemic response involves hard choices, are a vital part of how we *should* respond to Covid. Even if they are thin on the ground right now

Thanks to Braver Angels & David Zweig for engaging in this debate on the primary effects of the first year of the pandemic (540,000 deaths), the secondary effects (one year of learning loss for kids, unemployment, isolation), and things that we did right and wrong 1/ www.youtube.com/watch?v=59Gg...

Excellent primer on Tylenol (acetaminophen/paracetamol) in pregnancy from @jeremyfaust.bsky.social which just happens to quote me insidemedicine.substack.com/p/tylenol-ha...

Key “His supporters don’t trust the agencies he oversees, and his detractors don’t trust him.” Public Health is certainly a political issue - it is about how much we invest in human lives and wellbeing, so how could it not be? But it should never be *politicized* www.nytimes.com/2025/09/07/u...

And we certainly know that millions of lives have been *saved* by the very vaccines that the Secretary has singled out for attack

"Reality is that which, when you stop believing in it, doesn't go away." - Philip K. Dick

The point of this is that freedom and reality are connected. And that those who would deprive us of freedom are frightened of reality because it will be there after they are gone