Ancestral sequence reconstruction analysis indicates the S1/S2 insertion in the SARS-CoV-2 spike gene likely interrupted a codon Abstract. The genome of the SARS-CoV-2 virus has a 12-nucleotide insertion that produced a furin cleavage site at the S1/S2 junction of its spike protein.

I still wonder whether it was ever in a bat and not picked up after bat -> (non-human) mammal : it looks like this likely interrupted a codon 👇

academic.oup.com/ve/advance-a...

it's a population graph (filled area type) where year is the x axis and population in millions is the Y axis. It shows a steep decline from 1520 to 1545m and by 1576, the population has bottomed out. "Collapse of population in Mexico during the 16th century, attributed in part to repeated cocoliztli epidemics" "Figure 1. The 16th-century population collapse in Mexico, based on estimates of Cook and Simpson (1). The 1545 and 1576 cocoliztli epidemics appear to have been hemorrhagic fevers caused by an indigenous viral agent and aggravated by unusual climatic conditions. The Mexican population did not recover to pre-Hispanic levels until the 20th century."

In 1519, the year Spaniards arrived in Mexico, the population there was between 15 - 30 million.

By 1600, that dwindled to 2 million.

For lots of reasons, but as much as 70% of those deaths were the result of an UNKNOWN hemorrhagic fever.

Let's talk about the mystery of the COCOLIZTLI epidemics.

22-Oct 2022 headline from The Economist A new paper claims SARS-CoV-2 bears signs of genetic engineering But it has yet to be peer reviewed. And others strongly disagree

🧵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

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...

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...

Good science needs time.

Finally, a functional furin cleavage site found in the S1/S2 junction of a bat coronavirus. 🧪

www.biorxiv.org/content/10.1...

Women in the US are now being forced to have babies and carry in the most painful way possible.

The #autism announcement yesterday was not based at all on science. The correlations found in that 1 study are not sound: the follow up times were unbalanced, leading to bias and misleading associations.

Occultation! Venus is about to disappear behind the 5% lit Moon! #astronomy #astrophotography #Occultation #Moon #Venus @stormhour.com @photohour.bsky.social 1/2

My favorite thing: one of the CDC's COVID-19 risk factors is vaccination status, so one has an increased risk when discussing the COVID-19 vaccine prior to being vaccinated.

So meta! And so meaningless from the ACIP.

This #ACIP is not helping Americans.

Listening to the ACIP meeting in the background....

When voting, there were several comments about postponing the Hep B vote until a future meeting, but the motion was actually that the Hep B vote be postponed indefinitely.

Several times, though I don't know the cause - could be supply, demand, or just unrelated.

Thanks for posting this. I'm Type 1 and very much need one. It's also good for this craze to not catch on and not disturb the supply/distribution for those who truly need them.

Excellent news and hard work pays off - one of our studies, "Health outcomes of women with Gestational Diabetes Mellitus in North West London: a 10-year longitudinal study" accepted in BMJ Public Health 🥳🎉

Scientists Begin Testing Bird Flu Vaccine in Seals

#Birdflu still circulating: Scientists are testing a #birdflu vaccine in seals. If results show promise, the shots could be given to endangered Hawaiian monk seals. #H5N1 birdflu virus has devastated marine mammals globally. It tore thru Argentina's Valdés Peninsula killing ~17,400 seal pups 👇

Flags should have been at half mast at some point for those lost from the dropped PEPFAR programs.

My latest for @jama.com:

@zachhensel.bsky.social and I have a new paper on the origin of SARS-CoV-2! 🧪

There are a lot of reviews on the topic already, so we tried to do something different: characterize "lab leak" scenarios, and directly address those on SARS-CoV-2's furin cleavage site.▫️1/9

doi.org/10.5802/crbi...

It's good that you've experienced it - it's quite a different experience as a Type 1. One of the drawbacks with widespread use now is having several assume I don't need it (this has happened at the gym a few times).

Our 2021 review on COVID #vaccines was open access and provides a full report of effectiveness. Thanks to @carlzimmer.com and @apoorvanyt.bsky.social for their terrific article in NYT 👍

www.nature.com/articles/s41...

www.nytimes.com/2025/09/02/h...

How RFK Jr.’s misguided science on mRNA vaccines is shaping policy − a vaccine expert examines the false claims Chaos at the CDC and the sharp move away from mRNA vaccines has public health experts alarmed.

There was a slew of false statements made about COVID19 mRNA vaccines yesterday.

I can’t recommend highly enough this article from May by Dr. Deborah Fuller to clear up a lot of the chaff.

10 - I couldn't see the maps so guessed on that one!

Exclusive | RFK Jr., HHS to Link Autism to Tylenol Use in Pregnancy and Folate Deficiencies Kennedy’s autism report, touted by Trump, will suggest that using the pain reliever during pregnancy might be linked to the developmental disorder.

Show me these data and I will find you at least 30 confounders. The language will be most important, particularly how strong (that is, poor) are the report's claims of causality.

www.wsj.com/health/healt...

Kennedy described Geier's actions more as establishing a call for expressions of interest for others, rather than him taking on a single study, despite Geier himself having been granted sole access to a vast database.

So, what is Geier (employee? subcontractor?) doing at the HHS?

Lots of disturbing takeaways from the RFK Jr hearing, most prominently that he's listening only to Bhattacharya and Makary - non-experts - about vaccines rather than others (or reading any papers).

However, there's another major question:

RFK Jr., American Psycho He needs to go. Now.

He is a predator. He will prey upon the nation and the world if he is not stopped.

Necessary reading from @gregggonsalves.bsky.social

www.thenation.com/article/soci...

The 16th Ebola Virus Disease Outbreak in Bulape Health Zone, Kasai, Democratic Republic of the Congo: A new spillover event from an unknown reservoir host Background The Democratic Republic of the Congo (DRC) is currently facing concurrent outbreaks including mpox, cholera and malaria (1-4). The Ministry of Public Health, DRC has declared the 16th Ebola...

In under 24h following the newly identified outbreak of #Ebola in the DRC, the virus has been isolated, sequenced and the virus sequence data made publicly available.
virological.org/t/the-16th-e...

RFK Jr.’s tenure as HHS Secretary has been a disgrace. He’s destroying our public health system and putting millions of lives at risk.

He is wholly unfit to serve in this role and should resign immediately.

Opinion | Robert F. Kennedy Jr., the CDC and Me I was fired after 29 days because I held the line and insisted on rigorous scientific review.

gift link to dr. susan monarez’s piece in the wall street journal this morning.

Strange that they're still forcing kids to go to school.

State Plans to End School Vax Mandates, First to Do So Florida's controversial surgeon general compared the requirements to 'slavery'

Florida plans to end school vaccination mandates, the first to do so. The state's controversial surgeon general compared the requirements to "slavery." Joseph Ladapo says "people have a right to make their own decisions, informed decisions"👇

Your periodic reminder that mRNA vaccines are a scientific and public health game-changer. Those that have been approved have passed stringent efficacy and safety checks. They protect you and your child against potentially fatal diseases. You may, however, get a sore arm.