New preprint out on the origin of the SARS-CoV-2 BA.2.86 variant ('Pirola'). Our results challenge the widely held view that this variant emerged during a single long-term infection.
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biorxiv.org/content/10.110…
The BA.2.86 variant was first detected in July 2023. It carried >30 unusual mutations in the Spike protein. It rapidly spread and displaced all other SARS-CoV-2 lineages, and essentially all strains in circulation now are direct descendent of BA.2.86.
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idsociety.org/covid-19-real-…

I tend to like Americans, as individuals, and I believe the US has, on balance, been a force for good in the world over the last ~100 years, despite its recurrent overseas episodes of brutality. Though, I don't like where the US is going, both internally and internationally.
1/ As an example, the recent H5N1 outbreaks in cows suggest that the US administration has become deeply dysfunctional. I've worked with the CDC in the past. They were not always nice and friendly, but they were always on top of things.
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If and when Western liberal democracy goes down the drain, it won't be due to the silly antics of some vegan, gender-fluid, body-pierced, tree-hugging, pink-haired, face-masked, genocide-protesting students.
1/ Rather, I predict the fall of Western liberal democracy would be to blame on respectable, 'perma-outraged', "concerned", priggish, 'free-speech-for-me - but-not-for-thee' authoritarians in the thrall of the latest moral panic du jour - whatever idiocy may befall them next.
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In the early stages of the pandemic, I got very concerned about public health messaging aiming at terrorising people into submission rather than providing information that would help them to process the situation and try to do what's best for them.
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https://twitter.com/ballouxfrancois/status/1341776138608193542

I was particularly alarmed by the doomsday rhetoric of the 'eternal pandemic narrative' that was taking hold. I made many enemies among 'Covid-conscious' people for trying to push back against this dystopian vision.
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https://twitter.com/BallouxFrancois/status/1475839293490929670

New open access paper out in @NatureEcoEvo
TLDR:
- Humans pass on more viruses to other vertebrates than they do to us
- Generalist viruses (with broad host range) require fewer mutations to infect a novel host
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nature.com/articles/s4155… We started by downloading and analysing all publicly available viral genomes. One of our initial objectives was to test whether this data could be leveraged for pathogen surveillance. The answer at this stage is that it is likely too biased as a robust surveillance tool.
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Whatever the future ICJ/ICC rulings may bring, I'm now convinced that Israel's response to the Oct 7 atrocities qualifies as a genocide, in its intent, effect and result.
1/ This doesn't mean that the Gaza genocide is uniquely evil. Genocides happened throughout history, and are happening today in several places on earth, and will happen again in the future. "Never again" sadly is an empty slogan.
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This paper reports on 'passaged' SARS-CoV-2 variants passaged in 'humanised' mice (ie. carrying human ACE2).
I can see no justification for this work. There's essentially zero scientific interest in this experiment, but a tiny, but genuine, risk of it going wrong.
1/ Humanised mice are a meh model for the study of SARS-CoV-2 in humans. More fundamentally, we've known for ~150 years that 'passaging' a virus in a host makes it more virulent in said host. The study adds nothing new to our understanding on this.
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https://twitter.com/BallouxFrancois/status/1441559791156043780

Is Hamas an intolerant, theocratic, ethnocentric movement largely intent on genocide (among other things).
Hell yeah ...
1/ Is Hezbollah an intolerant, theocratic, ethnocentric movement largely intent on genocide (among other things).
Hell yeah ...
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A thread on civilian casualties in Gaza.
The Gazan MoH reports 22,000 recorded deaths so far (~70% children and women). This is likely a significant underestimate as many of those killed have not been accounted for to date (eg. still under rubble).
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reliefweb.int/report/occupie… We can produce estimates for the actual number of civilian deaths by extrapolating from UNRWA staff and healthcare worker casualties.
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Whether we believe Israel's 'special operation' in Gaza is rightful and justified, or not, essentially everyone should be able to agree that the Gaza operation, in the way it's been pursued by Israel, has been a total disaster.
1/ It's a disaster for the people being bombed and starved now, and for long-term prospects of peace in the Middle East.
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This piece is overlooking the most important point. If re-infections become less severe on average. This does not mean that no one will experience a more severe 2nd or 3rd infection that the first.
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Why Covid is still flooring some people
bbc.com/news/health-67… We have to think about this in terms of probability distributions around the mean severity for the 1st, 2nd, 3st ... infection, with individual cases drawn from those distributions .
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https://twitter.com/BallouxFrancois/status/1479524727630745603

A few comments on Mycoplasma pneumoniae.
It is an atypical bacterium as it has no cell wall. It causes generally mild respiratory infections ("walking pneumonia"). There's no good reason to refer to it as "white lung syndrome".
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cdc.gov/pneumonia/atyp… Mycoplasma pneumoniae infections happen all year round with a peak in winter. There is also a ~3-7 year periodicity, with a bigger epidemic roughly every ~4 year. This pattern predates the Covid-19 pandemic and has been observed over the past decades.
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gov.uk/government/pub…

I thought a lot about this graph - not because it came as a shock to me; it's in line with other data - but because it captures the complexity, and the often irrational perception of the relative impact of the pandemic on death rates, relative to other health challenges.
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https://twitter.com/ActuaryByDay/status/1716813737225793738

The pandemic had a significant impact on deaths rates, everywhere, largely irrespectively of the stringency of the suppression / mitigation enforced locally.
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If I were a doomer, and I'd monetise my Twitter takes, I'd predict:
- IDF enters Gaza, gets bogged down, suffers heavy casualties, and causes huge civilian loss of life
- Hezbollah enters conflict, West Bank / East Jerusalem riot, bored Talibans + other nutters get involved
1/ - Ukraine counter-offensive against Russia falters due to reduced US support due to redirection of help to Middle East
- Hindu nationalist support for Israel further poisons relationship with Pakistan, and blows up up into regional war
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SARS-CoV-2 does NOT cause immunodeficiency. Other viruses do (eg. HIV or measles).

That does not mean it never causes post-infection immunological sequelea, such as long-term inflammation, in particular in people who have been very ill.
1/ SARS-CoV-2 is NOT neurotropic. Other viruses are (e.g. influenza or Varicella zoster virus).

That does not mean it can never be found in the brain or never causes neurological symptoms, in particular in people who have been very ill.
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This study, which is currently making the rounds in the media, looked for organ damage in 259 people who had been hospitalised for Covid, and compared them to 52 younger, leaner, fitter, healthier controls from the community ...
1/ Now, it is expected that a significant fraction of patients hospitalised for Covid experience severe sequelae, in particular if they were infected in the pre-vaccine, pre-omicron stages of the pandemic.
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The Joint Committee on Vaccination and Immunisation (JCVI) advising on UK vaccine policy published its rationale for 2023 Covid vaccine boosters to be offered to everyone aged ≥65, to those otherwise at high risk to Covid, and to their close contacts.
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gov.uk/government/pub… This represents ~25-26M people who will be eligible for the winter 2023 Covid booster. This 'at increased risk group' is estimated to represent ~99% of expected future hospitalisations and deaths due to Covid.
The guidance is in line with other European countries.
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I'm getting very annoyed with the neurotic focus on Covid by a fraction of health professionals. To be brutally honest, I consider those who obsess over Covid as the sole threat to health, unless they're professional Covid grifters, as 'public health minimisers', at best.
1/ The Covid pandemic was a severe health crisis. It could be anticipated in early 2020, and it was nasty. The globally fairly poor response to it didn't help, but it's largely over now, even the WHO says so, and we're facing worse challenges right now.
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https://twitter.com/BallouxFrancois/status/1238837160779841537

This article is puzzling. While it engages with an actual problem, medical disinformation indeed kills, it does so from a 'scientific fundamentalist' perspective. It posits there's a dogma, an unquestionable truth decreed by the 'church of science'.
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jamanetwork.com/journals/jaman… And, from this premise, it follows that those who question any aspect of the dogma, however minor, or whose views are not canon, need to be chastised as heretics or apostates to science. It is, ironically, one of the least scientific articles I've ever come across.
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I took a mini-break from Twitter because I felt I had to think about the 'Proximal Origins' (PO) saga, without being distracted by the constant Twitter noise.

Having thought about it more, my take is that it is a disaster and a tragedy.
1/ Actually, I believe it is largely a tragedy in the 'Greek theatre' sense of it, where the main protagonist(s) believe they can outwit fate because they’re clever and they know better, and eventually they bring doom and opprobrium on themselves through their own actions.
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Interesting article in the NYT.
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https://twitter.com/DLeonhardt/status/1680915764126138370

I made essentially the same arguments in a thread three months ago (arguably not from a US centric perspective).
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https://twitter.com/BallouxFrancois/status/1642962788740997120