H5N1 bird flu has a mortality rate close to 100% in chicken. When the virus is detected in a chicken farm, all animals are being euthanised to reduce their suffering and limit the risk of spread to other animals and humans.
1/ Culling all the chicken in a farm where H5N1 is circulating is the correct response, epidemiologically, ethically and morally, and it is standard procedure globally.
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This is a brilliant - if technical and terse - reanalysis of the modelling that led to the double spillover claims for SARS-CoV-2. I feel it is fair to say that it puts to rest, once for all, the previous evidence published in favour of a multiple spillover scenario.
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https://twitter.com/nizzaneela/status/1895301911982776475

That said, in the grand scheme of things, it actually doesn't matter that much - besides correcting the scientific record.
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I've been challenged to provide evidence for the IDF sniping kids, and torture/rape of prisoners.
Bear with me.
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https://twitter.com/BallouxFrancois/status/1874844354021646554

Children sniped 1
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edition.cnn.com/2024/07/26/wor…

The genocide in Gaza is awful. Though, it is not unique in terms of human suffering with horrible atrocities being committed right now in other places (e.g. Syria, the Congo or Sudan). This raises the question as to why Gaza gets so much more attention.
1/ One answer is that Israel is held to higher standards than say the Taliban or the Janjaweed. This is obviously true, but it is also fair and should be uncontroversial. Israel is treated as a liberal democracy, and benefits from all the advantages that come with such a status.
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New preprint. We investigated if it is possible to predict what SARS-CoV-2 mutations will emerge and spread in the future.
Somewhat surprisingly, we can to a large extent predict which mutations will become dominant, and which ones won't.
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biorxiv.org/content/10.110… We analysed ~15M genomes. Of the ~200k possible (αα) mutations, we've seen about half so far, with the rate of new mutations tapering off. We computed a range of physicochemical metrics for all mutations, and define mutational fitness by their frequency in the population.
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This 'scientific' article which incidentally is a total mess, makes the bizarre argument that the principle of proportionality, a central tenet of the laws of war, should be subordinated to a party in a conflict feeling they are the 'good guys'.
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tandfonline.com/doi/full/10.10… This is a remarkably stupid and immoral argument which goes against any, if not all, value(s) of international law, which is there largely to protect the civilian population, and innocents, against the exactions of self-righteous génocidaires.
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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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