Archive for SARS-CoV-2

Nature squeakbits [26 February 2026]

Posted in Books, pictures, Running, Travel with tags , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , on April 16, 2026 by xi'an

In this issue of Nature, uncovering the fundamental (and Ig-Nobel worth) reason why basketball shoes are squeaking, the reason being a shockwave travelling through the sole!, two tribunes against nuclear testing and “must & should” towards a successor to the START treaty… While we should ask & act for a global and if not unilateral nuclear disarmament! This alas coïncides with France announcing the increase of its nuclear arsenal and the extension of its “umbrella” to several EU countries…

And another coverage of the deplorable Trump administration dismantling the biodefense and pandemic preparedness branches of the US NIAID, presumably a late under-the-belt jab at the national institute Anthony Fauci directed for 38 years. Meaning one of the forefronts for pandemic research and vaccine development has been dismantled. Plus the US EPA revoking the 2009 statement that climate change is endangering the US population and removing greenhouse-gas emission rules. In tune with the Drill, baby, drill! motto of the Trump supporters more interested in their short-term profits than in the long-term (no-)future of the country. Paradoxically sitting in the same issue as a comment calling for a policy-making assessment of avoidable climate-change risks. Illustrated by London’s drownin’ below

And a summary of their conclusions from 23 of the 27 members (from 27 countries) of the Scientific Advisory Group for the Origin of Novel Pathogens for the WHO. After 3.5 years of debate on the origin of COVID-19! Four hypotheses are examined and other hoaxes and conspiracies are debunked.

Another political entry about the EU and its Horizon Europe programme (that is funding my ERC Synergy grant) baring (researchers from) Chinese research organisations from applying for its grants in sensitive methodologies, in order to prevent “the undesired transfer of IP”. Following similar and earlier actions in the US with the (newspeak!) China Initiative launched by Trump 1.0 that turned into a witch hunt.

An exciting 228 metres of rock and mud providing a window on the past 23 million year weather. Obtained from the West Antarctica Ice Sheet.

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Nature snapshots

Posted in Books, Kids, pictures, Statistics, University life with tags , , , , , , , , , , , , , , , , on July 13, 2024 by xi'an

As I was waiting for my wife when visiting the Doges’ Palace in Venice last week, I read most of one of the issues of Nature I had brought with me to the Serenissima (after they arrived by bulk the week before for unclear reasons).

  • One of the editorials is about AI-assisted design of mathematical conjectures. Reminding me of grant panels I took part in where candidates in pure maths were often focussing on solving one or many conjectures, as opposed to more applied branches (like statistics).
  • Two entries about France, one about Macron’s idea of a European DARPA, unlikely to convince European partners after his calling most unnecessarily an election and bringing the extreme-right to its apex since the Vichy régime. Another one about the super mega campus Paris-Saclay unable to settle on a form of leadership and hence elect a president. Federalist versus centralised… Once again, thanks to Macron’s reckless gamble, his current Ministry for Higher Education may be in need of a position next month and could return to heading the campus.
  • Worrying coverage of bird flu in US cows (not yet pigs on the wing but worrying enough) and of zombie cells that should have died and that new treatments can fight way better.
  • A reflection on coming up with a treaty against AI weapons with autonomous kill decisions but isn’t it too late?!
  • Building design that would avoid total collapse of a failing building, as in South Florida four years ago. But solely for new ones, unfortunately.  (And the connection with lizards escapes me, except for managing to escape by loosing a tail…)
  • A biography of Daniel Kahneman, decision-theorist, 2002 Nobel economics (aka Bank of Sweden) Prize, author of Thinking, Slow and Fast, and spending the WW II in occupied France hiding from round-ups by the Vichy police.

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best science graphic of the week?!

Posted in Statistics with tags , , , , , , on January 24, 2023 by xi'an

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Bayesian phylogeographic inference of SARS-CoV-2

Posted in Books, Statistics, Travel, University life with tags , , , , , , , , , , , , , , , , , on December 14, 2020 by xi'an

Nature Communications of 10 October has a paper by Philippe Lemey et al. (incl. Marc Suchard) on including travel history and removing sampling bias on the study of the virus spread. (Which I was asked to review for a CNRS COVID watch platform, Bibliovid.)

The data is made of curated genomes available in GISAID on March 10, that is, before lockdown even started in France. With (trustworthy?) travel history data for over 20% of the sampled patients. (And an unwelcome reminder that Hong Kong is part of China, at a time of repression and “mainlandisation” by the CCP.)

“we model a discrete diffusion process between 44 locations within China, including 13 provinces, one municipality (Beijing), and one special administrative area (Hong Kong). We fit a generalized linear model (GLM) parameterization of the discrete diffusion process…”

The diffusion is actually a continuous-time Markov process, with a phylogeny that incorporates nodes associated with location. The Bayesian analysis of the model is made by MCMC, since, contrary to ABC, the likelihood can be computed by Felsenstein’s pruning algorithm. The covariates are used to calibrate the Markov process transitions between locations. The paper also includes a posterior predictive accuracy assessment.

“…we generate Markov jump estimates of the transition histories that are averaged over the entire posterior in our Bayesian inference.”

In particular the paper describes “travel-aware reconstruction” analyses that track the spatial path followed by a virus until collection, as below. The top graph represents the posterior probability distribution of this path.Given the lack of representativity, the authors also develop an additional “approach that adds unsampled taxa to assess the sensitivity of inferences to sampling bias”, although it mostly reflects the assumptions made in producing the artificial data. (With a possible connection with ABC?). If I understood correctly, they added 458 taxa for 14 locations,

An interesting opening made in the conclusion about the scalability of the approach:

“With the large number of SARS-CoV-2 genomes now available, the question arises how scalable the incorporation of un-sampled taxa will be. For computationally expensive Bayesian inferences, the approach may need to go hand in hand with down-sampling procedures or more detailed examination of specific sub-lineages.”

In the end, I find it hard, as with other COVID-related papers I read, to check how much the limitations, errors, truncations, &tc., attached with the data at hand impact the validation of this philogeographic reconstruction, and how the model can help further than reconstructing histories of contamination at the (relatively) early stage.

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