Sebastian Duchene

In analyses of ancient HBV, we argue that prior sensitivity is more important than tests of temporal signal. We provide some guidelines for assessing the reliability of estimates derived form the molecular clock. (3/3)

We describe the relationship between two fundamental concepts in molecular evolution, the phylodynamic threshold and measurably evolving populations, and the role of tests of temporal signal. (2/3)

I thought I’d share a recent article in collaboration with Ariane Weber and Sanni Översti ( @mpi) , and Julia Kende (
@pasteur.fr).

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

Summary in replies (1/3)

In analyses of ancient HBV, we argue that prior sensitivity is more important than tests of temporal signal. We provide some guidelines for assessing the reliability of estimates derived form the molecular clock. (3/3)

We describe the relationship between two fundamental concepts in molecular evolution, the phylodynamic threshold and measurably evolving populations, and the role of tests of temporal signal. (2/3)

The Next Pandemic? A Scenario. It began with a chimpanzee-trekking tour of a remote forest in Uganda and ended with the outbreak of a deadly new disease. And all because of health cuts and the disruption of a wild animal habitat.

If you have not yet, it is so worth reading (and re-reading) this post by medical historian @honigsbaum.bsky.social because it is so hauntingly realistic and well researched it makes your nails curl.

The Next Pandemic? A Scenario. open.substack.com/pub/markhoni...

Postdoctoral positions in epidemic mathematical/statistical modelling - Research Job description We are recruiting postdocs to contribute to research projects in the Mathematical Modelling of Infectious Diseases Unit, at Institut Pasteur in Paris. The candidates will be expected t...

New postdoc positions with a number of exciting epidemic modelling projects opening in our Unit at @pasteur.fr in beautiful Paris. Deadline for applications: 26th June.
research.pasteur.fr/en/job/postd...

I'm super proud to share this piece of work, led by @nrascovan.bsky.social, @avanzich.bsky.social and @marialopopolo.bsky.social. See details in Maria's post here:

You might be wondering why we haven't updated outbreak.info for months.

Well, the reason is that GISAID cut our access in January - as they did others. Without telling us.

After a ♾️ back and forth, that is now permanent.

More on that soon - and why GISAID should not be trusted with critical data.

For simple estimands, treating everything as Gaussian works unreasonably well! But lots to learn from less simple estimands. @avehtari.bsky.social has a nice case study examining this (part of our forthcoming book on workflow) users.aalto.fi/~ave/casestu...

The recency and geographical origins of the bat viruses ancestral to SARS-CoV and SARS-CoV-2 Recombination-aware evolutionary analyses of the entire genomes of SARS-CoV-1-like and SARS-CoV-2-like viruses indicate that SARS-CoV-1 and SARS-CoV-2 descend from bat coronaviruses that circulated as...

Sooo happy to finally have this one published!! (3 years in the making… 👀) A comprehensive investigation into the recency and geographical origins of both SARS-CoVs that spilled to humans in the past few decades, now in @cp-cell.bsky.social www.cell.com/cell/fulltex...