We show we can quantify the relative fitness of each lineage and identify genetic changes linked to the emergence of new, fitter lineages. This provides testable biological hypotheses about genetic variants in each pathogen that are driving the changes in population fitness of that pathogen. 8/n - ThreadSky

noemielefrancq.bsky.social • 58 days ago

We show we can quantify the relative fitness of each lineage and identify genetic changes linked to the emergence of new, fitter lineages. This provides testable biological hypotheses about genetic variants in each pathogen that are driving the changes in population fitness of that pathogen. 8/n

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aakhmetz.bsky.social•51 days ago

Noémie, thank you for your great work! I wonder, if I investigate the spread of TB at given location and have a co-circulating multi-drug resistant TB and non-resistant TB, would this approach and phylogeny allow me to estimate (=quantify) the relative fitness of MDR-TB vs non-resistant TB?

noemielefrancq.bsky.social•51 days ago

Yes, but the method will even go beyond simply MDR/non-MDR and find what precise clades are spreading differently in your population. That's exactly what we did in the paper for the dataset of Samara, Russia.

gpollara.bsky.social•57 days ago

Fabulous work and very interested in this implication. A sort of reverse discovery, trying to understand what drives changes in pathogen fitness.

noemielefrancq.bsky.social•58 days ago

We tested phylowave using a simulation study. Its ability to recover lineages depends on the time between emergence and the dates of sequences, with lineages with only small fitness advantages requiring sequences covering longer time periods, as expected. 9/n

noemielefrancq.bsky.social•58 days ago

Importantly, phylowave is robust to uneven and limited observation. For example, we tested the framework on subsampled SARS-CoV-2 phylogenies of only 150 sequences and were still able to detect nearly all the lineages.

This makes phylowave applicable to a wide range of pathogens! 10/n

noemielefrancq.bsky.social•58 days ago

Phylowave code is available on GitHub. While it is not packaged, it comes with a full readme and description of best practices. All you need to start is R and a timed phylogeny. If you have any questions or suggestions, feel free to open an issue/drop me a message! 11/n
https://buff.ly/3PEj32l

noemielefrancq.bsky.social•58 days ago

Developing this was a journey! Many thanks to the people who helped me along the way! Loréna Duret, super master student, my supervisors @hsalje.bsky.social and @julianparkhill.bsky.social and colleagues at Institut Pasteur @sylvainbrisse.bsky.social Valérie Bouchez. 12/n

noemielefrancq.bsky.social•58 days ago

I am now working @ethzurich.bsky.social @ETH_BSSE with @tanjastadler.bsky.social and @neher.io with an ETH fellowship to develop more phylodynamic frameworks for large-scale datasets. Very excited to start this new year! 13/n

gpollara.bsky.social•57 days ago

@skyview.social unroll

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