Simon Dellicour

The BEAST X logo - an octopus wrapping its noodley appendages round the letter X.

BEAST X v10.5.0 finally released – you can't just do beta releases forever. github.com/beast-dev/be...

Details and instructions for installing on the BEAST website: beast.community

Our study on the development and comparative performance of novel landscape phylogeography approaches has now been published in @pnas.org: lnkd.in/d5yuYwk6. A study led at the @ulbruxelles.bsky.social and @kuleuvenuniversity.bsky.social, and mainly conducted with the support of the F.R.S.-FNRS

Phylogenetic insights into the transmission dynamics of arthropod-borne viruses - Nature Reviews Genetics Arthropod-borne viruses have a substantial impact on global health, with climate change and urbanization exacerbating their emergence. Integrating genomic surveillance and phylogenetic models with eco...

Phylogenetic insights into the transmission dynamics of arthropod-borne viruses

www.nature.com/articles/s41...

Great work by Verity Hill and team

Interested in using phylogenetics to study arboviruses? Our new review in @natrevgenet.nature.com‬ by @viralverity.bsky.social‬, @sdellicour.bsky.social‬, and Marta Giovanetti has you covered!

📖 👉 rdcu.be/epH2U

Short 🧵

#SFP2025 is just starting. Lets talk about plant pathology!

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...

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...

Comparative phylogeography and recombination patterns of SARS CoV-1 and SARS CoV-2 related viruses. Both are derived from recent recombinations in their host bats, and then emerged in human hundreds of miles from their wild reservoirs.

www.cell.com/cell/fulltex...

Nouvelle étude sur l’origine géographique des virus de chauve-souris ancêtres des virus responsables du SRAS et de la COVID-19 - Actualités de l'ULB

🦇🦠 Nouvelle étude sur l’origine des virus de chauve-souris liés au SRAS et à la COVID-19 : le SARS-CoV-2 serait arrivé à Wuhan trop vite pour avoir été transporté naturellement par des chauves-souris.

👉 bit.ly/4m3Fb4Y
@mariusgilbert.bsky.social @sdellicour.bsky.social

A study performed with Fabiana Gámbaro, @maudejacquot.bsky.social, @lequimelab.eu, @guybaele.bsky.social, @mariusgilbert.bsky.social, Oliver Pybus, @msuchard.bsky.social, and @lemeylab.bsky.social - 8/8

GitHub - sdellicour/seraphim: R package for studying environmental rasters and phylogenetic informed movements (Dellicour et al. 2016, Bioinformatics; Dellicour et al. 2016, BMC Bioinf.) R package for studying environmental rasters and phylogenetic informed movements (Dellicour et al. 2016, Bioinformatics; Dellicour et al. 2016, BMC Bioinf.) - sdellicour/seraphim

Continuous phylogeographic simulations and landscape phylogeographic analyses were all conducted using new functions implemented in the R package “seraphim” available at github.com/sdellicour/s..., which now also comes with new dedicated tutorials. - 7/8

Our open-source methods are all available on GitHub (github.com/sdellicour/l...) and can be used to investigate the drivers of viral spread, with potential benefits for a better understanding of virus ecology and epidemiology. - 6/8

The results of our analyses enable us to formulate clear guidelines for the use of three complementary landscape phylogeographic approaches that have sufficient statistical power and low rates of false positives. - 5/8

that can test the impact of continuous environmental factors on the diffusion velocity of viral lineages. In order to evaluate the different methods, we also implemented two simulation frameworks to test and compare their statistical performance. - 4/8

In particular, landscape phylogeographic approaches use phylogeographic reconstructions to investigate the impact of environmental factors on the spatial spread of viruses. What we did in this study: we improved existing approaches and developed three novel landscape phylogeographic methods - 3/8

The context: the fast rate of evolution in RNA viruses implies that their evolutionary and ecological processes occur on the same time scale. Genome sequences of these pathogens can therefore contain information about the processes that govern their transmission and dispersal. - 2/8

Comparative performance of novel viral landscape phylogeography approaches The fast rate of evolution in RNA viruses implies that their evolutionary and ecological processes occur on the same time scale. Genome sequences of these pathogens can therefore contain information a...

Check out our latest study "Comparative performance of novel viral landscape phylogeography approaches", which is now available as a preprint on bioRxiv: www.biorxiv.org/content/10.1.... @ulbruxelles.bsky.social @ulbrecherche.bsky.social - 1/8

Spatial risk modelling of highly pathogenic avian influenza in France: Fattening duck farm activity matters In this study, we present a comprehensive analysis of the key spatial risk factors and predictive risk maps for HPAI infection in France, with a focus on the 2016–17 and 2020–21 epidemic waves. Our fi...

📢 New paper out! 🦆
Our latest study on HPAI in France and risk mapping has just been published doi.org/10.1371/jour...
@epidesa.bsky.social @inrae-france.bsky.social @anses-fr.bsky.social ENVT ULB

Lecture essentielle pour comprendre ce qui est occupé à se passer dans l'administration américaine.

with a continuous phytogeographic reconstruction that you conducted for a virus spreading in (animal) populations, feel free to contact us to extend the above figure with the estimates based on your dataset. The resulting figure and comparison will then be at your disposal (7/7)

GitHub - sdellicour/dispersal_capacities: Input files and scripts related to our study entitled "How fast are viruses spreading in the wild?", and which provides a framework for comparing the dispersa... Input files and scripts related to our study entitled "How fast are viruses spreading in the wild?", and which provides a framework for comparing the dispersal capacity of viruses (Dellic...

Overall, we here propose a comprehensive framework that can be used to compare how fast various viruses can spread, and which can be extended to analysis of further datasets: github.com/sdellicour/d.... If you would like to compare the dispersal capacity and pattern associated (6/7)

These results mostly reflect the dispersal capacity of the main infected host species but also, in some cases, the likely signature of rapid and/or long-distance dispersal events driven by human-mediated movements through animal trade (5/7)

We then use these two dispersal metrics to compare the dispersal pattern and capacity of various viruses spreading in animal populations. Our comparative analysis reveals a broad range of IBD patterns and diffusion coefficients (4/7)

a lineage dispersal velocity, a diffusion coefficient, and an isolation-by-distance (IBD) signal metric. Our results reveal that the diffusion coefficient and IBD signal metrics appear to be robust to the number of samples considered for the phylogeographic reconstruction (3/7)

In this study conducted at @ulbruxelles.bsky.social, we first evaluate dispersal metrics that can be estimated from the analysis of genomic data collected during viral epidemics. We implemented a simulation framework to evaluate the robustness of three dispersal metrics to the sampling effort: (2/7)

How fast are viruses spreading in the wild? Check out our latest study now published in @plosbiology.bsky.social: doi.org/10.1371/jour.... A study performed with Paul Bastide, Pauline Rocu, Denis Fargette, Olivier Hardy, @msuchard.bsky.social, @stephaneguindon.bsky.social, and Philippe Lemey (1/7)

Modeling the velocity of evolving lineages and predicting dispersal patterns
www.pnas.org/doi/10.1073/...

Scientists confront a mystery: Why have U.S. bird flu cases been so mild? The H5N1 bird flu outbreak in the U.S. has so far been shockingly mild. Researchers have some theories as to why.

This is a brilliant article from @helenbranswell.bsky.social about H5N1 that I think everyone should read, but I’m a bit worried that people may have the wrong takeaway despite its thoroughness:

www.statnews.com/2024/12/02/b...

Bird flu in Canada may have mutated to become more transmissible to humans Scientists are racing to understand what a hospitalized teen’s case of bird flu may mean for future outbreaks

I spoke to @mscribe.bsky.social @theguardian.com about the H5N1 case in BC.

More and more human cases are occurring, along with mutations that indicate further human adaptation.

We need to treat these cases like a warning, because that is what they are.

www.theguardian.com/world/2024/n...

Digital Pandemic Preparedness This programme will develop a blueprint for digital health systems that can be deployed during pandemics, create a funding model for implementation, and…

Another opportunity to come work @universityofoxford.bsky.social on the @oxmartinschool.bsky.social project on *Digital Pandemic Preparedness* together with Profs. Christl Donnelly, Christophe Fraser, Melinda Mills, Michael Parker, Luca Ferretti and me.

my.corehr.com/pls/uoxrecru...

The preliminary sequence from the H5N1 human case in British Columbia has been posted and it is not good news. The virus potentially has a quasispecies at HA residue 226 (H3 numbering). This is bad news because we know that mutations at residue 226 can increase binding to human receptors. 1/