iiinova — where your digital self keeps evolving

Reposted by Simon Dellicour

Gytis Dudas @evogytis.bsky.social · 22/09/2026

baltic v1.0.0 is live! Get it via pip or clone from Github repo. Now with documentation (baltic.readthedocs.io) & a gallery of tutorials & examples (phylo-baltic.github.io/baltic-gallery, still WIP). Huge thanks to @barney-potter.bsky.social for all the initiative & help along the way. #ViroSky

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Raphaëlle K @raph-klitting.bsky.social · 17/09/2026

3) We show that epidemic dynamics were associated with climatic conditions (temperature and precipitation, which shape mosquito density and activity), but that climate alone cannot account for the decline in transmission at the end of the epidemic.

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Colin Carlson @colincarlson.bsky.social · 18/06/2026

Potential postdoc opportunity! We're looking for someone to do Good Work Fast at the interface between zoonotic disease ecology and global climate and land-use projections. Strong skills in statistics and geospatial modeling are the non-negotiable here. In-person in New Haven. More essential info 👉

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heerens.bsky.social @heerens.bsky.social · 11/06/2026

Super stoked to share that our Opinion article is now online at @cp-trendsgenetics.bsky.social!!! With "our" I mean: @teuneverts.bsky.social, @sdellicour.bsky.social and myself!! Here is a link to our piece: authors.elsevier.com/a/1nFgD_3rsx...

authors.elsevier.com

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Kristian G. Andersen @kgandersen.bsky.social · 18/05/2026

Amazing speed from the teams in Uganda and the DRC - impressive! Three genomes released so far - a few quick takes: 1️⃣ New genomes ~equidistant from 2007 and 2012 outbreaks. 2️⃣ Represents new spillover from reservoir. 3️⃣ Limited diversity, so too early to speculate on timing. Great work ⭐!

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Nick Loman @pathogenomenick.bsky.social · 08/05/2026

First genome sequence from Andes hantavirus strain from ongoing ship outbreak posted on Virological: virological.org/t/complete-s... courtesy Swiss National Reference Centre for Emerging Viral Infections, Geneva University Hospitals, University of Zurich

virological.org

Complete sequence of Orthohantavirus andesense virus: Swiss resident 2026

Posted on behalf of the Swiss National Reference Center for Emerging Viral Infections, Geneva University Hospitals and the Institute of Medical Virology, University of Zurich (Partner Laboratory Natio...

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Colin Carlson @colincarlson.bsky.social · 09/04/2026

New in @science.org ‼️ In the most comprehensive study to date, we show that wildlife trade is driving animal-to-human zoonotic spillover at a planetary scale, with +1 spillover per host every 10 years. Live animal markets and illegal trade pose even greater risks. 🔓 www.science.org/doi/10.1126/...

Wildlife trade drives animal-to-human pathogen transmission over 40 years

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Simon Dellicour @sdellicour.bsky.social · 25/03/2026

The application note presenting this new version has been published today in Bioinformatics: 👉 academic.oup.com/bioinformati... The “seraphim” R package is available on GitHub, along with a detailed manual, tutorials, and associated example files: 👉 lnkd.in/dT-8WydN - 4/4

academic.oup.com

SERAPHIM 2.0: an extended toolbox for studying phylogenetically informed movements

AbstractSummary. We report the second version of the R package “seraphim”, a toolbox developed to process and analyze the output of spatially explicit phyl

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Simon Dellicour @sdellicour.bsky.social · 25/03/2026

“seraphim” is an evolving toolbox mainly developed at the Spatial Epidemiology Lab (SpELL) at the @ulbruxelles.bsky.social, with the support of the FNRS and in collaboration with Oliver Pybus, @lemeylab.bsky.social, Rebecca Rose, and @nfaria.bsky.social - 3/4

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Simon Dellicour @sdellicour.bsky.social · 25/03/2026

This toolbox can, e.g., be used to investigate the impact of environmental factors on the dispersal history and dynamics of viral lineages, estimate lineage dispersal statistics, map continuous phylogeographic reconstructions of viral spread, or conduct continuous phylogeographic simulations - 2/4

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Simon Dellicour @sdellicour.bsky.social · 25/03/2026

Ten years after the release of version 1.0, we are happy to announce version 2.0 of the toolbox “seraphim”, our R package for studying phylogenetically informed movements in molecular epidemiology studies - 1/4

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Ellie Bourgikos @ebourgikos.bsky.social · 12/01/2026

🦟📄 New preprint! Our first large-scale phylodynamic study of Jamestown Canyon virus (JCV) reveals how mosquito ecology shapes the evolution, persistence, and spread of this understudied arbovirus in North America. Read it here! www.biorxiv.org/content/10.6...

biorxiv.org

Evolutionary history of Jamestown Canyon virus disentangles complex multi-vector ecology

Jamestown Canyon virus (JCV) is a re-emerging mosquito-borne virus of increasing concern in North America. It has been historically understudied, leading to significant gaps in our understanding of it...

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Reposted by Simon Dellicour

Raphaëlle K @raph-klitting.bsky.social · 12/01/2026

I am very glad to share the preprint for our latest study on the 2024-2025 chikungunya virus outbreak on Réunion island, with primary data produced thanks to the massive efforts performed by Marie-C Jaffar and Etienne Frumence and analyses led by Simon Dellicour. www.medrxiv.org/content/10.6...

medrxiv.org

Unravelling the epidemiological and dispersal dynamics of the 2024-2025 chikungunya virus outbreak on Reunion island

Reunion island just experienced a massive chikungunya virus outbreak in 2024-2025, with more than 54,000 confirmed cases. This is the second major chikungunya outbreak on the island, following the fir...

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Simon Dellicour @sdellicour.bsky.social · 12/01/2026

This study is the result of a collaborative effort involving Etienne Frumence, @raph-klitting.bsky.social, @kylaserres.bsky.social, Yucai Shao, Muriel Vincent, Mandev Gill, @msuchard.bsky.social, @lemeylab.bsky.social, Xavier de Lamballerie, and Marie-Christine Jaffar-Bandjee. 9/9

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Simon Dellicour @sdellicour.bsky.social · 12/01/2026

While a short-term resurgence of viral transmission cannot be excluded, the impact of herd immunity constitutes an encouraging outcome that should at least contribute to limiting the spread of the virus in the upcoming seasons. 7/9

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Simon Dellicour @sdellicour.bsky.social · 12/01/2026

with frequent exchanges among distant residential areas. In addition, we show that the decrease in transmission rate leading to the end of the epidemic can, at least to a large extent, be attributed to the population immunity resulting from both the current and the 2005-2006 epidemic. 6/9

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Simon Dellicour @sdellicour.bsky.social · 12/01/2026

with viral transition events being more frequent from and toward more populated areas. While we find that dispersal events were on average more likely between geographically close locations, our analyses also reveal that the transmission chain was overall spatially intermixed, 5/9

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Simon Dellicour @sdellicour.bsky.social · 12/01/2026

Harnessing this genomic dataset, we used a set of phylodynamic and phylogeographic approaches to unravel the paths taken by the transmission chain and the external factors having impacted its dynamics on the island. Our analyses highlight a dispersal pattern in line with a gravity-model dynamic 4/9

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Simon Dellicour @sdellicour.bsky.social · 12/01/2026

In this study, we generated and analysed more than 3,000 time-stamped and geo-referenced near-full chikungunya virus genomes collected throughout the recent 2024-2025 outbreak, constituting one of the most comprehensive genomic datasets ever assembled for a non-COVID-19 viral epidemic. 3/9

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Simon Dellicour @sdellicour.bsky.social · 12/01/2026

It has been assessed that this new outbreak finds its origin in a single introduction event into the island, offering a unique opportunity to exploit viral genomic data to understand the epidemiological and dispersal dynamics of the introduced transmission chain. 2/9

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Simon Dellicour @sdellicour.bsky.social · 12/01/2026

Our latest study dedicated to the massive 2024-2025 chikungunya virus outbreak on Réunion island is now available as a preprint on medRxiv: doi.org/10.64898/202.... With more than 54,000 confirmed cases this is the second major chikungunya outbreak on the island, following the 1° one 20 yrs ago. 1/9

doi.org

Unravelling the epidemiological and dispersal dynamics of the 2024-2025 chikungunya virus outbreak on Reunion island

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Simon Dellicour @sdellicour.bsky.social · 12/11/2025

Our findings provide guidelines for implementing the complementary BFadj to detect and mitigate sampling bias in discrete phylogeographic inference using CTMC modeling (9/9)

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Simon Dellicour @sdellicour.bsky.social · 12/11/2025

levels of sampling bias, estimating their type I and type II error rates. Our results show that BFadj complements the BFstd by reducing type I errors at the cost increasing type II errors for inferred transition events, while improving type I and type II errors in root location inference (8/9)

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Simon Dellicour @sdellicour.bsky.social · 12/11/2025

which incorporates information on the relative abundance of samples by location when inferring support for transition events and root location inference without requiring additional data. Using a simulation framework, we assess the statistical performance of BFstd and BFadj under varying (7/9)

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Simon Dellicour @sdellicour.bsky.social · 12/11/2025

As such data is not necessarily available, alternative approaches that rely solely on available genomic data are needed. In this study, we assess the performance of a modification of the BFstd, the adjusted Bayes factor (BFadj), (6/9)

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Simon Dellicour @sdellicour.bsky.social · 12/11/2025

Existing methods to correct sampling bias in discrete phylogeographic analyses using continuous-time Markov chain (CTMC) model, often require additional epidemiological information to balance the sampling effort among locations (5/9)

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Simon Dellicour @sdellicour.bsky.social · 12/11/2025

and is typically followed by a Bayes factor (BF) test to assess the statistical support. In the standard BF (BFstd) test, the relative abundance of the involved trait states is not considered, which can be problematic in the case of unbalanced sampling (4/9)

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Simon Dellicour @sdellicour.bsky.social · 12/11/2025

Bayesian phylogeographic inference is widely used in molecular epidemiological studies to reconstruct the dispersal history of pathogens. Discrete phylogeographic analysis treats geographic locations as discrete traits and infers lineage transition events among them, (3/9)

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Simon Dellicour @sdellicour.bsky.social · 12/11/2025

A study conducted at the Spatial Epidemiology Lab (SpELL, spell.ulb.be) of the @ulbruxelles.bsky.social, led by Fabiana Gámbaro, with also the contributions and help of Maylis Layan, @guybaele.bsky.social, and Bram Vrancken, as well as the support of the F.R.S.-FNRS (2/9)

spell.ulb.be

Spatial Epidemiology Lab

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Simon Dellicour @sdellicour.bsky.social · 12/11/2025

Check out our new study entitled "Navigating sampling bias in discrete phylogeographic analysis: assessing the performance of an adjusted Bayes factor" and now published in Molecular Biology & Evolution: academic.oup.com/mbe/article/... (1/9)

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Chiara Poletto @chpoletto.bsky.social · 24/10/2025

Our analysis of modelling practices, data use, and science-policy interactions during the COVID-19 pandemic is out on @eurosurveillance.org this week. www.eurosurveillance.org/content/10.2... Wonderful collaborative effort conducted in the context of mood-h2020.eu Read the thread below 👇

mood-h2020.eu

Home - MOOD project

MOnitoring Outbreaks for Disease surveillance in a data science context Innovative and collaborative tools and services for early detection, assessment, and monitoring of current and potential infecti...

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Reposted by Simon Dellicour

Caspar Geenen @caspargeenen.bsky.social · 17/10/2025

In the COVID-19 Omicron surge, #KULeuven combined contact tracing with sequencing. Only 1/3 of contacts shared the same strain 🤯, so most people misperceived where they got infected. @thibaut-jonathan.bsky.social and team show how to assess contact tracing accuracy in the future! #IDSky #EpiSky

sciencedirect.com

A novel methodology for assessing contact tracing precision: Phylogenetic validation of a contact tracing program for COVID-19 in Belgium

During the COVID-19 pandemic, contact tracing was widely used to limit virus propagation and implement targeted disease control measures. It can howev…

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Simon Dellicour @sdellicour.bsky.social · 29/09/2025

A huge thank you to @kylaserres.bsky.social for having coordinated the logistical aspects of this edition, as well as to the FNRS and @ulbruxelles.bsky.social for their support

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Simon Dellicour @sdellicour.bsky.social · 29/09/2025

A great opportunity to present and discuss about current research projects in the respective teams and beyond, enhancing interdisciplinarity, and opening new collaboration opportunities

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Simon Dellicour @sdellicour.bsky.social · 29/09/2025

Ongoing at the @ulbruxelles.bsky.social: the 4th edition of the Health Geography and Spatial Epidemiology workshop organised by the homonymous FNRS contact group (www.healthgeographygroup.eu)

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Andrew Rambaut (🐏🎀) @arambaut.bsky.social · 02/07/2025

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

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Simon Dellicour @sdellicour.bsky.social · 26/06/2025

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

lnkd.in

This link will take you to a page that’s not on LinkedIn

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Reposted by Simon Dellicour

Nathan Grubaugh @nathangrubaugh.bsky.social · 09/06/2025

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 🧵

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Société Française de Phytopathologie @sfp-france.bsky.social · 20/05/2025

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

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Reposted by Simon Dellicour

Spyros Lytras @spyroslytras.bsky.social · 10/05/2025

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...

cell.com

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...

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Stuart Neil @tetherin.bsky.social · 07/05/2025

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...

cell.com

The recency and geographical origins of the bat viruses ancestral to SARS-CoV and SARS-CoV-2

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ULBRecherche @ulbrecherche.bsky.social · 07/05/2025

🦇🦠 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

bit.ly

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

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