Our first WiLiMan project paper is out #wilimanid! 🎉 We modelled how host genetics might shape Chronic Wasting Disease (CWD) dynamics in wild reindeer (Rangifer tarandus). Read here: doi.org/10.1016/j.ec... (Photo: Olav Strand/NINA) | 1/12

What happens to a sexually transmitted pathogen during a pandemic with social distancing measures?! We have a new paper out from the genome epidemiology team at NIPH! Led by Kristian Alfsnes. Read here: 👾https://doi.org/10.1099/mgen.0.001479 | 1/13

If lost there's no going back: "...the lab holds the world’s largest repository of gonorrhea isolates — over 50,000, dating back to 1988 when the CDC began to collect them."

www.statnews.com/2025/04/05/c...

Perspective from @kgandersen.bsky.social, Purushotham, Lutz, & @edythparker.bsky.social "Immunological drivers of zoonotic virus emergence, evolution, and endemicity." authors.elsevier.com/a/1ks2e3qNrU...

Postdoc Opportunity

Got a PhD in disease evolution, or something similarly hardcore? Know your way around phylodynamics? Good. We need you.

If you’re up for real-world research getting hands-on with fieldwork, sequencing, and making sense of viral evolution, apply here: jobs.inrae.fr/en/ot-25456.

We present JUNIPER, our outbreak reconstruction tool that incorporates within-host variants, models missing data, and scales to large, sparsely sampled datasets to achieve state-of-the-art performance. Led by @ivan_specht et al. @sabeti_lab. www.medrxiv.org/content/10.1... 1/12 🧵

Important and timely analysis! The observation of a lower mutation rate in cattle compared to birds highlights the need for host-specific clock rates.

📢 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

First genome sequence from the Ugandan Ebolavirus outbreak with analysis: virological.org/t/990 and first filovirus genome submitted to Pathoplexus database: pathoplexus.org/seq/PP_0011C.... Great (and rapid) work from the National Health Laboratory, UVRI and partners.

Given these efforts, graduate student, Praneeth G., in the lab asked himself the question "have we ever found any evidence of Q226L in "the wild"?"

And the answer is yes.

In SRR29377776 from June 2024, collected from a mouse on, presumably, a farm.

Data:
www.ncbi.nlm.nih.gov/sra/?term=SR...

Receptor switching is one of the key steps in adaptation of animal influenza viruses to humans. Studies shows that is requires only a single mutation to do that. The widespread circulation of AI in cattle is playing with fire. www.science.org/doi/10.1126/...

Study estimating the dispersal capacity of viruses using genomic data. Pretty cool figure!

New post on some preliminary – but troubling – signals about the direction H5N1 might be taking: kucharski.substack.com/p/h5n1-influ...

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/

The final version of our study using pseudovirus deep mutational scanning to measure the effects of mutations influenza H5 hemagglutinin to inform viral surveillance is now published in PLoS Biology:
journals.plos.org/plosbiology/...

8/115 of farm workers in a convenience sample positive for H5N1 - original study here: www.cdc.gov/mmwr/volumes...

Straight from the cellars of NIPH, we have a paper out on pneumococcal lineage (GPSC) dynamics in response to childhood vaccination. Resuscitating freeze-dried cultures was a substantial effort, but worked surprisingly well. Have a look if interested! genomemedicine.biomedcentral.com/articles/10....