🚨 Exciting new work out today led by @carolinecummings.bsky.social! Do bats host deadly viruses? Yes - but only specific bats (that just happen to be found in a lot of places!). Challenging some big ideas in the zoonosis world with data. Well done Caroline and team!!

Last week, we were lucky to host an international workshop on Pandemic Risk Scenarios for the 21st Century, with generous support from PAX sapiens and @viralemergence.org. Lots of lessons learned from climate and biodiversity science on how to design useful models and imagine better futures!

🦇🦠 New preprint - in a long-term effort led by the amazing @mayajuman.bsky.social, we've shown that the ML tools developed by @viralemergence.org let us efficiently screen museum collections for pathogens with pandemic potential 🎉🔓 www.biorxiv.org/content/10.1...

Excited to share our study reporting the first Sin Nombre virus (SNV) genome sequences from the Northwestern U.S., and the first ever from a vole host. www.biorxiv.org/content/10.1...

Honored to be featured in WSU’s “Q&A with a Graduate Student.” I talk about my path, current work, and the role of mentorship (special mention to my PI, @stephseifertphd.bsky.social) and collaboration in advancing my research goals. Full Q&A: vetmed.wsu.edu/qa-with-grad...

New preprint! 🥳🎉 We looked at viral coinfection patterns at the largest scale ever in wildlife. We found a strong association among CoVs, PMVs, and influenza A, and higher coinfection rates in wildlife trade; plus, evidence that bats accumulate persistent infections. www.biorxiv.org/content/10.1...

v1.0.0 of CoinfectionSimulator.jl is out! I think I'm starting to get a feel for coding in #JuliaLang style. You can use this simulator to model multiple directly transmitted infections in a host population, including different disease types and interactions between them. github.com/japilo/Coinf...

Like I said: a small part of a much bigger project, which I'll let @faustobustos.bsky.social tell you about - including a much longer-term effort to figure out how to improve WHO and PAHO case definitions / syndromic surveillance / clinical treatment for very hard to distinguish endemic arboviruses.

One thing that makes this project special to me - Fausto and I adapted these algorithms from the @viralemergence.org codebase, where we've been using them to predict wildlife reservoirs of viruses like coronaviruses, hantaviruses, and paramyxoviruses. 🦇🦠🔓 www.thelancet.com/journals/lan...

Just another example among many of how NSF's investment in our Center - and specifically, in a program that uses open science and the good, ethical, runs-on-your-laptop, pre-chatbot kind of AI/ML to understand fundamental biology - has had broader benefits for public health and clinical medicine.

NEW! 🚨🦠 We trained ML algorithms to identify the clinical presentations that best distinguish pediatric dengue, chikungunya, and Zika. One notable finding: afebrile dengue may be being missed. A small part of a big project led by @faustobustos.bsky.social, out now 🔓 www.thelancet.com/journals/lan...

The next release will be a major one that makes the package more Julian, as per some helpful comments by @ctrlalttim.com. I may have learned the basics of coding in Julia, but I'm still teaching myself to think beyond my R approach to scientific programs and organize my code differently.

v 0.3.0 of CoinfectionSimulator.jl is out, now with a more logical implementation of species pair interaction strength in `prep_interaction_matrix`. github.com/japilo/Coinf...

5️⃣ Since 2023, discussions about creating an "IPCC for Pandemics" have been taken up by the UN Foundation, the National Academy of Medicine, and academic orgs like Fiocruz and Verena. Now the fight heads to Geneva. If the ball doesn't start rolling at World Health Assembly 2026, expect it in 2027.

🚨 Very, very big news. Today, a global coalition - including members of the IPCC, IPBES, and WHO expert advisors, as well as independent virologists, epidemiologists, and lawyers - started the process of creating an "IPCC for Pandemics." 🔓 www.thelancet.com/journals/lan... 🧵 Five things to know 👉

👋 We’re still collecting responses!! We’d love your input if you’re in an adjacent field — already seeing some super cool questions that make me so excited for the workshop.

Newest software stuff from team @viralemergence.org and maybe the most widely-useful thing we've developed? Huge congrats to Alexander and Steph, this is such an amazing bioinformatics tool. (Just wait until you see what they're doing with it!)

This is a really great project led by two PhD students in our group, and I can already tell it's going to lead to a really fun workshop. Consider participating if you're a virologist / disease ecologist / something more like that than not like that!

🚨 Our team just released a reproducible Docker pipeline for RNAseq assembly and annotation designed for nonmodel organisms! We're using it to explore how bats manage viral infections, but it's built for broad utility in wildlife transcriptomics. @viralemergence.org www.biorxiv.org/content/10.1...

🚨 New publication out today. Bats are over 1480 species. In this latest article, we discuss the diversity within bats and their immune systems. Elegantly led by the Becker and Frank laboratories. nyaspubs.onlinelibrary.wiley.com/doi/10.1111/... @danjbecker.bsky.social @bat-lady.bsky.social

🦠🌿🐦🧪 How can biodiversity monitoring help global efforts in disease surveillance? With ✨ fantastic ✨ colleagues from @viralemergence.org and the @geobon.org working group on One Health, we try to identify three key lessons for the future. 🧵 A short thread! academic.oup.com/bioscience/a...

Check out our new paper describing a wildlife disease data standard!

Do you study wildlife disease? Don't just share your sequences - share your testing data! We've developed a minimum data standard and an R package to help you, and wrote a little how-to-share-data handbook for disease ecology and One Health surveillance projects 🦇🦟🦠🗺️🔢 www.nature.com/articles/s41...

Virus researchers! Please consider participating in this project - it would be a huge help to our lab, and we think it'll lead to some really exciting synthesis. Plus, you'll get an invitation to participate in a workshop later in the project! 🦠😷

All of this AND food systems are the #1 driver of pandemic risk! www.nature.com/articles/s44...

🧬🦠🌍 What are the big, cross-scale questions shaping the ecology and evolution of emerging viruses? @torrelavelle.bsky.social and I are building a list of 100 questions + want your input. Help map the future of EEID — fill out & share our short survey! 🔗 airtable.com/appTW4ZoSFjR...

A brief update on this today: we are still down $1.25m in our final year, and down a still-unknown amount - could be less, could be $2.5m more - starting in September. No one has stepped in to save us. If you are a philanthropy looking to take action, we still need your help. 🫂

If you’re at @eeid2025.bsky.social Come see my poster tomorrow, and let’s talk about viral evolution!

Last year, I helped organize a workshop hosted by Fiocruz and the National Academy of Medicine to consider an "IPCC for pandemics" and explore the intersection of climate change and pandemic risk. You can read the proceedings now 🎉🇧🇷 nam.edu/perspectives...

This important commentary from Victor Dzau (NAM/GPMB), Lourdes Oliveira Aguiar (Fiocruz), and Joy Phumaphi (GPMB) also outlines the case for a new channel for scientific assessment, synthesis, and policy advice on pandemic risk (e.g., an "IPCC for pandemics") nam.edu/perspectives...

An update from the team on the uncertain future of our program and the impact of NSF budget cuts. Please share and reach out 🦠

It's hard to overstate how devastating these cuts will be for our incredible group of people working on these important questions.

I’m one of those four postdocs. Fight the budget cuts, for the sake of pandemic prevention.

An update from the team on the uncertain future of our program and the impact of NSF budget cuts. Please share and reach out 🦠

Check out @stephseifertphd.bsky.social's amazing work with bat cell lines in The Scientist! www.the-scientist.com/bat-cells-in...

Some coverage of our recent work on Oropouche virus. Big lingering questions: Where are these midges? Are we at risk in the United States? Is climate change contributing to bigger epidemics? ysph.yale.edu/news-article...

I talked to Nature about the latest development at NSF, which is a five-alarm fire for American science. The scale of immediate impact is massive. We narrowly escaped this affecting @viralemergence.org for now, but will have to shut down in a few months if this stays. www.nature.com/articles/d41...

What does this mean in practical terms? We don't have a great handle on how Oropouche virus is maintained in nature (more on this later...) or whether it could spread in the United States - especially when this is all the data we have on where the midge vectors are found.

Turns out, that's only seven studies between 1961 and 2024. Still, a fair bit of work to extract the data, summarize it, make sense of methodological differences, and come to a conclusion about public health risks. Our open data initiatives can save us some time on #1 and #2 before outbreaks start.

🦟🦠 NEW! We looked at every experiment going back to the 1960s, and found that mosquitoes are almost certainly not primary or secondary vectors of Oropouche virus - a common claim in both the scientific literature and public health communication. #EpiSky #IDSky 😷🧪 journals.plos.org/plosntds/art...

Hey disease ecologists: We're still doing that open data thing. A few months ago, we hired two amazing data scientists, and they'd love to work with you to help you use this data standard (and a new R package!!) to get your data into a FAIR repository. Please reach out if you want to work with us!

Updated preprint: "A minimum data standard for wildlife disease research and surveillance." With: ✏️ A new version of the standard 💻 A new R package to help you format your data 🦇 A retrospective mini-study of data sharing rates Preprint here: ecoevorxiv.org/repository/v... Got data? Reach out! 🦠🧪

Public health journalists: We have a new paper coming on April 30! Currently under embargo, but the headline is "Oropouche virus is probably transmitted by midges, not mosquitoes - but it's been horribly understudied for decades." Ping us if you're keen!

Research on the #bat innate #ImmuneResponse to pathogens is hindered by a lack of lab reagents. @fviromics.bsky.social @stephseifertphd.bsky.social @virology.bsky.social &co generate new bat #CellLines, enabling studies on viral susceptibility & immune responses @plosbiology.org 🧪 plos.io/4jkXukf

The first really big comparative immunology study from @viralemergence.org - some bat cells can be infected with Zika virus, others can't, and we're getting to the bottom of why. First step in a long journey to understand how some bats are different, and what that means for human health!

Are bats tolerant of all viruses? With a comparative -omics approach, we show that Egyptian fruit bat cells show both antiviral and pro-inflammatory immune responses to infection with Zika virus while our Jamaican fruit bat cells are not susceptible. www.biorxiv.org/content/10.1...

Huge congrats to the leads and especially @stephseifertphd.bsky.social, who is doing amazing work scaling science from viral phenotypes up to ecosystem and pandemic related questions. (If any journalists want to cover this amazing study, you should reach out to her!) bsky.app/profile/step...

🚨🦠 New from @viralemergence.org: Can mpox become endemic worldwide? Where did borealpox come from? Where could the next smallpox jump from animals into populations with dwindling susceptibility? We use AI/ML and viral genomics to make some educated guesses. 🔓😷🧪 www.nature.com/articles/s42...

🚨Excited to share our latest research published in @commsbio.bsky.social , where we've developed a predictive model that integrates both host ecological traits and viral genomic features to identify potential reservoir hosts for Orthopoxviruses, including mpox virus. www.nature.com/articles/s42...

The Data Life Cycle is a useful narrative device to understand how data flow within a project. But understanding how it fits with complex model pipelines has been awkward. So we wrote a thing! It's called the Model Life Cycle, and it's now out in PLOS Comp Biol: 🧪 journals.plos.org/ploscompbiol...