Lightnews — Scholar-powered news

First Sin Nombre virus (Orthohantavirus sinnombreense) genome sequences from the Northwestern United States

9 28

Reposted by Verena

Steph N. Seifert, PhD @stephseifertphd.bsky.social · 21d

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...

We report the first Sin Nombre virus (SNV) genome sequences from the Northwestern United States and the first SNV sequences recovered from voles. Analysis of samples collected from 189 individual rode...

Q&A with graduate student Ricardo Rivero

1 5 5

Reposted by Verena

Ricardo Rivero H. 💻🧬 @ricardoriveroh.bsky.social · 25d

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...

WSU graduate student Ricardo Rivero is working to uncover the rules that govern how viruses evolve — insights that could one day help predict viral behavior and guide public health responses. A PhD st...

vetmed.wsu.edu

2 4

Reposted by Verena

Colin Carlson @colincarlson.bsky.social · 28d

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...

Figure 3 of our paper, which shows viral coinfection networks at the virus level

3 47 91

Reposted by Verena

Dr. July Pilowsky @pilowsky.me · Aug 14

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...

Release v1.0.0 · japilo/CoinfectionSimulator.jl

This version is more Julian in structure, and uses abstract types to manage simulation parameters, host populations, and disease strains. The simulations are more broken down into a network of help...

github.com

4 10

Reposted by Verena

Colin Carlson @colincarlson.bsky.social · Aug 6

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.

A table of syndromic features that best distinguish dengue, chikungunya, and Zika

1 2 3

Reposted by Verena

Colin Carlson @colincarlson.bsky.social · Aug 6

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...

Optimising predictive models to prioritise viral discovery in zoonotic reservoirs

Despite the global investment in One Health disease surveillance, it remains difficult and costly to identify and monitor the wildlife reservoirs of novel zoonotic viruses. Statistical models can guid...

www.thelancet.com

1 1 2

Reposted by Verena

Colin Carlson @colincarlson.bsky.social · Aug 6

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.

1 2 7

Reposted by Verena

Colin Carlson @colincarlson.bsky.social · Aug 6

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...

Paper title: "Comparison of dengue, chikungunya, and Zika among children in Nicaragua across 18 years: a single-centre, prospective cohort study"

Figure beneath it shows classification rates for different diseases and the most informative variables in each model

1 8 33

Reposted by Verena

Dr. July Pilowsky @pilowsky.me · Jul 30

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.

1 1 4

Reposted by Verena

Dr. July Pilowsky @pilowsky.me · Jul 30

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...

Release v0.3.0 · japilo/CoinfectionSimulator.jl

Version 0.3.0 has improved implementation of interaction strengths in prep_interaction_matrix. Previously, interaction_strength determined the standard deviation of draws from a normal distribution...

github.com

1 2 5

Reposted by Verena

Colin Carlson @colincarlson.bsky.social · Jul 17

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.

1 3 14

Reposted by Verena

Colin Carlson @colincarlson.bsky.social · Jul 17

🚨 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 👉

Pathways to an Intergovernmental Panel on Pandemics: lessons from the IPCC and IPBES

Colin J Carlson, Christopher H Trisos, Ben Oppenheim, Shweta Bansal, Sara E Davies, Aïda Diongue-Niang, Victoria Y Fan, John D Kraemer,
Rachel Golden Kroner, Lawrence O Gostin, David T S Hayman, Marion Koopmans, Torre E Lavelle, Carlos G das Neves, Zoe O’Donoghue,
Laura M Pereira, Benjamin Roche, Matiangai Sirleaf, Kayla Zamanian, Carlos Zambrana-Torrelio, Alexandra L Phelan

Pandemics pose a global threat to human wellbeing, justice, economies, and ecosystems and are comparable with other planetary crises such as climate change and biodiversity loss in terms of urgency and impact. The global community would benefit from a dedicated scientific synthesis body to assess pandemic risks and solutions. In this Personal View, we explore proposals for an Intergovernmental Panel on Pandemics and assess potential pathways to its creation. Learning lessons from the Intergovernmental Panel on Climate Change (IPCC) and the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (IPBES) might help national governments and international organisations to chart a course through important decisions about format, governance, operations, scientific scope and process, and ability to recommend policies that make the world safer.

5 120 310

Reposted by Verena

Hailey Robertson @haileyrobertson.bsky.social · Jul 16

👋 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.

The Carlson Lab @ Yale @carlsonlab.bsky.social · Jul 16

Viral -ologists of all kinds - molecular, ecological, evolutionary - if you haven't yet, consider joining our horizon scan study and help us identify 100 questions that are guiding where your field is going! Fill in the survey and get an invite to a workshop:

📝 airtable.com/appTW4ZoSFjR...

Airtable is a low-code platform for building collaborative apps. Customize your workflow, collaborate, and achieve ambitious outcomes. Get started for free.

TATAT: a containerized software for generating annotated coding transcriptomes from raw RNA-seq data

7 3

Reposted by Verena

Colin Carlson @colincarlson.bsky.social · Jul 14

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!)

Steph N. Seifert, PhD @stephseifertphd.bsky.social · Jul 14

🚨 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...

Motivation: Many transcriptome creation workflows are not standardized, are difficult to install or share, prone to breaking as dependencies update or cease to be maintained and are resource intensive...

1 5 11

Reposted by Verena

Colin Carlson @colincarlson.bsky.social · Jul 16

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!

The Carlson Lab @ Yale @carlsonlab.bsky.social · Jul 16

Viral -ologists of all kinds - molecular, ecological, evolutionary - if you haven't yet, consider joining our horizon scan study and help us identify 100 questions that are guiding where your field is going! Fill in the survey and get an invite to a workshop:

📝 airtable.com/appTW4ZoSFjR...

Airtable is a low-code platform for building collaborative apps. Customize your workflow, collaborate, and achieve ambitious outcomes. Get started for free.

TATAT: a containerized software for generating annotated coding transcriptomes from raw RNA-seq data

4 4

Reposted by Verena

Steph N. Seifert, PhD @stephseifertphd.bsky.social · Jul 14

🚨 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...

Motivation: Many transcriptome creation workflows are not standardized, are difficult to install or share, prone to breaking as dependencies update or cease to be maintained and are resource intensive...

Bats are recognized to have distinct immune systems from other vertebrates that may allow them to host virulent pathogens without showing disease. However, these flying mammals are also incredibly di...

1 10 25

Reposted by Verena

Arinjay Banerjee @banerjeelab.ca · Jul 3

🚨 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

NYAS Publications

nyaspubs.onlinelibrary.wiley.com

10 23

Reposted by Verena

Timothée Poisot @ctrlalttim.com · Jun 30

🦠🌿🐦🧪 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...

Biodiversity science and biosurveillance are fellow travelers

The failure to meet the Aichi targets to alleviate global biodiversity decline (Nature 2020) was a wake-up call to the biodiversity monitoring community (T

academic.oup.com

1 21 34

Reposted by Verena

Collin Schwantes @collin-schwantes.bsky.social · Jun 23

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

The Carlson Lab @ Yale @carlsonlab.bsky.social · Jun 23

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...

A minimum data standard for wildlife disease research and surveillance - Scientific Data

Scientific Data - A minimum data standard for wildlife disease research and surveillance

www.nature.com

3 4

Reposted by Verena

The Carlson Lab @ Yale @carlsonlab.bsky.social · Jun 23

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...

A minimum data standard for wildlife disease research and surveillance - Scientific Data

Scientific Data - A minimum data standard for wildlife disease research and surveillance

www.nature.com

25 48

Reposted by Verena

Colin Carlson @colincarlson.bsky.social · Jun 17

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! 🦠😷

Hailey Robertson @haileyrobertson.bsky.social · Jun 17

🧬🦠🌍 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...

Airtable is a low-code platform for building collaborative apps. Customize your workflow, collaborate, and achieve ambitious outcomes. Get started for free.

1 24 28

Reposted by Verena

Colin Carlson @colincarlson.bsky.social · Jun 17

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

1 22 65

Reposted by Verena

Hailey Robertson @haileyrobertson.bsky.social · Jun 17

🧬🦠🌍 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...

Airtable is a low-code platform for building collaborative apps. Customize your workflow, collaborate, and achieve ambitious outcomes. Get started for free.