Nathan Grubaugh

Forecasting the Next Pandemic Led by scientists from Yale and the University of Oklahoma, the Viral Emergence Research Initiative (Verena) is one of the largest pandemic prevention research

Very special to wake up today to a profile of @viralemergence.org from Yale. We’re in month eight of turmoil right now, and it’s hard to focus on the science, but the truth is: we have a lot more work to do.

ysph.yale.edu/news-article...

So I pleased to announce the conceptual spawn of FigTree: PearTree (acronym still to be finalised). If you want to dive right in it is hosted as a web app here: artic-network.github.io/peartree (click the “Example...” button for immediate candy and then click every button you can find).

Postbac positions available in experimental and computational biology working on #virusevolution, tick-borne viruses and computational drug discovery! Reach out if you’d like to discuss projects in the #QVEU at NIH-NIAID. Please share with any talented undergrads or MS students you know!

Now published: our work using phylodynamics from surveillance data to quantify and experimentally validate the fitness impact of antibiotic resistance determinants & how this changes with patterns of antibiotic use: www.nature.com/articles/s41...

You know that annoying NSF form "List every coauthor/co-PI from the last 4y" ?

At @cevianlabs.io we built a free tool that drafts the COI form from your PDF CV in minutes. Check it out 👇

Want to know what 5128 primers looks like?! Lead author @chaneykalinich.bsky.social is happy to show you!

Something very different and cool for my lab. Sequencing a 4.4mb TB genome using the Artic-style PCR amplicon method with >5128 primers in two reactions 🤯

Enables culture-free WGS for TB!

journals.asm.org/doi/10.1128/...

A webpage section listing three resources related to measles virus genomic epidemiology. The first item shows an icon and the heading ‘Measles virus genomic epidemiology’ with a subheading ‘A primer on measles virus genomic epidemiology and why we do it.’ The second item shows an icon and the heading ‘artic-measles/400/v1.0.0 Primer Scheme’ with a description of the ARTIC-network primer scheme for sequencing measles virus. The third item shows an icon and the heading ‘ARTIC-network MEV wet-lab protocol’ with a description of the wet-lab protocol for sequencing MEV using the artic-measles/400/v1.0.0 primer scheme.

A webpage section titled ‘User‑interface pipelines using Epi2me,’ displaying four items. The first item shows an icon with the heading ‘amplicon‑nf: Running the pipeline in EPI2ME’ and describes using EPI2ME to run the ARTIC amplicon‑nf pipeline without the command line. The second item shows an icon with the heading ‘amplicon‑nf: Running the pipeline in EPI2ME for Illumina Data,’ again describing use of EPI2ME to run the amplicon‑nf pipeline without the command line. The third item shows an icon with the heading ‘amplicon‑nf: Running the pipeline in EPI2ME for Oxford Nanopore Data,’ with the same description. The fourth item shows an icon with the heading ‘amplicon‑nf: Viewing outputs of the pipeline in EPI2ME,’ describing how to view outputs of the amplicon‑nf pipeline within EPI2ME.

A webpage section titled ‘Command line interface pipeline SOPs.’ The first item shows an icon with the heading ‘Fieldbioinformatics: viral amplicon sequencing bioinformatics SOP’ and labels indicating ‘Nanopore | bioinformatics.’ A second section titled ‘Phylogenetics and Interpretation’ includes an icon with the heading ‘MeV Phylogenetics’ and a description stating it contains resources and protocols for measles virus alignment and phylogenetics.

ARTIC 2 measles resources are live!

As part of the Wellcome Trust funded ARTIC 2 project we have developed a collection of measles virus resources that are now openly available at artic.network/viruses/mev

Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny - Nature Methods This Resource paper presents a global SARS-CoV-2 phylogenetic tree of 4,471,579 high-quality genomes consistently constructed by Viridian, an efficient amplicon-aware assembler.

A long time ago in a galaxy far away, there was a SARS-CoV-2 pandemic. Our paper, led by @martibartfast.bsky.social
a) correcting errors in 4.5 million genomes & their phylogeny
b) improving representation of the Global South in public data
www.nature.com/articles/s41...
(thread 1/n)

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🚨2 new pre-prints🚨

✅ Molecular scale: "Deconstructing empirical fitness seascapes across scales of granularity."

✅ Host-parasite scale: "Learning virulence-transmission relationships using causal inference."

My department at Washington State University is recruiting an Assistant or Associate Professor in vector-borne disease 🕷️🦟🦠

Full job description is linked below.

Come join us on the Palouse!

Antibody escape drives emergence of diverse spike haplotypes resembling variants of concern in persistent SARS-CoV-2 infections Snell et al. develop sequencing methodology to identify full-length spike haplotypes and show that persistent SARS-CoV-2 infections drive divergent haplotype emergence, accelerating viral evolution an...

This is finally out.

Very short take home. All the variation in spike that produced the immune escape characteristics of Omicron can occur in one single persistently infected individual over the period of a year.

This is why persistent infections matter

www.cell.com/cell-reports...

PacBio Sells Short Read Tech To Illumina PacBio has finally sold their short read sequencing assets to Illumina for ~$50M.

PacBio folds its short-read sequencing hand.
-Sad for us because Omniome's tech (the current Onso instrument) was promising for its Q40 reads that help those interested in calling rare variants accurately (like me).
-Sad for them too because $$$

aseq.substack.com/p/pacbio-sel...

A long-term dream of mine has been to bridge @viralemergence.org's work on AI/ML-driven viral risk assessment with AI/ML-driven work on drug discovery. This would make a great topic for this fellowship here at Yale! If you're interested in applying, reach out. medicine.yale.edu/biomedical-d...

❤️

Our paper on the Genomic Epidemiology of DENV2/3 in Colombia and the Americas is finally out @cp-cellreports.bsky.social, check it out: www.sciencedirect.com/science/arti...

Big thanks to my collaborators @lambod50.bsky.social, @viralverity.bsky.social, @nathangrubaugh.bsky.social, and many others!

Check out our new print that combines dense sequencing and phylodynamics to uncover a bunch of 😎 things about an understudied virus.

- Doesn't evolve for 10 months a year ✅
- Uses some mossies for maintenance, others for spread ✅
- Established in Northeast for ~300 years ✅

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...

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

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...

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...

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...

🦟📄 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...

noice. Is that The Rob + mushrooms? looks like some sort of choose your own adventure.

My favs are Garbage, Sweetballs, and when I'm in the mood, The King.

It used to be Next Door but they closed

or One6Three

Atticus

Microbial Evolution: Impacts on Human Health Call for Papers A defining characteristic of infectious diseases is that they evolve. The consequences of this evolution are among the most pressing medical issues facing humanity, including emerging pandemics, antibiotic resistance, and the success or failure of vaccines. Pathogen evolution profoundly influences virulence, transmission, and responses to a broad array of human interventions. While the evolutionary dynamics of pathogens have historically been challenging to study, large-scale genomic sequencing, novel computational tools, and experimental methods are rapidly changing the field. We encourage submissions on the broad topic of the evolution of infectious diseases. This Special Issue aims to feature research that blends evolutionary approaches to understanding pathogen heterogeneity and ongoing genetic change in clinical samples and models of human infection. It also seeks to highlight opportunities to design treatment and prevention strategies that remain effective in the face of ongoing pathogen evolution. Submission – open until January 31, 2027 Guest editors Robert Woods, MD PhD, University of Michigan Camilo Barbosa, PhD, University of Michigan Silvie Huijben, PhD, Arizona State University

🚨Call for papers🚨
Microbial Evolution: Impacts on Human Health
in the society journal Evolution, Medicine, and Public Health

Guest Editors: Bob Woods, Silvie Huijben & Camilo Barbosa
EIC: me

This will be great, please submit and share!
academic.oup.com/emph/pages/m...

Vector-Pathogen Interactions: From Vector Biology to Innovative Control Strategies | Keystone Symposia Join us at the Keystone Symposia on Vector-Pathogen Interactions: From Vector Biology to Innovative Control Strategies, February 2027, in Geneva, with field leaders!

👀There will be a Keystone Symposium with a focus on Vector-Pathogen Interactions to be held in Geneva, Switzerland in February 2027. It should be a great meeting and hope to see you there! www.keystonesymposia.org/conferences/...

Children will die with RFK Jr.'s new vaccine recommendations. We're NOT doing the "experts disagree" game. The US vaccine schedule was painstakingly constructed through a deep & thorough process by experts with unquestionable expertise. This is policy by fiat. It is pre-meditated murder. 1/

I cannot emphasize this enough, if you're cold-emailing me applying to my lab I would so much rather get the bulleted broken list of genuine interests than whatever letter ChatGPT spits out in its stead

If you're training with me, I'm working with you not an LLM. I want to see who you are!

December 25 The Company of the Ring leaves Rivendell at dusk.

December 25th. The day the Fellowship departs Rivendell to destroy the One Ring.

Whatever you celebrate, may you have the courage to take the first steps to defy and endure against the dark, and rekindle light into the world.

Graph showing temperature anomaly and other covariates' effects on "RISc" score globally and by region

NEW!🦠🌡️ : What makes a "dengue year" like 2023-24? It's hard to pin down an answer unless you can homogenize out all the spatial variation and temporal trends. But once you do, the answer is pretty clean: dengue years are hot years.

Last one of the year (unless...?) 👉 www.medrxiv.org/content/10.6...