In collaboration with Nicola Muller, and led by @lambod50.bsky.social, we have a new preprint out that's all about reassortment! www.biorxiv.org/content/10.6...
Using TargetedBeast, we built massive (9000 tips!) Bayesian phylogenies of North American H5Nx viruses, and inferred the host...
Check out the preprint of a project I had the pleasure of working on with Nicola Mueller and Louise Moncla on North American H5 reassortment! Feel free to reach out with questions or thoughts!
Amidst all the craziness in the world it's great to see folks like Dr. Legall providing critical perspectives on microbiology and the state of science. Please consider subscribing! substack.com/@noahlegall?...
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!
What makes bird flu spill over to humans? 4y funded PhD in the genomics and molecular virology behind zoonosis of avian influenza A virus, working with @tompeacock.bsky.social and others between Liverpool, Pirbright, and Uppsala!
open to applications until next week!
Our lab's paper describing the North American H5N1 epizootic is out now in Nature! So thrilled to have this out, and congratulations to @lambod50.bsky.social for all the fantastic work on this: www.nature.com/articles/s41...
Our lab's first paper is out! Led by Jordan Ort, we developed NextClade datasets that enable rapid H5 clade assignment via NextClade. We deployed these during the start of the H5 cattle outbreak, and we finally published the paper in Virus Evolution academic.oup.com/ve/article/1...
Check out this cool preprint on Dengue epidemiology in Colombia! It was a pleasure to work with Ricardo on some of these interesting phylodynamic analyses!
Important work from Tavis Anderson and our Penn-CEIRR USDA colleagues:
www.science.org/doi/10.1126/...
U.S. citizen interested in grad studies at the University of British Columbia in Vancouver (Canada)?
Grad programs are re-opening applications of US programs for one week. With expedited decisions.
U.S. Applicant Week:
www.grad.ubc.ca/us-applicant...
#AcademicChatter #Canada #GradSchool
A tricky thing about modern society is that no one has any idea when they don’t die.
Like, the number of lives saved by controlling air pollution in America is probably over 200,000 per year, but the number of people who think their life was saved by controlling air pollution is zero.
Please watch. Powerful and chilling. 1: ‘Do not obey in advance.’ 20: ‘Be as courageous as you can!’
1/3 How long do you think it takes for highly pathogenic avian flu H5N1 sequences to be uploaded to GISAID after collection? How long should it be? In this commentary, we find a median delay of 228 days, with half the countries taking more than 6 months. rdcu.be/eeZGU @naturebiotech.bsky.social
I'm hopping on the market for postdocs outside the US...
...as soon as I finish some new analyses for a manuscript.
Lmk if there are any good leads! I've been collecting random ones here and there, but it's more daunting now that my home country appears to be off the table.
In study led by @ckikawa.bsky.social & Andrea Loes, we use new assay to measure ~10,000 neutralization titers to recent influenza strains & show titers correlate w evolutionary success of viral strains
Similar data could help forecast evolution for vaccine selection
www.biorxiv.org/content/10.1...
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.
Today @natmedicine.bsky.social published our study showing the older individuals born prior to 1968 have more antibodies that cross-react to #H5N1 relative to younger individuals. If H5N1 causes a pandemic, children will likely be the most susceptible. 1/2
www.nature.com/articles/s41...
Highly suggest folks read up about Lysenkosism because it feels like that is where we are heading.
Check out some really cool work on canine influenza that was just published! Awesome collaborative team and looking forward to learning more about this very understudied pathogen!
Figure 2. Visualizing a knowledge graph ontology. (a) Representing subject–predicate–object (SPO) triples in a graph format. (b) The current data ecosystem; each dotted box represents a type of tabular dataset that may contain many of the individual SPO triples. (c) A domain-specific ontology to represent an outbreak. Nodes (circles) represent instances of a class, with the bolded text above or below as labels with the node classes. To the left or right of each node are the properties of that node. (d) The full ontology and schema for the zoonotic risk knowledge graph. The graph schema adheres to the ontology.
Timely work on data integration for flu spillover prediction from @haileyrobertson.bsky.social and collaborators: "Understanding ecological systems using knowledge graphs: an application to highly pathogenic avian influenza" 🔓 academic.oup.com/bioinformati...
stopover duration of waterfowl predicts HPAI infection probability in backyard poultry from waterfowl, but ttiming has no effect. virulence and immunity impact the transmission risk to backyard poultry.
👉 www.nature.com/articles/s41...
New research alert! 🚨
Our paper describing the first evidence of the novel H18N12 Flu in Albiventris bats is out in @natureportfolio.nature.com Scientific Reports.
Huge shoutout to my friend and colleague Daniel for leading this work.
www.nature.com/articles/s41...
New paper led by Rohan Simkin exploring global patterns of zoonotic hosts in the wildland-urban interface. WUIs are a complex and expanding contact zone with many potential host species that are likely to be consequential for spillover transmission on a rapidly urbanizing planet. bit.ly/WUI-zdx
Preprint out by me, Greg Albery, Barbara Han (@bahanbug.bsky.social ), and Amy Sweeny about how coinfection dynamics affect our ability to measure parasite/pathogen diversity. This research was funded by @viralemergence.org. ecoevorxiv.org/repository/v... 🧪🧵(1/4)
We get data *from* the WHO. Without this, we're flying blind with data regarding evolution of infectious agents globally, putting us behind if we need to develop vaccines & treatments, just for one aspect. This puts the whole country at risk.
Call your senators! Do it today! It's better than wallowing
Very excited to see this paper out in the world. Absolutely monumental effort by @gorkalasso.bsky.social et al. to predict which filoviruses are likely to infect which bat species. Check out the thread below for details!
Top panels: graphs showing increases in spillover events, extinction rates, and temperature anomalies over the last few centuries. Bottom panel: a map of 10 pandemics since the year 1900. Four were linked to agriculture, two to wildlife use, and one to climate change.
🚨😷🧪 NEW: A growing body of evidence shows that pandemics, biodiversity loss, and climate change are part of a broader polycrisis - but there are no simple solutions. A sweeping overview of "Pathogens and planetary change" for the first issue of @natrevbiodiv.bsky.social, out now 🔓 rdcu.be/d6lHl
Hi! I'm new to blue sky, and I have a new preprint out! 🥳🥳 This work is the first chapter of my dissertation: biorxiv.org/content/10.1... The study was completed with the @viralemergence.org with support from @danjbecker.bsky.social, @colincarlson.bsky.social, and Amanda Vicente-Santos ☺️🦇⚕️🦠👩🔬 (1/5)
