iiinova — where your digital self keeps evolving

Louise H. Moncla @lhmoncla.bsky.social · 28/09/2026

Due to some really great work from the @nextstrain.org team, it is now easier to put together new builds! We've recently released H7Nx and H10Nx builds onto the main avian-flu page along with all the standard features. Check them out! nextstrain.org/avian-flu/h1...

nextstrain.org

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IDDjobs @iddjobs.org · 25/09/2026

Postdoc (London, UK) Develop new methods for pathogen genomic epidemiology with @ceciletk.bsky.social at Imperial College London @mrc-outbreak.bsky.social More details: iddjobs.org/jobs/2596

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Louise H. Moncla @lhmoncla.bsky.social · 23/09/2026

Our lab just put out a new preprint! Led by Maria Maltepes, we've been working with @tavisanderson.bsky.social and @alexey-markin.bsky.social to understand how host species impacts the fundamentals of how influenza viruses evolve. TLDR, reassortment and selection rates vary widely across species.

scholar.google.com

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Louise H. Moncla @lhmoncla.bsky.social · 25/08/2026

Which virology journals have a quick submit to review/editorial reject decision? We've had two papers sit at journals for > a month and then be editorially rejected, and are trying to find journals that will at least reject quickly. We are not shooting for the stars, just reasonable journals

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nitanother.bsky.social @nitanother.bsky.social · 17/08/2026

We're hiring multiple post docs to work on spatial and quantitative models of infectious disease! For details and application materials: psu.wd1.myworkdayjobs.com/PSU_Academic... and see our lab website here: humidlab.com

psu.wd1.myworkdayjobs.com

Postdoctoral Scholar - Bharti Lab

APPLICATION INSTRUCTIONS: CURRENT PENN STATE EMPLOYEE (faculty, staff, technical service, or student), please login to Workday to complete the internal application process. Please do not apply here, a...

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Ed Hutchinson @socialinfluenza.bsky.social · 23/07/2026

🚨New Pre-Print!🚨 Want to search for variation in influenza A virus sequences, but find the amount of data overwhelming? Wondering if new avian flu strains have signs of mammalian adaptation? The #Flu-MutationExplorer, a new online tool, can help (1/n) www.biorxiv.org/content/10.6...

An image in the style of an Andy Warhol screen print showing influenza virions in a variety of colours. (Image credit Ed Hutchinson and Naina Nair, MRC-University of Glasgow Centre for Virus Research)

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Louise H. Moncla @lhmoncla.bsky.social · 23/07/2026

Led by Anna Jaeger and Elena Cruz-Adames, we have a new preprint out on within-sample diversity and local spread of H5N1 in Pennsylvania! www.biorxiv.org/content/10.6.... We developed a sequencing protocol and bioinformatic pipeline to sequence residual RNA from H5+ wild and domestic birds in PA.

biorxiv.org

Within- and between-host dynamics of highly pathogenic avian influenza in domestic birds from Pennsylvania farms and live bird markets

Since late 2021, highly pathogenic avian influenza viruses (HPAI) of the H5 subtype clade 2.3.4.4b have spread across the Americas, devastating wildlife, agricultural animals, and resulting in dozens ...

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Louise H. Moncla @lhmoncla.bsky.social · 13/07/2026

As a young PI, it can feel like everything is out of our control. But today, we used our lab meeting to have each person draft and submit comments on the OMB rule. It felt really good to prioritize this within the work day for our lab, and it felt more empowering to do it as a group.

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Hensley Lab @scottehensley.bsky.social · 05/07/2026

Do you live in Philly? Has your cat been acting crazy? Well, it is likely this craziness is not due to H5N1 infection--but rather the fact that your cat is a cat. In this new preprint with @lhmoncla.bsky.social we find low H5N1 seroprevalence rates in Philly cats. www.biorxiv.org/content/10.6...

biorxiv.org

Clade 2.3.4.4b H5N1 influenza virus and SARS-CoV-2 seroprevalence among owned and feral cats in Philadelphia and surrounding communities

Clade 2.3.4.4b H5NX influenza viruses have spread widely in birds since 2020. In addition to causing disease in birds, these viruses have infected a variety of mammals, including humans. Clade 2.3.4.4...

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Chris Brooke @christopherbrooke.bsky.social · 14/05/2026

Excited to announce that we are moving the lab to Minneapolis to join the University of Minnesota Department of Microbiology & Immunology and Institute on Infectious Diseases this summer!! We will be hiring so please reach out if interested in viral evolution, viral immunology, etc.!!

Sunset view of the Mississippi river and beautiful downtown Minneapolis

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Gytis Dudas @evogytis.bsky.social · 22/04/2026

Please share! My lab has an open fully-funded PhD position at Vilnius University's Life Sciences Center in Lithuania. The PhD project will involve identifying missing orthomyxovirus segments from public sequence data. Applicants must hold an MSc by June & have bioinformatics experience. 1/2

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Louise H. Moncla @lhmoncla.bsky.social · 20/04/2026

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...

biorxiv.org

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Ed Hutchinson @socialinfluenza.bsky.social · 05/03/2026

🚨New Influenza Tool🚨 Interested in IAV mutations? Looking for markers of mammalian adaptation? Frustrated by converting between IAV numbering systems? The #Flu-MutationExplorer, a new tool from @cvrbioinfo.bsky.social and @royalvetcollege.bsky.social, is here to help: flu-gdb.cvr.gla.ac.uk (1/n)

A 3x3 grid of coloured images of influenza virus particles in the style of an Andy Warhol screen print. Image credit Naina Nair / Ed Hutchinson (MRC-University of Glasgow Centre for Virus Research)

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Louise H. Moncla @lhmoncla.bsky.social · 02/03/2026

Big news for those of us clicking around on trees all the time!

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Louise H. Moncla @lhmoncla.bsky.social · 11/02/2026

Cool opportunity to work on avian flu with a great team! lnu.se/en/meet-linn...

lnu.se

Vacancies page

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Dr Emma Hodcroft @firefoxx66.bsky.social · 20/11/2025

1/ 🚀 Exciting news: we’ve just released the first Nextclade dataset for Enterovirus D68 (EV-D68), developed in collaboration with the European Non-Polio Enterovirus Network (ENPEN). 👉🏻 Check out the dataset on Nextclade! clades.nextstrain.org?dataset-name... #EVD68 #Enterovirus #OpenData

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Louise H. Moncla @lhmoncla.bsky.social · 19/11/2025

Last week, a human in Washington was hospitalized for H5N5, the first human case of highly pathogenic H5N5 in the US. doh.wa.gov/newsroom/h5n.... Thanks to work from Anna Jaeger and Stephen Shank in our lab, we've added this strain to our North American phylogeny: nextstrain.org/groups/moncl...

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Louise H. Moncla @lhmoncla.bsky.social · 15/10/2025

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...

academic.oup.com

Development of avian influenza A(H5) virus datasets for Nextclade enables rapid and accurate clade assignment

Abstract. The 2022 panzootic of highly pathogenic avian influenza (HPAI) A(H5) viruses has led to unprecedented transmission to multiple mammalian species.

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Louise H. Moncla @lhmoncla.bsky.social · 14/08/2025

I've always loved Ted Chiang and his writing

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Alexey Markin @alexey-markin.bsky.social · 11/08/2025

TreeSort is out at MBE! Fresh off the press so DOI below is not yet working, but you can find the article here: academic.oup.com/mbe/article/... 💡If you want to apply it to your data - please see the tutorial here github.com/flu-crew/Tre...

academic.oup.com

Revealing Reassortment in Influenza A Viruses with TreeSort

Abstract. Reassortment among influenza A viruses (IAV) facilitates evolution and has been associated with interspecies transmission and pandemics. We intro

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Louise H. Moncla @lhmoncla.bsky.social · 25/07/2025

Emma is great, and leading the way on making better ways to share and aggreggate data. This is an awesome opportunity!!

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Katherine Xue @ksxue.bsky.social · 17/07/2025

The Xue lab at UC Irvine is looking for a staff scientist to support our work investigating how microbes interact and evolve in the gut microbiome! Open to a wide range of previous experience levels, see ad for more. recruit.ap.uci.edu/JPF09601

recruit.ap.uci.edu

Junior, Assistant, or Associate Specialist – Xue Lab

University of California, Irvine is hiring. Apply now!

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Gregg Gonsalves @gregggonsalves.bsky.social · 09/06/2025

This is incredibly courageous and brave. Support NIH staffers. They stuck out their necks for us. Now we have to have their backs.

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Louise H. Moncla @lhmoncla.bsky.social · 19/03/2025

This is so useful! Very good to know that someone is looking

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Erik Karlsson @eakarlsson.bsky.social · 25/02/2025

The Virology Unit at IPC has 3 positions open in #OneHealth: *Postdoc – Reconstructing Past Outbreaks *Postdoc – Environmental Surveillance *Clinical Manager These aren’t just jobs. They’re front-row seats to global health in action. Ready? tinyurl.com/57rvxcau #ViroSky #IDSky 🦠🔬🧬🥼🧪

tinyurl.com

Institut Pasteur du Cambodge on LinkedIn: The Institut Pasteur du Cambodge (IPC) is looking for: -…

The Institut Pasteur du Cambodge (IPC) is looking for: - 𝐏𝐨𝐬𝐭𝐝𝐨𝐜𝐭𝐨𝐫𝐚𝐥 𝐑𝐞𝐬𝐞𝐚𝐫𝐜𝐡𝐞𝐫 – 𝐒𝐞𝐫𝐨𝐥𝐨𝐠𝐲 𝐚𝐭 𝐭𝐡𝐞 𝐇𝐮𝐦𝐚𝐧-𝐀𝐧𝐢𝐦𝐚𝐥…

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Louise H. Moncla @lhmoncla.bsky.social · 28/02/2025

This week @scottehensley.bsky.social and I briefed the Pennsylvania state House Agriculture and Rural Affairs and Health committees on H5N1. It was super interesting and useful, and we got some great questions. www.youtube.com/live/yRxdeG9..., we got one question that I would like to crowd source:

youtube.com

YouTube

Share your videos with friends, family, and the world

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Thijs Kuiken @thijskuiken.bsky.social · 17/02/2025

What is happening in the USA, including U.S. government censorship of research, is unacceptable. The least we can do is to state our opposition publicly. Please have a look at this declaration and--if you agree--put your name to it. docs.google.com/document/u/0...

docs.google.com

Declaration To Defend Research Against Government Censorship

Declaration To Defend Research Against U.S. Government Censorship, V.1.1 Drafted by Lisa Schiff (@lschiff.bsky.social), Alice Meadows (@alicemeadows.bsky.social), Catherine Mitchell (@camitchell.bsky....

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Louise H. Moncla @lhmoncla.bsky.social · 13/02/2025

It made me so happy to see that MMWR is back!

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Louise H. Moncla @lhmoncla.bsky.social · 05/02/2025

I agree with Scott. This is important because: 1. This shows that cattle are susceptible to other H5N1 viruses, not just B3.13. 2. D1.1 viruses are currently transmitting really efficiently through wild birds in North America, and are very widespread. ...

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Shenglai @shenglai.bsky.social · 03/02/2025

Our next #IFEEAI webinar speaker is @lhmoncla.bsky.social , Assistant Professor @upenn.edu Title: Intensive transmission in wild, migratory birds drove rapid geographic dissemination and repeated spillovers of #H5N1 #birdflu into agriculture in North America.

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Dave Levitan @davelevitan.bsky.social · 28/01/2025

Per an NIH source: “Discussions with colleagues have suggested that if the universities all come together and raise hell about the delays to funding caused by not holding meetings, that might move the needle. From every state. There are well-funded universities in red states that will be impacted.”

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Louise H. Moncla @lhmoncla.bsky.social · 28/01/2025

Call your senators! Do it today! It's better than wallowing

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Louise H. Moncla @lhmoncla.bsky.social · 10/01/2025

Our lab's 2nd preprint is now on bioRxiv! Led by Jordan Ort, we made H5 datasets that enable rapid clade assignment with Nextclade. We released these builds in the spring (due to cow flu) & finally wrote the paper! TLDR: it's fast, easy, accurate, and we hope, useful www.biorxiv.org/content/10.1...

biorxiv.org

Development of avian influenza A(H5) virus datasets for Nextclade enables rapid and accurate clade assignment

The ongoing panzootic of highly pathogenic avian influenza (HPAI) A(H5) viruses is the largest in history, with unprecedented transmission to multiple mammalian species. Avian influenza A viruses of t...

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Louise H. Moncla @lhmoncla.bsky.social · 10/01/2025

I'm co-organizing a symposium and we are looking for people who do cool work on infectious disease and climate change! Who is doing cool stuff in that space?

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Jessica Metcalf @jessmetcalf.bsky.social · 09/12/2024

Senior Postdoctoral Research position open in EEB Princeton puwebp.princeton.edu/AcadHire/app...

puwebp.princeton.edu

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Kai Kupferschmidt @kakape.bsky.social · 06/12/2024

If an #H5N1 pandemic starts tomorrow or in three months, there will be little mystery as to how it happened. The conditions are all there. They have been for a while. So in some ways the more interesting question to me at the moment is: Why aren’t we in a pandemic yet? Story here, 🧵 to come: 🧪#IDSky

science.org

Why hasn’t the bird flu pandemic started?

Some scientists examining mutations found in H5N1 viruses fear major outbreak is imminent but others says pathogen remains unpredictable

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Louise H. Moncla @lhmoncla.bsky.social · 25/11/2024

This truly makes me queasy. I really hope no one drinks this milk

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Louise H. Moncla @lhmoncla.bsky.social · 17/11/2024

Additional information from Scott and Jesse

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Louise H. Moncla @lhmoncla.bsky.social · 17/11/2024

Last week, a teenager in British Columbia contracted H5N1, the first human case acquired in Canada. The BC CDC and and Canadian Food Inspection Agency have released sequences from this infected person and domestic and wild birds sampled in BC, which we've just added to Nextstrain. A thread:

nextstrain.org

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Louise H. Moncla @lhmoncla.bsky.social · 14/05/2024

New tool announcement! Thanks to a lot of work from Jordan Ort (an awesome student in the lab), with help from @richardneher , Todd Davis, Tommy Lam, and Sam Shepard, the H5s are now on Nextclade! clades.nextstrain.org A thread below:

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Kristian G. Andersen @kgandersen.bsky.social · 03/05/2024

Preliminary report on genomic epidemiology of the 2024 H5N1 influenza A virus outbreak in U.S. cattle. Thanks to everyone who contributed to this and, of course, first and foremost the data producers and those involved in the response. virological.org/t/preliminar...

virological.org

Preliminary report on genomic epidemiology of the 2024 H5N1 influenza A virus outbreak in U.S. cattle (Part 1 of 2)

Due to length constraints on virological.org posts, we are splitting this report into two parts that should be read as a single report. This is Part 1, containing Background, Data, Methods, and Findi...

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Louise H. Moncla @lhmoncla.bsky.social · 01/04/2024

In response to the H5N1 infections in cows and now a human in Texas, we've just updated our North America specific H5Nx Nextstrain build with the cow and goat sequences, which are viewable under "Species-grouped: Ruminant": nextstrain.org/groups/moncl.... A few notes.

nextstrain.org

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Louise H. Moncla @lhmoncla.bsky.social · 25/03/2024

Such a great resource, and wonderful to see this in print! Can recommend for anyone getting into genomic epidemiology.

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