iiinova — where your digital self keeps evolving

Louise H. Moncla @lhmoncla.bsky.social · 09/10/2026

This has really flown further under the radar, but these proposed NIH peer review changes are really bad! I just submitted my comment, and I hope others do too. You have until October 13: rfi.grants.nih.gov?s=6a2b1c22c3...

rfi.grants.nih.gov

Request For Information

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George O'Toole (he/him/his) @geiselbiofilm.bsky.social · 07/10/2026

Pls share:The Department of Microbiology at the University of Georgia invites applications for a tenure track Associate or Full professor position in Medical Mycology, beginning August 1, 2027. www.ugajobsearch.com/postings/508...

ugajobsearch.com

Associate Professor or Professor of Microbiology in Medical Mycology

The Department of Microbiology at the University of Georgia invites applications for a nine-month, tenure-track position in Medical Mycology at the rank of Associate or Full Professor, with an anticip...

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Louise H. Moncla @lhmoncla.bsky.social · 05/10/2026

My first PhD student defended today, and honestly, it was the best. Truly nothing feels better than getting to watch trainees mature into independent scientists.

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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

auspice

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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

Finally, the preprint is on biorxiv here: scholar.google.com/citations?vi...

scholar.google.com

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

This has been a super fun and long project. We could not have done this without substantial help from @tavisanderson.bsky.social and @alexey-markin.bsky.social who developed TreeSort. We hope others find our pipeline useful, and made it available with example data here: github.com/moncla-lab/t...

github.com

GitHub - moncla-lab/treesort-pipeline

Contribute to moncla-lab/treesort-pipeline development by creating an account on GitHub.

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

by the host they are circulating in. This evolutionary flexibility could be one reason why these viruses are so good at host switching. We also show that in its reservoir H3 evolution is marked by high reassortment rates that rapidly turn over lineages, with little selection. And swine are weird!

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

than non-reassortants, suggesting a potential fitness advantage. We also find host-specific differences in segment reassortment patterns, although we don't know why that is. Overall, these data suggest that the roles of mutation and reassortment in driving H3Nx evolution is fundamentally shaped

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

In mammal hosts, we see the opposite: lower reassortment rates, but higher rates of selection. Swine viruses are unique in that they harbor high reassortment and selection, supporting their potential to generate new diversity. In swine, reassortant viruses are also more likely to persist

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

reservoir host (birds) and in each spillover host (dogs, horses, humans, swine). In birds, we find barely any selection, but tons of reassortment. Reassortant lineages are short-lived on average, turn over frequently, and operate especially to bring in new NA subtypes.

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

of H3Nx viruses from these species, and then developed a pipeline to quantify reassortment in technical replicate, allowing us to quantify patterns of selection and reassortment with statistical uncertainty. We could then measure how selection and reassortment rates and patterns operate in the

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

Understanding host switching is a challenging problem, in part because natural instances of host jumps are rare. H3Nx viruses are a unique group of influenza viruses that circulate in wild birds, but have established long-term lineages in horses, dogs, pigs, and humans. Maria curated a huge dataset

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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

testing, and for all the individuals who have collectively worked on HPAI outbreak response

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

Overall, our data suggest that these outbreaks do provide opportunities for viral evolution, and support the strategy of stamping out transmission. We've made all our data and pipelines available, which you can find here: github.com/moncla-lab/h.... Huge thank you to PADLS lab staff for diagnostic

github.com

GitHub - moncla-lab/hpai-comm-pa: Repository for all files related to analysis of HPAI H5NX sequence data from commercial birds in PA

Repository for all files related to analysis of HPAI H5NX sequence data from commercial birds in PA - moncla-lab/hpai-comm-pa

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

samples retaining signatures of shared transmission linkage. Finally, we find evidence of transmission between PA and NY live bird markets, and show that these settings support a high degree of circulating diversity and may benefit from enhanced biosecurity precautions.

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

collected from the same outbreak. These samples are pooled poultry samples, sometimes up to 11 swabs, so this sharing could reflect pooling, transmission through wide bottlenecks, or some other process. Regardless, these data suggest a fair bit of diversity circulating within outbreaks, with...

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

adaptive mutations, including PB2 D710N, suggesting that these mutations, while rare, can be circulating in settings that would allow exposure to humans. In contrast to human studies that find very limited shared diversity, we find a high rate of shared within-sample variants from samples ...

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

Using a combination of phylogenetic and within-sample variant analyses, we trace evolution and transmission across 3 commercial farm outbreaks and 2 live bird market outbreak in Pennsylvania from 2023-2025. We find overall low within-sample diversity, but a few instances of known ...

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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

evolution is pretty fundamentally linked to the ecology and spread of LPAI viruses, which we should probably surveil and understand better. Huge thank you to all the people at USDA who generated these sequence data, to @lambod50.bsky.social and Nicola for all their fantastic work on this!

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

Together, this study suggests that reassortment is frequent, seasonal, and mostly driven by viral prevalence and mixing with LPAIs. This suggests that aspects of reassortment (timing, host, locations) may be more predictable if we understood transmission better. Our data also suggest that HPAI

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

Using these time-varying rates, we show that the probability of reassortment in the 6 months leading up to the emergence of B3.13 and D1.1 was ~0.15, meaning that viruses evolving during particular times of year are likely to be reassortants, regardless of whether reassortment was beneficial.

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

We find that that reassortment is frequent, seasonal and mostly driven by mixing between high and low path viruses. Peaks in HPAI reassortment are best predicted by LPAI cases, indicating that LPAI ecology plays a major role in the timing of HPAI reassortment.

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

Next, Nicola developed a new version of CoalRE that allows reassortment to be modelled as a function of prevalence. We inferred the full reassortment network and measured reassortment rates over time, and used a GLM to assess whether cases of HPAI or LPAI correlated with reassortment.

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

generating less. Ducks contributed the most to transmission, and contributed about half of all reassortant segments! So ducks are really the source of new H5 genotypes in North America, making them a useful target for surveillance.

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

flyway, and time of genotype origins as a proxy for reassortment. We find that genotypes mostly arise in flyways and hosts proportional to what you would expect based on the transmission they support, with the Central flyway and geese generating more reassortment than you would expect, and cattle

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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

One note is that the NA sequence is currently not shown in the neuraminidase tree. It looks like we have an issue with purging out divergent NA subtypes, which we are working on fixing.

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

From a quick look at the sequences, neither 627K or 701N are present in PB2, and the HA does not appear to have any known adaptive mutations. Thank you to the Washington State Department of Health for the rapid data generation and sharing. Hoping that this person recovers well.

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

could reflect unsampled infections/transmission chains in wild, North American birds prior to spillover. Enhanced surveillance/data would be useful for determining how widely and persistently these H5N5s are circulating, and for tracking their dissemination across the continent.

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

Across all gene segments, this human strain clusters with sequences sampled from gulls and ringed seals in Nova Scotia (Atlantic Flyway) and Nunavut (Atlantic, but very far North), which is a bit surprising. The HA sequence does have a few mutations from its closest relative, so this ..

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

This human strain clusters with the A6 genotype viruses (Genoflu nomenclature), which include numerous H5N5 viruses that were introduced to North America from Europe. Though introduction patterns vary across the segment trees, these H5N5s always cluster together and descend from Europe.

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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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