Louise H. Moncla
@lhmoncla.bsky.social
Assistant Professor of Pathobiology at the University of Pennsylvania. We use trees to study RNA virus evolution and transmission, with a focus on avian influenza. viruses, sequencing, phylogenetics, pop gen. She/her https://lmoncla.github.io/monclalab/
🚨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...
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.
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 ...
biorxiv.org
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.
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...
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...
biorxiv.org
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.!!
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
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
🚨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)
Big news for those of us clicking around on trees all the time!
Andrew Rambaut (🐏🎀)@arambaut.bsky.social · 5mo agoThe first version of FigTree was released nearly 20 years ago and it is still widely used (including by me). But there are currently 85 issues on the GitHub repo (github.com/rambaut/figt...) and some of them I don’t really like the look of.
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
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...
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...
Ecology and spread of the North American H5N1 epizootic - Nature
The panzootic of highly pathogenic H5N1 since 2021 was driven by around nine introductions into the Atlantic and Pacific flyways, followed by rapid dissemination through wild migratory birds, primaril...
nature.com
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...
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.
academic.oup.com
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...
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
academic.oup.com
Molecular Biology and Evolution@molbioevol.bsky.social · 12mo ago@alexey-markin.bsky.social @tavisanderson.bsky.social et al. introduce TreeSort, a tool for identifying recent and ancestral reassortment events on datasets with thousands of influenza A virus genomes. 🔗 doi.org/10.1093/molbev/msaf133 #evobio #molbio #virus
Emma is great, and leading the way on making better ways to share and aggreggate data. This is an awesome opportunity!!
Dr Emma Hodcroft@firefoxx66.bsky.social · last yr.📢New job posting!📢 Are you excited by the idea of building global infrastructure to make pathogen sequencing more accessible, interpretable, and equitable? 🧑🏻💻🧬 My group at @swisstph.ch has an opening working with ARTIC2, @pathoplexus.org, & Loculus - read on! 1/5
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
Junior, Assistant, or Associate Specialist – Xue Lab
University of California, Irvine is hiring. Apply now!
recruit.ap.uci.edu
This is incredibly courageous and brave. Support NIH staffers. They stuck out their necks for us. Now we have to have their backs.
Stand Up for Science!@standupforscience.net · last yr.🚨BREAKING: 300+ NIH employees call out the harm of censorship & politicized science in scathing email to Bhattacharya, demanding an end to political interference, a lift on funding freezes, & rehiring of fired staff whose work saves lives. This is historic - insiders are blowing the whistle. 🧵(1/5)
This is so useful! Very good to know that someone is looking
David Bacsik@dbacsik.bsky.social · last yr.1/ How has H5N1 affected this year’s flu season in Seattle? Despite ongoing outbreaks in birds & cattle nationally, we detected zero H5N1 cases in 675 influenza A-positive specimens tested at UW Medicine.
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 🦠🔬🧬🥼🧪
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…
tinyurl.com
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:
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Has anyone ever been to a MEEGID meeting, and if so, what did you think? www.elsevier.com/events/confe...
Meegid XVII | Elsevier
17th International Conference on Molecular Epidemiology and Evolutional Genetics of Infectious Diseases
elsevier.com
Really lovely work here lead by Janathan Pekar, @worobey.bsky.social @peacockflu.bsky.social @influenzal.bsky.social and many others.
Tom Peacock@peacockflu.bsky.social · last yr.Our analysis of the second incursion of H5N1 viruses (genotype D1.1) into dairy cattle in the US is now posted to virological virological.org/t/timing-and...
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...
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....
docs.google.com
Dear Virology Community, please see ASV’s statement to our members and the scientific community. asv.org/asv-statemen...
ASV Statement for our Members | American Society for Virology
Our American Society for Virology (ASV) promotes the study and combatting of viruses, more than ever recognizing their importance and responding to them with research and education. Our academic…
asv.org
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. ...
Hensley Lab@scottehensley.bsky.social · last yr.This is big because: 1. This is evidence of a 2nd avian-->cattle H5N1 introduction. 2. The D1.1 genotype was found in the severe case in British Columbia and the deadly case in Louisiana. It is possible that this genotype has an easier time adapting to human cells. www.statnews.com/2025/02/05/u...
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.
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.”
