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/
https://lmoncla.github.io/monclalab/
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
October 15, 2025 at 3:44 PM
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...
I've always loved Ted Chiang and his writing
As always, Ted Chiang is great in this interview.
cdh.princeton.edu/blog/2025/08...
cdh.princeton.edu/blog/2025/08...
August 14, 2025 at 2:16 PM
I've always loved Ted Chiang and his writing
Reposted by Louise H. Moncla
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...
💡If you want to apply it to your data - please see the tutorial here github.com/flu-crew/Tre...
August 11, 2025 at 1:34 PM
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...
💡If you want to apply it to your data - please see the tutorial here github.com/flu-crew/Tre...
Emma is great, and leading the way on making better ways to share and aggreggate data. This is an awesome opportunity!!
📢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
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
July 25, 2025 at 3:30 PM
Emma is great, and leading the way on making better ways to share and aggreggate data. This is an awesome opportunity!!
Reposted by Louise H. Moncla
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/JPF09601
Junior, Assistant, or Associate Specialist – Xue Lab
University of California, Irvine is hiring. Apply now!
recruit.ap.uci.edu
July 17, 2025 at 8:32 PM
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/JPF09601
Reposted by Louise H. Moncla
This is incredibly courageous and brave. Support NIH staffers. They stuck out their necks for us. Now we have to have their backs.
🚨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 historic - insiders are blowing the whistle.
🧵(1/5)
June 9, 2025 at 12:18 PM
This is incredibly courageous and brave. Support NIH staffers. They stuck out their necks for us. Now we have to have their backs.
This is so useful! Very good to know that someone is looking
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.
March 19, 2025 at 6:51 PM
This is so useful! Very good to know that someone is looking
Reposted by Louise H. Moncla
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 🦠🔬🧬🥼🧪
*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
February 25, 2025 at 2:59 PM
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 🦠🔬🧬🥼🧪
*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 🦠🔬🧬🥼🧪
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
Share your videos with friends, family, and the world
www.youtube.com
February 28, 2025 at 6:01 PM
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:
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
www.elsevier.com
February 24, 2025 at 4:01 PM
Has anyone ever been to a MEEGID meeting, and if so, what did you think? www.elsevier.com/events/confe...
Really lovely work here lead by Janathan Pekar, @worobey.bsky.social @peacockflu.bsky.social @influenzal.bsky.social and many others.
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...
Timing and molecular characterisation of the transmission to cattle of H5N1 influenza A virus genotype D1.1, clade 2.3.4.4b
Jonathan E. Pekar, Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, UK Thomas P. Peacock, The Pirbright Institute, Woking, UK, GU24 0NF; Department of Infectious Disease, Imper...
virological.org
February 24, 2025 at 3:53 PM
Really lovely work here lead by Janathan Pekar, @worobey.bsky.social @peacockflu.bsky.social @influenzal.bsky.social and many others.
Reposted by Louise H. Moncla
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/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
February 17, 2025 at 6:48 AM
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/document/u/0...
Reposted by Louise H. Moncla
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
February 13, 2025 at 9:20 PM
Dear Virology Community, please see ASV’s statement to our members and the scientific community. asv.org/asv-statemen...
It made me so happy to see that MMWR is back!
An H5N1 serosurvey paper was released in MMWR Weekly today . Three of 150 vets had detectable neutralizing or HAI antibodies.
www.cdc.gov/mmwr/volumes...
www.cdc.gov/mmwr/volumes...
Notes from the Field: Seroprevalence of Highly ...
This report describes evidence of recent highly pathogenic avian influenza infection among three veterinary practitioners.
www.cdc.gov
February 13, 2025 at 10:33 PM
It made me so happy to see that MMWR is back!
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.
...
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.
...
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...
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...
USDA milk testing shows different strain of H5N1 bird flu in Nevada dairy herds
The USDA said four Nevada dairy herds were infected with an H5N1 bird flu strain that has circulated in wild birds, making prospects for containment in cows appear dim.
www.statnews.com
February 5, 2025 at 8:00 PM
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.
...
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.
...
Reposted by Louise H. Moncla
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.
Title: Intensive transmission in wild, migratory birds drove rapid geographic dissemination and repeated spillovers of #H5N1 #birdflu into agriculture in North America.
February 3, 2025 at 8:35 PM
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.
Title: Intensive transmission in wild, migratory birds drove rapid geographic dissemination and repeated spillovers of #H5N1 #birdflu into agriculture in North America.
Reposted by Louise H. Moncla
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.”
“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.”
January 28, 2025 at 12:45 AM
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.”
“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.”
Call your senators! Do it today! It's better than wallowing
January 28, 2025 at 2:55 PM
Call your senators! Do it today! It's better than wallowing
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...
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...
www.biorxiv.org
January 10, 2025 at 10:21 PM
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...
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?
January 10, 2025 at 9:44 PM
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?
Reposted by Louise H. Moncla
Really proud to share our preprint describing early adaptation of H5N1 to US dairy cattle, and showing how these mutations enhance the ability of the virus to infect other mammals, such as pigs and humans.
With @influenzal.bsky.social @vidhid.bsky.social @drclairesmith.bsky.social and many more!
With @influenzal.bsky.social @vidhid.bsky.social @drclairesmith.bsky.social and many more!
Polymerase mutations underlie adaptation of H5N1 influenza virus to dairy cattle and other mammals.
In early 2024, an unprecedented outbreak of H5N1 high pathogenicity avian influenza was detected in dairy cattle in the USA. The epidemic remains uncontrolled, with spillbacks into poultry, wild birds...
www.biorxiv.org
January 7, 2025 at 7:59 AM
Really proud to share our preprint describing early adaptation of H5N1 to US dairy cattle, and showing how these mutations enhance the ability of the virus to infect other mammals, such as pigs and humans.
With @influenzal.bsky.social @vidhid.bsky.social @drclairesmith.bsky.social and many more!
With @influenzal.bsky.social @vidhid.bsky.social @drclairesmith.bsky.social and many more!
Reposted by Louise H. Moncla
Really excited to share that my postdoctoral work on HPAI in North America is now preprinted! Please feel free to reach out with any feedback and thoughts! www.biorxiv.org/content/10.1...
Intensive transmission in wild, migratory birds drove rapid geographic dissemination and repeated spillovers of H5N1 into agriculture in North America
Since late 2021, a panzootic of highly pathogenic H5N1 avian influenza virus has driven significant morbidity and mortality in wild birds, domestic poultry, and mammals. In North America, infections i...
www.biorxiv.org
December 20, 2024 at 10:44 PM
Really excited to share that my postdoctoral work on HPAI in North America is now preprinted! Please feel free to reach out with any feedback and thoughts! www.biorxiv.org/content/10.1...
Just in time for the holidays, our lab has just submitted our first lab led paper www.biorxiv.org/content/10.1...! We use phylodynamics to reconstruct how H5N1 got to North America and spread so rapidly. Full thread coming post holidays, but for now, super proud of @lambod50.bsky.social
Intensive transmission in wild, migratory birds drove rapid geographic dissemination and repeated spillovers of H5N1 into agriculture in North America
Since late 2021, a panzootic of highly pathogenic H5N1 avian influenza virus has driven significant morbidity and mortality in wild birds, domestic poultry, and mammals. In North America, infections i...
www.biorxiv.org
December 20, 2024 at 10:44 PM
Just in time for the holidays, our lab has just submitted our first lab led paper www.biorxiv.org/content/10.1...! We use phylodynamics to reconstruct how H5N1 got to North America and spread so rapidly. Full thread coming post holidays, but for now, super proud of @lambod50.bsky.social
Reposted by Louise H. Moncla
Senior Postdoctoral Research position open in EEB Princeton puwebp.princeton.edu/AcadHire/app...
puwebp.princeton.edu
December 9, 2024 at 6:29 PM
Senior Postdoctoral Research position open in EEB Princeton puwebp.princeton.edu/AcadHire/app...
Reposted by Louise H. Moncla
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
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
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
www.science.org
December 6, 2024 at 12:54 PM
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
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