Gage Moreno
@gagekmoreno.bsky.social
Postdoc in the Sabeti Lab. Interested in the genomic epidemiology, evolution, and pathogenicity of RNA viruses 🦠🏳️🌈
Pinned
Gage Moreno
@gagekmoreno.bsky.social
· Apr 9
Geospatial and demographic patterns of SARS-CoV-2 spread in Massachusetts from over 130,000 genomes
Despite intensive study, gaps remain in our understanding of SARS-CoV-2 transmission patterns during the COVID-19 pandemic, in part due to limited contextual metadata accompanying most large genomic s...
www.medrxiv.org
I’m thrilled to share our latest preprint! We analyzed >130,000 SARS-CoV-2 genomes from MA to investigate complex transmission dynamics—from statewide patterns, within specific facilities, and at the individual level 🦠🧬
Check out the preprint here ⬇️
www.medrxiv.org/content/10.1...
Check out the preprint here ⬇️
www.medrxiv.org/content/10.1...
I’m thrilled to share our latest preprint! We analyzed >130,000 SARS-CoV-2 genomes from MA to investigate complex transmission dynamics—from statewide patterns, within specific facilities, and at the individual level 🦠🧬
Check out the preprint here ⬇️
www.medrxiv.org/content/10.1...
Check out the preprint here ⬇️
www.medrxiv.org/content/10.1...
Geospatial and demographic patterns of SARS-CoV-2 spread in Massachusetts from over 130,000 genomes
Despite intensive study, gaps remain in our understanding of SARS-CoV-2 transmission patterns during the COVID-19 pandemic, in part due to limited contextual metadata accompanying most large genomic s...
www.medrxiv.org
April 9, 2025 at 7:11 PM
I’m thrilled to share our latest preprint! We analyzed >130,000 SARS-CoV-2 genomes from MA to investigate complex transmission dynamics—from statewide patterns, within specific facilities, and at the individual level 🦠🧬
Check out the preprint here ⬇️
www.medrxiv.org/content/10.1...
Check out the preprint here ⬇️
www.medrxiv.org/content/10.1...
Reposted by Gage Moreno
Geospatial and demographic patterns of SARS-CoV-2 spread in Massachusetts from over 130,000 genomes https://www.medrxiv.org/content/10.1101/2025.04.04.25324273v1
April 6, 2025 at 3:43 PM
Geospatial and demographic patterns of SARS-CoV-2 spread in Massachusetts from over 130,000 genomes https://www.medrxiv.org/content/10.1101/2025.04.04.25324273v1
Excited to have played a small role in this one! Outbreak reconstruction tool that incorporates within-host variants, models missing data, and scales to large, sparsely sampled datasets. Check it out ⬇️
JUNIPER: Reconstructing Transmission Events from Next-Generation Sequencing Data at Scale https://www.medrxiv.org/content/10.1101/2025.03.02.25323192v1
March 6, 2025 at 4:29 PM
Excited to have played a small role in this one! Outbreak reconstruction tool that incorporates within-host variants, models missing data, and scales to large, sparsely sampled datasets. Check it out ⬇️
Reposted by Gage Moreno
🐦⬛🔬Bird Flu (H5N1) – what’s the deal? 🤔
@pardissabeti.bsky.social joined @scishow.bsky.social
to break it all down—its origins, where it stands today, and why it matters. 🦠🐦 Here’s a sneak peek! 👀 Want the full story? Head to the SciShow's YouTube channel: youtu.be/5CyVi4UzKxE?... 🎥✨
@pardissabeti.bsky.social joined @scishow.bsky.social
to break it all down—its origins, where it stands today, and why it matters. 🦠🐦 Here’s a sneak peek! 👀 Want the full story? Head to the SciShow's YouTube channel: youtu.be/5CyVi4UzKxE?... 🎥✨
February 25, 2025 at 4:58 PM
🐦⬛🔬Bird Flu (H5N1) – what’s the deal? 🤔
@pardissabeti.bsky.social joined @scishow.bsky.social
to break it all down—its origins, where it stands today, and why it matters. 🦠🐦 Here’s a sneak peek! 👀 Want the full story? Head to the SciShow's YouTube channel: youtu.be/5CyVi4UzKxE?... 🎥✨
@pardissabeti.bsky.social joined @scishow.bsky.social
to break it all down—its origins, where it stands today, and why it matters. 🦠🐦 Here’s a sneak peek! 👀 Want the full story? Head to the SciShow's YouTube channel: youtu.be/5CyVi4UzKxE?... 🎥✨
Reposted by Gage Moreno
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 Gage Moreno
🎉 Huge congrats to Dr. Jon Arizti Sanz for winning the 2025 Imperial Alumni Award from his alma mater, @imperialcollegeldn.bsky.social! 👏 This award honors game-changers & problem-solvers, and Jon has been just that in the Sabeti Lab & beyond! Read more ->🔗 bit.ly/4htWbhD
Jon Arizti Sanz
Imperial alumnus Jon Arizti Sanz is revolutionising the field of infectious disease diagnostics and pandemic prevention.
bit.ly
January 24, 2025 at 3:58 PM
🎉 Huge congrats to Dr. Jon Arizti Sanz for winning the 2025 Imperial Alumni Award from his alma mater, @imperialcollegeldn.bsky.social! 👏 This award honors game-changers & problem-solvers, and Jon has been just that in the Sabeti Lab & beyond! Read more ->🔗 bit.ly/4htWbhD
Reposted by Gage Moreno
🧪 #PublicHealth is under attack in the US, and among those to fall may be a mainstay of #EpiSky and #MedSky : The CDC's MMWR. We at Broadly Epi want to introduce an open, searchable MMWR database as a response. It's a work in progress, but we will keep at it. www.broadlyepi.com/broadly-epi-...
Broadly Epi MMWR Archive Database - Broadly Epi
Explore Public Health Records with the Broadly Epi MMWR Archive Database What is the Broadly Epi MMWR Archive Database? Created as a collaborative effort among…
www.broadlyepi.com
January 24, 2025 at 12:55 AM
🧪 #PublicHealth is under attack in the US, and among those to fall may be a mainstay of #EpiSky and #MedSky : The CDC's MMWR. We at Broadly Epi want to introduce an open, searchable MMWR database as a response. It's a work in progress, but we will keep at it. www.broadlyepi.com/broadly-epi-...
Reposted by Gage Moreno
Robust disease surveillance for novel pathogens isn’t just a matter of public health preparedness, but also national security, and need to guard against deliberate threats. As the tools for engineering dangerous pathogens become more ubiquitous, threats increase
My essay in @statnews.com
My essay in @statnews.com
Continuing surveillance of emerging disease threats is vital for public health, national security
“Basic public health protections help augment our national security protections,” particularly when it comes to emerging disease threats, write Scott Gottlieb and Mark B. McClellan.
www.statnews.com
January 12, 2025 at 1:16 AM
Robust disease surveillance for novel pathogens isn’t just a matter of public health preparedness, but also national security, and need to guard against deliberate threats. As the tools for engineering dangerous pathogens become more ubiquitous, threats increase
My essay in @statnews.com
My essay in @statnews.com
Reposted by Gage Moreno
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 Gage Moreno
Reposted by Gage Moreno
North American HPAI panzootic was driven by ∼8 independent introductions into North America via the Atlantic and Pacific Flyways. Transmission via Anseriformes, shorebirds, Galliformes. Songbirds, raptors, and owls dead-end hosts (1/2)
👉 biorxiv.org/content/10.1...
👉 biorxiv.org/content/10.1...
January 6, 2025 at 12:30 AM
North American HPAI panzootic was driven by ∼8 independent introductions into North America via the Atlantic and Pacific Flyways. Transmission via Anseriformes, shorebirds, Galliformes. Songbirds, raptors, and owls dead-end hosts (1/2)
👉 biorxiv.org/content/10.1...
👉 biorxiv.org/content/10.1...
Reposted by Gage Moreno
Reposted by Gage Moreno
Fancy some light Christmas reading? I’m happy to share our new preprint, covering the impact and cutting edge improvements to PrimalScheme!
Preprint: www.biorxiv.org/content/10.1...
Preprint: www.biorxiv.org/content/10.1...
PrimalScheme: open-source community resources for low-cost viral genome sequencing
Viral genome sequencing using the ARTIC protocol has been a vital tool for understanding the spread of epidemics including Ebola, Zika, COVID-19 and Mpox and has seen widespread adoption due to its lo...
www.biorxiv.org
December 23, 2024 at 10:37 AM
Fancy some light Christmas reading? I’m happy to share our new preprint, covering the impact and cutting edge improvements to PrimalScheme!
Preprint: www.biorxiv.org/content/10.1...
Preprint: www.biorxiv.org/content/10.1...
Reposted by Gage Moreno
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 Gage Moreno
Sharing our work expanding SARS-CoV-2 style tiled amplicon sequencing for whole bacteria genomes directly from clinical samples, showing examples with M.tb (>4 mb) and Strep pneumo (>2 mb).
Led by Chaney Kalinich, Freddy Gonzalez, & Seth Redmond
www.biorxiv.org/content/10.1...
Led by Chaney Kalinich, Freddy Gonzalez, & Seth Redmond
www.biorxiv.org/content/10.1...
December 20, 2024 at 8:45 PM
Sharing our work expanding SARS-CoV-2 style tiled amplicon sequencing for whole bacteria genomes directly from clinical samples, showing examples with M.tb (>4 mb) and Strep pneumo (>2 mb).
Led by Chaney Kalinich, Freddy Gonzalez, & Seth Redmond
www.biorxiv.org/content/10.1...
Led by Chaney Kalinich, Freddy Gonzalez, & Seth Redmond
www.biorxiv.org/content/10.1...
Reposted by Gage Moreno
✨ Get a glimpse behind the scenes of this year’s holiday card! 🎥💫 Watch the magic come to life here: bit.ly/4gFdvjp
We hope it brings a little extra holiday cheer your way! 🎄💖
We hope it brings a little extra holiday cheer your way! 🎄💖
Behind the Scenes: Creating the Sabeti Lab's Holiday
Take a sneak peek into the magic behind the Sabeti Lab's holiday card! 🎄✨ A huge shoutout to our amazing holiday card crew for bringing this vision to life, and an extra-special thank you to Omayma Dalal for capturing the magic and creating this beautiful video. Happy Holidays from all of us!
bit.ly
December 19, 2024 at 5:52 PM
✨ Get a glimpse behind the scenes of this year’s holiday card! 🎥💫 Watch the magic come to life here: bit.ly/4gFdvjp
We hope it brings a little extra holiday cheer your way! 🎄💖
We hope it brings a little extra holiday cheer your way! 🎄💖
Reposted by Gage Moreno
What better way to kick off our Bluesky journey than with our annual holiday card? 🌟 Celebrate unity, humanity, and the milestones shaping a brighter future with us. Happy Holidays! 🎄✨ bit.ly/3Dsr6wk
December 19, 2024 at 5:39 PM
What better way to kick off our Bluesky journey than with our annual holiday card? 🌟 Celebrate unity, humanity, and the milestones shaping a brighter future with us. Happy Holidays! 🎄✨ bit.ly/3Dsr6wk
Reposted by Gage Moreno
Pasteurized retail dairy enables genomic surveillance of H5N1 avian influenza virus in United States cattle https://www.medrxiv.org/content/10.1101/2024.12.12.24318872v1
December 13, 2024 at 6:46 PM
Pasteurized retail dairy enables genomic surveillance of H5N1 avian influenza virus in United States cattle https://www.medrxiv.org/content/10.1101/2024.12.12.24318872v1
Reposted by Gage Moreno
There is a new alternative to the MCC summary tree in BEAST X - the 'highest independent posterior sub-tree reconstruction' or HIPSTR tree. First implemented over 5 years ago (something distracted us from writing it up) we now have a preprint describing it: www.biorxiv.org/content/10.1...
HIPSTR: highest independent posterior subtree reconstruction in TreeAnnotator X
In Bayesian phylogenetic and phylodynamic studies it is common to summarise the posterior distribution of trees with a time-calibrated consensus phylogeny. While the maximum clade credibility (MCC) tr...
eur02.safelinks.protection.outlook.com
December 11, 2024 at 1:05 PM
There is a new alternative to the MCC summary tree in BEAST X - the 'highest independent posterior sub-tree reconstruction' or HIPSTR tree. First implemented over 5 years ago (something distracted us from writing it up) we now have a preprint describing it: www.biorxiv.org/content/10.1...
Reposted by Gage Moreno
Spread-gl: visualising pathogen dispersal in a high-performance browser application https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btae721/7914009 🧬🖥️🧪 https://github.com/GuyBaele/SpreadGL
December 9, 2024 at 9:00 PM
Spread-gl: visualising pathogen dispersal in a high-performance browser application https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btae721/7914009 🧬🖥️🧪 https://github.com/GuyBaele/SpreadGL
Reposted by Gage Moreno
Today Pathoplexus announces the inclusion of a new viral pathogen: mpox (previously known as monkeypox).
Within the context of the current mpox outbreaks and ongoing health concerns, Pathoplexus aims to support sequence sharing to improve both understanding and response.
1/7
Within the context of the current mpox outbreaks and ongoing health concerns, Pathoplexus aims to support sequence sharing to improve both understanding and response.
1/7
December 9, 2024 at 7:15 PM
Today Pathoplexus announces the inclusion of a new viral pathogen: mpox (previously known as monkeypox).
Within the context of the current mpox outbreaks and ongoing health concerns, Pathoplexus aims to support sequence sharing to improve both understanding and response.
1/7
Within the context of the current mpox outbreaks and ongoing health concerns, Pathoplexus aims to support sequence sharing to improve both understanding and response.
1/7
Reposted by Gage Moreno
Here's a new starter pack for researchers at the Broad Institute of MIT and Harvard!
November 22, 2024 at 1:26 AM
Here's a new starter pack for researchers at the Broad Institute of MIT and Harvard!
Reposted by Gage Moreno
Excited to share our new preprint “Establishing methods to monitor H5N1 influenza virus in dairy cattle milk”. A HUGE collaborative effort between the Sabeti lab @broadinstitute.org and the Mass DPH and MDAR 🧵👇 (1/n)
medrxiv.org/cgi/content/...
medrxiv.org/cgi/content/...
Establishing methods to monitor H5N1 influenza virus in dairy cattle milk
Highly Pathogenic Avian Influenza strain H5N1 has caused a multi-state outbreak among US dairy cattle, spreading across 15 states and infecting hundreds of herds since its onset. We rapidly developed ...
medrxiv.org
December 6, 2024 at 2:53 PM
Excited to share our new preprint “Establishing methods to monitor H5N1 influenza virus in dairy cattle milk”. A HUGE collaborative effort between the Sabeti lab @broadinstitute.org and the Mass DPH and MDAR 🧵👇 (1/n)
medrxiv.org/cgi/content/...
medrxiv.org/cgi/content/...
Reposted by Gage Moreno
Receptor switching is one of the key steps in adaptation of animal influenza viruses to humans. Studies shows that is requires only a single mutation to do that. The widespread circulation of AI in cattle is playing with fire. www.science.org/doi/10.1126/...
A single mutation in bovine influenza H5N1 hemagglutinin switches specificity to human receptors
In 2024, several human infections with highly pathogenic clade 2.3.4.4b bovine influenza H5N1 viruses in the United States raised concerns about their capability for bovine-to-human or even human-to-h...
www.science.org
December 6, 2024 at 7:08 AM
Receptor switching is one of the key steps in adaptation of animal influenza viruses to humans. Studies shows that is requires only a single mutation to do that. The widespread circulation of AI in cattle is playing with fire. www.science.org/doi/10.1126/...