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...

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...

medrxiv.org

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 ⬇️

medRxivpreprint@medrxivpreprint.bsky.social · 2y ago

JUNIPER: Reconstructing Transmission Events from Next-Generation Sequencing Data at Scale https://www.medrxiv.org/content/10.1101/2025.03.02.25323192v1

🐦‍⬛🔬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?... 🎥✨

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 · 2y ago

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...

🎉 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

🧪 #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-...

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

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.

statnews.com

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!

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...

biorxiv.org

www.cdc.gov/media/releas...

First H5 Bird Flu Death Reported in United States

A person with severe avian influenza A(H5N1) illness (

cdc.gov

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...

www.nytimes.com/2024/12/23/h...

Mpox Is Spreading in Congo’s Capital, Threatening Global Efforts to Contain the Virus

Our reporter went to Congo, where the mpox epidemic has reached the teeming capital, infecting children and their mothers, who sell sex to survive.

nytimes.com

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...

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...

biorxiv.org

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...

biorxiv.org

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...

✨ 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! 🎄💖

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

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

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

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

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

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

Here's a new starter pack for researchers at the Broad Institute of MIT and Harvard!

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/...

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

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...

science.org

Couldn’t find a virology starter pack so here’s one to get the ball rolling. Repost/reply if you are a virologist so I can find and add you to the list! go.bsky.app/SinqoJU

Our new GenSpectrum.org dashboard has finally launched! Using Influenza H5N1, RSV and SARS-CoV-2 data from INSDC and West Nile virus data from @pathoplexus.org, it enables fast and interactive analyses of genome sequencing data similar to CoV-Spectrum. 1/5

Fabulous work with colleagues in Burundi, who took up Mpox sequencing to understand the situation AND are willing to share pre-publication, shows the expanding tree, and evidence for several introductions not taking off. In progress virological.org/t/preliminar...

Preliminary analysis of 98 genomic sequences of MPXV clade Ib cases from Burundi, July to September 2024

Preliminary analysis of 98 genomic sequences of MPXV clade Ib cases from Burundi, July to September 2024 Introduction A large mpox clade Ib virus outbreak started in the province of South Kivu in th...

virological.org

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:

Study of bovine H5N1 influenza strain in ferrets. Intramammary infection leads to transmission of the virus to dams. Would be good to know what is being done to monitor disease in calves www.biorxiv.org/content/10.1...

Bovine H5N1 influenza virus infection is transmitted by milk causing mortality in suckling neonates

The spread of H5N1 clade 2.3.4.4b in dairy herds raises concerns about zoonotic transmission due to the high viral load in milk, a key point of contact between livestock and humans. H5N1 clade 2.3.4.4...

biorxiv.org