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 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 ⬇️

🐦‍⬛🔬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. ...

🎉 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

🧪 #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

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!

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...

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...

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

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! 🎄💖

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...

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/...

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/...

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...

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...

ARTIC have primers for #Marburg virus! (MVD) labs.primalscheme.com/detail/artic... #molecularepidemiology #pathogen #pathogensurviellance #bioinformatics #epidemiology #virus #outbreak #clinicalvirology

Highly Pathogenic Avian Influenza A (H5N1) clade 2.3.4.4b Virus detected in dairy cattle https://www.biorxiv.org/content/10.1101/2024.04.16.588916v1

In a Matters Arising at Nature Communications, we discuss πN/πS for detecting within-host natural selection. We also estimate the fraction of nonsynonymous mutations that is beneficial in #SARSCoV2. Grateful to Haogao Gu & Leo Poon for the collaboration. 1/12 www.nature.com/articles/s41...

Have you been wondering what's going on with avian influenza in North America? Check out our lab's @nextstrain narrative on phylodynamic analysis of H5Nx evolution and transmission here! nextstrain.org/groups/moncl...

Excited to *finally* have @mfarjo.bsky.social 's fantastic paper on SARS-CoV-2 within-host evolutionary dynamics during acute infection published at JVI: journals.asm.org/doi/10.1128/...

I hope this preprint is useful for folks tracking SARS-CoV-2 lineages from wastewater sequences! @ssutcliffe.bsky.social led this group effort by 9 teams from 6 countries. We tested 9 tools to find & quantify lineages in a simulated mixture of BA.1, BA.2, and Delta. Some take-homes: 1/n

In new study led by Frances Welsh, we map how mutations to influenza affect neutralization by antibodies from humans of various ages   We find differences in mutation effects among age groups   Virus seems to evolve especially to escape antibodies of teenagers   www.biorxiv.org/content/10.1...

We like saliva, but we wanted to see what others think about (sp)it 🤤 My main takeaways: 1. Others do also like the idea of saliva, if they feel they can trust it. 2. Different testing experiences during the pandemic impact preferences - these should be considered before broad implementation. 🧪🧬👩‍🔬

New paper from "SEARCH" just landed! By sequencing 80k+ SARS2 genomes from San Diego & Baja, we looked at connectedness between waves since the start of the pandemic. Clear heterogeneity over time and very limited effect of the US-Mexico border 'closure'. t.co/AdtUN7VuKK

Public Service Announcement: "A popular and incorrect view on the evolution of virulence, frequently expressed in the context of SARS-CoV-2, is that in the long run, pathogens will tend to evolve to be decreasingly virulent" From www.nature.com/articles/s41...