Author selfie—but this one feels different. Our newest @sabeti_lab paper came out as conflict escalated between Israel & Iran, our birth countries. A reminder of how fragile the world can be & a reminder of what’s possible: across borders & conflict, individuals can still choose to build together.
Thank you to Sierra Leone Ministry of Health and National Public Health Agency for their inspired leadership in the #mpox response and to Danaher for supporting them by donating 10,000 Cepheid Xpert diagnostic tests
Proud of my crew @fathom.info who turned around a version of our “Lookout” platform in just six hours after receiving data for the Sierra Leone outbreak.
We've been working with Pardis and Christian since 2020, and while the circumstances are devastating, we've been building for moments like this.
Sierra Leone is battling an mpox variant, G.1, that is rapidly spreading—25% hospitalized, thousands likely infected, cases doubling every two weeks, and now detected in the US & Europe. The country is responding. The world must join them. time.com/7291478/sier...
🎉 Congrats to Dr. Laura Luebbert ( @lauraluebbert.com ) for receiving the 2025 FutureHouse Fellowship! She’ll develop AI tools to detect viral sequences in genomic data & analyze virome data from 4,000+ people. Creator of gget & champion of open science—go Laura! 🧬🙌
We’re thrilled to share that our Sentinel team (a collaboration between the @sabetilab.bsky.social & ACEGID/IGH) has been selected as a Finalist for #100andChange! 🎉
Learn more here: 100andchange.org
#100andChange #LeverforChange #SocialImpact #Philanthropy
Sharing a #studymix2025 🎶 — for @Harvard students grinding through finals 📚 #AgainstAllOdds #Statistics students prepping for #APStatistics exams 🧮 & good people everywhere wrapping up the year 🙌 —some new and old favorites that keep me inspired and grooving💥 open.spotify.com/playlist/315...
Delighted to share my tribute to Christian Happi in this year’s #TIME100.
A brilliant scientist, a relentless leader, and a dear friend—his work has transformed outbreak response across Africa, built a genomic powerhouse in Nigeria, and is inspiring a generation. @TIME
time.com/collections/...
Earlier this year, Sabeti Lab members traveled to 🇳🇬 to work with our incredible partners at ACEGID/IGH on LAMP diagnostics & Lassa virus sequencing. We're so grateful for this ongoing collaboration 🌍🤝 For more moments from the trip, check out our Instagram!
Big congratulations to Dr. Jon Arizti Sanz for being named a 2025 Schmidt Science Fellow! 🎉 The fellowship empowers early career scientists to pivot into new fields, lead interdisciplinary research, and tackle global challenges. We’re so proud of him! 💥🌍 read more -> bit.ly/4ciXAGk
We will keep a close look out, thanks to our academic and public health partnership that makes this possible. Here is a team selfie, including our project lead @drelyse.bsky.social and some of our awesome @sabetilab.bsky.social @broadinstitute.org & the Mass DPH team. (10/10)
By establishing and validating these methods, we were positioned to partner with @MassDPH and @MassDeptAgr to support mandatory H5N1 testing in milk from cattle dairy farms across the state. Starting from August 2023, and continuing today, regular testing has yet to reveal a positive result. (9/10)
At higher sample concentrations (>500 cp/uL), hybrid-selected RNA-Seq libraries produced the most complete genomes, while an Amp-Seq protocol performed best at lower concentrations. (8/10)
We were also able to produce near-complete genomes from even ultra-pasteurized milk using 3 library construction methods — RNA-Seq, hybrid-selected RNA-Seq, and Amp-Seq — and in samples with copy numbers as low as 14 H5N1 cp/uL. (7/10)
Of our 214 commercial milk samples, 55 (26%) tested positive for H5N1 RNA by dPCR, while 48 (22%) tested positive by qPCR. Most positive samples were from processing plants in four states with reported H5N1 outbreaks: Colorado, Idaho, Michigan, and Texas. (6/10)
We also assessed a variety of pre-processing and extraction protocols for H5N1 detection and sequencing. All three tested extraction kits demonstrated similar recovery, and fat content and pre-centrifugation did not significantly affect detection. (5/10)
With 214 store-bought milk samples from 20 states, we evaluated dPCR & qPCR assays for H5N1 w/primers targeting the H5 subtype of HA gene. All assays performed well w/minimal optimization – dPCR was slightly more sensitive – & bovine Ribonuclease P gene served as an effective positive control.(4/10)
The best time to set up testing is indeed before any cases, but setting up testing requires positive cases for validation. A classic conundrum, that here was solved by ready access to positive samples are our store shelves – commercial milk – and spurred by a collaboration with @BostonGlobe. (3/10)
With an H5N1 outbreak spreading through dairy cattle in multiple states, we looked to develop and optimize diagnostic and surveillance capabilities in Massachusetts before a single case had reached New England. (2/10)
The @SabetiLab is excited to share our EID journal paper “Establishing methods to monitor H5N1 influenza virus in dairy cattle milk.” A collaboration led by @drelyse.bsky.social and a partnership between @broadinstitute.org , Mass DPH, Mass Dept. of Agr., & the CDC bit.ly/42gKYLo
More thank you's to: @kgandersen.bsky.social, @dannyjpark.bsky.social , @glipsnort.bsky.social , Bronwyn MacInnis, Christian Happy, Jacob E. Lemieux, Al Ozonoff, Michael D. Mitzenmacher, and @benfry.com 16/17
Thanks to everyone involved in this project: Patrick Varilly, Mark Schifferli, Katherine Yang, @timbrrr.bsky.social , Paul Cronan, Olivia Glennon, Olivia Jacks, Ellory Laning, Libby Marrs, Kyle Oba, Shannon Yeung, @edythparker.bsky.social , Ifeanyi Omah, Jonathan Pekar, @lauraluebbert.com 16/17
Now more than ever, we're excited to see how making Bayesian phylogenetics broadly usable for a much wider audience can enhance real-time tracking and strengthen public health responses to emerging outbreaks. 15/17
While Delphy focuses on early outbreak response, its core concept—EMATs—has broader potential. Any Bayesian phylogenetics calculation can be adapted to EMATs. We welcome community efforts to integrate EMATs into existing tools for everyone's benefit.
#Phylogenetics 14/17
Delphy rethinks Bayesian phylogenetics using EMATs instead of implicit trees + Felsenstein tree likelihood, opening the door to:
⚡ Faster outbreak analysis
🎯 Better sampling
🧩 Richer modeling
📊 New analysis tools
And we’re just getting started.
13/17
We tested Delphy’s scalability with simulated outbreaks having 100 to 100K samples over 6 months of growth. Inferred trees and parameters matched ground truth in all but one case. The 100K run finished in <15 hrs (ESS 248)—likely the largest full Bayesian phylo run to date. 🚀
#ScalableTech 12/17
Stay up to date on the #H5N1 outbreak with Delphy’s daily-updated results 👉 delphy.fathom.info/us-h5n1-latest.
Uses Andersen Lab’s avian flu sequences (1944 as of Mar 22, 2025) and exact dates from GenBank.
Delphy assumes exponential growth—for now.
#OutbreakResponse 11/17
We’re now applying Delphy to the ongoing H5N1 outbreak in U.S. cattle. It captures key dynamics: 🐄 Initial spillover in TX (early 2024), 🌾 gradual spread across states, 🌄 localized CO outbreaks (spring–summer), 🌉 spread to CA (summer–fall).
#H5N1 #Phylogenetics #OutbreakResponse 10/17
By Feb 8, 2020, Delphy could've detected separate early SARS-CoV-2 introductions into Europe & N. America that exhibited onward transmission. Even as early as Feb 1, key outbreak parameters like mutation rate & tMRCA were already coming into focus.
#SARSCoV2 #Phylogenetics #OutbreakResponse 9/17
To demo Delphy as a frontline tool, we simulated how it could’ve inferred key insights week-by-week during the early SARS-CoV-2 pandemic using GISAID data—applying minimal filtering to reflect the urgency and limited knowledge of a real-time outbreak. 8/17
