I want to thank everyone involved in this huge effort:
@broadinstitute.org @broadclinicallabs.bsky.social @pardissabeti.bsky.social @lakrasil.bsky.social @dannyjpark.bsky.social @massdph.bsky.social @sabetilab.bsky.social and so many others 🤗

This study illustrates that the combination of genomic and demographic data can yield a much more detailed understanding of the complexity of transmission patterns as they unfold across different geographic scales than either type of data alone

While we recognize the scale of SARS-CoV-2 genomic surveillance is no longer feasible, sequencing 500/wk was enough to detect emerging lineages and identify growth earliest. However, sequencing 50/wk was enough to detect lineages along the same timeline as we would have otherwise

While qualitative, we saw a sharp drop in infections among 5–11-year-olds after vaccines became available to that group. This decline—seen in both school and public testing—suggests substantial short-term protection from infection.

Across two genomic methods we found that more recent vaccination and booster doses reduced the likelihood of transmission. Boosted individuals ~35% less likely to initiate transmission than unvaccinated people.

In schools, colleges, and SNFs, we found much stronger evidence of within-facility transmission among student and resident-aged than among staff-aged. Staff-aged individuals had lower viral relatedness to their facility, suggesting more involvement in community transmission

We then examined within-facility transmission across colleges, schools, SNFs, and workplaces. Facilities overall had 2.7x more closely related virus pairs (within 2 mutations from each other) than community samples—evidence of sustained transmission in these settings.

Across three major Omicron lineages, new variants reached 50% frequency in college settings 4–13 days earlier than elsewhere. This early rise wasn’t observed in when colleges were out of session (during BA.5*), suggesting unique features of colleges that accelerate spread.

We leveraged demographic information (age + facility) in our dataset to explore how different settings shaped SARS-CoV-2 transmission. Colleges, in particular, emerged as early indicators of new variant spread—often detecting variant growth days before other sectors.

We also show that SARS-CoV-2 moved more quickly between metro areas than it did to the primarily rural areas between them. Overall, we find that viruses diffuse throughout the entire state in about 2 months

New variants became prevalent more quickly in the Boston suburbs than in other regional cities, despite more frequent external introductions into the latter—highlighting the role of local transmission from initial introductions into Boston in driving early variant spread.

Using high-resolution spatial and temporal data, we tracked the introduction and spread of six Omicron lineages across Massachusetts. Urban areas played a central role—both as entry points for new lineages and as key drivers of their dissemination.

Our analyses fall into 4 main categories:
1) How do viruses enter and move within MA?
2) What are the demographic drivers of transmission?
3) How did vaccination/boosting work against infection and transmission?
4) How much sequencing did we need to detect lineages?

The Broad Clinical Labs generated >130k SC2 genomes 🧬 between Nov 2021 and Jan 2023. We were able to match >85k individuals to metadata like age, sex, city of residence, facility of collection, and vaccination status

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...

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 www.medrxiv.org/content/10.1101/2025.04....

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.
...

Jon Arizti Sanz Imperial alumnus Jon Arizti Sanz is revolutionising the field of infectious disease diagnostics and pandemic prevention.

🎉 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-...

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.

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

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...

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!

First H5 Bird Flu Death Reported in United States A person with severe avian influenza A(H5N1) illness (

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

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...

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.

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

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...

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...

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...

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...