Lightnews — Scholar-powered news

Gage Moreno @gagekmoreno.bsky.social · Apr 9

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 🤗

3

Gage Moreno @gagekmoreno.bsky.social · Apr 9

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

1 2

Gage Moreno @gagekmoreno.bsky.social · Apr 9

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

1 2

Gage Moreno @gagekmoreno.bsky.social · Apr 9

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.

1 2

Gage Moreno @gagekmoreno.bsky.social · Apr 9

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.

1 1 4

Gage Moreno @gagekmoreno.bsky.social · Apr 9

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

1 2

Gage Moreno @gagekmoreno.bsky.social · Apr 9

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.

1 2

Gage Moreno @gagekmoreno.bsky.social · Apr 9

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.

1 2

Gage Moreno @gagekmoreno.bsky.social · Apr 9

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.

1 2

Gage Moreno @gagekmoreno.bsky.social · Apr 9

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

1 2

Gage Moreno @gagekmoreno.bsky.social · Apr 9

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.

1 2

Gage Moreno @gagekmoreno.bsky.social · Apr 9

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.

1 2

Gage Moreno @gagekmoreno.bsky.social · Apr 9

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?

1 1

Gage Moreno @gagekmoreno.bsky.social · Apr 9

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

1 1

Gage Moreno @gagekmoreno.bsky.social · Apr 9

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...

www.medrxiv.org

1 6 12

Reposted by Gage Moreno

medRxivpreprint @medrxivpreprint.bsky.social · Apr 6

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

1 4

Gage Moreno @gagekmoreno.bsky.social · Mar 6

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 · Mar 6

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

1

Reposted by Gage Moreno

sabetilab.bsky.social @sabetilab.bsky.social · Feb 25

🐦‍⬛🔬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?... 🎥✨

5 8

Reposted by Gage Moreno

Louise H. Moncla @lhmoncla.bsky.social · Feb 5

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 · Feb 5

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...

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

4 25 45

Reposted by Gage Moreno

sabetilab.bsky.social @sabetilab.bsky.social · Jan 24

🎉 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

1 3

Reposted by Gage Moreno

Broadly Epi @broadlyepi.com · Jan 24

🧪 #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

7 200 850

Reposted by Gage Moreno

Scott Gottlieb, MD @scottgottliebmd.bsky.social · Jan 12

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.

www.statnews.com

4 54 190

Reposted by Gage Moreno

Tom Peacock @peacockflu.bsky.social · Jan 7

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...

www.biorxiv.org

9 160 350

Reposted by Gage Moreno

Duncan MacCannell @drm.bsky.social · Jan 7

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

First H5 Bird Flu Death Reported in United States

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

www.cdc.gov

8 9