Evidence map›Paper›PMID 40236398›Full record

ArticlemedRxiv : the preprint server for health sciences2025

Geospatial and demographic patterns of SARS-CoV-2 spread in Massachusetts from over 130,000 genomes.

Gage K Moreno, Taylor Brock-Fisher, Lydia A Krasilnikova, Steve F Schaffner, Meagan Burns, Carolyn E Casiello, Katelyn S Messer, Brittany Petros, Ivan Specht, Katherine C DeRuff and 12 more

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in medRxiv : the preprint server for health sciences, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

22 authors.

Gage K MorenoBroad Institute of Harvard and MIT, Cambridge, MA, USA.ORCID 0000-0003-4738-5318
Taylor Brock-FisherBroad Institute of Harvard and MIT, Cambridge, MA, USA.ORCID 0009-0000-5388-9315
Lydia A KrasilnikovaBroad Institute of Harvard and MIT, Cambridge, MA, USA.ORCID 0000-0003-4163-706X
Steve F SchaffnerBroad Institute of Harvard and MIT, Cambridge, MA, USA.
Meagan BurnsMassachusetts Department of Public Health, Boston, MA, USA.ORCID 0000-0001-7802-4721
Carolyn E CasielloMassachusetts Department of Public Health, Boston, MA, USA.
Katelyn S MesserBroad Institute of Harvard and MIT, Cambridge, MA, USA.
Brittany PetrosBroad Institute of Harvard and MIT, Cambridge, MA, USA.ORCID 0000-0003-2110-7475
Ivan SpechtBroad Institute of Harvard and MIT, Cambridge, MA, USA.ORCID 0000-0003-2834-8191
Katherine C DeRuffBroad Institute of Harvard and MIT, Cambridge, MA, USA.ORCID 0000-0001-6011-4323
Katherine J SiddleDepartment of Molecular Microbiology and Immunology, Brown University, Providence, RI, USA.ORCID 0000-0002-1799-7295
Christine LorethBroad Institute of Harvard and MIT, Cambridge, MA, USA.ORCID 0000-0002-9626-7820
Nicholas A FitzgeraldBroad Institute of Harvard and MIT, Cambridge, MA, USA.
Heather M RookeBroad Institute of Harvard and MIT, Cambridge, MA, USA.
Stacey B GabrielBroad Institute of Harvard and MIT, Cambridge, MA, USA.
Sandra SmoleMassachusetts Department of Public Health, Boston, MA, USA.ORCID 0000-0001-9414-8521
Shirlee WohlMassachusetts Department of Public Health, Boston, MA, USA.ORCID 0000-0002-0311-3348
Daniel J ParkBroad Institute of Harvard and MIT, Cambridge, MA, USA.
Lawrence C MadoffMassachusetts Department of Public Health, Boston, MA, USA.ORCID 0000-0003-2589-7777
Catherine M BrownMassachusetts Department of Public Health, Boston, MA, USA.
Bronwyn L MacInnisBroad Institute of Harvard and MIT, Cambridge, MA, USA.
Pardis C SabetiBroad Institute of Harvard and MIT, Cambridge, MA, USA.

Funding

Viral Genomics: evolution, spread, and host interactionsU19AI110818 · NIAID · BROAD INSTITUTE, INC. · PI SABETI, PARDIS CHRISTINE · 2014 to 2024
$66.5M
Medical Scientist Training ProgramT32GM007753 · NIGMS · HARVARD UNIVERSITY (MEDICAL SCHOOL) · PI WALENSKY, LOREN DAVID · 1985 to 2021
$50.0M
Medical Scientist Training ProgramT32GM144273 · NIGMS · HARVARD MEDICAL SCHOOL · PI David Shumway Jones, Jacqueline A. Lees · 2022 to 2026
$14.7M
Partners Healthcare Training Program in Precision and Genomic MedicineT32HG010464 · NHGRI · MASSACHUSETTS GENERAL HOSPITAL · PI HEIDI L REHM, JORDAN W SMOLLER · 2019 to 2026
$3.1M
NHGRI NIH HHS T32 HG010464NIAID NIH HHS U19 AI110818NIGMS NIH HHS T32 GM007753NIGMS NIH HHS T32 GM144273
6 · The paper itself

Abstract

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 surveillance datasets. We analyzed over 130,000 SARS-CoV-2 genomes, over 85,000 with matched epidemiological data, collected in Massachusetts from November 2021 to January 2023, to investigate viral transmission dynamics at high resolution. The data were drawn from diagnostic testing at >600 facilities representing schools, workplaces, public testing, and other sectors, and encompass the emergence of six major viral lineages, each representing a new outbreak. We found urban areas as key hubs for new lineage introduction and interurban transmission as facilitating spread throughout the state. Young adults, especially those on college campuses, served as early indicators of emerging lineage dominance. Resident-aged populations in college campuses and nursing homes exhibited a higher likelihood of being linked to within-facility transmission, while staff-aged at those facilities were more linked to their surrounding community. Individuals with recent vaccine doses, including boosters, had a lower likelihood of initiating transmission. This dataset shows the value of linking genomic and epidemiologic data at scale for higher resolution insights into viral dynamics and their implication for public health strategy.

Identifiers

PMID40236398
PMCPMC11998852

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.