Evidence map›Paper›PMID 36198312›Full record

ArticleMed (New York, N.Y.)2022

Multimodal surveillance of SARS-CoV-2 at a university enables development of a robust outbreak response framework.

Brittany A Petros, Jillian S Paull, Christopher H Tomkins-Tinch, Bryn C Loftness, Katherine C DeRuff, Parvathy Nair, Gabrielle L Gionet, Aaron Benz, Taylor Brock-Fisher, Michael Hughes and 54 more

Open access · hybridAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Med (New York, N.Y.), 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.

0numbers the graph read from it
0cells of the map it votes in
24citing papers in PubMed
3.1field-weighted citation impact, top 7% of its field
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

24 citing papers in PubMed, 31 citations in OpenAlex.

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  8. Identifying changes in viral fitness using population genetic structure.Proceedings of the National Academy of Sciences of the United States of America · 2024
    Article
  9. Increased Pediatric Respiratory Syncytial Virus Case Counts Following the Emergence of SARS-CoV-2 Can Be Attributed to Changes in Testing.Clinical infectious diseases : an official publication of the Infectious Diseases Society of America · 2024
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  15. Review
  16. Inferring Viral Transmission Pathways from Within-Host Variation.medRxiv : the preprint server for health sciences · 2023
    Article
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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

64 authors at 9 institutions in 1 country.

Brittany A PetrosBroad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard-MIT Program in Health Sciences and Technology, Cambridge, MA 02139, USA; Harvard/MIT MD-PhD Program, Boston, MA 02115, USA; Systems, Synthetic, and Quantitative Biology PhD Program, Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.
Jillian S PaullBroad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Systems, Synthetic, and Quantitative Biology PhD Program, Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA. Electronic address: jpaull@broadinstitute.org.
Christopher H Tomkins-TinchBroad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA. Electronic address: tomkinsc@broadinstitute.org.
Bryn C LoftnessBroad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Computer Science and Engineering, Colorado Mesa University, Grand Junction, CO 81501, USA; Complex Systems and Data Science PhD Program, University of Vermont, Burlington, VT 05405, USA; Vermont Complex Systems Center, University of Vermont, Burlington, VT 05405, USA. Electronic address: bloftnes@broadinstitute.org.
Katherine C DeRuffBroad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Parvathy NairHoward Hughes Medical Institute, Chevy Chase, MD 20815, USA.
Gabrielle L GionetBroad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Aaron BenzDegree Analytics, Inc., Austin, TX 78758, USA.
Taylor Brock-FisherBroad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Michael HughesColorado Mesa University, Grand Junction, CO 81501, USA.
Leonid YurkovetskiyProgram in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA.
Shandukani MulaudziHarvard Program in Bioinformatics and Integrative Genomics, Harvard Medical School, Boston, MA 02115, USA.
Emma LeenermanColorado Mesa University, Grand Junction, CO 81501, USA.
Thomas NyalileProgram in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA.
Gage K MorenoBroad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Ivan SpechtBroad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Kian SaniBroad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Gordon AdamsBroad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Simone V BabetDepartment of Civil, Environmental, and Architectural Engineering, University of Colorado, Boulder, CO 80309, USA.
Emily BaronCOVIDCheck Colorado, LLC, Denver, CO 80202, USA.
Jesse T BlankColorado Mesa University, Grand Junction, CO 81501, USA.
Chloe BoehmBroad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Princeton University Molecular Biology Department, Princeton, NJ 08544, USA.
Yolanda Botti-LodovicoBroad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Jeremy BrownColorado Mesa University, Grand Junction, CO 81501, USA.
Adam R BuiskerColorado Mesa University, Grand Junction, CO 81501, USA.
Timothy BurchamFathom Information Design, Boston, MA 02114, USA.
Lily ChylekBroad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Paul CronanFathom Information Design, Boston, MA 02114, USA.
Ann DauphinProgram in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA.
Valentine DesreumauxDepartment of Civil, Environmental, and Architectural Engineering, University of Colorado, Boulder, CO 80309, USA.
Megan DossWarrior Diagnostics, Inc., Loveland, CO 80538, USA.
Belinda FlynnColorado Mesa University, Grand Junction, CO 81501, USA.
Adrianne Gladden-YoungBroad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Olivia GlennonFathom Information Design, Boston, MA 02114, USA.
Hunter D HarmonColorado Mesa University, Grand Junction, CO 81501, USA.
Thomas V HookDepartment of Civil, Environmental, and Architectural Engineering, University of Colorado, Boulder, CO 80309, USA.
Anton KaryDepartment of Biological Sciences, Colorado Mesa University, Grand Junction, CO 81501, USA.
Clay KingDepartment of Mathematics and Statistics, Colorado Mesa University, Grand Junction, CO 81501, USA.
Christine LorethBroad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Libby MarrsFathom Information Design, Boston, MA 02114, USA.
Kyle J McQuadeDepartment of Biological Sciences, Colorado Mesa University, Grand Junction, CO 81501, USA.
Thorsen T MiltonDepartment of Civil, Environmental, and Architectural Engineering, University of Colorado, Boulder, CO 80309, USA.
Jada M MulfordDepartment of Biological Sciences, Colorado Mesa University, Grand Junction, CO 81501, USA.
Kyle ObaFathom Information Design, Boston, MA 02114, USA.
Leah PearlmanBroad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Mark SchifferliFathom Information Design, Boston, MA 02114, USA.
Madelyn J SchmidtColorado Mesa University, Grand Junction, CO 81501, USA.
Grace M TandusDepartment of Civil, Environmental, and Architectural Engineering, University of Colorado, Boulder, CO 80309, USA.
Andy TylerColorado Mesa University, Grand Junction, CO 81501, USA.
Megan E VodzakBroad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Kelly Krohn BevillDepartment of Computer Science and Engineering, Colorado Mesa University, Grand Junction, CO 81501, USA.
Andres ColubriBroad Institute of MIT and Harvard, Cambridge, MA 02142, USA; University of Massachusetts Medical School, Worcester, MA 01655, USA.
Bronwyn L MacInnisBroad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
A Zeynep OzsoyDepartment of Biological Sciences, Colorado Mesa University, Grand Junction, CO 81501, USA.
Eric ParrieCOVIDCheck Colorado, LLC, Denver, CO 80202, USA.
Kari SholtesDepartment of Computer Science and Engineering, Colorado Mesa University, Grand Junction, CO 81501, USA; Department of Civil, Environmental, and Architectural Engineering, University of Colorado, Boulder, CO 80309, USA.
Katherine J SiddleBroad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.
Ben FryFathom Information Design, Boston, MA 02114, USA.
Jeremy LubanBroad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA; Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01655, USA; Massachusetts Consortium on Pathogen Readiness, Boston, MA 02115, USA.
Daniel J ParkBroad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
John MarshallColorado Mesa University, Grand Junction, CO 81501, USA.
Amy BronsonPhysician Assistant Program, Department of Kinesiology, Colorado Mesa University, Grand Junction, CO 81501, USA.
Stephen F SchaffnerBroad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Pardis C SabetiBroad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; Massachusetts Consortium on Pathogen Readiness, Boston, MA 02115, USA; Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA.
Broad Institute · USColorado Mesa University · USUniversity of Colorado Boulder · USHarvard University · USUniversity of Massachusetts Chan Medical School · USConcord Consortium · USHoward Hughes Medical Institute · USPrinceton University · USUniversity of Vermont · US

Funding

Viral Genomics: evolution, spread, and host interactionsU19AI110818 · NIAID · BROAD INSTITUTE, INC. · PI NEAFSEY, DANIEL E · 2014 to 2024
$66.5M
Medical Scientist Training ProgramT32GM007753 · NIGMS · HARVARD UNIVERSITY (MEDICAL SCHOOL) · PI WALENSKY, LOREN DAVID · 1985 to 2021
$50.0M
Training Program in Bioinformatics and Integrative GenomicsT32HG002295 · NHGRI · MASSACHUSETTS INSTITUTE OF TECHNOLOGY · PI Peter J Park · 2001 to 2026
$15.8M
Medical Scientist Training ProgramT32GM144273 · NIGMS · HARVARD MEDICAL SCHOOL · PI David Shumway Jones, Jacqueline A. Lees · 2022 to 2026
$14.7M
West African Emerging Infectious Disease Research Center (WA-EIDRC)U01AI151812 · NIAID · SCRIPPS RESEARCH INSTITUTE, THE · PI ANDERSEN, KRISTIAN GRAUGAARD, GARRY, ROBERT F · 2020 to 2024
$13.2M
The HUSH complex in HIV-1 latencyR37AI147868 · NIAID · UNIV OF MASSACHUSETTS MED SCH WORCESTER · PI JEREMY LUBAN · 2019 to 2026
$6.4M
Insight into the Ebola virus glycoprotein fusion mechanism gleaned from the 2013-2016 epidemic GP-A82V variantR01AI148784 · NIAID · UNIV OF MASSACHUSETTS MED SCH WORCESTER · PI LUBAN, JEREMY · 2020 to 2024
$4.1M
NHGRI NIH HHS T32 HG002295NIAID NIH HHS R01 AI148784NIAID NIH HHS R37 AI147868NIAID NIH HHS U01 AI151812NIAID NIH HHS U19 AI110818NIGMS NIH HHS T32 GM007753NIGMS NIH HHS T32 GM144273
6 · The paper itself

Abstract

backgroundUniversities are vulnerable to infectious disease outbreaks, making them ideal environments to study transmission dynamics and evaluate mitigation and surveillance measures. Here, we analyze multimodal COVID-19-associated data collected during the 2020-2021 academic year at Colorado Mesa University and introduce a SARS-CoV-2 surveillance and response framework.

methodsWe analyzed epidemiological and sociobehavioral data (demographics, contact tracing, and WiFi-based co-location data) alongside pathogen surveillance data (wastewater and diagnostic testing, and viral genomic sequencing of wastewater and clinical specimens) to characterize outbreak dynamics and inform policy. We applied relative risk, multiple linear regression, and social network assortativity to identify attributes or behaviors associated with contracting SARS-CoV-2. To characterize SARS-CoV-2 transmission, we used viral sequencing, phylogenomic tools, and functional assays.

findingsAthletes, particularly those on high-contact teams, had the highest risk of testing positive. On average, individuals who tested positive had more contacts and longer interaction durations than individuals who never tested positive. The distribution of contacts per individual was overdispersed, although not as overdispersed as the distribution of phylogenomic descendants. Corroboration via technical replicates was essential for identification of wastewater mutations.

conclusionsBased on our findings, we formulate a framework that combines tools into an integrated disease surveillance program that can be implemented in other congregate settings with limited resources.

fundingThis work was supported by the National Science Foundation, the Hertz Foundation, the National Institutes of Health, the Centers for Disease Control and Prevention, the Massachusetts Consortium on Pathogen Readiness, the Howard Hughes Medical Institute, the Flu Lab, and the Audacious Project.

Indexed as

COVID-19SARS-CoV-2Contact TracingDisease OutbreaksHumansUnited StatesUniversitiesFoundational researchgenomic epidemiologylineage characterizationmultimodal surveillancerisk identification and mitigationSARS-CoV-2social network analysisuniversity outbreak responseviral genomic sequencingwastewater sequencing methodswastewater surveillance

Identifiers

PMID36198312
PMCPMC9482833
OpenAlexW4296260841

What OpenQuestion holds

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LicenceCC BY
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Registered trials

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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.