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Petros BA, Paull JS, Tomkins-Tinch CH, Loftness BC, DeRuff KC, Nair P, Gionet GL, Benz A, Brock-Fisher T, Hughes M, Yurkovetskiy L, Mulaudzi S, Leenerman E, Nyalile T, Moreno GK, Specht I, Sani K, Adams G, Babet SV, Baron E, Blank JT, Boehm C, Botti-Lodovico Y, Brown J, Buisker AR, Burcham T, Chylek L, Cronan P, Dauphin A, Desreumaux V, Doss M, Flynn B, Gladden-Young A, Glennon O, Harmon HD, Hook TV, Kary A, King C, Loreth C, Marrs L, McQuade KJ, Milton TT, Mulford JM, Oba K, Pearlman L, Schifferli M, Schmidt MJ, Tandus GM, Tyler A, Vodzak ME, Krohn Bevill K, Colubri A, MacInnis BL, Ozsoy AZ, Parrie E, Sholtes K, Siddle KJ, Fry B, Luban J, Park DJ, Marshall J, Bronson A, Schaffner SF, Sabeti PC. Multimodal surveillance of SARS-CoV-2 at a university enables development of a robust outbreak response framework. MED 2022; 3:883-900.e13. [PMID: 36198312 PMCID: PMC9482833 DOI: 10.1016/j.medj.2022.09.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 09/06/2022] [Accepted: 09/12/2022] [Indexed: 12/27/2022]
Abstract
BACKGROUND Universities 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. METHODS We 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. FINDINGS Athletes, 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. CONCLUSIONS Based 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. FUNDING This 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.
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Affiliation(s)
- Brittany A Petros
- Broad 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 Paull
- Broad 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.
| | - Christopher H Tomkins-Tinch
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.
| | - Bryn C Loftness
- Broad 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.
| | | | - Parvathy Nair
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | | | - Aaron Benz
- Degree Analytics, Inc., Austin, TX 78758, USA
| | | | | | - Leonid Yurkovetskiy
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Shandukani Mulaudzi
- Harvard Program in Bioinformatics and Integrative Genomics, Harvard Medical School, Boston, MA 02115, USA
| | | | - Thomas Nyalile
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Gage K Moreno
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ivan Specht
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kian Sani
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Gordon Adams
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Simone V Babet
- Department of Civil, Environmental, and Architectural Engineering, University of Colorado, Boulder, CO 80309, USA
| | - Emily Baron
- COVIDCheck Colorado, LLC, Denver, CO 80202, USA
| | - Jesse T Blank
- Colorado Mesa University, Grand Junction, CO 81501, USA
| | - Chloe Boehm
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Princeton University Molecular Biology Department, Princeton, NJ 08544, USA
| | | | - Jeremy Brown
- Colorado Mesa University, Grand Junction, CO 81501, USA
| | | | | | - Lily Chylek
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Paul Cronan
- Fathom Information Design, Boston, MA 02114, USA
| | - Ann Dauphin
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Valentine Desreumaux
- Department of Civil, Environmental, and Architectural Engineering, University of Colorado, Boulder, CO 80309, USA
| | - Megan Doss
- Warrior Diagnostics, Inc., Loveland, CO 80538, USA
| | - Belinda Flynn
- Colorado Mesa University, Grand Junction, CO 81501, USA
| | | | | | | | - Thomas V Hook
- Department of Civil, Environmental, and Architectural Engineering, University of Colorado, Boulder, CO 80309, USA
| | - Anton Kary
- Department of Biological Sciences, Colorado Mesa University, Grand Junction, CO 81501, USA
| | - Clay King
- Department of Mathematics and Statistics, Colorado Mesa University, Grand Junction, CO 81501, USA
| | | | - Libby Marrs
- Fathom Information Design, Boston, MA 02114, USA
| | - Kyle J McQuade
- Department of Biological Sciences, Colorado Mesa University, Grand Junction, CO 81501, USA
| | - Thorsen T Milton
- Department of Civil, Environmental, and Architectural Engineering, University of Colorado, Boulder, CO 80309, USA
| | - Jada M Mulford
- Department of Biological Sciences, Colorado Mesa University, Grand Junction, CO 81501, USA
| | - Kyle Oba
- Fathom Information Design, Boston, MA 02114, USA
| | - Leah Pearlman
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | | | - Grace M Tandus
- Department of Civil, Environmental, and Architectural Engineering, University of Colorado, Boulder, CO 80309, USA
| | - Andy Tyler
- Colorado Mesa University, Grand Junction, CO 81501, USA
| | - Megan E Vodzak
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kelly Krohn Bevill
- Department of Computer Science and Engineering, Colorado Mesa University, Grand Junction, CO 81501, USA
| | - Andres Colubri
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; University of Massachusetts Medical School, Worcester, MA 01655, USA
| | | | - A Zeynep Ozsoy
- Department of Biological Sciences, Colorado Mesa University, Grand Junction, CO 81501, USA
| | - Eric Parrie
- COVIDCheck Colorado, LLC, Denver, CO 80202, USA
| | - Kari Sholtes
- Department 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 Siddle
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Ben Fry
- Fathom Information Design, Boston, MA 02114, USA
| | - Jeremy Luban
- Broad 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 Park
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - John Marshall
- Colorado Mesa University, Grand Junction, CO 81501, USA
| | - Amy Bronson
- Physician Assistant Program, Department of Kinesiology, Colorado Mesa University, Grand Junction, CO 81501, USA
| | | | - Pardis C Sabeti
- Broad 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
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