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Multimodal surveillance of SARS-CoV-2 at a university enables development of a robust outbreak response framework.
Petros, Brittany A; Paull, Jillian S; Tomkins-Tinch, Christopher H; Loftness, Bryn C; DeRuff, Katherine C; Nair, Parvathy; Gionet, Gabrielle L; Benz, Aaron; Brock-Fisher, Taylor; Hughes, Michael; Yurkovetskiy, Leonid; Mulaudzi, Shandukani; Leenerman, Emma; Nyalile, Thomas; Moreno, Gage K; Specht, Ivan; Sani, Kian; Adams, Gordon; Babet, Simone V; Baron, Emily; Blank, Jesse T; Boehm, Chloe; Botti-Lodovico, Yolanda; Brown, Jeremy; Buisker, Adam R; Burcham, Timothy; Chylek, Lily; Cronan, Paul; Dauphin, Ann; Desreumaux, Valentine; Doss, Megan; Flynn, Belinda; Gladden-Young, Adrianne; Glennon, Olivia; Harmon, Hunter D; Hook, Thomas V; Kary, Anton; King, Clay; Loreth, Christine; Marrs, Libby; McQuade, Kyle J; Milton, Thorsen T; Mulford, Jada M; Oba, Kyle; Pearlman, Leah; Schifferli, Mark; Schmidt, Madelyn J; Tandus, Grace M; Tyler, Andy; Vodzak, Megan E.
  • Petros BA; 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 S
  • Paull JS; 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. Electronic address: jpaull@broadinstitute.org.
  • Tomkins-Tinch CH; Broad 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.
  • Loftness BC; 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, Unive
  • DeRuff KC; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
  • Nair P; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
  • Gionet GL; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
  • Benz A; Degree Analytics, Inc., Austin, TX 78758, USA.
  • Brock-Fisher T; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
  • Hughes M; Colorado Mesa University, Grand Junction, CO 81501, USA.
  • Yurkovetskiy L; Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA.
  • Mulaudzi S; Harvard Program in Bioinformatics and Integrative Genomics, Harvard Medical School, Boston, MA 02115, USA.
  • Leenerman E; Colorado Mesa University, Grand Junction, CO 81501, USA.
  • Nyalile T; Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA.
  • Moreno GK; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
  • Specht I; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
  • Sani K; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
  • Adams G; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
  • Babet SV; Department of Civil, Environmental, and Architectural Engineering, University of Colorado, Boulder, CO 80309, USA.
  • Baron E; COVIDCheck Colorado, LLC, Denver, CO 80202, USA.
  • Blank JT; Colorado Mesa University, Grand Junction, CO 81501, USA.
  • Boehm C; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Princeton University Molecular Biology Department, Princeton, NJ 08544, USA.
  • Botti-Lodovico Y; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
  • Brown J; Colorado Mesa University, Grand Junction, CO 81501, USA.
  • Buisker AR; Colorado Mesa University, Grand Junction, CO 81501, USA.
  • Burcham T; Fathom Information Design, Boston, MA 02114, USA.
  • Chylek L; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
  • Cronan P; Fathom Information Design, Boston, MA 02114, USA.
  • Dauphin A; Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA.
  • Desreumaux V; Department of Civil, Environmental, and Architectural Engineering, University of Colorado, Boulder, CO 80309, USA.
  • Doss M; Warrior Diagnostics, Inc., Loveland, CO 80538, USA.
  • Flynn B; Colorado Mesa University, Grand Junction, CO 81501, USA.
  • Gladden-Young A; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
  • Glennon O; Fathom Information Design, Boston, MA 02114, USA.
  • Harmon HD; Colorado Mesa University, Grand Junction, CO 81501, USA.
  • Hook TV; Department of Civil, Environmental, and Architectural Engineering, University of Colorado, Boulder, CO 80309, USA.
  • Kary A; Department of Biological Sciences, Colorado Mesa University, Grand Junction, CO 81501, USA.
  • King C; Department of Mathematics and Statistics, Colorado Mesa University, Grand Junction, CO 81501, USA.
  • Loreth C; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
  • Marrs L; Fathom Information Design, Boston, MA 02114, USA.
  • McQuade KJ; Department of Biological Sciences, Colorado Mesa University, Grand Junction, CO 81501, USA.
  • Milton TT; Department of Civil, Environmental, and Architectural Engineering, University of Colorado, Boulder, CO 80309, USA.
  • Mulford JM; Department of Biological Sciences, Colorado Mesa University, Grand Junction, CO 81501, USA.
  • Oba K; Fathom Information Design, Boston, MA 02114, USA.
  • Pearlman L; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
  • Schifferli M; Fathom Information Design, Boston, MA 02114, USA.
  • Schmidt MJ; Colorado Mesa University, Grand Junction, CO 81501, USA.
  • Tandus GM; Department of Civil, Environmental, and Architectural Engineering, University of Colorado, Boulder, CO 80309, USA.
  • Tyler A; Colorado Mesa University, Grand Junction, CO 81501, USA.
  • Vodzak ME; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Med (N Y) ; 2022 Sep 19.
Article in English | MEDLINE | ID: covidwho-2031561
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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Full text: Available Collection: International databases Database: MEDLINE Type of study: Diagnostic study / Experimental Studies / Prognostic study Language: English Year: 2022 Document Type: Article

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Full text: Available Collection: International databases Database: MEDLINE Type of study: Diagnostic study / Experimental Studies / Prognostic study Language: English Year: 2022 Document Type: Article