Phylogeographic and genetic network assessment of COVID-19 mitigation protocols on SARS-CoV-2 transmission in university campus residencesResearch in context
Joel O. Wertheim,
Tetyana I. Vasylyeva,
Robert J. Wood,
Kalen Cantrell,
Soraya Piña Contreras,
Aryeh Feldheim,
Ravi Goyal,
Jennifer L. Havens,
Rob Knight,
Louise C. Laurent,
Niema Moshiri,
Robert Neuhard,
Shashank Sathe,
Alysson Satterlund,
Angela Scioscia,
Angela Y. Song,
Robert T. Schooley,
Cheryl M. Anderson,
Natasha K. Martin,
Stefan Aigner,
Kristian G. Andersen,
Nathan A. Baer,
Maryann Betty,
Amanda Birmingham,
Anelizze Castro-Martinez,
Willi Cheung,
Peter De Hoff,
Kathleen M. Fisch,
Alison J. King,
Karthik Gangavarapu,
Abbas Hakim,
Benjamin Henson,
Kristen Jepsen,
Christina H. Mac,
Toan T. Ngo,
Kelly N. Nguyen,
Tyler R. Ostrander,
Sarah Perkins,
Ashley Plascencia,
Andrea Rivera,
Ariana Rivera,
Rodolfo A. Salido,
Kieran C. Saucedo,
Madison Schwab,
Allison L. Steedman,
Anthony Veder,
Alana Weiss,
Gene W. Yeo,
Mark Zeller
Affiliations
Joel O. Wertheim
Department of Medicine, University of California San Diego, La Jolla, CA, USA; Corresponding author.
Tetyana I. Vasylyeva
Department of Medicine, University of California San Diego, La Jolla, CA, USA; Department of Population Health and Disease Prevention, University of California Irvine, Irvine, CA, USA
Robert J. Wood
Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA
Kalen Cantrell
Department of Computer Science & Engineering, University of California San Diego, La Jolla, CA, USA
Soraya Piña Contreras
Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA
Aryeh Feldheim
Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA
Ravi Goyal
Department of Medicine, University of California San Diego, La Jolla, CA, USA
Jennifer L. Havens
Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA, USA
Rob Knight
Department of Pediatrics, University of California San Diego, La Jolla, CA, USA; Department of Bioengineering, University of California San Diego, La Jolla, CA, USA; Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA; Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA; Halıcıoğlu Data Science Institute, University of California San Diego, La Jolla, CA, USA
Louise C. Laurent
Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, CA, USA; University of California San Diego, La Jolla, CA, USA
Niema Moshiri
Department of Computer Science & Engineering, University of California San Diego, La Jolla, CA, USA
Robert Neuhard
University of California San Diego, La Jolla, CA, USA
Shashank Sathe
Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, CA, USA; University of California San Diego, La Jolla, CA, USA
Alysson Satterlund
University of California San Diego, La Jolla, CA, USA
Angela Scioscia
Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA
Angela Y. Song
University of California San Diego, La Jolla, CA, USA
Robert T. Schooley
Department of Medicine, University of California San Diego, La Jolla, CA, USA
Cheryl M. Anderson
Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA
Natasha K. Martin
Department of Medicine, University of California San Diego, La Jolla, CA, USA
Summary: Background: Congregate living provides an ideal setting for SARS-CoV-2 transmission in which many outbreaks and superspreading events occurred. To avoid large outbreaks, universities turned to remote operations during the initial COVID-19 pandemic waves in 2020 and 2021. In late-2021, the University of California San Diego (UC San Diego) facilitated the return of students to campus with comprehensive testing, vaccination, masking, wastewater surveillance, and isolation policies. Methods: We performed molecular epidemiological and phylogeographic analysis of 4418 SARS-CoV-2 genomes sampled from UC San Diego students during the Omicron waves between December 2021 and September 2022, representing 58% of students with confirmed SARS-CoV-2 infection. We overlaid these analyses across on-campus residential information to assess the spread and persistence of SARS-CoV-2 within university residences. Findings: Within campus residences, SARS-CoV-2 transmission was frequent among students residing in the same room or suite. However, a quarter of pairs of suitemates with concurrent infections had distantly related viruses, suggesting separate sources of infection during periods of high incidence in the surrounding community. Students with concurrent infections residing in the same building were not at substantial increased probability of being members of the same transmission cluster. Genetic network and phylogeographic inference indicated that only between 3.1 and 12.4% of infections among students could be associated with transmission within buildings outside of individual suites. The only super-spreading event we detected was related to a large event outside campus residences. Interpretation: We found little evidence for sustained SARS-CoV-2 transmission within individual buildings, aside from students who resided in the same suite. Even in the face of heightened community transmission during the 2021–2022 Omicron waves, congregate living did not result in a heightened risk for SARS-CoV-2 transmission in the context of the multi-pronged mitigation strategy. Funding: SEARCH Alliance: Centers for Disease Control and Prevention (CDC) BAA (75D301-22-R-72097) and the Google Cloud Platform Research Credits Program. J.O.W.: NIH–NIAID (R01 AI135992). T.I.V.: Branco Weiss Fellowship and Newkirk Fellowship. L.L.: University of California San Diego.
