SARS-CoV-2 diversity and transmission on a university campus across two academic years during the pandemic

Institutions of higher education (IHEs) have been a focus of SARS-CoV-2 transmission studies but there is limited information on how viral diversity and transmission at IHEs changed as the pandemic progressed. Here we analyze 3606 viral genomes from unique COVID-19 episodes collected at a public university in Seattle, Washington (WA) from September 2020 to September 2022. Across the study period, we found evidence of frequent viral transmission among university affiliates with 60% (n=2153) of viral genomes from campus specimens genetically identical to at least one other campus specimen. Moreover, viruses from students were observed in transmission clusters at a higher frequency than in the overall dataset while viruses from symptomatic infections were observed in transmission clusters at a lower frequency. Though only a small percentage of community viruses were identified as possible descendants of viruses isolated in university study specimens, phylodynamic modelling suggested a high rate of transmission events from campus into the local community, particularly during the 2021-2022 academic year. We conclude that viral transmission was common within the university population throughout the study period but that not all university affiliates were equally likely to be involved. In addition, the transmission rate from campus into the surrounding community may have increased during the second year of the study, possibly due to return to in-person instruction. ### Competing Interest Statement GSG has received research grants and/or research support from the US National Institutes of Health, the University of Washington, the Bill & Melinda Gates Foundation, Gilead Sciences, Alere Technologies, Merck & Co., Janssen Pharmaceutica, Cerus Corporation, ViiV Healthcare, Bristol-Myers Squibb, Roche Molecular Systems, Abbott Molecular Diagnostics, and THERA Technologies/TaiMed Biologics, Inc, all outside of the submitted work. JAE reports grants to her institution from AstraZeneca, GlaxoSmithKline, Merck, and Pfizer and acts as a consultant for Abbvie, Ark Biopharma, AstraZeneca, GlaxoSmithKline, Meissa Vaccines, Merck, Moderna, Pfizer, and Sanofi Pasteur. MB has performed consulting for Allovir, Symbio, and Evrys Bio and has received research support from Merck. CML reports that her spouse is an employee of Bayer. HYC reports consulting for Ellume, Pfizer, and the Bill and Melinda Gates Foundation; has served on advisory boards for Vir, Merck and Abbvie; has conducted CME teaching with Medscape, Vindico, and Clinical Care Options; and has received research funding from Gates Ventures, and support and reagents from Ellume and Cepheid outside of the submitted work. All other authors have no competing interests to report. ### Funding Statement This work was supported by a Howard Hughes Medical Institute Covid Supplement Award to TB and by the United States Senate and House of Representatives, Bill 748, Coronavirus Aid, Relief, and Economic Security Act. MIP is an ARCS Foundation scholar. TB is a Howard Hughes Medical Institute Investigator. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: The IRB of the University of Washington gave ethical approval for this work. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes All SARS-CoV-2 genomes used in this study have been deposited to GISAID (https://gisaid.org/). Additional data and software files are available on github (https://github.com/amcasto/huskytesting\_SARSCoV2genomics\_First2Years). [https://github.com/amcasto/huskytesting\_SARSCoV2genomics\_First2Years][1] [1]: https://github.com/amcasto/huskytesting_SARSCoV2genomics_First2Years