Genomic Epidemiology of SARS-CoV-2 Transmission among University Students in Western Pennsylvania.

BACKGROUND: SARS-CoV-2 control on college campuses is challenging given communal living and student social dynamics. Understanding SARS-CoV-2 transmission among college students is important for the development of optimal control strategies.

METHODS: SARS-CoV-2 nasal swabs were collected from University of Pittsburgh students for symptomatic testing and asymptomatic surveillance from August 2020 through April 2021 from three campuses. Whole-genome sequencing (WGS) was performed on 308 samples and contact tracing information collected from students was used to identify transmission clusters.

RESULTS: We identified 31 Pangolin lineages of SARS-CoV-2, the majority belonging to B.1.1.7 (Alpha) and B.1.2 lineages. Contact tracing identified 142 (46%) students clustering with each other; WGS identified 53 putative transmission clusters involving 216 (70%) students. WGS identified transmissions that were missed by contact tracing. However, 84 (27%) cases could not be linked by either WGS or contact tracing. Clusters were most frequently linked to students residing in the same dormitory, off-campus roommates, friends, or athletic activities.

CONCLUSION: The majority of SARS-CoV-2 positive samples clustered by WGS, indicating significant transmission across campuses. The combination of WGS and contact tracing maximized the identification of SARS-CoV-2 transmission on campus. WGS can be used as a strategy to mitigate, and further prevent transmission among students.