Genomic Epidemiology of Severe Acute Respiratory Syndrome Coronavirus 2 Transmission Among University Students in Western Pennsylvania

J Infect Dis. 2023 Jun 28;228(1):37-45. doi: 10.1093/infdis/jiad041.

Abstract

Background: Severe acute respiratory syndrome coronavirus 2 (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 swab samples were collected from University of Pittsburgh students for symptomatic testing and asymptomatic surveillance from August 2020 through April 2021 from 3 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 students (46%) clustering with each other; WGS identified 53 putative transmission clusters involving 216 students (70%). WGS identified transmissions that were missed by contact tracing. However, 84 cases (27%) 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.

Conclusions: 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.

Keywords: SARS-CoV-2; contact tracing; transmission; university; whole-genome sequencing.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • COVID-19* / epidemiology
  • Genomics
  • Humans
  • Pennsylvania / epidemiology
  • SARS-CoV-2* / genetics
  • Students
  • Universities

Supplementary concepts

  • SARS-CoV-2 variants