Genomic surveillance of SARS-CoV-2 Omicron variants on a university campus

Novel variants continue to emerge in the SARS-CoV-2 pandemic. University testing programs may provide timely epidemiologic and genomic surveillance data to inform public health responses. We conducted testing from September 2021 to February 2022 in a university setting and indoor CoV-2 by RT-PCR; whole genome sequencing identified 209 Delta and 1,730 Omicron genomes of the 1,939 total sequenced. Compared to Delta, Omicron had a shorter median serial interval between genetically identical, symptomatic infections within households (2 versus 6 days, P = 0.021). Omicron also demonstrated a greater basic reproductive number (2.4 versus 1.8), and a 1.07 (95% confidence interval: 0.58, 1.57; P < 0.0001) higher mean case value. Despite near universal vaccination and stringent mitigation measures, Omicron rapidly displaced the Delta variant to become the predominant viral strain and led to a surge in cases in a university population.

Ana A Weil, Kyle G Luiten, Amanda M Casto, Julia C Bennett, Jessica O'Hanlon, Peter D Han, Luis S Gamboa, Evan McDermott, Melissa Truong, Geoffrey S Gottlieb, Zack Acker, Caitlin R Wolf, Ariana Magedson, Eric J Chow, Natalie K Lo, Lincoln C Pothan, Devon McDonald, Tessa C Wright, Kathryn M McCaffrey, Marlin D Figgins, Janet A Englund, Michael Boeckh, Christina M Lockwood, Deborah A Nickerson, Jay Shendure, Trevor Bedford, James P Hughes, Lea M Starita, Helen Y Chu