Genomic surveillance of SARS-CoV-2 Omicron variants on a university campus
Ana A. Weil, Kyle G Luiten, Amanda M. Casto, Julia C. Bennett, Jessica O’Hanlon, Peter D. Han, Luis S. Gamboa, Evan McDermot, Melissa Truong, Geoffrey S. Gottlieb, Zack Acker, Caitlin R. Wolf, Ariana Magedson, Eric J. Chow, Natalie Lo, Lincoln C. Pothan, Devon McDonald, Tessa Wright, Kathryn 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
Abstract
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 population under vaccination and indoor mask mandates. A total of 3,048 of 24,393 individuals tested positive for SARS-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 peak reproductive number (2.4 versus 1.8), and a 1.07 (95% confidence interval: 0.58, 1.57; P < 0.0001) higher mean cycle threshold 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.