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 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 and Helen Y. Chu
Additional contact information
Ana A. Weil: University of Washington
Kyle G. Luiten: University of Washington
Amanda M. Casto: University of Washington
Julia C. Bennett: University of Washington
Jessica O’Hanlon: University of Washington
Peter D. Han: Brotman Baty Institute
Luis S. Gamboa: Brotman Baty Institute
Evan McDermot: Brotman Baty Institute
Melissa Truong: Brotman Baty Institute
Geoffrey S. Gottlieb: University of Washington
Zack Acker: Brotman Baty Institute
Caitlin R. Wolf: University of Washington
Ariana Magedson: University of Washington
Eric J. Chow: University of Washington
Natalie K. Lo: University of Washington
Lincoln C. Pothan: Brotman Baty Institute
Devon McDonald: University of Washington
Tessa C. Wright: University of Washington
Kathryn M. McCaffrey: Brotman Baty Institute
Marlin D. Figgins: Fred Hutchinson Cancer Research Center
Janet A. Englund: University of Washington
Michael Boeckh: Fred Hutchinson Cancer Research Center
Christina M. Lockwood: Brotman Baty Institute
Deborah A. Nickerson: University of Washington
Jay Shendure: Brotman Baty Institute
Trevor Bedford: Fred Hutchinson Cancer Research Center
James P. Hughes: University of Washington
Lea M. Starita: Brotman Baty Institute
Helen Y. Chu: University of Washington

Nature Communications, 2022, vol. 13, issue 1, 1-12

Abstract: 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

Date: 2022
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DOI: 10.1038/s41467-022-32786-z

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