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Genomic surveillance of SARS-CoV-2 Omicron variants on a university campus.
Weil, Ana A; Luiten, Kyle G; Casto, Amanda M; Bennett, Julia C; O'Hanlon, Jessica; Han, Peter D; Gamboa, Luis S; McDermot, Evan; Truong, Melissa; Gottlieb, Geoffrey S; Acker, Zack; Wolf, Caitlin R; Magedson, Ariana; Chow, Eric J; Lo, Natalie K; Pothan, Lincoln C; McDonald, Devon; Wright, Tessa C; McCaffrey, Kathryn M; Figgins, Marlin D; Englund, Janet A; Boeckh, Michael; Lockwood, Christina M; Nickerson, Deborah A; Shendure, Jay; Bedford, Trevor; Hughes, James P; Starita, Lea M; Chu, Helen Y.
  • Weil AA; Department of Medicine, University of Washington, Seattle, WA, USA. anaweil@uw.edu.
  • Luiten KG; Department of Medicine, University of Washington, Seattle, WA, USA.
  • Casto AM; Department of Medicine, University of Washington, Seattle, WA, USA.
  • Bennett JC; Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
  • O'Hanlon J; Department of Medicine, University of Washington, Seattle, WA, USA.
  • Han PD; Department of Medicine, University of Washington, Seattle, WA, USA.
  • Gamboa LS; Brotman Baty Institute, Seattle, WA, USA.
  • McDermot E; Department of Genome Sciences, University of Washington, Seattle, WA, USA.
  • Truong M; Brotman Baty Institute, Seattle, WA, USA.
  • Gottlieb GS; Department of Genome Sciences, University of Washington, Seattle, WA, USA.
  • Acker Z; Brotman Baty Institute, Seattle, WA, USA.
  • Wolf CR; Brotman Baty Institute, Seattle, WA, USA.
  • Magedson A; Department of Medicine, University of Washington, Seattle, WA, USA.
  • Chow EJ; Environmental Health & Safety Department, University of Washington, Seattle, WA, USA.
  • Lo NK; Department of Global Health, University of Washington, Seattle, WA, USA.
  • Pothan LC; Brotman Baty Institute, Seattle, WA, USA.
  • McDonald D; Department of Medicine, University of Washington, Seattle, WA, USA.
  • Wright TC; Department of Medicine, University of Washington, Seattle, WA, USA.
  • McCaffrey KM; Department of Medicine, University of Washington, Seattle, WA, USA.
  • Figgins MD; Department of Medicine, University of Washington, Seattle, WA, USA.
  • Englund JA; Brotman Baty Institute, Seattle, WA, USA.
  • Boeckh M; Department of Global Health, University of Washington, Seattle, WA, USA.
  • Lockwood CM; Department of Medicine, University of Washington, Seattle, WA, USA.
  • Nickerson DA; Department of Medicine, University of Washington, Seattle, WA, USA.
  • Shendure J; Brotman Baty Institute, Seattle, WA, USA.
  • Bedford T; Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
  • Hughes JP; Seattle Children's Research Institute, Department of Pediatrics, University of Washington, Seattle, WA, USA.
  • Starita LM; Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
  • Chu HY; Brotman Baty Institute, Seattle, WA, USA.
Nat Commun ; 13(1): 5240, 2022 09 06.
Article in English | MEDLINE | ID: covidwho-2008277
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.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: SARS-CoV-2 / COVID-19 Type of study: Observational study Topics: Vaccines / Variants Limits: Humans Language: English Journal: Nat Commun Journal subject: Biology / Science Year: 2022 Document Type: Article Affiliation country: S41467-022-32786-z

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Full text: Available Collection: International databases Database: MEDLINE Main subject: SARS-CoV-2 / COVID-19 Type of study: Observational study Topics: Vaccines / Variants Limits: Humans Language: English Journal: Nat Commun Journal subject: Biology / Science Year: 2022 Document Type: Article Affiliation country: S41467-022-32786-z