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

Nat Commun. 2022 Sep 6;13(1):5240. doi: 10.1038/s41467-022-32786-z.


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.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • COVID-19* / epidemiology
  • COVID-19* / prevention & control
  • Genome, Viral / genetics
  • Genomics
  • Humans
  • RNA, Viral / analysis
  • RNA, Viral / genetics
  • SARS-CoV-2* / genetics
  • Universities


  • RNA, Viral

Supplementary concepts

  • SARS-CoV-2 variants