Baseline Sequencing Surveillance of Public Clinical Testing, Hospitals, and Community Wastewater Reveals Rapid Emergence of SARS-CoV-2 Omicron Variant of Concern in Arizona, USA
Matthew F. Smith, Steven C. Holland, Mihyun B. Lee, James C. Hu, Nghia C. Pham, Regan A. Sullins, LaRinda A. Holland, Tianchen Mu, Alexis W. Thomas, Remington Fitch, Erin M. Driver, Rolf U. Halden, Michelle Villegas-Gold, Sheri Sanders, Jennifer L. Krauss, Lora Nordstrom, Mary Mulrow, Michael White, Vel Murugan, Efrem S. Lim
Abstract
SARS-CoV-2 continues to evolve new variants throughout the pandemic. However, the temporal dynamics of how SARS-CoV-2 variants emerge to become the dominant circulating variant is not precisely known. Genomic sequencing surveillance offers unique insights into how SARS-CoV-2 spreads in communities and the lead-up to hospital cases during a surge. Specifically, baseline sequencing surveillance through random selection of positive diagnostic specimens provides a representative outlook of the virus lineages circulating in a geographic region. Here, we investigated the emergence of the Omicron variant of concern in Arizona by leveraging baseline genomic sequence surveillance of public clinical testing, hospitals, and community wastewater. We tracked the spread and evolution of the Omicron variant as it first emerged in the general public, and its rapid shift in hospital admissions in the state health system. This study demonstrates the timescale of public health preparedness needed to respond to an antigenic shift in SARS-CoV-2.