Omicron-associated mutations were documented during November 2021, at least a week before the first U.S. case identified via clinical testing on December 1 in community wastewater according to a new report from the Centers for Disease Control and Prevention (CDC). The detection of Omicron-associated mutations in community wastewater provides strong early evidence that the Omicron variant was likely present in California, Colorado, New York, and Texas in November, before it was found by clinical testing.
Variant tracking data from wastewater can be used as a complement to clinical testing for early detection of emerging variants, which can help guide decisions about allocation of clinical and public health resources, testing strategies, and public health messaging.
The United States designated the B.1.1.529 (Omicron) variant of SARS-CoV-2 a variant of concern on November 30, 2021, and the first U.S. Omicron COVID-19 case was reported on December 1. By December 18, Omicron was estimated to account for 37.9% of U.S. COVID-19 cases. Early warning systems, such as sewage (wastewater) surveillance, can help track the spread of SARS-CoV-2 variants across communities.
The wastewater surveillance programs in the four states were the first to detect evidence of Omicron in community wastewater. Variant tracking data from wastewater cannot confirm the presence of a specific variant because the methods used cannot determine whether all variant-defining mutations are present on a single genome.
However, conditions that increase confidence in the results include detection of multiple variant-associated mutations; linked mutations (i.e., on the same sequence read), or unique mutations not shared by other known variants; RNA concentration data consistent with emergence (e.g., low initial concentrations, increasing over time); the reporting of clinical cases in the area; detections in consecutive samples or via multiple methods; and RNA concentration or sequence abundance data for multiple variant-associated mutations trending together.
The National Wastewater Surveillance System (NWSS) comprises 43 health departments funded by CDC to provide data on presence of and trends in SARS-CoV-2 infections that are independent of clinical testing. In addition to total SARS-CoV-2 testing, some health departments track SARS-CoV-2 variants by detecting variant-associated mutations in wastewater.
Health departments in four states (California, Colorado, New York, and Texas) were the first wastewater surveillance programs to detect evidence of Omicron in community wastewater. The CDC report describes the initial detections in wastewater during November 21–December 16, 2021, and the interpretative framework for these types of data.