Notes from the Field: Early Evidence of the SARS-CoV-2 B.1.1.529 (Omicron) Variant in Community Wastewater — United States, November–December 2021

Early Evidence of the SARS-CoV-2 B.1.1.529 (Omicron) Variant in Community Wastewater — United States, November–December 2021 Amy E. Kirby, PhD1; Rory M. Welsh, PhD1; Zachary A. Marsh, MPH1; Alexander T. Yu, PhD2; Duc J. Vugia, MD2; Alexandria B. Boehm, PhD3; Marlene K. Wolfe, PhD4; Bradley J. White5; Shannon R. Matzinger, PhD6; Allison Wheeler, MSPH6; Laura Bankers, PhD6; Kevin Andresen, MPH6; Cristal Salatas, MSGH6; New York City Department of Environmental Protection; Devon A. Gregory, PhD7,8,9; Marc C. Johnson, PhD7; Monica Trujillo, PhD10; Sherin Kannoly, PhD8; Davida S. Smyth, PhD11; John J. Dennehy, PhD8,9; Nicolae Sapoval12; Katherine Ensor, PhD12; Todd Treangen, PhD12; Lauren B. Stadler, PhD12; Loren Hopkins, PhD12,13

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. This report describes the initial detections in wastewater during November 21-December 16, 2021, and the interpretative framework for these types of data. This activity was reviewed by CDC and was conducted consistent with applicable federal law and CDC policy. §

California
The California Department of Public Health and academic partners use mutation-specific reverse transcription-polymerase chain reaction (RT-PCR) and sequencing to track  (Table). Results from these samples were available on December 2; at that time, two clinical COVID-19 cases attributed to Omicron had been identified in California, but none from these communities. By December 17, del143-145 mutations were detected at all 10 sampled sewersheds in California communities.

Colorado
The Colorado Department of Public Health and Environment conducts biweekly SARS-CoV-2 wastewater testing at 21 sewersheds, § § using sequencing to track variants. Thirteen Omicron-associated mutations were detected in a sample collected on December 2, 2021. At that time, only one travelassociated Omicron case had been reported in Colorado. No Omicron-associated mutations were detected in the samples collected on December 6; however, by December 16, Omicronassociated mutations were detected at 19 of 21 sewersheds.

New York City
The New York City Department of Environmental Protection tracks variants in wastewater by sequencing weekly samples collected from 14 sewersheds ¶ ¶, *** (3). Twelve Omicron-associated mutations were detected in a sample collected on November 21. By December 4, the date the wastewater data were reported, one Omicron case had been identified in a resident of the sewershed. Samples collected on November 28 from this same sewershed and from another sewershed contained Omicron-associated mutations, as reported to the health department on December 17.

Houston, Texas
The Houston Health Department conducts weekly wastewater testing at 39 sewersheds in the city and uses sequencing to ¶ Quantitative SARS-CoV-2 measurements in untreated sewage can provide information on changes in total SARS-CoV-2 infection in the community contributing to that wastewater treatment plant. That area is known as the sewershed. ** https://www.protocols.io/view/quantification-of-sars-cov-  track variants. † † † Sequencing detected six Omicron-associated mutations in samples collected on November 29 from seven sewersheds across the city. The first clinical detection of Omicron in the city was reported on December 1. The number of Omicron-positive sites, as well as the number of Omicronassociated mutations detected, increased over the subsequent 2 weeks.

Discussion
The wastewater surveillance programs in these 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 † † † https://www.medrxiv.org/content/10.1101/2021.09.08.21263279v1 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 variantassociated mutations trending together. Limitations of variant tracking in wastewater include detections inconsistent with the current epidemiology, low quality sequence data, sporadic detections, detection of a single variant-associated mutation, and conflicting trends in concentration or abundance data for mutations associated with the same variant. Reporting times >1 week can limit the usefulness of this data.
The detection of Omicron-associated mutations in community wastewater provides strong early evidence that the Omicron variant was likely present or more widely distributed in these communities than originally indicated by clinical testing alone; 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. 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.