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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
Weekly / January 21, 2022 / 71(3);103–105
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 (View author affiliations)
View suggested citationThe United States designated the B.1.1.529 (Omicron) variant of SARS-CoV-2 (the virus that causes COVID-19) a variant of concern on November 30, 2021, and the first U.S. Omicron COVID-19 case was reported on December 1 (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 (2).
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 variants in wastewater collected daily from 10 sewersheds.¶,** Omicron-associated mutations delHV69–70 (also seen with Alpha variant [B.1.1.7 and Q lineages])†† and del143–145 were detected in samples collected November 25 and November 30, 2021, from two Northern California communities (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 travel-associated Omicron case had been reported in Colorado. No Omicron-associated mutations were detected in the samples collected on December 6; however, by December 16, Omicron-associated 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 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 Omicron-associated 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 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. 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.
Acknowledgments
Rebecca Schneider, New York City Department of Health and Mental Hygiene; Houston Health Department; Houston Public Works; Pamela Brown, Yanlai Lai, Ryker Penn, Houston Health Department Bureau of Laboratory Services; Yunxi Liu, Rice University Stadler Lab and Treangen Lab; Rice University Spatial Studies Laboratory.
Corresponding author: Amy Kirby, agk1@cdc.gov.
1Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, CDC; 2California Department of Public Health; 3Stanford University, Stanford, California; 4Rollins School of Public Health, Emory University, Atlanta, Georgia; 5Verily Life Sciences, South San Francisco, California; 6Colorado Department of Public Health and Environment; 7University of Missouri-School of Medicine, Columbia, Missouri; 8Queens College, The City University of New York, New York; 9Biology Doctoral Program, The Graduate Center, The City University of New York, New York; 10Queensborough Community College, The City University of New York, New York; 11Texas A&M University-San Antonio, San Antonio, Texas; 12Rice University, Houston, Texas; 13Houston Health Department, Houston, Texas.
All authors have completed and submitted the International Committee of Medical Journal Editors form for disclosure of potential conflicts of interest. Loren Hopkins reports an honorarium from Baylor College of Medicine for speaking at a conference. Lauren B. Stadler reports institutional support from the National Science Foundation to purchase laboratory equipment and from the Houston Health Department. Katherine Ensor reports institutional support from the Houston Health Department for analysis of samples, unpaid presidency of the American Statistical Association, and unpaid membership on the Institute of Pure and Applied Mathematics Board of Trustees. John J. Dennehy reports institutional support from the New York City Department of Environmental Protection and research reagents from Qiagen, Inc. Davida S. Smyth reports support from the City University of New York and the Department of Environmental Protection, and support from the National Science Foundation outside the current work. Monica Trujillo reports contract support from the New York City Department of Environmental Protection. Devon A. Gregory reports a grant from the National Institutes of Health (NIH). Marc C. Johnson reports a grant from NIH. Allison Wheeler reports support from the Colorado Department of Public Health and Environment. Bradley J. White reports paid employment by Verily Life Sciences, and stock ownership in Verily Life Sciences as part of compensation. Marlene K. Wolfe reports consulting fees from Verily Life Sciences. No other potential conflicts of interest were disclosed.
* https://covid.cdc.gov/covid-data-tracker/#variant-proportions (Accessed January 10, 2022).
† https://www.cdc.gov/healthywater/surveillance/wastewater-surveillance/wastewater-surveillance.html
§ 45 C.F.R. part 46, 21 C.F.R. part 56; 42 U.S.C. Sect. 241(d); 5 U.S.C. Sect. 552a; 44 U.S.C. Sect. 3501 et seq.
¶ 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-2-variant-mutations-hv6-b2qmqdu6
†† https://www.researchsquare.com/article/rs-1083575/v1
§§ https://covid19.colorado.gov/covid-19-monitoring-in-wastewater
¶¶ https://www.medrxiv.org/content/10.1101/2021.03.21.21253978v1
*** https://www.medrxiv.org/content/10.1101/2021.07.26.21261142v1
††† https://www.medrxiv.org/content/10.1101/2021.09.08.21263279v1
References
- CDC COVID-19 Response Team. SARS-CoV-2 B.1.1.529 (Omicron) variant—United States, December 1–8, 2021. MMWR Morb Mortal Wkly Rep 2021;70:1731–4. https://doi.org/10.15585/mmwr.mm7050e1 PMID:34914670
- Kirby AE, Walters MS, Jennings WC, et al. Using wastewater surveillance data to support the COVID-19 response—United States, 2020–2021. MMWR Morb Mortal Wkly Rep 2021;70:1242–4. https://doi.org/10.15585/mmwr.mm7036a2 PMID:34499630
- Trujillo M, Cheung K, Gao A, et al. Protocol for safe, affordable, and reproducible isolation and quantitation of SARS-CoV-2 RNA from wastewater. PLoS One 2021;16:e0257454. https://doi.org/10.1371/journal.pone.0257454 PMID:34555079
Abbreviation: RT-PCR = reverse transcription–polymerase chain reaction.
* https://www.protocols.io/view/quantification-of-sars-cov-2-variant-mutations-hv6-b2qmqdu6
† https://www.medrxiv.org/content/10.1101/2021.03.21.21253978v1
§ https://www.medrxiv.org/content/10.1101/2021.07.26.21261142v1
¶ https://www.medrxiv.org/content/10.1101/2021.09.08.21263279v1
Suggested citation for this article: Kirby AE, Welsh RM, Marsh ZA, et al. 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. MMWR Morb Mortal Wkly Rep 2022;71:103–105. DOI: http://dx.doi.org/10.15585/mmwr.mm7103a5.
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