Top 5 Takeaways

1. Omicron Detection: The Omicron variant was first detected in U.S. community wastewater in late November 2021.
2. Early Surveillance: Wastewater surveillance provided early evidence of Omicron, ahead of clinical testing.
3. Geographical Spread: Initial detections were reported in California, Colorado, New York, and Texas.
4. Methodology: Health departments used mutation-specific RT-PCR and sequencing to identify Omicron-associated mutations.
5. Public Health Implications: Wastewater data can complement clinical testing for early variant detection, aiding public health decisions.

Original Article Author and Citation

Corresponding Author

Amy Kirby, agk1@cdc.gov

Suggested Citation

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

Summary

The B.1.1.529 (Omicron) variant of SARS-CoV-2 was designated a variant of concern in the U.S. on November 30, 2021. Wastewater surveillance systems in California, Colorado, New York, and Texas detected Omicron-associated mutations in community wastewater samples between November 21 and December 16, 2021, providing early evidence of the variant’s presence before widespread clinical detection.

Methods

The National Wastewater Surveillance System (NWSS) funded 43 health departments to monitor SARS-CoV-2 in wastewater. Health departments in California, Colorado, New York, and Texas used mutation-specific RT-PCR and sequencing to detect Omicron-associated mutations in wastewater samples collected from various sewersheds.

Discussion

Wastewater surveillance programs in these states were the first to detect Omicron in community wastewater. Although wastewater data cannot confirm the presence of a specific variant, the detection of multiple variant-associated mutations, linked mutations, and consistent RNA concentration trends can increase confidence in the results. Limitations include inconsistent detections, low-quality sequence data, and reporting delays.

Conclusion

The detection of Omicron-associated mutations in wastewater provided early evidence of the variant’s presence, complementing clinical testing. This early detection can guide public health decisions regarding resource allocation, testing strategies, and public health messaging.

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