. 2022 Jan 21;71(3):103–105. doi: 10.15585/mmwr.mm7103a5

TABLE. Detection of mutations associated with the SARS-CoV-2 B.1.1.529 (Omicron) variant in wastewater — California, Colorado, New York City, and Houston, Texas, November 21–December 16, 2021.

Location	Sample date	Test method	Results
California
Sewershed A	Nov 25, 2021	Mutation-specific RT-PCRs targeting delHV69–70 and del143–145*	Both mutations detected at <1,000 genomic copies/gram wastewater solids
Sewershed B	Nov 30, 2021	Mutation-specific RT-PCRs targeting delHV69–70 and del143–145*	Both mutations detected at <1,000 genomic copies/gram wastewater solids
	Dec 2, 2021	Mutation-specific RT-PCRs targeting delHV69–70 and del143–145*	Both mutations detected at <1,000 genomic copies/gram wastewater solids
	Dec 2, 2021	Partial sequencing of S-gene using ARTIC v4 73R, 74L primers	Detected 9 bp insertion mutation in s214EPE and 3 bp N211I deletion
Sewersheds (10 sites)	Dec 17, 2021	Mutation-specific RT-PCR targeting del143–145*	Mutations detected at >4,500 genomic copies/gram wastewater solids
Sewersheds (10 sites)	10 of 10 sites	Mutation-specific RT-PCR targeting del143–145*
Colorado
Sewersheds (21 sites)	Dec 2, 2021	SARS-CoV-2-enriched tiled amplicon sequencing	Detected 13 of 17 Omicron-associated mutations
	One of 21 sites	SARS-CoV-2-enriched tiled amplicon sequencing	Detected 13 of 17 Omicron-associated mutations
	Dec 6, 2021	SARS-CoV-2-enriched tiled amplicon sequencing	No Omicron-associated mutations detected
	Zero of 21 sites	SARS-CoV-2-enriched tiled amplicon sequencing	No Omicron-associated mutations detected
	Dec 9, 2021	SARS-CoV-2-enriched tiled amplicon sequencing	Detected between four and 13 of 17 Omicron-associated mutations depending on the site
	Five of 21 sites	SARS-CoV-2-enriched tiled amplicon sequencing
	Dec 13, 2021	SARS-CoV-2-enriched tiled amplicon sequencing	Detected between six and 14 of 17 Omicron-associated mutations, depending on the site
	12 of 21 sites	SARS-CoV-2-enriched tiled amplicon sequencing
	Dec 16, 2021	SARS-CoV-2-enriched tiled amplicon sequencing	Detected between 12 and 14 of 17 Omicron-associated mutations, depending on the site
	19 of 21 sites	SARS-CoV-2-enriched tiled amplicon sequencing
New York City
Sewershed A	Nov 21, 2021	Short-read sequencing of S-gene amplicon^†,§	Detected 12 Omicron-associated mutations including eight mutations unique to Omicron
Sewershed A	Nov 28, 2021	Short-read sequencing of S-gene amplicon^†,§	Detected 12 Omicron-associated mutations including eight mutations unique to Omicron
Sewershed B	Nov 28, 2021	Short-read sequencing of S-gene amplicon^†,§	Detected 12 Omicron-associated mutations including eight mutations unique to Omicron
Houston, Texas
Sewersheds (39 sites)	Nov 29, 2021	SARS-CoV-2-enriched tiled amplicon sequencing using ARTIC v3 primers^¶	Detected six Omicron-associated mutations
	Seven of 39 sites		Detected six Omicron-associated mutations
	Dec 6, 2021	SARS-CoV-2-enriched tiled amplicon sequencing using ARTIC v3 primers^¶	Detected 14 Omicron-associated mutations
	25 of 39 sites		Detected 14 Omicron-associated mutations
	Dec 13, 2021	SARS-CoV-2-enriched tiled amplicon sequencing using ARTIC v3 primers^¶	Detected 18 Omicron-associated mutations
	35 of 39 sites		Detected 18 Omicron-associated mutations

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