Omicron may have been in NYC before it was discovered in South Africa

A study of wastewater in New York City shows that the omicron variant of COVID-19 was probably in the city before scientists in South Africa discovered the omicron variant existed and was more widely spread than originally indicated by clinical testing.

The New York City Department of Environmental Protection has been tracking variants in wastewater by sequencing weekly samples collected from 14 sewersheds. It found 12 omicron-associated mutations in a sample collected on November 21, according to a publication by the Centers for Disease Control and Prevention (CDC).

That means the variant could have been in New York City before South African scientists first announced on November 25, 2021 that they had discovered the variant.

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The first omicron case in the U.S. was reported on Dec. 1.  The CDC says that by December 4, the date the wastewater data were reported, an omicron case had been identified in a New York City resident.

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.

Scientists says that 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.

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They do say that conditions that increase confidence in the results include the detection of multiple variant-associated mutations.

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.