Early Introduction and Community Transmission of SARS-CoV-2 Omicron Variant, New York, New York, USA

Dakai Liu; Yexiao Cheng; Hangyu Zhou; Lulan Wang; Roberto Hurtado Fiel; Yehudah Gruenstein; Jean Jingzi Luo; Vishnu Singh; Eric Konadu; Keither James; Calvin Lui; Pengcheng Gao; Carl Urban; Nishant Prasad; Sorana Segal-Maurer; Esther Wurzberger; Genhong Cheng; Aiping Wu; William Harry Rodgers


Emerging Infectious Diseases. 2023;29(2):371-380. 

In This Article

Abstract and Introduction


The Omicron variant of SARS-CoV-2 has become dominant in most countries and has raised significant global health concerns. As a global commerce center, New York, New York, USA, constantly faces the risk for multiple variant introductions of SARS-CoV-2. To elucidate the introduction and transmission of the Omicron variant in the city of New York, we created a comprehensive genomic and epidemiologic analysis of 392 Omicron virus specimens collected during November 25–December 11, 2021. We found evidence of 4 independent introductions of Omicron subclades, including the Omicron subclade BA.1.1 with defining substitution of R346K in the spike protein. The continuous genetic divergence within each Omicron subclade revealed their local community transmission and co-circulation in New York, including both household and workplace transmissions supported by epidemiologic evidence. Our study highlights the urgent need for enhanced genomic surveillance and effective response planning for better prevention and management of emerging SARS-CoV-2 variants.


During the global pandemic of SARS-CoV-2, novel variants have continuously emerged.[1] Some variants constitute an increased risk to global public health and are being monitored as variants of concern by the World Health Organization (WHO). The Omicron variant was detected from patients in Botswana and South Africa in November 2021;[2] it was designated as the fifth variant of concern. Since its detection, it rapidly spread across the world and became the predominant variant in several countries.[3] Omicron has a higher number of mutations than previously detected variants. Of note, some mutations located in the receptor-binding domain (RBD) of the spike (S) protein altered the immune escape ability of Omicron.[4–6] The 69–70 deletion in the S gene of Omicron can be characterized by the failure to detect the S gene using certain diagnostic tests,[7] known as the S gene target failure (SGTF). In the context of the global dominance of Delta and Omicron, some studies defined the Omicron case as the presence of SGTF and the Delta case as the absence of SGTF in the test samples.[8–10] Three studies reported the genomic, epidemiologic, and clinical analysis of early Omicron introductions;[10–12] combining viral genome analysis with epidemiologic evidence supports the study of introduction and community transmission patterns of emerging viruses.

As a major cosmopolitan city, New York, New York, USA (NYC), has been at risk for multiple variant introductions of SARS-CoV-2 during the COVID-19 pandemic.[13–15] Studies have shown that a patient infected with the Omicron variant attended a large indoor convention with attendees from 52 US jurisdictions and 30 foreign countries during November 19–November 21, 2021, in NYC; a total of 119 event-associated cases were identified after the investigation.[16,17] In addition, some Omicron-associated mutations were detected in wastewater in NYC on November 21, 2021.[18] This evidence indicates that the Omicron variant was introduced to NYC early in its outbreak. Shortly after its introduction, Omicron replaced Delta as the dominant variant in NYC (https://www1.nyc.gov/site/doh/covid/covid-19-data-variants.page), suggesting potential community transmission.

In this study, we performed whole-genome sequencing for 392 Omicron viruses obtained from persons in NYC during November 25–December 11, 2021. These dates encompass the expected early Omicron introduction into the city. Using the epidemiologic and genetic data of these sequencing samples, we determined the introduction and community transmission pattern of early Omicron in NYC. This study was reviewed and approved by the NewYork-Presbyterian Queens Hospital Institutional Review Board (IRB no. 13740321).