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

Discussion

Since the first detections in November 2021, the Omicron variant has gained global attention for its increased transmissibility and immune escape.^[23] It was identified in 87 countries within 3 weeks^[2] and established itself as the global dominant variant within a few months.^[3] Although several measures were implemented to reduce the introduction and spread of SARS-CoV-2 into the United States, 22 states reported ≥1 case of Omicron as of December 8, 2021.^[24] As a major cosmopolitan city, NYC has been challenged with multiple introductions of different variants of SARS-CoV-2 during the pandemic.^[13–15] The high contact rates observed in densely populated cities may promote community transmissions of the virus.^[25]

Our analyses suggest that there have been 4 main independent introductions of different Omicron subclades into NYC from regions including Africa, Europe, and North America during the early outbreak of Omicron. Those introductions were followed by subsequent community transmission across NYC. Similarly, the rapid local spread after early Omicron introductions was observed in Finland,^[10] Denmark,^[11] and Mexico City.^[12] In addition, through the combination of genome sequencing analysis and epidemiologic studies of SARS-CoV-2 patients in individual districts of NYC, we discovered evidence of both household and workplace transmission patterns. Our observation of multiple Omicron introductions followed by onward transmission during a 17-day period highlights the potential for introductions of emerging variants to spread locally. Therefore, after emerging variant outbreaks, timely enhanced tracking and monitoring of travelers and subsequent transmission reduction interventions are urgently needed to ensure that those introductions do not result in widespread community transmission.

Given the limited sequencing coverage and surveillance, we were unable to determine the first case of the introduction for each of 4 clades in our study and its subsequent transmission chain. Differences in sampling and sequencing may bias results and make accurate estimation of introduction times difficult. In addition, the possible convergent evolution of viruses within immunocompromised or immunocompetent hosts in NYC could complicate interpretation. As more genomes of Omicron viruses are being sequenced, we expect to be able to further elucidate the origins of Omicron introductions and chain of the community transmission.

Our analysis also highlights the importance of timely genomic surveillance, which can reduce the effects of emerging variants.^[26] Through genomic surveillance, we can make an initial assessment of the risk for the emerging variant by its mutation profile and growth advantage.^[2] Analysis of sequenced data can augment testing strategies to monitor the variant in real-time without whole-genome sequencing. For example, SGTF can be used as a proxy for Omicron during the early days of an outbreak.^[8–10] In addition, the introduction and transmission pattern of the emerging variants can be elucidated using viral sequences. Early identification of the emerging variant outbreak provided by genomic surveillance could aid us in making timely and appropriate policy responses, including enhanced tracking and monitoring of travelers and social control measures. Therefore, combining real-time genomic and epidemiologic surveillance is critical for effective responses for tracking, understanding, and controlling infectious disease outbreaks.

Emerging Infectious Diseases. 2023;29(2):371-380. © 2023 Centers for Disease Control and Prevention (CDC)