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**, and William Harry Rodgers**
*These authors contributed equally to this article.
**Co-correspondence authors
NewYork-Presbyterian Queens Hospital, Flushing, New York, USA (D. Liu, J.J. Luo, V. Singh, E. Konadu, K. James, C. Lui, P. Gao, C. Urban, N. Prasad, S. Segal-Maurer, W.H. Rodgers); Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China (Y. Cheng, H. Zhou, A. Wu); Suzhou Institute of Systems Medicine, Suzhou, China (Y. Cheng, H. Zhou, A. Wu); University of California, Los Angeles, California, USA (L. Wang, G. Cheng); Kaiser Permanente Health, North Valley, California, USA (R.H. Fiel); LabQ Diagnostics, Brooklyn, New York, USA (Y. Gruenstein, E. Wurzberger); Weill Cornell Medical College, New York (J.J. Luo, C. Urban, N. Prasad, S. Segal-Maurer, W.H. Rodgers)
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.
Early Introduction and Community Transmission of SARS-CoV-2 Omicron Variant, New York, New York, USA by Dakai Liu et al. Emerging Infectious Diseases.