Dataset Information

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

ABSTRACT: 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.

SUBMITTER: Liu D

PROVIDER: S-EPMC9881774 | biostudies-literature | 2023 Feb

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

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

Liu Dakai D Cheng Yexiao Y Zhou Hangyu H Wang Lulan L Fiel Roberto Hurtado RH Gruenstein Yehudah Y Luo Jean Jingzi JJ Singh Vishnu V Konadu Eric E James Keither K Lui Calvin C Gao Pengcheng P Urban Carl C Prasad Nishant N Segal-Maurer Sorana S Wurzberger Esther E Cheng Genhong G Wu Aiping A Rodgers William Harry WH

Emerging infectious diseases 20230201 2

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 ev ...[more]

PMID: 36692451

Similar Datasets

Project description:BackgroundUnderstanding community transmission of SARS-CoV-2 variants of concern (VOCs) is critical for disease control in the post pandemic era. The Delta variant (B.1.617.2) emerged in late 2020 and became the dominant VOC globally in the summer of 2021. While the epidemiological features of the Delta variant have been extensively studied, how those characteristics shaped community transmission in urban settings remains poorly understood.MethodsUsing high-resolution contact tracing data and testing records, we analyze the transmission of SARS-CoV-2 during the Delta wave within New York City (NYC) from May 2021 to October 2021. We reconstruct transmission networks at the individual level and across 177 ZIP code areas, examine network structure and spatial spread patterns, and use statistical analysis to estimate the effects of factors associated with COVID-19 spread.ResultsWe find considerable individual variations in reported contacts and secondary infections, consistent with the pre-Delta period. Compared with earlier waves, Delta-period has more frequent long-range transmission events across ZIP codes. Using socioeconomic, mobility and COVID-19 surveillance data at the ZIP code level, we find that a larger number of cumulative cases in a ZIP code area is associated with reduced within- and cross-ZIP code transmission and the number of visitors to each ZIP code is positively associated with the number of non-household infections identified through contact tracing and testing.ConclusionsThe Delta variant produced greater long-range spatial transmission across NYC ZIP code areas, likely caused by its increased transmissibility and elevated human mobility during the study period. Our findings highlight the potential role of population immunity in reducing transmission of VOCs. Quantifying variability of immunity is critical for identifying subpopulations susceptible to future VOCs. In addition, non-pharmaceutical interventions limiting human mobility likely reduced SARS-CoV-2 spread over successive pandemic waves and should be encouraged for reducing transmission of future VOCs.

Dataset Information

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

Publications

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

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets