ABSTRACT
Background
Monitoring the emergence and spread of SARS-CoV-2 variants is an important public health objective. We investigated how the Gamma variant was established in New York City (NYC) in early 2021 in the presence of travel restrictions that aimed to prevent viral spread from Brazil, the country where the variant was first identified.
Methods
We performed phylogeographic analysis on 15,967 Gamma sequences sampled between March 10th through May 1st, 2021, to identify geographic sources of Gamma lineages introduced into NYC. We identified locally circulating Gamma transmission clusters and inferred the timing of their establishment in NYC.
Results
We identified 16 phylogenetically-distinct Gamma clusters established in NYC (cluster sizes ranged 2-108 genomes); most of them were introduced from Florida and Illinois and only one directly from Brazil. By the time the first Gamma case was reported by genomic surveillance in NYC on March 10th, the majority (57%) of circulating Gamma lineages had already been established in the city for at least two weeks.
Conclusions
Although travel from Brazil to the US was restricted from May 2020 through the end of the study period, this restriction did not prevent Gamma from becoming established in NYC as most introductions occurred from domestic locations.
Keywords: SARS-CoV-2, Gamma Variant, New York City, Travel restrictions, public health
Contributor Information
Tetyana I Vasylyeva, Department of Medicine, University of California San Diego, La Jolla, CA, USA.
Courtney E Fang, New York City Public Health Laboratory, New York City Department of Health and Mental Hygiene, New York, NY, USA.
Michelle Su, New York City Public Health Laboratory, New York City Department of Health and Mental Hygiene, New York, NY, USA.
Jennifer L Havens, Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA, US.
Edyth Parker, Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, US.
Jade C Wang, New York City Public Health Laboratory, New York City Department of Health and Mental Hygiene, New York, NY, USA.
Mark Zeller, Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, US.
Anna Yakovleva, Medical Sciences Division, University of Oxford, Oxford, UK.
Gabriel W Hassler, Department of Computational Medicine, University of California Los Angeles, Los Angeles, CA, USA.
Moinuddin A Chowdhury, New York City Public Health Laboratory, New York City Department of Health and Mental Hygiene, New York, NY, USA.
Kristian G Andersen, Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, US.
Scott Hughes, New York City Public Health Laboratory, New York City Department of Health and Mental Hygiene, New York, NY, USA.
Joel O Wertheim, Department of Medicine, University of California San Diego, La Jolla, CA, USA.
Supplementary Material
Associated Data
This section collects any data citations, data availability statements, or supplementary materials included in this article.