Introduction and Establishment of SARS-CoV-2 Gamma Variant in New York City in Early 2021

T. Vasylyeva, Courtney E. Fang, Michelle Su, J. L. Havens, Edyth Parker, Jade C. Wang, M. Zeller, A. Yakovleva, G. Hassler, Moinuddin A. Chowdhury, K. Andersen, S. Hughes, J. Wertheim
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引用次数: 4

Abstract

Background. Monitoring the emergence and spread of SARS-CoV-2 variants is an important public health objective. Travel restrictions, aimed to prevent viral spread, have major economic consequences and unclear effectiveness despite considerable research. We investigated the introduction and establishment of the Gamma variant in New York City (NYC) in 2021. Methods. We performed phylogeographic analysis on 15,967 Gamma sequences available on GISAID and 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. Findings. We identified 16 phylogenetically-distinct Gamma clusters established in NYC (cluster sizes ranged 2-108 genomes). Most of the NYC clusters were introduced from Florida and Illinois; only one was introduced from outside the United States (US). 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. Interpretation. Despite the expansion of SARS-CoV-2 genomic surveillance in NYC, there was a substantial gap between Gamma variant introduction and establishment in January/February 2021, and its identification by genomic surveillance in March 2021. 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.
2021年初纽约市SARS-CoV-2 γ变体的引入和建立
背景。监测SARS-CoV-2变体的出现和传播是一项重要的公共卫生目标。旨在防止病毒传播的旅行限制造成了严重的经济后果,尽管进行了大量研究,但效果尚不明确。我们调查了2021年在纽约市(NYC)引入和建立Gamma变体的情况。方法。我们对GISAID上提供的15967个伽马序列进行了系统地理学分析,并在2021年3月10日至5月1日期间取样,以确定引入纽约市的伽马谱系的地理来源。我们确定了当地传播的伽马传播集群,并推断了它们在纽约市建立的时间。发现。我们确定了在纽约市建立的16个系统发育上不同的Gamma集群(集群大小范围为2-108个基因组)。纽约市的大多数集群都是从佛罗里达州和伊利诺伊州引进的;只有一种是从美国以外引进的。到3月10日纽约市基因组监测报告第一例伽玛病例时,大多数(57%)的流行伽玛谱系已经在该市建立了至少两周。解释。尽管纽约市扩大了SARS-CoV-2基因组监测,但从2021年1月/ 2月引入和建立伽玛变体到2021年3月通过基因组监测发现伽玛变体之间存在很大差距。尽管从2020年5月到研究期结束,从巴西到美国的旅行受到限制,但这一限制并没有阻止Gamma在纽约成立,因为大多数引入都发生在国内。
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