Effective public response to a pandemic relies upon accurate measurement of the extent and dynamics of an outbreak. Viral genome sequencing has emerged as a powerful approach to link seemingly unrelated cases, and large-scale sequencing surveillance can inform on critical epidemiological parameters. Here, we report the analysis of 864 SARS-CoV-2 sequences from cases in the New York City metropolitan area during the COVID-19 outbreak in spring 2020. The majority of cases had no recent travel history or known exposure, and genetically linked cases were spread throughout the region. Comparison to global viral sequences showed that early transmission was most linked to cases from Europe. Our data are consistent with numerous seeds from multiple sources and a prolonged period of unrecognized community spreading. This work highlights the complementary role of genomic surveillance in addition to traditional epidemiological indicators.

中文翻译：

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测序确定了纽约市地区多次早期引入的 SARS-CoV-2

对大流行的有效公众反应依赖于对爆发的程度和动态的准确测量。病毒基因组测序已成为一种将看似无关的病例联系起来的有力方法，大规模测序监测可以为关键的流行病学参数提供信息。在这里，我们报告了对 2020 年春季 COVID-19 爆发期间纽约市大都市区病例的 864 条 SARS-CoV-2 序列的分析。大多数病例没有近期旅行史或已知接触史，并且与基因相关的病例遍布整个地区。与全球病毒序列的比较表明，早期传播与来自欧洲的病例最为相关。我们的数据与来自多个来源的众多种子和长期未被识别的社区传播一致。