Sequencing analysis of the spread of SARS-CoV2 in the Greater New York City region

ABSTRACT

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 means to link seemingly unrelated cases, and large-scale sequencing surveillance can inform on critical epidemiological parameters. Here, we report analysis of 156 SARS-CoV2 sequences from individuals in the New York City metropolitan area during the initial stages of the 2020 COVID-19 outbreak. The majority of samples had no recent travel history or known exposure. Comparison to global viral sequences showed that the majority of sequences were most related to samples from Europe. Our data are consistent with numerous seed transmissions and a period of unrecognized community spreading. This work highlights the complementary role of genomic surveillance to traditional epidemiological indicators.