Introductions and early spread of SARS-CoV-2 in the New York City area

Gonzalez-Reiche AS; Hernandez MM; Sullivan MJ; Ciferri B; Alshammary H; Obla A; Fabre S; Kleiner G; Polanco J; Khan Z; Alburquerque B; van de Guchte A; Dutta J; Francoeur N; Melo BS; Oussenko I; Deikus G; Soto J; Sridhar SH; Wang YC; Twyman K; Kasarskis A; Altman DR; Smith M; Sebra R; Aberg J; Krammer F; Garcia-Sastre A; Luksza M; Patel G; Paniz-Mondolfi A; Gitman M; Sordillo EM; Simon V; van Bakel H

Science, Vol.369, No.6501, 297-+, 2020

DOI10.1126/science.abc1917 Export Citation

Introductions and early spread of SARS-CoV-2 in the New York City area

Gonzalez-Reiche AS, Hernandez MM, Sullivan MJ, Ciferri B, Alshammary H, Obla A, Fabre S, Kleiner G, Polanco J, Khan Z, Alburquerque B, van de Guchte A, Dutta J, Francoeur N, Melo BS, Oussenko I, Deikus G, Soto J, Sridhar SH, Wang YC, Twyman K, Kasarskis A, Altman DR, Smith M, Sebra R, Aberg J, Krammer F, Garcia-Sastre A, Luksza M, Patel G, Paniz-Mondolfi A, Gitman M, Sordillo EM, Simon V, van Bakel H

New York City (NYC) has emerged as one of the epicenters of the current severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic. To identify the early transmission events underlying the rapid spread of the virus in the NYC metropolitan area, we sequenced the virus that causes coronavirus disease 2019 (COVID-19) in patients seeking care at the Mount Sinai Health System. Phylogenetic analysis of 84 distinct SARS-CoV-2 genomes indicates multiple, independent, but isolated introductions mainly from Europe and other parts of the United States. Moreover, we found evidence for community transmission of SARS-CoV-2 as suggested by clusters of related viruses found in patients living in different neighborhoods of the city.