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

Gonzalez-Reiche, Ana S.; Hernandez, Matthew M.; Sullivan, Mitchell J.; Ciferri, Brianne; Alshammary, Hala; Obla, Ajay; Fabre, Shelcie; Kleiner, Giulio; Polanco, Jose; Khan, Zenab; Alburquerque, Bremy; van de Guchte, Adriana; Dutta, Jayeeta; Francoeur, Nancy; Melo, Betsaida Salom; Oussenko, Irina; Deikus, Gintaras; Soto, Juan; Sridhar, Shwetha Hara; Wang, Ying-Chih; Twyman, Kathryn; Kasarskis, Andrew; Altman, Deena R.; Smith, Melissa; Sebra, Robert; Aberg, Judith; Krammer, Florian; García-Sastre, Adolfo; Luksza, Marta; Patel, Gopi; Paniz-Mondolfi, Alberto; Gitman, Melissa; Sordillo, Emilia Mia; Simon, Viviana; van Bakel, Harm

New York City (NYC) has emerged as one of the epicenters of the current 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 causing COVID-19 in patients seeking care at the Mount Sinai Health System. Phylogenetic analysis of 84 distinct SARS-CoV2 genomes indicates multiple, independent but isolated introductions mainly from Europe and other parts of the United States. Moreover, we find 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.