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

Gonzalez-Reiche, Ana S; Hernandez, Matthew M; Sullivan, Mitchell; 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 Rose; Smith, Melissa; Sebra, Robert; Aberg, Judith; Krammer, Florian; Garcia-Sarstre, 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-CoV2 pandemic. To identify the early events underlying the rapid spread of the virus in the NYC metropolitan area, we sequenced the virus causing COVID19 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-CoV2 as suggested by clusters of related viruses found in patients living in different neighborhoods of the city.