Introductions and early spread of SARS-CoV-2 in the New York City area
Ana S. Gonzalez‐Reiche, Matthew M. Hernandez, Mitchell J. Sullivan, Brianne Ciferri, Hala Alshammary, Ajay Obla, Shelcie Fabre, Giulio Kleiner, José Polanco, Zenab Khan, Bremy Alburquerque, Adriana van de Guchte, Jayeeta Dutta, Nancy Francoeur, Betsaida Salom Melo, Irina Oussenko, Gintaras Deikus, Juan Soto, Shwetha Hara Sridhar, Ying‐Chih Wang, Kathryn Twyman, Andrew Kasarskis, Deena R. Altman, Melissa Smith, Robert Sebra, Judith A. Aberg, Florian Krammer, Adolfo García‐Sastre, Marta Łuksza, Gopi Patel, Alberto Paniz‐Mondolfi, Melissa Gitman, Emilia Mia Sordillo, Viviana Simon, Harm van Bakel
Abstract
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.