Detection and Genetic Characterization of Community-Based SARS-CoV-2 Infections - New York City, March 2020

To limit introduction of SARS-CoV-2, the virus that causes coronavirus disease 2019 (COVID-19), the US restricted travel from China on Feb 2, 2020, and from Europe on Mar 13. To determine whether local transmission of SARS-CoV-2 could be detected, the New York City (NYC) Department of Health and Mental Hygiene (DOHMH) conducted deidentified sentinel surveillance at six NYC hospital emergency departments (EDs) during Mar 1--20. On Mar 8, while testing availability for SARS-CoV-2 was still limited, DOHMH announced sustained community transmission of SARS-CoV-2. At this time, twenty-six NYC residents had confirmed COVID-19, and ED visits for influenza-like illness increased, despite decreased influenza virus circulation. The following week, on Mar 15, when only seven of the 56 (13%) patients with known exposure histories had exposure outside of NYC, the level of community SARS-CoV-2 transmission status was elevated from sustained community transmission to widespread community transmission. Through sentinel surveillance during Mar 1--20, DOHMH collected 544 specimens from patients with influenza- like symptoms (ILS) who had negative test results for influenza and, in some instances, other respiratory pathogens.