Before the Surge: Molecular Evidence of SARS-CoV-2 in New York City Prior to the First Report

Hernandez, M. M.; Gonzalez-Reiche, A. S.; Alshammary, H.; Fabre, S.; Khan, Z.; van De Guchte, A.; Obla, A.; Ellis, E.; Sullivan, M. J.; Tan, J.; Alburquerque, B.; Soto, J.; Wang, C.-Y.; Sridhar, S. H.; Wang, Y.-C.; Smith, M.; Sebra, R.; Paniz-Mondolfi, A. E.; Gitman, M. R.; Nowak, M. D.; Cordon-Cardo, C.; Luksza, M.; Krammer, F.; van Bakel, H.; Simon, V.; Sordillo, E. M.

New York City (NYC) emerged as a coronavirus disease 2019 (COVID-19) epicenter in March 2020, but there is limited information regarding potentially unrecognized severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections before the first reported case. We utilized a sample pooling strategy to screen for SARS-CoV-2 RNA in de-identified, respiratory pathogen-negative nasopharyngeal specimens from 3,040 patients across our NYC health system who were evaluated for respiratory symptoms or influenza-like illness during the first 10 weeks of 2020. We obtained complete SARS-CoV-2 genome sequences from samples collected between late February and early March. Additionally, we detected SARS-CoV-2 RNA in pooled specimens collected in the week ending 25 January 2020, indicating that SARS-CoV-2 caused sporadic infections in NYC a full month before the first officially documented case.