Molecular evidence of SARS-CoV-2 in New York before the first pandemic wave

Hernandez, Matthew M.; Gonzalez-Reiche, Ana S.; Alshammary, Hala; Fabre, Shelcie; Khan, Zenab; van De Guchte, Adriana; Obla, Ajay; Ellis, Ethan; Sullivan, Mitchell J.; Tan, Jessica; Alburquerque, Bremy; Soto, Juan; Wang, Ching-Yi; Sridhar, Shwetha Hara; Wang, Ying-Chih; Smith, Melissa; Sebra, Robert; Paniz-Mondolfi, Alberto E.; Gitman, Melissa R.; Nowak, Michael D.; Cordon-Cardo, Carlos; Luksza, Marta; Krammer, Florian; van Bakel, Harm; Simon, Viviana; Sordillo, Emilia Mia

Numerous reports document the spread of SARS-CoV-2, but there is limited information on its introduction before the identification of a local case. This may lead to incorrect assumptions when modeling viral origins and transmission. Here, we utilize a sample pooling strategy to screen for previously undetected SARS-CoV-2 in de-identified, respiratory pathogen-negative nasopharyngeal specimens from 3,040 patients across the Mount Sinai Health System in New York. The patients had been previously evaluated for respiratory symptoms or influenza-like illness during the first 10 weeks of 2020. We identify SARS-CoV-2 RNA from specimens collected as early as 25 January 2020, and complete SARS-CoV-2 genome sequences from multiple pools of samples collected between late February and early March, documenting an increase prior to the later surge. Our results provide evidence of sporadic SARS-CoV-2 infections a full month before both the first officially documented case and emergence of New York as a COVID-19 epicenter in March 2020.