The global pandemic of Coronavirus disease 2019 (COVID-19), caused by Severe Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), has highlighted the importance of surveillance efforts to closely monitor the transmission and evolution of viral pathogens. I will present how the Mount Sinai Health System Pathogen Surveillance Program has applied high-throughput sequencing of SARS-CoV-2 genomes from COVID-19 patients, in combination with molecular epidemiology, to identify the timing and origins of early introductions of SARS-CoV-2 in the New York City metropolitan area and its continued spread. NYC was one of the first affected large cities in the world and an early epicenter of the pandemic. I will further outline how genomic technologies can be applied to precisely delineate outbreaks in quarantine and healthcare settings.

Learning objectives:

1. Understand how we can use next-generation sequencing to track the spread and diversity of SARS-CoV-2

2. Understand how limitations in testing obscured our view of early viral introductions 

3. Identify and evaluate the contribution of asymptomatic carriers in the transmission of SARS-CoV-2