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

Area of Science:

• Public Health
• Infectious Disease Epidemiology
• Virology

Background:

• Travel restrictions were implemented to limit SARS-CoV-2 introduction into the U.S.
• New York City (NYC) experienced a rapid increase in COVID-19 cases and community transmission.
• Limited testing capacity initially hampered the detection of local SARS-CoV-2 spread.

Purpose of the Study:

• To determine the extent of local SARS-CoV-2 transmission in NYC.
• To assess the utility of sentinel surveillance for early outbreak detection.
• To identify the origins of SARS-CoV-2 introductions into NYC.

Main Methods:

• Deidentified sentinel surveillance was conducted in six NYC hospital emergency departments from March 1-20.
• Specimens from patients with influenza-like illness (ILI) and negative influenza tests were collected.
• SARS-CoV-2 testing and genetic sequencing were performed by the CDC.

Main Results:

• Of 544 specimens tested, 36 (6.6%) were positive for SARS-CoV-2.
• Genetic sequencing revealed that most positive specimens were similar to strains circulating in Europe.
• Findings suggested introductions from Europe, other U.S. locations, and local transmission within NYC.

Conclusions:

• Sentinel surveillance is crucial for detecting and monitoring community transmission of novel respiratory viruses.
• Rapid implementation of surveillance systems and genetic sequencing capacity are vital for timely public health interventions.
• Early detection of SARS-CoV-2 in NYC informed containment and mitigation strategies.