Mount Sinai Study Finds First Cases of COVID-19 in New York City are Primarily from European and US Sources First definitive molecular epidemiology study of SARS-CoV-2 in New York City to describe the route by which the virus arrived

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New York City’s first confirmed COVID-19 cases are from primarily European and United States sources, according to the first molecular epidemiology study of SARS-CoV-2. The study, published in the journal Science and led by Icahn School of Medicine at Mount Sinai (ISMMS) researchers, is the first to trace the source of these cases and show that the SARS-CoV-2 epidemic in New York City predominately arose through untracked transmission between the United States and Europe, with limited evidence to support any direct introductions from China, where the virus originated, or other locations in Asia. The researchers also documented early community spread of SARS-CoV-2 in New York City during that time.

New York City has become one of the major epicenters of SARS-CoV-2 infections in the US with more than 4,000 fatalities in the metropolitan area. The government instituted targeted screening of suspected coronavirus disease 2019 (COVID-19) cases and a series of successive nation-wide travel restrictions to curtail SARS-CoV-2 introductions into the US from outbreak hotspots in China, Iran, and later mainland European countries to the continental United States. Despite these measures, the first SARS-CoV-2 case in New York State was identified in New York City by the end of February. Knowing the time the virus came to New York and the route it took is essential for evaluating and designing effective containment strategies.

The team of researchers from the Icahn Institute for Data Science and Genomic Technology, the Global Health and Emerging Pathogens Institute, and the Departments of Microbiology, Pathology, and Genetics and Genomic Sciences sequenced 90 SARS-CoV-2 genomes from 84 of over 800 confirmed COVID-19 positive cases within the Mount Sinai Health System.

“We sequenced genomes from COVID-19 cases identified up to March 18,” said Harm van Bakel, PhD, Assistant Professor of Genetics and Genomic Sciences at ISMMS. “These cases were drawn from 21 New York City neighborhoods across four boroughs (Manhattan, Bronx, Queens and Brooklyn), as well as two towns in neighboring Westchester County.”

The team then analyzed these sequences together with all 2,363 publicly available SARS-CoV-2 genomes from around the world to determine the most likely origin of the SARS-CoV-2 strains infecting these metro New York City residents who sought care at Mount Sinai.

“Phylogenetic analysis of 84 distinct SARS-CoV2 genomes indicates multiple independent but isolated introductions mainly from Europe and other parts of the United States. In addition, clusters of related viruses found in patients living in different neighborhoods of the city provide strong evidence of community transmission of SARS-CoV2 in the city prior to March 18, 2020,” said van Bakel.

“These results show that SARS-CoV-2 came to the New York City area predominately via Europe through untracked transmissions." said Viviana Simon, MD, PhD, Professor of Microbiology and Infectious Diseases at ISMMS. "Only one of the cases studied was infected with a virus that was a clear candidate for introduction from Asia, and that virus is most closely related to viral isolates from Seattle, Washington. The study also suggests that the virus was likely circulating as early as late-January 2020 in the New York City area. This underscores the urgent need for early and continued broad testing to identify untracked transmission clusters in the community."

Precision surveillance of pathogens allows researchers to infer both the source and timing by which a pathogen entered a community. In the COVID-19 pandemic, we are fortunate to have many thousands of SARS-CoV-2 sequences collected at https://www.gisaid.org/ by the efforts of clinicians and researchers around the globe. The Pathogen Surveillance Program at ISMMS is a multidisciplinary institutional infrastructure that generates timely high resolution genetic information on pathogens in the large and diverse patient population seeking care at the Mount Sinai Health System and integrates these data into clinical operations to support both research and clinical care at the Mount Sinai Health System.

The Research reported in this paper was supported by the Office of Research Infrastructure of the National Institutes of Health (NIH) under award numbers S10OD018522 and S10OD026880 as well as Mount Sinai Health System institutional funds. Protocols established for this study were in part based on influenza virus sequencing protocols established with the support of CRIP (Center for Research on Influenza Pathogenesis), an NIH funded Center of Excellence for Influenza Research and Surveillance (CEIRS, contract number HHSN272201400008C). The content is solely the responsibility of the authors and does not necessarily represent the official views of the NIH.