Coronavirus Entered New York City Mainly From Europe, Genomic Studies Suggest

COV-IRT member Chris Mason at Weill Cornell Medicine is featured in this article where he discusses his work sequencing viruses from patients in New York.

From genomeweb

NEW YORK – The SARS-CoV-2 virus that is causing the COVID-19 pandemic appears to have entered New York City mainly from Europe, according to independent viral genome sequencing studies from researchers at the Icahn School of Medicine at Mount Sinai, New York University Grossman School of Medicine, and Weill Cornell Medicine.

New York State has been hit hardest by the COVID-19 pandemic in the US, with 160,000 cases and more than 7,000 coronavirus-related deaths as of late Wednesday, including 87,000 cases and more than 5,000 deaths in New York City alone.

In order to trace the origin and spread of the disease in NYC, researchers have so far sequenced SARS-CoV-2 genomes from hundreds of COVID-19 patients in the city, conducting phylogenetic analyses that led them to similar conclusions.

A team led by Harm van Bakel, Viviana Simon, and Emilia Sordillo at Mount Sinai generated SARS-CoV-2 genome sequences from 84 patients seeking care at hospitals belonging to the Mount Sinai Health System between Feb. 29 and March 18.

According to a paper they recently submitted as a preprint to MedRxiv, the virus likely came to NYC through “multiple, independent but isolated introductions mainly from Europe and other parts of the United States.” In addition, there is “evidence for community transmission of SARS-CoV-2 as suggested by clusters of related viruses found in patients living in different neighborhoods of the city,” they wrote.

For their study, the Mount Sinai researchers sequenced 90 SARS-CoV-2 genomes from 84 patients, which came from 21 neighborhoods in Manhattan, the Bronx, Queens, and Brooklyn, as well as from two towns in Westchester County. After whole-genome amplification of the viral genome, samples were sequenced on Pacific Biosciences Sequel 1 and Illumina MiSeq instruments, followed by genome assembly and phylogenetic analysis.

In their analysis, the scientists compared the NYC isolates with 2,363 viral genome sequences in the GISAID (Global Initiative on Sharing All Influenza Data) EpiCoV database. The NYC isolates turned out to be distributed across the phylogenetic tree, which they said is consistent with multiple independent introductions.

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