Dataset Information

Introductions and early spread of SARS-CoV-2 in the New York City area.

ABSTRACT: New York City (NYC) has emerged as one of the epicenters of the current SARS-CoV-2 pandemic. To identify the early transmission events underlying the rapid spread of the virus in the NYC metropolitan area, we sequenced the virus causing COVID-19 in patients seeking care at the Mount Sinai Health System. Phylogenetic analysis of 84 distinct SARS-CoV2 genomes indicates multiple, independent but isolated introductions mainly from Europe and other parts of the United States. Moreover, we find 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.

SUBMITTER: Gonzalez-Reiche AS

PROVIDER: S-EPMC7259823 | biostudies-literature | 2020 May

REPOSITORIES: biostudies-literature

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Introductions and early spread of SARS-CoV-2 in the New York City area.

Gonzalez-Reiche Ana S AS Hernandez Matthew M MM Sullivan Mitchell J MJ Ciferri Brianne B Alshammary Hala H Obla Ajay A Fabre Shelcie S Kleiner Giulio G Polanco Jose J Khan Zenab Z Alburquerque Bremy B van de Guchte Adriana A Dutta Jayeeta J Francoeur Nancy N Melo Betsaida Salom BS Oussenko Irina I Deikus Gintaras G Soto Juan J Sridhar Shwetha Hara SH Wang Ying-Chih YC Twyman Kathryn K Kasarskis Andrew A Altman Deena R DR Smith Melissa M Sebra Robert R Aberg Judith J Krammer Florian F García-Sastre Adolfo A Luksza Marta M Patel Gopi G Paniz-Mondolfi Alberto A Gitman Melissa M Sordillo Emilia Mia EM Simon Viviana V van Bakel Harm H

Science (New York, N.Y.) 20200529 6501

New York City (NYC) has emerged as one of the epicenters of the current severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic. To identify the early transmission events underlying the rapid spread of the virus in the NYC metropolitan area, we sequenced the virus that causes coronavirus disease 2019 (COVID-19) in patients seeking care at the Mount Sinai Health System. Phylogenetic analysis of 84 distinct SARS-CoV-2 genomes indicates multiple, independent, but isolated introduction ...[more]

PMID: 32471856

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Project description:Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a novel coronavirus that was first reported in Wuhan, China in December of 2019 and has since caused a global pandemic resulting in millions of deaths and tens of millions of patients testing positive for infection. Analysis of different viral strains has identified a D614G change in the spike protein that is correlated with the virus becoming more transmissible. While studies have shown G614 viruses to be more transmissible, the effects of this mutation on the host response, especially on the cellular level, are yet to be fully elucidated. In this experiment we infected NHBE cells with the Washington (D614) strain or the New York (G614) strains of SARS-CoV-2. We generated RNA sequencing data at three different time points to improve our understanding of how the intracellular host response differs between infections with these two strains. We analyzed these data with a bioinformatics pipeline that identifies differentially expressed genes, enriched Gene Ontology terms and dysregulated signaling pathways. We detected over 2,000 differentially expressed genes, over 600 Gene Ontology terms, and 29 affected pathways between the two treatments. Many of these entities play a role in immune signaling and response. When comparing the different strains and different time points we found more overall similarities between matched time points than across different time points with the same strain. When specifically comparing the affected pathways, we saw that the 24hr time point of the New York strain was more similar to the 12hr time point of the Washington strain with a large number of pathways related to translation being inhibited in both strains at these time points. These results suggest that D614G substitution in the spike protein, combined with other nonsynonymous changes in the viral gene products cause distinct responses in infected host cells, especially relating to how quickly translation is dysregulated after infection. These observed differences in the intracellular host response to infection could play a role in driving the increase in pathogenicity and mortality seen in the New York outbreaks versus the Washington outbreaks at the beginning of the SARS-CoV-2 pandemic.

Dataset Information

Introductions and early spread of SARS-CoV-2 in the New York City area.

Publications

Introductions and early spread of SARS-CoV-2 in the New York City area.

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