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Introductions and early spread of SARS-CoV-2 in the New York City area.
Science. 2020 07 17; 369(6501):297-301.Sci

Abstract

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 introductions mainly from Europe and other parts of the United States. Moreover, we found 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.

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Authors+Show Affiliations

Gonzalez-Reiche AS
Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Hernandez MM
Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA. The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Sullivan MJ
Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Ciferri B
Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Alshammary H
Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Obla A
Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Fabre S
Clinical Microbiology Laboratory, Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Kleiner G
Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Polanco J
Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA. Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Khan Z
Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Alburquerque B
Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA. The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
van de Guchte A
Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Dutta J
Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Francoeur N
Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Melo BS
Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA. Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Oussenko I
Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA. Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Deikus G
Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA. Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Soto J
Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA. Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Sridhar SH
Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA. Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Wang YC
Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA. Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Twyman K
The Mount Sinai Data Office, Mount Sinai Health System, New York, NY 10029, USA.
Kasarskis A
Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA. Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA. The Mount Sinai Data Office, Mount Sinai Health System, New York, NY 10029, USA.
Altman DR
Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA. Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Smith M
Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA. Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Sebra R
Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA. Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA. Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA. Sema4, Stamford, CT 06902, USA.
Aberg J
Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Krammer F
Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA. The Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
García-Sastre A
Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA. Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA. The Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA. The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Luksza M
Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA. Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Patel G
Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Paniz-Mondolfi A
The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Gitman M
The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Sordillo EM
The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA. harm.vanbakel@mssm.edu viviana.simon@mssm.edu emilia.sordillo@mssm.edu.
Simon V
Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA. harm.vanbakel@mssm.edu viviana.simon@mssm.edu emilia.sordillo@mssm.edu. Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA. The Mount Sinai Data Office, Mount Sinai Health System, New York, NY 10029, USA.
van Bakel H
Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA. harm.vanbakel@mssm.edu viviana.simon@mssm.edu emilia.sordillo@mssm.edu. Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.

MeSH

AdultAgedAged, 80 and overBetacoronavirusCOVID-19Coronavirus InfectionsEpidemiological MonitoringFemaleGenome, ViralGeography, MedicalHumansMaleMiddle AgedNew York CityPandemicsPhylogenyPneumonia, ViralResidence CharacteristicsSARS-CoV-2Young Adult

Pub Type(s)

Journal Article
Research Support, N.I.H., Extramural

Language

eng

PubMed ID

32471856

Citation

Gonzalez-Reiche, Ana S., et al. "Introductions and Early Spread of SARS-CoV-2 in the New York City Area." Science (New York, N.Y.), vol. 369, no. 6501, 2020, pp. 297-301.
Gonzalez-Reiche AS, Hernandez MM, Sullivan MJ, et al. Introductions and early spread of SARS-CoV-2 in the New York City area. Science. 2020;369(6501):297-301.
Gonzalez-Reiche, A. S., Hernandez, M. M., Sullivan, M. J., Ciferri, B., Alshammary, H., Obla, A., Fabre, S., Kleiner, G., Polanco, J., Khan, Z., Alburquerque, B., van de Guchte, A., Dutta, J., Francoeur, N., Melo, B. S., Oussenko, I., Deikus, G., Soto, J., Sridhar, S. H., ... van Bakel, H. (2020). Introductions and early spread of SARS-CoV-2 in the New York City area. Science (New York, N.Y.), 369(6501), 297-301. https://doi.org/10.1126/science.abc1917
Gonzalez-Reiche AS, et al. Introductions and Early Spread of SARS-CoV-2 in the New York City Area. Science. 2020 07 17;369(6501):297-301. PubMed PMID: 32471856.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Introductions and early spread of SARS-CoV-2 in the New York City area. AU - Gonzalez-Reiche,Ana S, AU - Hernandez,Matthew M, AU - Sullivan,Mitchell J, AU - Ciferri,Brianne, AU - Alshammary,Hala, AU - Obla,Ajay, AU - Fabre,Shelcie, AU - Kleiner,Giulio, AU - Polanco,Jose, AU - Khan,Zenab, AU - Alburquerque,Bremy, AU - van de Guchte,Adriana, AU - Dutta,Jayeeta, AU - Francoeur,Nancy, AU - Melo,Betsaida Salom, AU - Oussenko,Irina, AU - Deikus,Gintaras, AU - Soto,Juan, AU - Sridhar,Shwetha Hara, AU - Wang,Ying-Chih, AU - Twyman,Kathryn, AU - Kasarskis,Andrew, AU - Altman,Deena R, AU - Smith,Melissa, AU - Sebra,Robert, AU - Aberg,Judith, AU - Krammer,Florian, AU - García-Sastre,Adolfo, AU - Luksza,Marta, AU - Patel,Gopi, AU - Paniz-Mondolfi,Alberto, AU - Gitman,Melissa, AU - Sordillo,Emilia Mia, AU - Simon,Viviana, AU - van Bakel,Harm, Y1 - 2020/05/29/ PY - 2020/04/10/received PY - 2020/05/27/accepted PY - 2020/5/31/pubmed PY - 2020/7/31/medline PY - 2020/5/31/entrez SP - 297 EP - 301 JF - Science (New York, N.Y.) JO - Science VL - 369 IS - 6501 N2 - 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 introductions mainly from Europe and other parts of the United States. Moreover, we found 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. SN - 1095-9203 UR - https://www.unboundmedicine.com/medline/citation/32471856/Introductions_and_early_spread_of_SARS_CoV_2_in_the_New_York_City_area_ DB - PRIME DP - Unbound Medicine ER -