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

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

doi:10.1126/science.abc1917

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

Science. 2020 Jul 17;369(6501):297-301. doi: 10.1126/science.abc1917. Epub 2020 May 29.

Authors

Ana S Gonzalez-Reiche^#¹, Matthew M Hernandez^#^{2

3}, Mitchell J Sullivan¹, Brianne Ciferri¹, Hala Alshammary², Ajay Obla¹, Shelcie Fabre⁴, Giulio Kleiner², Jose Polanco^{1

2}, Zenab Khan¹, Bremy Alburquerque^{1

3}, Adriana van de Guchte¹, Jayeeta Dutta¹, Nancy Francoeur¹, Betsaida Salom Melo^{1

5}, Irina Oussenko^{1

5}, Gintaras Deikus^{1

5}, Juan Soto^{1

5}, Shwetha Hara Sridhar^{1

5}, Ying-Chih Wang^{1

5}, Kathryn Twyman⁶, Andrew Kasarskis^{1

5

6}, Deena R Altman^{1

7}, Melissa Smith^{1

5}, Robert Sebra^{1

5

8

9}, Judith Aberg⁷, Florian Krammer^{2

10}, Adolfo García-Sastre^{2

7

10

11}, Marta Luksza^{1

12}, Gopi Patel⁵, Alberto Paniz-Mondolfi³, Melissa Gitman³, Emilia Mia Sordillo^#¹³, Viviana Simon^#^{14

5

6}, Harm van Bakel^#^{15

8}

Affiliations

¹ Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
² Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
³ The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
⁴ Clinical Microbiology Laboratory, Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
⁵ Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
⁶ The Mount Sinai Data Office, Mount Sinai Health System, New York, NY 10029, USA.
⁷ Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
⁸ Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
⁹ Sema4, Stamford, CT 06902, USA.
¹⁰ The Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
¹¹ The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
¹² Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
¹³ 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.
¹⁴ 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.
¹⁵ 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.

^# Contributed equally.

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.

Publication types

Research Support, N.I.H., Extramural

MeSH terms

Adult
Aged
Aged, 80 and over
Betacoronavirus / genetics*
COVID-19
Coronavirus Infections / epidemiology*
Coronavirus Infections / mortality
Coronavirus Infections / transmission*
Epidemiological Monitoring
Female
Genome, Viral*
Geography, Medical
Humans
Male
Middle Aged
New York City / epidemiology
Pandemics
Phylogeny
Pneumonia, Viral / epidemiology*
Pneumonia, Viral / mortality
Pneumonia, Viral / transmission*
Residence Characteristics
SARS-CoV-2
Young Adult

Abstract

Publication types

MeSH terms

Grants and funding