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Sequencing identifies multiple early introductions of SARS-CoV-2 to the New York City region.
Maurano, Matthew T; Ramaswami, Sitharam; Zappile, Paul; Dimartino, Dacia; Boytard, Ludovic; Ribeiro-Dos-Santos, André M; Vulpescu, Nicholas A; Westby, Gael; Shen, Guomiao; Feng, Xiaojun; Hogan, Megan S; Ragonnet-Cronin, Manon; Geidelberg, Lily; Marier, Christian; Meyn, Peter; Zhang, Yutong; Cadley, John; Ordoñez, Raquel; Luther, Raven; Huang, Emily; Guzman, Emily; Arguelles-Grande, Carolina; Argyropoulos, Kimon V; Black, Margaret; Serrano, Antonio; Call, Melissa E; Kim, Min Jae; Belovarac, Brendan; Gindin, Tatyana; Lytle, Andrew; Pinnell, Jared; Vougiouklakis, Theodore; Chen, John; Lin, Lawrence H; Rapkiewicz, Amy; Raabe, Vanessa; Samanovic, Marie I; Jour, George; Osman, Iman; Aguero-Rosenfeld, Maria; Mulligan, Mark J; Volz, Erik M; Cotzia, Paolo; Snuderl, Matija; Heguy, Adriana.
  • Maurano MT; Institute for Systems Genetics, NYU Grossman School of Medicine, New York, New York 10016, USA.
  • Ramaswami S; Department of Pathology, NYU Grossman School of Medicine, New York, New York 10016, USA.
  • Zappile P; Genome Technology Center, Division of Advanced Research Technologies, Office of Science and Research, NYU Langone Health, New York, New York 10016, USA.
  • Dimartino D; Genome Technology Center, Division of Advanced Research Technologies, Office of Science and Research, NYU Langone Health, New York, New York 10016, USA.
  • Boytard L; Genome Technology Center, Division of Advanced Research Technologies, Office of Science and Research, NYU Langone Health, New York, New York 10016, USA.
  • Ribeiro-Dos-Santos AM; Center for Biospecimen Research and Development, NYU Langone Health, New York, New York 10016, USA.
  • Vulpescu NA; Institute for Systems Genetics, NYU Grossman School of Medicine, New York, New York 10016, USA.
  • Westby G; Department of Pathology, NYU Grossman School of Medicine, New York, New York 10016, USA.
  • Shen G; Institute for Systems Genetics, NYU Grossman School of Medicine, New York, New York 10016, USA.
  • Feng X; Department of Pathology, NYU Grossman School of Medicine, New York, New York 10016, USA.
  • Hogan MS; Genome Technology Center, Division of Advanced Research Technologies, Office of Science and Research, NYU Langone Health, New York, New York 10016, USA.
  • Ragonnet-Cronin M; Department of Pathology, NYU Grossman School of Medicine, New York, New York 10016, USA.
  • Geidelberg L; Department of Pathology, NYU Grossman School of Medicine, New York, New York 10016, USA.
  • Marier C; Institute for Systems Genetics, NYU Grossman School of Medicine, New York, New York 10016, USA.
  • Meyn P; Department of Pathology, NYU Grossman School of Medicine, New York, New York 10016, USA.
  • Zhang Y; MRC Centre for Global Infectious Disease Analysis and Department of Infectious Disease Epidemiology, Imperial College London, London W2 1PG, United Kingdom.
  • Cadley J; MRC Centre for Global Infectious Disease Analysis and Department of Infectious Disease Epidemiology, Imperial College London, London W2 1PG, United Kingdom.
  • Ordoñez R; Genome Technology Center, Division of Advanced Research Technologies, Office of Science and Research, NYU Langone Health, New York, New York 10016, USA.
  • Luther R; Genome Technology Center, Division of Advanced Research Technologies, Office of Science and Research, NYU Langone Health, New York, New York 10016, USA.
  • Huang E; Genome Technology Center, Division of Advanced Research Technologies, Office of Science and Research, NYU Langone Health, New York, New York 10016, USA.
  • Guzman E; Institute for Systems Genetics, NYU Grossman School of Medicine, New York, New York 10016, USA.
  • Arguelles-Grande C; Department of Pathology, NYU Grossman School of Medicine, New York, New York 10016, USA.
  • Argyropoulos KV; Institute for Systems Genetics, NYU Grossman School of Medicine, New York, New York 10016, USA.
  • Black M; Department of Pathology, NYU Grossman School of Medicine, New York, New York 10016, USA.
  • Serrano A; Institute for Systems Genetics, NYU Grossman School of Medicine, New York, New York 10016, USA.
  • Call ME; Department of Pathology, NYU Grossman School of Medicine, New York, New York 10016, USA.
  • Kim MJ; Institute for Systems Genetics, NYU Grossman School of Medicine, New York, New York 10016, USA.
  • Belovarac B; Department of Pathology, NYU Grossman School of Medicine, New York, New York 10016, USA.
  • Gindin T; Genome Technology Center, Division of Advanced Research Technologies, Office of Science and Research, NYU Langone Health, New York, New York 10016, USA.
  • Lytle A; Center for Biospecimen Research and Development, NYU Langone Health, New York, New York 10016, USA.
  • Pinnell J; Department of Pathology, NYU Grossman School of Medicine, New York, New York 10016, USA.
  • Vougiouklakis T; Department of Pathology, NYU Grossman School of Medicine, New York, New York 10016, USA.
  • Chen J; Department of Pathology, NYU Grossman School of Medicine, New York, New York 10016, USA.
  • Lin LH; Department of Dermatology, NYU Grossman School of Medicine, New York, New York 10016, USA.
  • Rapkiewicz A; Department of Dermatology, NYU Grossman School of Medicine, New York, New York 10016, USA.
  • Raabe V; Department of Pathology, NYU Grossman School of Medicine, New York, New York 10016, USA.
  • Samanovic MI; Department of Pathology, NYU Grossman School of Medicine, New York, New York 10016, USA.
  • Jour G; Department of Pathology, NYU Grossman School of Medicine, New York, New York 10016, USA.
  • Osman I; Department of Pathology, NYU Grossman School of Medicine, New York, New York 10016, USA.
  • Aguero-Rosenfeld M; Department of Pathology, NYU Grossman School of Medicine, New York, New York 10016, USA.
  • Mulligan MJ; Medical Center IT, NYU Langone Health, New York, New York 10016, USA.
  • Volz EM; Department of Pathology, NYU Grossman School of Medicine, New York, New York 10016, USA.
  • Cotzia P; Department of Pathology, NYU Grossman School of Medicine, New York, New York 10016, USA.
  • Snuderl M; Division of Infectious Diseases and Immunology, Department of Medicine and NYU Langone Vaccine Center, NYU Grossman School of Medicine, New York, New York 10016, USA.
  • Heguy A; Division of Infectious Diseases and Immunology, Department of Medicine and NYU Langone Vaccine Center, NYU Grossman School of Medicine, New York, New York 10016, USA.
Genome Res ; 30(12): 1781-1788, 2020 12.
Article in English | MEDLINE | ID: covidwho-889658
ABSTRACT
Effective public response to a pandemic relies upon accurate measurement of the extent and dynamics of an outbreak. Viral genome sequencing has emerged as a powerful approach to link seemingly unrelated cases, and large-scale sequencing surveillance can inform on critical epidemiological parameters. Here, we report the analysis of 864 SARS-CoV-2 sequences from cases in the New York City metropolitan area during the COVID-19 outbreak in spring 2020. The majority of cases had no recent travel history or known exposure, and genetically linked cases were spread throughout the region. Comparison to global viral sequences showed that early transmission was most linked to cases from Europe. Our data are consistent with numerous seeds from multiple sources and a prolonged period of unrecognized community spreading. This work highlights the complementary role of genomic surveillance in addition to traditional epidemiological indicators.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: Phylogeny / Genome, Viral / Pandemics / Whole Genome Sequencing / SARS-CoV-2 / COVID-19 Type of study: Observational study / Prognostic study / Randomized controlled trials Limits: Female / Humans / Male Country/Region as subject: North America Language: English Journal: Genome Res Journal subject: Molecular Biology / Genetics Year: 2020 Document Type: Article Affiliation country: Gr.266676.120

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Full text: Available Collection: International databases Database: MEDLINE Main subject: Phylogeny / Genome, Viral / Pandemics / Whole Genome Sequencing / SARS-CoV-2 / COVID-19 Type of study: Observational study / Prognostic study / Randomized controlled trials Limits: Female / Humans / Male Country/Region as subject: North America Language: English Journal: Genome Res Journal subject: Molecular Biology / Genetics Year: 2020 Document Type: Article Affiliation country: Gr.266676.120