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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, USA.
  • Ramaswami S; Department of Pathology, NYU Grossman School of Medicine, New York, USA.
  • Zappile P; Genome Technology Center, Division of Advanced Research Technologies, Office of Science and Research, NYU Langone Health, New York, USA.
  • Dimartino D; Genome Technology Center, Division of Advanced Research Technologies, Office of Science and Research, NYU Langone Health, New York, USA.
  • Boytard L; Genome Technology Center, Division of Advanced Research Technologies, Office of Science and Research, NYU Langone Health, New York, USA.
  • Ribeiro-Dos-Santos AM; Center for Biospecimen Research and Development, NYU Langone Health, New York, USA.
  • Vulpescu NA; Institute for Systems Genetics, NYU Grossman School of Medicine, New York, USA.
  • Westby G; Department of Pathology, NYU Grossman School of Medicine, New York, USA.
  • Shen G; Institute for Systems Genetics, NYU Grossman School of Medicine, New York, USA.
  • Feng X; Department of Pathology, NYU Grossman School of Medicine, New York, USA.
  • Hogan MS; Genome Technology Center, Division of Advanced Research Technologies, Office of Science and Research, NYU Langone Health, New York, USA.
  • Ragonnet-Cronin M; Department of Pathology, NYU Grossman School of Medicine, New York, USA.
  • Geidelberg L; Department of Pathology, NYU Grossman School of Medicine, New York, USA.
  • Marier C; Institute for Systems Genetics, NYU Grossman School of Medicine, New York, USA.
  • Meyn P; Department of Pathology, NYU Grossman School of Medicine, New York, USA.
  • Zhang Y; MRC Centre for Global Infectious Disease Analysis and Department of Infectious Disease Epidemiology, Imperial College London.
  • Cadley J; MRC Centre for Global Infectious Disease Analysis and Department of Infectious Disease Epidemiology, Imperial College London.
  • Ordoñez R; Genome Technology Center, Division of Advanced Research Technologies, Office of Science and Research, NYU Langone Health, New York, USA.
  • Luther R; Genome Technology Center, Division of Advanced Research Technologies, Office of Science and Research, NYU Langone Health, New York, USA.
  • Huang E; Genome Technology Center, Division of Advanced Research Technologies, Office of Science and Research, NYU Langone Health, New York, USA.
  • Guzman E; Institute for Systems Genetics, NYU Grossman School of Medicine, New York, USA.
  • Arguelles-Grande C; Department of Pathology, NYU Grossman School of Medicine, New York, USA.
  • Argyropoulos KV; Institute for Systems Genetics, NYU Grossman School of Medicine, New York, USA.
  • Black M; Department of Pathology, NYU Grossman School of Medicine, New York, USA.
  • Serrano A; Institute for Systems Genetics, NYU Grossman School of Medicine, New York, USA.
  • Call ME; Department of Pathology, NYU Grossman School of Medicine, New York, USA.
  • Kim MJ; Institute for Systems Genetics, NYU Grossman School of Medicine, New York, USA.
  • Belovarac B; Department of Pathology, NYU Grossman School of Medicine, New York, USA.
  • Gindin T; Genome Technology Center, Division of Advanced Research Technologies, Office of Science and Research, NYU Langone Health, New York, USA.
  • Lytle A; Center for Biospecimen Research and Development, NYU Langone Health, New York, USA.
  • Pinnell J; Department of Pathology, NYU Grossman School of Medicine, New York, USA.
  • Vougiouklakis T; Department of Pathology, NYU Grossman School of Medicine, New York, USA.
  • Chen J; Department of Pathology, NYU Grossman School of Medicine, New York, USA.
  • Lin LH; Department of Dermatology, NYU Grossman School of Medicine, New York, USA.
  • Rapkiewicz A; Department of Dermatology, NYU Grossman School of Medicine, New York, USA.
  • Raabe V; Department of Pathology, NYU Grossman School of Medicine, New York, USA.
  • Samanovic MI; Department of Pathology, NYU Grossman School of Medicine, New York, USA.
  • Jour G; Department of Pathology, NYU Grossman School of Medicine, New York, USA.
  • Osman I; Department of Pathology, NYU Grossman School of Medicine, New York, USA.
  • Aguero-Rosenfeld M; Department of Pathology, NYU Grossman School of Medicine, New York, USA.
  • Mulligan MJ; Medical Center IT, NYU Langone Health, New York, USA.
  • Volz EM; Department of Pathology, NYU Grossman School of Medicine, New York, USA.
  • Cotzia P; Department of Pathology, NYU Grossman School of Medicine, New York, USA.
  • Snuderl M; Division of Infectious Diseases and Immunology, Department of Medicine and NYU Langone Vaccine Center, NYU Grossman School of Medicine, New York, USA.
  • Heguy A; Department of Medicine, NYU Grossman School of Medicine, New York, USA.
medRxiv ; 2020 Aug 19.
Article in English | MEDLINE | ID: covidwho-828498
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 Type of study: Prognostic study Language: English Year: 2020 Document Type: Article Affiliation country: 2020.04.15.20064931

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Full text: Available Collection: International databases Database: MEDLINE Type of study: Prognostic study Language: English Year: 2020 Document Type: Article Affiliation country: 2020.04.15.20064931