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A Genomic Survey of SARS-CoV-2 Reveals Multiple Introductions into Northern California without a Predominant Lineage.
Deng, Xianding; Gu, Wei; Federman, Scot; du Plessis, Louis; Pybus, Oliver G; Faria, Nuno; Wang, Candace; Yu, Guixia; Pan, Chao-Yang; Guevara, Hugo; Sotomayor-Gonzalez, Alicia; Zorn, Kelsey; Gopez, Allan; Servellita, Venice; Hsu, Elaine; Miller, Steve; Bedford, Trevor; Greninger, Alexander L; Roychoudhury, Pavitra; Starita, Lea M; Famulare, Michael; Chu, Helen Y; Shendure, Jay; Jerome, Keith R; Anderson, Catie; Gangavarapu, Karthik; Zeller, Mark; Spencer, Emily; Andersen, Kristian G; MacCannell, Duncan; Paden, Clinton R; Li, Yan; Zhang, Jing; Tong, Suxiang; Armstrong, Gregory; Morrow, Scott; Willis, Matthew; Matyas, Bela T; Mase, Sundari; Kasirye, Olivia; Park, Maggie; Chan, Curtis; Yu, Alexander T; Chai, Shua J; Villarino, Elsa; Bonin, Brandon; Wadford, Debra A; Chiu, Charles Y.
Afiliación
  • Deng X; Department of Laboratory Medicine, University of California, San Francisco, California, USA.
  • Gu W; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, USA.
  • Federman S; Department of Laboratory Medicine, University of California, San Francisco, California, USA.
  • du Plessis L; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, USA.
  • Pybus OG; Department of Laboratory Medicine, University of California, San Francisco, California, USA.
  • Faria N; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, USA.
  • Wang C; Department of Zoology, University of Oxford, Oxford, UK.
  • Yu G; Department of Zoology, University of Oxford, Oxford, UK.
  • Pan CY; Department of Zoology, University of Oxford, Oxford, UK.
  • Guevara H; Department of Laboratory Medicine, University of California, San Francisco, California, USA.
  • Sotomayor-Gonzalez A; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, USA.
  • Zorn K; Department of Laboratory Medicine, University of California, San Francisco, California, USA.
  • Gopez A; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, USA.
  • Servellita V; California Department of Public Health, Richmond, California, USA.
  • Hsu E; California Department of Public Health, Richmond, California, USA.
  • Miller S; Department of Laboratory Medicine, University of California, San Francisco, California, USA.
  • Bedford T; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, USA.
  • Greninger AL; Department of Biochemistry and Biophysics, San Francisco, California, USA.
  • Roychoudhury P; Department of Laboratory Medicine, University of California, San Francisco, California, USA.
  • Starita LM; Department of Laboratory Medicine, University of California, San Francisco, California, USA.
  • Famulare M; Department of Laboratory Medicine, University of California, San Francisco, California, USA.
  • Chu HY; Department of Laboratory Medicine, University of California, San Francisco, California, USA.
  • Shendure J; Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.
  • Jerome KR; Brotman Baty Institute for Precision Medicine, Seattle, Washington, USA.
  • Anderson C; Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.
  • Gangavarapu K; Department of Laboratory Medicine, University of Washington, Seattle, WA, USA.
  • Zeller M; Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.
  • Spencer E; Department of Laboratory Medicine, University of Washington, Seattle, WA, USA.
  • Andersen KG; Brotman Baty Institute for Precision Medicine, Seattle, Washington, USA.
  • MacCannell D; Department of Genome Sciences, University of Washington, Seattle, WA, USA.
  • Paden CR; Institute for Disease Modeling, Bellevue, WA, USA.
  • Li Y; Brotman Baty Institute for Precision Medicine, Seattle, Washington, USA.
  • Zhang J; Department of Medicine, University of Washington, Seattle, WA, USA.
  • Tong S; Brotman Baty Institute for Precision Medicine, Seattle, Washington, USA.
  • Armstrong G; Department of Laboratory Medicine, University of Washington, Seattle, WA, USA.
  • Morrow S; Howards Hughes Medical Institute, Seattle, WA, USA.
  • Willis M; Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.
  • Matyas BT; Department of Laboratory Medicine, University of Washington, Seattle, WA, USA.
  • Mase S; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.
  • Kasirye O; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.
  • Park M; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.
  • Chan C; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.
  • Yu AT; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.
  • Chai SJ; United States Centers for Disease Control and Prevention, Atlanta, Georgia, USA.
  • Villarino E; United States Centers for Disease Control and Prevention, Atlanta, Georgia, USA.
  • Bonin B; United States Centers for Disease Control and Prevention, Atlanta, Georgia, USA.
  • Wadford DA; United States Centers for Disease Control and Prevention, Atlanta, Georgia, USA.
  • Chiu CY; United States Centers for Disease Control and Prevention, Atlanta, Georgia, USA.
medRxiv ; 2020 Mar 30.
Article en En | MEDLINE | ID: mdl-32511579
The COVID-19 pandemic caused by the novel coronavirus SARS-CoV-2 has spread globally, resulting in >300,000 reported cases worldwide as of March 21st, 2020. Here we investigate the genetic diversity and genomic epidemiology of SARS-CoV-2 in Northern California using samples from returning travelers, cruise ship passengers, and cases of community transmission with unclear infection sources. Virus genomes were sampled from 29 patients diagnosed with COVID-19 infection from Feb 3rd through Mar 15th. Phylogenetic analyses revealed at least 8 different SARS-CoV-2 lineages, suggesting multiple independent introductions of the virus into the state. Virus genomes from passengers on two consecutive excursions of the Grand Princess cruise ship clustered with those from an established epidemic in Washington State, including the WA1 genome representing the first reported case in the United States on January 19th. We also detected evidence for presumptive transmission of SARS-CoV-2 lineages from one community to another. These findings suggest that cryptic transmission of SARS-CoV-2 in Northern California to date is characterized by multiple transmission chains that originate via distinct introductions from international and interstate travel, rather than widespread community transmission of a single predominant lineage. Rapid testing and contact tracing, social distancing, and travel restrictions are measures that will help to slow SARS-CoV-2 spread in California and other regions of the USA.
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Idioma: En Revista: MedRxiv Año: 2020 Tipo del documento: Article País de afiliación: Estados Unidos Pais de publicación: Estados Unidos
Texto completo
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Idioma: En Revista: MedRxiv Año: 2020 Tipo del documento: Article País de afiliación: Estados Unidos Pais de publicación: Estados Unidos