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Genomic surveillance reveals multiple introductions of SARS-CoV-2 into Northern California.
Deng, Xianding; Gu, Wei; Federman, Scot; du Plessis, Louis; Pybus, Oliver G; Faria, Nuno R; Wang, Candace; Yu, Guixia; Bushnell, Brian; 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; Masinde, Godfred; Chan, Curtis; Yu, Alexander T; Chai, Shua J; Villarino, Elsa; Bonin, Brandon; Wadford, Debra A; Chiu, Charles Y.
  • Deng X; Department of Laboratory Medicine, University of California, San Francisco, CA, USA.
  • Gu W; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA.
  • Federman S; Department of Laboratory Medicine, University of California, San Francisco, CA, USA.
  • du Plessis L; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA.
  • Pybus OG; Department of Laboratory Medicine, University of California, San Francisco, CA, USA.
  • Faria NR; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA.
  • Wang C; Department of Zoology, University of Oxford, Oxford, UK.
  • Yu G; Department of Zoology, University of Oxford, Oxford, UK.
  • Bushnell B; Department of Pathobiology and Population Sciences, Royal Veterinary College, London, UK.
  • Pan CY; Department of Zoology, University of Oxford, Oxford, UK.
  • Guevara H; MRC Centre for Global Infectious Disease Analysis, J-IDEA, Imperial College London, London, UK.
  • Sotomayor-Gonzalez A; Department of Laboratory Medicine, University of California, San Francisco, CA, USA.
  • Zorn K; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA.
  • Gopez A; Department of Laboratory Medicine, University of California, San Francisco, CA, USA.
  • Servellita V; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA.
  • Hsu E; Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
  • Miller S; California Department of Public Health, Richmond, CA, USA.
  • Bedford T; California Department of Public Health, Richmond, CA, USA.
  • Greninger AL; Department of Laboratory Medicine, University of California, San Francisco, CA, USA.
  • Roychoudhury P; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA.
  • Starita LM; Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA.
  • Famulare M; Department of Laboratory Medicine, University of California, San Francisco, CA, USA.
  • Chu HY; Department of Laboratory Medicine, University of California, San Francisco, CA, USA.
  • Shendure J; Department of Laboratory Medicine, University of California, San Francisco, CA, USA.
  • Jerome KR; Department of Laboratory Medicine, University of California, San Francisco, CA, USA.
  • Anderson C; Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
  • Gangavarapu K; Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.
  • Zeller M; Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
  • Spencer E; Department of Laboratory Medicine, University of Washington, Seattle, WA, USA.
  • Andersen KG; Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
  • MacCannell D; Department of Laboratory Medicine, University of Washington, Seattle, WA, USA.
  • Paden CR; Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.
  • Li Y; Department of Genome Sciences, University of Washington, Seattle, WA, USA.
  • Zhang J; Institute for Disease Modeling, Bellevue, WA, USA.
  • Tong S; Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.
  • Armstrong G; Department of Medicine, University of Washington, Seattle, WA, USA.
  • Morrow S; Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.
  • Willis M; Department of Laboratory Medicine, University of Washington, Seattle, WA, USA.
  • Matyas BT; Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
  • Mase S; Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
  • Kasirye O; Department of Laboratory Medicine, University of Washington, Seattle, WA, USA.
  • Park M; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.
  • Masinde G; 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; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.
  • Villarino E; U.S. Centers for Disease Control and Prevention, Atlanta, GA, USA.
  • Bonin B; U.S. Centers for Disease Control and Prevention, Atlanta, GA, USA.
  • Wadford DA; U.S. Centers for Disease Control and Prevention, Atlanta, GA, USA.
  • Chiu CY; U.S. Centers for Disease Control and Prevention, Atlanta, GA, USA.
Science ; 369(6503): 582-587, 2020 07 31.
Article in English | MEDLINE | ID: covidwho-591377
ABSTRACT
The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread globally, with >365,000 cases in California as of 17 July 2020. We investigated the genomic epidemiology of SARS-CoV-2 in Northern California from late January to mid-March 2020, using samples from 36 patients spanning nine counties and the Grand Princess cruise ship. Phylogenetic analyses revealed the cryptic introduction of at least seven different SARS-CoV-2 lineages into California, including epidemic WA1 strains associated with Washington state, with lack of a predominant lineage and limited transmission among communities. Lineages associated with outbreak clusters in two counties were defined by a single base substitution in the viral genome. These findings support contact tracing, social distancing, and travel restrictions to contain the spread of SARS-CoV-2 in California and other states.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: Phylogeny / Pneumonia, Viral / Genome, Viral / Coronavirus Infections / Betacoronavirus Type of study: Observational study / Randomized controlled trials Limits: Humans Country/Region as subject: North America Language: English Journal: Science Year: 2020 Document Type: Article Affiliation country: Science.abb9263

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Full text: Available Collection: International databases Database: MEDLINE Main subject: Phylogeny / Pneumonia, Viral / Genome, Viral / Coronavirus Infections / Betacoronavirus Type of study: Observational study / Randomized controlled trials Limits: Humans Country/Region as subject: North America Language: English Journal: Science Year: 2020 Document Type: Article Affiliation country: Science.abb9263