Genomic surveillance reveals multiple introductions of SARS-CoV-2 into Northern California.

Betacoronavirus / genetics COVID-19 California / epidemiology Coronavirus Infections / epidemiology Epidemiological Monitoring Genome, Viral Humans Pandemics Phylogeny Pneumonia, Viral / epidemiology SARS-CoV-2 Sequence Alignment Ships Travel Washington

Journal

Science (New York, N.Y.)
ISSN: 1095-9203
Titre abrégé: Science
Pays: United States
ID NLM: 0404511

Informations de publication

Date de publication:
31 07 2020
Historique:
received: 27 03 2020
accepted: 03 06 2020
pubmed: 10 6 2020
medline: 13 8 2020
entrez: 10 6 2020
Statut: ppublish

Résumé

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.

Identifiants

DOI: 10.1126/science.abb9263 PMID: 32513865 PMC: PMC7286545
pubmed: 32513865
pii: science.abb9263
doi: 10.1126/science.abb9263
pmc: PMC7286545
doi:

Types de publication

Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

IM

Pagination

582-587

Subventions

Organisme : Medical Research Council
ID : MC_PC_19012
Pays : United Kingdom
Organisme : Medical Research Council
ID : MR/S019510/1
Pays : United Kingdom
Organisme : NCI NIH HHS
ID : K08 CA230156
Pays : United States
Organisme : NIAID NIH HHS
ID : U01 AI151812
Pays : United States
Organisme : Medical Research Council
ID : MR/R015600/1
Pays : United Kingdom

Commentaires et corrections

Type : UpdateOf

Informations de copyright

Copyright © 2020 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

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Auteurs

Xianding Deng (X)

Department of Laboratory Medicine, University of California, San Francisco, CA, USA.
UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA.
ORCID: 0000-0001-7648-4652

Wei Gu (W)

Department of Laboratory Medicine, University of California, San Francisco, CA, USA.
UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA.
ORCID: 0000-0002-2480-6645

Scot Federman (S)

Department of Laboratory Medicine, University of California, San Francisco, CA, USA.
UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA.
ORCID: 0000-0001-8712-3131

Louis du Plessis (L)

Department of Zoology, University of Oxford, Oxford, UK.
ORCID: 0000-0003-0352-6289

Oliver G Pybus (OG)

Department of Zoology, University of Oxford, Oxford, UK.
Department of Pathobiology and Population Sciences, Royal Veterinary College, London, UK.
ORCID: 0000-0002-8797-2667

Nuno R Faria (NR)

Department of Zoology, University of Oxford, Oxford, UK.
MRC Centre for Global Infectious Disease Analysis, J-IDEA, Imperial College London, London, UK.
ORCID: 0000-0001-8839-2798

Candace Wang (C)

Department of Laboratory Medicine, University of California, San Francisco, CA, USA.
UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA.

Guixia Yu (G)

Department of Laboratory Medicine, University of California, San Francisco, CA, USA.
UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA.
ORCID: 0000-0003-3248-9157

Brian Bushnell (B)

Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
ORCID: 0000-0002-8140-0131

Chao-Yang Pan (CY)

California Department of Public Health, Richmond, CA, USA.

Hugo Guevara (H)

California Department of Public Health, Richmond, CA, USA.

Alicia Sotomayor-Gonzalez (A)

Department of Laboratory Medicine, University of California, San Francisco, CA, USA.
UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA.
ORCID: 0000-0002-8930-745X

Kelsey Zorn (K)

Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA.
ORCID: 0000-0003-1227-2137

Allan Gopez (A)

Department of Laboratory Medicine, University of California, San Francisco, CA, USA.

Venice Servellita (V)

Department of Laboratory Medicine, University of California, San Francisco, CA, USA.

Elaine Hsu (E)

Department of Laboratory Medicine, University of California, San Francisco, CA, USA.

Steve Miller (S)

Department of Laboratory Medicine, University of California, San Francisco, CA, USA.
ORCID: 0000-0002-9188-3392

Trevor Bedford (T)

Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.
ORCID: 0000-0002-4039-5794

Alexander L Greninger (AL)

Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
Department of Laboratory Medicine, University of Washington, Seattle, WA, USA.
ORCID: 0000-0002-7443-0527

Pavitra Roychoudhury (P)

Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
Department of Laboratory Medicine, University of Washington, Seattle, WA, USA.
ORCID: 0000-0002-4567-8232

Lea M Starita (LM)

Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.
Department of Genome Sciences, University of Washington, Seattle, WA, USA.
ORCID: 0000-0003-2870-5099

Michael Famulare (M)

Institute for Disease Modeling, Bellevue, WA, USA.
ORCID: 0000-0001-9275-7454

Helen Y Chu (HY)

Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.
Department of Medicine, University of Washington, Seattle, WA, USA.

Jay Shendure (J)

Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.
Department of Laboratory Medicine, University of Washington, Seattle, WA, USA.
Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
ORCID: 0000-0002-1516-1865

Keith R Jerome (KR)

Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
Department of Laboratory Medicine, University of Washington, Seattle, WA, USA.
ORCID: 0000-0002-8212-3789

Catie Anderson (C)

Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.

Karthik Gangavarapu (K)

Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.

Mark Zeller (M)

Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.

Emily Spencer (E)

Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.

Kristian G Andersen (KG)

Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.
ORCID: 0000-0001-6431-5982

Duncan MacCannell (D)

U.S. Centers for Disease Control and Prevention, Atlanta, GA, USA.
ORCID: 0000-0002-8869-1840

Clinton R Paden (CR)

U.S. Centers for Disease Control and Prevention, Atlanta, GA, USA.
ORCID: 0000-0001-8701-8948

Yan Li (Y)

U.S. Centers for Disease Control and Prevention, Atlanta, GA, USA.

Jing Zhang (J)

U.S. Centers for Disease Control and Prevention, Atlanta, GA, USA.

Suxiang Tong (S)

U.S. Centers for Disease Control and Prevention, Atlanta, GA, USA.
ORCID: 0000-0001-8439-8826

Gregory Armstrong (G)

U.S. Centers for Disease Control and Prevention, Atlanta, GA, USA.

Scott Morrow (S)

San Mateo County Department of Public Health, San Mateo, CA, USA.
ORCID: 0000-0003-0849-1644

Matthew Willis (M)

Marin County Division of Public Health, San Rafael, CA, USA.

Bela T Matyas (BT)

Solano County Department of Public Health, Fairfield, CA, USA.

Sundari Mase (S)

Sonoma County Department of Public Health, Santa Rosa, CA, USA.

Olivia Kasirye (O)

Sacramento County Division of Public Health, Sacramento, CA, USA.
ORCID: 0000-0003-1385-0699

Maggie Park (M)

San Joaquin County Department of Public Health, Stockton, CA, USA.
ORCID: 0000-0001-8080-548X

Godfred Masinde (G)

San Francisco County Department of Public Health, San Francisco, CA, USA.

Curtis Chan (C)

San Francisco County Department of Public Health, San Francisco, CA, USA.

Alexander T Yu (AT)

California Department of Public Health, Richmond, CA, USA.
ORCID: 0000-0002-5502-9818

Shua J Chai (SJ)

California Department of Public Health, Richmond, CA, USA.
U.S. Centers for Disease Control and Prevention, Atlanta, GA, USA.
ORCID: 0000-0003-2048-2871

Elsa Villarino (E)

County of Santa Clara, Public Health Department, Santa Clara, CA, USA.

Brandon Bonin (B)

County of Santa Clara, Public Health Department, Santa Clara, CA, USA.

Debra A Wadford (DA)

California Department of Public Health, Richmond, CA, USA.
ORCID: 0000-0002-8630-427X

Charles Y Chiu (CY)

Department of Laboratory Medicine, University of California, San Francisco, CA, USA. charles.chiu@ucsf.edu.
UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA.
Department of Medicine, Division of Infectious Diseases, University of California, San Francisco, CA, USA.
ORCID: 0000-0003-2915-2094

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Classifications MeSH

questionsmedicales.fr › Virus › Virus à ARN › Virus à ARN à brin positif › Nidovirales › Coronaviridae › Coronavirus › Betacoronavirus › Genomic surveillance reveals multiple...
questionsmedicales.fr › Maladies de l'appareil respiratoire › Infections de l'appareil respiratoire › Pneumopathie infectieuse › Pneumopathie virale › COVID-19 › Genomic surveillance reveals multiple...
questionsmedicales.fr › Régions géographiques › Amériques › Amérique du Nord › États-Unis › États du Sud-Ouest des États-Unis › Californie › Genomic surveillance reveals multiple...
questionsmedicales.fr › Infection › Maladies virales › Infections à virus à ARN › Infections à Nidovirales › Infections à Coronaviridae › Infections à coronavirus › Genomic surveillance reveals multiple...
questionsmedicales.fr › Environnement et santé publique › Santé publique › Méthodes épidémiologiques › Surveillance épidémiologique › Genomic surveillance reveals multiple...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Génome › Génome microbien › Génome viral › Genomic surveillance reveals multiple...
questionsmedicales.fr › Eucaryotes › Animaux › Chordés › Vertébrés › Mammifères › Eutheria › Primates › Haplorhini › Catarrhini › Hominidae › Humains › Genomic surveillance reveals multiple...
questionsmedicales.fr › Environnement et santé publique › Santé publique › Épidémies de maladies › Épidémies › Pandémies › Genomic surveillance reveals multiple...
questionsmedicales.fr › Sciences de l'information › Phylogenèse › Genomic surveillance reveals multiple...
questionsmedicales.fr › Maladies de l'appareil respiratoire › Infections de l'appareil respiratoire › Pneumopathie infectieuse › Pneumopathie virale › Genomic surveillance reveals multiple...
questionsmedicales.fr › Virus › Virus à ARN › Virus à ARN à brin positif › Nidovirales › Coronaviridae › Coronavirus › Betacoronavirus › Virus du SRAS › SARS-CoV-2 › Genomic surveillance reveals multiple...
questionsmedicales.fr › Techniques d'investigation › Techniques génétiques › Alignement de séquences › Genomic surveillance reveals multiple...
questionsmedicales.fr › Technologie, industrie et agriculture › Transports › Navires › Genomic surveillance reveals multiple...
questionsmedicales.fr › Activités humaines › Voyage › Genomic surveillance reveals multiple...
questionsmedicales.fr › Régions géographiques › Amériques › Amérique du Nord › États-Unis › États du Pacifique › Washington › Genomic surveillance reveals multiple...