Phylogenetic analysis of SARS-CoV-2 in Boston highlights the impact of superspreading events.

Boston / epidemiology COVID-19 / epidemiology Disease Outbreaks Epidemiological Monitoring Genome, Viral Humans Phylogeny SARS-CoV-2 / genetics

Journal

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

Informations de publication

Date de publication:
05 02 2021
Historique:
received: 19 08 2020
accepted: 07 12 2020
pubmed: 12 12 2020
medline: 13 2 2021
entrez: 11 12 2020
Statut: ppublish

Résumé

Analysis of 772 complete severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes from early in the Boston-area epidemic revealed numerous introductions of the virus, a small number of which led to most cases. The data revealed two superspreading events. One, in a skilled nursing facility, led to rapid transmission and significant mortality in this vulnerable population but little broader spread, whereas other introductions into the facility had little effect. The second, at an international business conference, produced sustained community transmission and was exported, resulting in extensive regional, national, and international spread. The two events also differed substantially in the genetic variation they generated, suggesting varying transmission dynamics in superspreading events. Our results show how genomic epidemiology can help to understand the link between individual clusters and wider community spread.

Identifiants

DOI: 10.1126/science.abe3261 PMID: 33303686 PMC: PMC7857412
pubmed: 33303686
pii: science.abe3261
doi: 10.1126/science.abe3261
pmc: PMC7857412
mid: NIHMS1655344
pii:
doi:

Types de publication

Journal Article Research Support, N.I.H., Extramural

Langues

eng

Sous-ensembles de citation

IM

Subventions

Organisme : NHGRI NIH HHS
ID : K99 HG010669
Pays : United States
Organisme : NIAID NIH HHS
ID : R37 AI147868
Pays : United States
Organisme : NCEZID CDC HHS
ID : U01 CK000490
Pays : United States
Organisme : NIGMS NIH HHS
ID : U54 GM088558
Pays : United States
Organisme : NIAID NIH HHS
ID : R01 AI128344
Pays : United States
Organisme : NIAID NIH HHS
ID : U19 AI110818
Pays : United States
Organisme : ACL HHS
ID : U01CK000490
Pays : United States
Organisme : NIAID NIH HHS
ID : R01 AI148784
Pays : United States
Organisme : NHGRI NIH HHS
ID : R00 HG010669
Pays : United States

Commentaires et corrections

Type : UpdateOf
Type : CommentIn

Informations de copyright

Copyright © 2021 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

Références

Science. 2020 Oct 30;370(6516):564-570
pubmed: 32912998
Genome Biol. 2014;15(11):519
pubmed: 25403361
Emerg Infect Dis. 2021 Jan;27(1):
pubmed: 33075274
Science. 2020 May 8;368(6491):
pubmed: 32234805
MMWR Morb Mortal Wkly Rep. 2020 May 08;69(18):551-556
pubmed: 32379733
Nature. 2005 Nov 17;438(7066):355-9
pubmed: 16292310
N Engl J Med. 2020 May 21;382(21):2005-2011
pubmed: 32220208
Bioinformatics. 2018 Dec 1;34(23):4121-4123
pubmed: 29790939
Genome Biol. 2004;5(10):R80
pubmed: 15461798
MMWR Morb Mortal Wkly Rep. 2020 May 15;69(19):606-610
pubmed: 32407303
Mol Biol Evol. 2015 Jan;32(1):268-74
pubmed: 25371430
MMWR Morb Mortal Wkly Rep. 2020 Apr 10;69(14):411-415
pubmed: 32271722
Genome Biol. 2019 Nov 28;20(1):257
pubmed: 31779668
MMWR Morb Mortal Wkly Rep. 2020 May 22;69(20):632-635
pubmed: 32437338
J Vis Exp. 2016 Jul 02;(113):
pubmed: 27403729
Clin Infect Dis. 2020 Nov 25;:
pubmed: 33237993
Clin Infect Dis. 2020 Jul 15;:
pubmed: 32667967
Mol Biol Evol. 2013 Apr;30(4):772-80
pubmed: 23329690
Virus Evol. 2018 Jan 08;4(1):vex042
pubmed: 29340210
Wellcome Open Res. 2020 Apr 9;5:67
pubmed: 32685698
Cell. 2015 Jun 18;161(7):1516-26
pubmed: 26091036
Cell. 2020 Aug 20;182(4):812-827.e19
pubmed: 32697968
Bioinformatics. 2011 Nov 1;27(21):3070-1
pubmed: 21926124
Lancet Infect Dis. 2020 May;20(5):533-534
pubmed: 32087114
Virus Evol. 2016 Apr 09;2(1):vew007
pubmed: 27774300
JAMA. 2020 Jun 2;323(21):2191-2192
pubmed: 32338732

Auteurs

Jacob E Lemieux (JE)

Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA. lemieux@broadinstitute.org pardis@broadinstitute.org bronwyn@broadinstitute.org.
Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA.
ORCID: 0000-0002-2758-4005

Katherine J Siddle (KJ)

Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA.
Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.
ORCID: 0000-0002-1799-7295

Bennett M Shaw (BM)

Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA.
Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA.
ORCID: 0000-0002-0180-6802

Christine Loreth (C)

Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA.
ORCID: 0000-0002-9626-7820

Stephen F Schaffner (SF)

Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA.
Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.
Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Harvard University, Boston, MA, USA.
ORCID: 0000-0001-6699-3568

Adrianne Gladden-Young (A)

Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA.

Gordon Adams (G)

Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA.

Timelia Fink (T)

Massachusetts Department of Public Health, Boston, MA, USA.

Christopher H Tomkins-Tinch (CH)

Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA.
Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.
ORCID: 0000-0002-9114-6421

Lydia A Krasilnikova (LA)

Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA.
Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.
ORCID: 0000-0003-4163-706X

Katherine C DeRuff (KC)

Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA.
ORCID: 0000-0001-6011-4323

Melissa Rudy (M)

Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA.
ORCID: 0000-0003-0165-5669

Matthew R Bauer (MR)

Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA.
Harvard Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA 02115, USA.

Kim A Lagerborg (KA)

Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA.
Harvard Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA 02115, USA.
ORCID: 0000-0003-2490-2191

Erica Normandin (E)

Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA.
Department of Systems Biology, Harvard Medical School, Boston, MA, USA.
ORCID: 0000-0002-4996-6442

Sinéad B Chapman (SB)

Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA.
ORCID: 0000-0002-9454-2737

Steven K Reilly (SK)

Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA.
Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.
ORCID: 0000-0003-3140-1483

Melis N Anahtar (MN)

Department of Pathology, Massachusetts General Hospital, Boston, MA, USA.
ORCID: 0000-0003-0309-368X

Aaron E Lin (AE)

Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA.
Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.
ORCID: 0000-0001-7400-4125

Amber Carter (A)

Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA.

Cameron Myhrvold (C)

Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA.
Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.
ORCID: 0000-0002-8971-184X

Molly E Kemball (ME)

Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA.
Department of Systems Biology, Harvard Medical School, Boston, MA, USA.
ORCID: 0000-0002-6085-9314

Sushma Chaluvadi (S)

Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA.

Caroline Cusick (C)

Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA.
ORCID: 0000-0002-2743-9545

Katelyn Flowers (K)

Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA.

Anna Neumann (A)

Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA.
ORCID: 0000-0001-7115-8305

Felecia Cerrato (F)

Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA.
ORCID: 0000-0002-9086-7710

Maha Farhat (M)

Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
Division of Pulmonary and Critical Care, Massachusetts General Hospital, Boston, MA, USA.
ORCID: 0000-0002-3871-5760

Damien Slater (D)

Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA.
ORCID: 0000-0002-1115-0894

Jason B Harris (JB)

Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA.
Department of Pediatrics, Harvard Medical School, Boston, MA, USA.
ORCID: 0000-0003-3642-5126

John A Branda (JA)

Department of Pathology, Massachusetts General Hospital, Boston, MA, USA.

David Hooper (D)

Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA.

Jessie M Gaeta (JM)

Institute for Research, Quality, and Policy in Homeless Health Care, Boston Health Care for the Homeless Program, Boston, MA, USA.
Section of General Internal Medicine, Boston University Medical Center, Boston, MA, USA.

Travis P Baggett (TP)

Institute for Research, Quality, and Policy in Homeless Health Care, Boston Health Care for the Homeless Program, Boston, MA, USA.
Division of General Internal Medicine, Massachusetts General Hospital, Boston, MA, USA.
Department of Medicine, Harvard Medical School, Boston, MA, USA.

James O'Connell (J)

Institute for Research, Quality, and Policy in Homeless Health Care, Boston Health Care for the Homeless Program, Boston, MA, USA.
Division of General Internal Medicine, Massachusetts General Hospital, Boston, MA, USA.
Department of Medicine, Harvard Medical School, Boston, MA, USA.
ORCID: 0000-0002-2570-4253

Andreas Gnirke (A)

Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA.

Tami D Lieberman (TD)

Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA.
Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
ORCID: 0000-0001-5430-3937

Anthony Philippakis (A)

Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA.

Meagan Burns (M)

Massachusetts Department of Public Health, Boston, MA, USA.
ORCID: 0000-0001-7802-4721

Catherine M Brown (CM)

Massachusetts Department of Public Health, Boston, MA, USA.

Jeremy Luban (J)

Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA.
Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA.
Massachusetts Consortium on Pathogen Readiness, Boston, MA 02115, USA.
ORCID: 0000-0001-5650-4054

Edward T Ryan (ET)

Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA.
Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Harvard University, Boston, MA, USA.
Department of Medicine, Harvard Medical School, Boston, MA, USA.

Sarah E Turbett (SE)

Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA.
Department of Pathology, Massachusetts General Hospital, Boston, MA, USA.
Department of Medicine, Harvard Medical School, Boston, MA, USA.
ORCID: 0000-0002-3603-8110

Regina C LaRocque (RC)

Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA.
Department of Medicine, Harvard Medical School, Boston, MA, USA.
ORCID: 0000-0003-4558-0339

William P Hanage (WP)

Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA.
ORCID: 0000-0002-6319-7336

Glen R Gallagher (GR)

Massachusetts Department of Public Health, Boston, MA, USA.

Lawrence C Madoff (LC)

Massachusetts Department of Public Health, Boston, MA, USA.
University of Massachusetts Medical School, Infectious Diseases and Immunology, Worcester, MA 01655, USA.
ORCID: 0000-0003-2589-7777

Sandra Smole (S)

Massachusetts Department of Public Health, Boston, MA, USA.
ORCID: 0000-0001-9414-8521

Virginia M Pierce (VM)

Department of Pathology, Massachusetts General Hospital, Boston, MA, USA.
Pediatric Infectious Disease Unit, Massachusetts General Hospital for Children, Boston, MA, USA.
Department of Pathology, Harvard Medical School, Boston, MA, USA.
ORCID: 0000-0002-3723-1326

Eric Rosenberg (E)

Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA.
Department of Pathology, Massachusetts General Hospital, Boston, MA, USA.
ORCID: 0000-0002-8217-5458

Pardis C Sabeti (PC)

Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA. lemieux@broadinstitute.org pardis@broadinstitute.org bronwyn@broadinstitute.org.
Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.
Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Harvard University, Boston, MA, USA.
Massachusetts Consortium on Pathogen Readiness, Boston, MA 02115, USA.
Howard Hughes Medical Institute, 4000 Jones Bridge Rd, Chevy Chase, MD 20815, USA.
ORCID: 0000-0002-9843-1890

Daniel J Park (DJ)

Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA.
ORCID: 0000-0001-7226-7781

Bronwyn L MacInnis (BL)

Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA. lemieux@broadinstitute.org pardis@broadinstitute.org bronwyn@broadinstitute.org.
Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Harvard University, Boston, MA, USA.
Massachusetts Consortium on Pathogen Readiness, Boston, MA 02115, USA.
ORCID: 0000-0003-0082-968X

Articles similaires

Comprehensive comparative analysis and development of molecular markers for Lasianthus species based on complete chloroplast genome sequences.

Yue Zhang, Meifang Song, Deying Tang et al.
1.00
Genome, Chloroplast Phylogeny Genetic Markers Base Composition High-Throughput Nucleotide Sequencing

[Redispensing of expensive oral anticancer medicines: a practical application].

Lisanne N van Merendonk, Kübra Akgöl, Bastiaan Nuijen
1.00
Humans Antineoplastic Agents Administration, Oral Drug Costs Counterfeit Drugs

Smoking Cessation and Incident Cardiovascular Disease.

Jun Hwan Cho, Seung Yong Shin, Hoseob Kim et al.
1.00
Humans Male Smoking Cessation Cardiovascular Diseases Female

Evaluation of Low-Value Services Across Major Medicare Advantage Insurers and Traditional Medicare.

Ciara Duggan, Adam L Beckman, Ishani Ganguli et al.
1.00
Humans United States Aged Cross-Sectional Studies Medicare Part C

Classifications MeSH

questionsmedicales.fr › Régions géographiques › Villes › Boston › Phylogenetic analysis of SARS-CoV-2 in Boston...
questionsmedicales.fr › Maladies de l'appareil respiratoire › Infections de l'appareil respiratoire › Pneumopathie infectieuse › Pneumopathie virale › COVID-19 › Phylogenetic analysis of SARS-CoV-2 in Boston...
questionsmedicales.fr › Environnement et santé publique › Santé publique › Épidémies de maladies › Phylogenetic analysis of SARS-CoV-2 in Boston...
questionsmedicales.fr › Environnement et santé publique › Santé publique › Méthodes épidémiologiques › Surveillance épidémiologique › Phylogenetic analysis of SARS-CoV-2 in Boston...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Génome › Génome microbien › Génome viral › Phylogenetic analysis of SARS-CoV-2 in Boston...
questionsmedicales.fr › Eucaryotes › Animaux › Chordés › Vertébrés › Mammifères › Eutheria › Primates › Haplorhini › Catarrhini › Hominidae › Humains › Phylogenetic analysis of SARS-CoV-2 in Boston...
questionsmedicales.fr › Sciences de l'information › Phylogenèse › Phylogenetic analysis of SARS-CoV-2 in Boston...
questionsmedicales.fr › Virus › Virus à ARN › Virus à ARN à brin positif › Nidovirales › Coronaviridae › Coronavirus › Betacoronavirus › Virus du SRAS › SARS-CoV-2 › Phylogenetic analysis of SARS-CoV-2 in Boston...