Phylogenetic analysis of SARS-CoV-2 in the Boston area highlights the role of recurrent importation and superspreading events.

Journal

medRxiv : the preprint server for health sciences
Titre abrégé: medRxiv
Pays: United States
ID NLM: 101767986

Informations de publication

Date de publication:
25 Aug 2020
Historique:
pubmed: 2 9 2020
medline: 2 9 2020
entrez: 2 9 2020
Statut: epublish

Résumé

SARS-CoV-2 has caused a severe, ongoing outbreak of COVID-19 in Massachusetts with 111,070 confirmed cases and 8,433 deaths as of August 1, 2020. To investigate the introduction, spread, and epidemiology of COVID-19 in the Boston area, we sequenced and analyzed 772 complete SARS-CoV-2 genomes from the region, including nearly all confirmed cases within the first week of the epidemic and hundreds of cases from major outbreaks at a conference, a nursing facility, and among homeless shelter guests and staff. The data reveal over 80 introductions into the Boston area, predominantly from elsewhere in the United States and Europe. We studied two superspreading events covered by the data, events that led to very different outcomes because of the timing and populations involved. One produced rapid spread in a vulnerable population but little onward transmission, while the other was a major contributor to sustained community transmission, including outbreaks in homeless populations, and was exported to several other domestic and international sites. The same two events differed significantly in the number of new mutations seen, raising the possibility that SARS-CoV-2 superspreading might encompass disparate transmission dynamics. Our results highlight the failure of measures to prevent importation into MA early in the outbreak, underscore the role of superspreading in amplifying an outbreak in a major urban area, and lay a foundation for contact tracing informed by genetic data.

Identifiants

DOI: 10.1101/2020.08.23.20178236 PMID: 32869040 PMC: PMC7457619
pubmed: 32869040
doi: 10.1101/2020.08.23.20178236
pmc: PMC7457619
pii:
doi:

Types de publication

Preprint

Langues

eng

Subventions

Organisme : NIAID NIH HHS
ID : R01 AI148784
Pays : United States
Organisme : NIAID NIH HHS
ID : R37 AI147868
Pays : United States

Commentaires et corrections

Type : UpdateIn

Déclaration de conflit d'intérêts

Competing interests: J.E.L. has received consulting fees from Sherlock Biosciences. J.B. has been a consultant for T2 Biosystems, DiaSorin, and Roche Diagnostics. A.P. is a Venture Partner at Google Ventures. P.C.S. is a co-founder and shareholder of Sherlock Biosciences, and a Board member and shareholder of Danaher Corporation.

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Auteurs

Jacob E Lemieux (JE)

Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA.
Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA.

Katherine J Siddle (KJ)

Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA.
Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.

Bennett M Shaw (BM)

Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA.
Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA.

Christine Loreth (C)

Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA.

Stephen F Schaffner (SF)

Broad Institute of Harvard and MIT, 75 Ames 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.

Adrianne Gladden-Young (A)

Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA.

Gordon Adams (G)

Broad Institute of Harvard and MIT, 75 Ames 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, 75 Ames Street, Cambridge, MA 02142, USA.
Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.

Lydia A Krasilnikova (LA)

Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA.
Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.

Katherine C DeRuff (KC)

Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA.

Melissa Rudy (M)

Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA.

Matthew R Bauer (MR)

Broad Institute of Harvard and MIT, 75 Ames 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, 75 Ames Street, Cambridge, MA 02142, USA.
Harvard Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA 02115, USA.

Erica Normandin (E)

Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA.
Department of Systems Biology, Harvard Medical School, Boston, MA, USA.

Sinead B Chapman (SB)

Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA.

Steven K Reilly (SK)

Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA.
Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.

Melis N Anahtar (MN)

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

Aaron E Lin (AE)

Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA.
Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.

Amber Carter (A)

Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA.

Cameron Myhrvold (C)

Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA.
Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.

Molly E Kemball (ME)

Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA.
Department of Systems Biology, Harvard Medical School, Boston, MA, USA.

Sushma Chaluvadi (S)

Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA.

Caroline Cusick (C)

Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA.

Katelyn Flowers (K)

Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA.

Anna Neumann (A)

Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA.

Felecia Cerrato (F)

Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA.

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.

Damien Slater (D)

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

Jason B Harris (JB)

Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA.
Department of Pediatrics, Harvard Medical School, Boston, MA, USA.

John Branda (J)

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)

lnstitute 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.

Travis P Baggett (TP)

lnstitute 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.
Department of Medicine, Harvard Medical School, Boston, MA, USA.

James O'Connell (J)

lnstitute 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.
Department of Medicine, Harvard Medical School, Boston, MA, USA.

Andreas Gnirke (A)

Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA.

Tami D Lieberman (TD)

Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA.
lnstitute for Medical Engineering and Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.

Anthony Philippakis (A)

Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA.

Meagan Burns (M)

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

Catherine M Brown (CM)

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

Jeremy Luban (J)

Broad Institute of Harvard and MIT, 75 Ames 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.

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.

Regina C LaRocque (RC)

Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA.
Department of Medicine, Harvard Medical School, Boston, MA, USA.

William P Hanage (WP)

Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA.

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.

Sandra Smole (S)

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

Virginia M Pierce (VM)

Department of Pathology, Massachusetts General Hospital, Boston, MA, USA.
Pediatric Infectious Disease Unit, MassGeneral Hospital for Children, Boston, MA, USA.
Department of Pathology, Harvard Medical School, Boston, MA, USA.

Eric Rosenberg (E)

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

Pardis C Sabeti (PC)

Broad Institute of Harvard and MIT, 75 Ames 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.
Massachusetts Consortium on Pathogen Readiness, Boston, MA, 02115, USA.
Howard Hughes Medical Institute, 4000 Jones Bridge Rd, Chevy Chase, MD 20815.

Daniel J Park (DJ)

Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA.

Bronwyn L Maclnnis (BL)

Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, 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.

Classifications MeSH