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Phylogenetic analysis of SARS-CoV-2 in the Boston area highlights the role of recurrent importation and superspreading events.
Lemieux, Jacob E; Siddle, Katherine J; Shaw, Bennett M; Loreth, Christine; Schaffner, Stephen F; Gladden-Young, Adrianne; Adams, Gordon; Fink, Timelia; Tomkins-Tinch, Christopher H; Krasilnikova, Lydia A; DeRuff, Katherine C; Rudy, Melissa; Bauer, Matthew R; Lagerborg, Kim A; Normandin, Erica; Chapman, Sinead B; Reilly, Steven K; Anahtar, Melis N; Lin, Aaron E; Carter, Amber; Myhrvold, Cameron; Kemball, Molly E; Chaluvadi, Sushma; Cusick, Caroline; Flowers, Katelyn; Neumann, Anna; Cerrato, Felecia; Farhat, Maha; Slater, Damien; Harris, Jason B; Branda, John; Hooper, David; Gaeta, Jessie M; Baggett, Travis P; O'Connell, James; Gnirke, Andreas; Lieberman, Tami D; Philippakis, Anthony; Burns, Meagan; Brown, Catherine M; Luban, Jeremy; Ryan, Edward T; Turbett, Sarah E; LaRocque, Regina C; Hanage, William P; Gallagher, Glen R; Madoff, Lawrence C; Smole, Sandra; Pierce, Virginia M; Rosenberg, Eric.
Afiliación
  • Lemieux JE; Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA.
  • Siddle KJ; Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA.
  • Shaw BM; Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA.
  • Loreth C; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.
  • Schaffner SF; Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA.
  • Gladden-Young A; Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA.
  • Adams G; Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA.
  • Fink T; Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA.
  • Tomkins-Tinch CH; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.
  • Krasilnikova LA; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA.
  • DeRuff KC; Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA.
  • Rudy M; Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA.
  • Bauer MR; Massachusetts Department of Public Health, Boston, MA, USA.
  • Lagerborg KA; Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA.
  • Normandin E; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.
  • Chapman SB; Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA.
  • Reilly SK; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.
  • Anahtar MN; Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA.
  • Lin AE; Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA.
  • Carter A; Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA.
  • Myhrvold C; Harvard Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA 02115, USA.
  • Kemball ME; Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA.
  • Chaluvadi S; Harvard Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA 02115, USA.
  • Cusick C; Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA.
  • Flowers K; Department of Systems Biology, Harvard Medical School, Boston, MA, USA.
  • Neumann A; Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA.
  • Cerrato F; Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA.
  • Farhat M; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.
  • Slater D; Department of Pathology, Massachusetts General Hospital, Boston, MA, USA.
  • Harris JB; Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA.
  • Branda J; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.
  • Hooper D; Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA.
  • Gaeta JM; Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA.
  • Baggett TP; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.
  • O'Connell J; Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA.
  • Gnirke A; Department of Systems Biology, Harvard Medical School, Boston, MA, USA.
  • Lieberman TD; Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA.
  • Philippakis A; Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA.
  • Burns M; Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA.
  • Brown CM; Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA.
  • Luban J; Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA.
  • Ryan ET; Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
  • Turbett SE; Division of Pulmonary and Critical Care, Massachusetts General Hospital, Boston, MA, USA.
  • LaRocque RC; Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA.
  • Hanage WP; Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA.
  • Gallagher GR; Department of Pediatrics, Harvard Medical School, Boston, MA, USA.
  • Madoff LC; Department of Pathology, Massachusetts General Hospital, Boston, MA, USA.
  • Smole S; Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA.
  • Pierce VM; lnstitute for Research, Quality, and Policy in Homeless Health Care, Boston Health Care for the Homeless Program, Boston, MA, USA.
  • Rosenberg E; Section of General Internal Medicine, Boston University Medical Center, Boston.
medRxiv ; 2020 Aug 25.
Article en En | MEDLINE | ID: mdl-32869040
ABSTRACT
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.
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Texto completo: 1 Colección: 01-internacional Banco de datos: MEDLINE Idioma: En Revista: MedRxiv Año: 2020 Tipo del documento: Article País de afiliación: Estados Unidos
Texto completo
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XML
PubMed Links
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Texto completo: 1 Colección: 01-internacional Banco de datos: MEDLINE Idioma: En Revista: MedRxiv Año: 2020 Tipo del documento: Article País de afiliación: Estados Unidos