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

Jacob E. Lemieux; Katherine J. Siddle; Bennett M. Shaw; Christine Loreth; Stephen F. Schaffner; Adrianne Gladden-Young; Gordon Adams; Timelia Fink; Christopher H. Tomkins-Tinch; Lydia A. Krasilnikova; Katherine C. DeRuff; Melissa Rudy; Matthew R. Bauer; Kim A. Lagerborg; Erica Normandin; Sinéad B. Chapman; Steven K. Reilly; Melis N. Anahtar; Aaron E. Lin; Amber Carter; Cameron Myhrvold; Molly E. Kemball; Sushma Chaluvadi; Caroline Cusick; Katelyn Flowers; Anna Neumann; Felecia Cerrato; Maha Farhat; Damien Slater; Jason B. Harris; John A. Branda; David Hooper; Jessie M. Gaeta; Travis P. Baggett; James O'Connell; Andreas Gnirke; Tami D. Lieberman; Anthony Philippakis; Meagan Burns; Catherine M. Brown; Jeremy Luban; Edward T. Ryan; Sarah E. Turbett; Regina C. LaRocque; William P. Hanage; Glen R. Gallagher; Lawrence C. Madoff; Sandra Smole; Virginia M. Pierce; Eric Rosenberg; Pardis C. Sabeti; Daniel J. Park; Bronwyn L. MacInnis

doi:10.1126/science.abe3261

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

Jacob E. Lemieux, Katherine J. Siddle, Bennett M. Shaw, Christine Loreth, Stephen F. Schaffner, Adrianne Gladden-Young, Gordon Adams, Timelia Fink, Christopher H. Tomkins-Tinch, Lydia A. Krasilnikova, Katherine C. DeRuff, Melissa Rudy, Matthew R. Bauer, Kim A. Lagerborg, Erica Normandin, Sinéad B. Chapman, Steven K. Reilly, Melis N. Anahtar, Aaron E. Lin, Amber CarterCameron Myhrvold, Molly E. Kemball, Sushma Chaluvadi, Caroline Cusick, Katelyn Flowers, Anna Neumann, Felecia Cerrato, Maha Farhat, Damien Slater, Jason B. Harris, John A. Branda, David Hooper, Jessie M. Gaeta, Travis P. Baggett, James O'Connell, Andreas Gnirke, Tami D. Lieberman, Anthony Philippakis, Meagan Burns, Catherine M. Brown, Jeremy Luban, Edward T. Ryan, Sarah E. Turbett, Regina C. LaRocque, William P. Hanage, Glen R. Gallagher, Lawrence C. Madoff, Sandra Smole, Virginia M. Pierce, Eric Rosenberg, Pardis C. Sabeti, Daniel J. Park, Bronwyn L. MacInnis

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183 Scopus citations

Abstract

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.

Original language	English (US)
Article number	eabe3261
Journal	Science
Volume	371
Issue number	6529
DOIs	https://doi.org/10.1126/science.abe3261
State	Published - Feb 5 2021
Externally published	Yes

All Science Journal Classification (ASJC) codes

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Lemieux, J. E., Siddle, K. J., Shaw, B. M., Loreth, C., Schaffner, S. F., Gladden-Young, A., Adams, G., Fink, T., Tomkins-Tinch, C. H., Krasilnikova, L. A., DeRuff, K. C., Rudy, M., Bauer, M. R., Lagerborg, K. A., Normandin, E., Chapman, S. B., Reilly, S. K., Anahtar, M. N., Lin, A. E., ... MacInnis, B. L. (2021). Phylogenetic analysis of SARS-CoV-2 in Boston highlights the impact of superspreading events. Science, 371(6529), Article eabe3261. https://doi.org/10.1126/science.abe3261

@article{34b49daa0b98451eb74671abe79e6d3b,

title = "Phylogenetic analysis of SARS-CoV-2 in Boston highlights the impact of superspreading events",

abstract = "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.",

author = "Lemieux, {Jacob E.} and Siddle, {Katherine J.} and Shaw, {Bennett M.} and Christine Loreth and Schaffner, {Stephen F.} and Adrianne Gladden-Young and Gordon Adams and Timelia Fink and Tomkins-Tinch, {Christopher H.} and Krasilnikova, {Lydia A.} and DeRuff, {Katherine C.} and Melissa Rudy and Bauer, {Matthew R.} and Lagerborg, {Kim A.} and Erica Normandin and Chapman, {Sin{\'e}ad B.} and Reilly, {Steven K.} and Anahtar, {Melis N.} and Lin, {Aaron E.} and Amber Carter and Cameron Myhrvold and Kemball, {Molly E.} and Sushma Chaluvadi and Caroline Cusick and Katelyn Flowers and Anna Neumann and Felecia Cerrato and Maha Farhat and Damien Slater and Harris, {Jason B.} and Branda, {John A.} and David Hooper and Gaeta, {Jessie M.} and Baggett, {Travis P.} and James O'Connell and Andreas Gnirke and Lieberman, {Tami D.} and Anthony Philippakis and Meagan Burns and Brown, {Catherine M.} and Jeremy Luban and Ryan, {Edward T.} and Turbett, {Sarah E.} and LaRocque, {Regina C.} and Hanage, {William P.} and Gallagher, {Glen R.} and Madoff, {Lawrence C.} and Sandra Smole and Pierce, {Virginia M.} and Eric Rosenberg and Sabeti, {Pardis C.} and Park, {Daniel J.} and MacInnis, {Bronwyn L.}",

year = "2021",

month = feb,

day = "5",

doi = "10.1126/science.abe3261",

language = "English (US)",

volume = "371",

journal = "Science",

issn = "0036-8075",

publisher = "American Association for the Advancement of Science",

number = "6529",

}

Lemieux, JE, Siddle, KJ, Shaw, BM, Loreth, C, Schaffner, SF, Gladden-Young, A, Adams, G, Fink, T, Tomkins-Tinch, CH, Krasilnikova, LA, DeRuff, KC, Rudy, M, Bauer, MR, Lagerborg, KA, Normandin, E, Chapman, SB, Reilly, SK, Anahtar, MN, Lin, AE, Carter, A, Myhrvold, C, Kemball, ME, Chaluvadi, S, Cusick, C, Flowers, K, Neumann, A, Cerrato, F, Farhat, M, Slater, D, Harris, JB, Branda, JA, Hooper, D, Gaeta, JM, Baggett, TP, O'Connell, J, Gnirke, A, Lieberman, TD, Philippakis, A, Burns, M, Brown, CM, Luban, J, Ryan, ET, Turbett, SE, LaRocque, RC, Hanage, WP, Gallagher, GR, Madoff, LC, Smole, S, Pierce, VM, Rosenberg, E, Sabeti, PC, Park, DJ & MacInnis, BL 2021, 'Phylogenetic analysis of SARS-CoV-2 in Boston highlights the impact of superspreading events', Science, vol. 371, no. 6529, eabe3261. https://doi.org/10.1126/science.abe3261

TY - JOUR

T1 - Phylogenetic analysis of SARS-CoV-2 in Boston highlights the impact of superspreading events

AU - Lemieux, Jacob E.

AU - Siddle, Katherine J.

AU - Shaw, Bennett M.

AU - Loreth, Christine

AU - Schaffner, Stephen F.

AU - Gladden-Young, Adrianne

AU - Adams, Gordon

AU - Fink, Timelia

AU - Tomkins-Tinch, Christopher H.

AU - Krasilnikova, Lydia A.

AU - DeRuff, Katherine C.

AU - Rudy, Melissa

AU - Bauer, Matthew R.

AU - Lagerborg, Kim A.

AU - Normandin, Erica

AU - Chapman, Sinéad B.

AU - Reilly, Steven K.

AU - Anahtar, Melis N.

AU - Lin, Aaron E.

AU - Carter, Amber

AU - Myhrvold, Cameron

AU - Kemball, Molly E.

AU - Chaluvadi, Sushma

AU - Cusick, Caroline

AU - Flowers, Katelyn

AU - Neumann, Anna

AU - Cerrato, Felecia

AU - Farhat, Maha

AU - Slater, Damien

AU - Harris, Jason B.

AU - Branda, John A.

AU - Hooper, David

AU - Gaeta, Jessie M.

AU - Baggett, Travis P.

AU - O'Connell, James

AU - Gnirke, Andreas

AU - Lieberman, Tami D.

AU - Philippakis, Anthony

AU - Burns, Meagan

AU - Brown, Catherine M.

AU - Luban, Jeremy

AU - Ryan, Edward T.

AU - Turbett, Sarah E.

AU - LaRocque, Regina C.

AU - Hanage, William P.

AU - Gallagher, Glen R.

AU - Madoff, Lawrence C.

AU - Smole, Sandra

AU - Pierce, Virginia M.

AU - Rosenberg, Eric

AU - Sabeti, Pardis C.

AU - Park, Daniel J.

AU - MacInnis, Bronwyn L.

PY - 2021/2/5

Y1 - 2021/2/5

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=85099827259&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85099827259&partnerID=8YFLogxK

U2 - 10.1126/science.abe3261

DO - 10.1126/science.abe3261

M3 - Article

C2 - 33303686

AN - SCOPUS:85099827259

SN - 0036-8075

VL - 371

JO - Science

JF - Science

IS - 6529

M1 - eabe3261

ER -

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

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