Transmission from vaccinated individuals in a large SARS-CoV-2 Delta variant outbreak

Katherine J Siddle; Lydia A Krasilnikova; Gage K Moreno; Stephen F Schaffner; Johanna Vostok; Nicholas A Fitzgerald; Jacob E Lemieux; Nikolaos Barkas; Christine Loreth; Ivan Specht; Christopher H Tomkins-Tinch; Jillian S Paull; Beau Schaeffer; Bradford P Taylor; Bryn Loftness; Hillary Johnson; Petra L Schubert; Hanna M Shephard; Matthew Doucette; Timelia Fink; Andrew S Lang; Stephanie Baez; John Beauchamp; Scott Hennigan; Erika Buzby; Stephanie Ash; Jessica Brown; Selina Clancy; Seana Cofsky; Luc Gagne; Joshua Hall; Rachel Harrington; Gabrielle L Gionet; Katherine C DeRuff; Megan E Vodzak; Gordon C Adams; Sabrina T Dobbins; Sarah D Slack; Steven K Reilly; Lisa M Anderson; Michelle C Cipicchio; Matthew T DeFelice; Jonna L Grimsby; Scott E Anderson; Brendan S Blumenstiel; James C Meldrim; Heather M Rooke; Gina Vicente; Natasha L Smith; Katelyn S Messer; Faye L Reagan; Zoe M Mandese; Matthew D Lee; Marianne C Ray; Marissa E Fisher; Maesha A Ulcena; Corey M Nolet; Sean E English; Katie L Larkin; Kyle Vernest; Sushma Chaluvadi; Deirdre Arvidson; Maurice Melchiono; Theresa Covell; Vaira Harik; Taylor Brock-Fisher; Molly Dunn; Amanda Kearns; William P Hanage; Clare Bernard; Anthony Philippakis; Niall J Lennon; Stacey B Gabriel; Glen R Gallagher; Sandra Smole; Lawrence C Madoff; Catherine M Brown; Daniel J Park; Bronwyn L MacInnis; Pardis C Sabeti

doi:10.1016/j.cell.2021.12.027

Transmission from vaccinated individuals in a large SARS-CoV-2 Delta variant outbreak

Cell. 2022 Feb 3;185(3):485-492.e10. doi: 10.1016/j.cell.2021.12.027. Epub 2021 Dec 23.

Authors

Katherine J Siddle¹, Lydia A Krasilnikova², Gage K Moreno³, Stephen F Schaffner⁴, Johanna Vostok⁵, Nicholas A Fitzgerald³, Jacob E Lemieux⁶, Nikolaos Barkas³, Christine Loreth³, Ivan Specht⁷, Christopher H Tomkins-Tinch², Jillian S Paull⁸, Beau Schaeffer⁹, Bradford P Taylor⁹, Bryn Loftness³, Hillary Johnson⁵, Petra L Schubert⁵, Hanna M Shephard¹⁰, Matthew Doucette⁵, Timelia Fink⁵, Andrew S Lang⁵, Stephanie Baez⁵, John Beauchamp⁵, Scott Hennigan⁵, Erika Buzby⁵, Stephanie Ash⁵, Jessica Brown⁵, Selina Clancy⁵, Seana Cofsky⁵, Luc Gagne⁵, Joshua Hall⁵, Rachel Harrington⁵, Gabrielle L Gionet³, Katherine C DeRuff³, Megan E Vodzak³, Gordon C Adams³, Sabrina T Dobbins³, Sarah D Slack³, Steven K Reilly³, Lisa M Anderson³, Michelle C Cipicchio³, Matthew T DeFelice³, Jonna L Grimsby³, Scott E Anderson³, Brendan S Blumenstiel³, James C Meldrim³, Heather M Rooke³, Gina Vicente³, Natasha L Smith³, Katelyn S Messer³, Faye L Reagan³, Zoe M Mandese³, Matthew D Lee³, Marianne C Ray³, Marissa E Fisher³, Maesha A Ulcena³, Corey M Nolet³, Sean E English³, Katie L Larkin³, Kyle Vernest³, Sushma Chaluvadi³, Deirdre Arvidson¹¹, Maurice Melchiono¹¹, Theresa Covell¹¹, Vaira Harik¹², Taylor Brock-Fisher¹³, Molly Dunn¹³, Amanda Kearns¹³, William P Hanage⁹, Clare Bernard³, Anthony Philippakis³, Niall J Lennon³, Stacey B Gabriel³, Glen R Gallagher⁵, Sandra Smole⁵, Lawrence C Madoff⁵, Catherine M Brown⁵, Daniel J Park³, Bronwyn L MacInnis¹⁴, Pardis C Sabeti¹⁵

Affiliations

¹ Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA. Electronic address: kjsiddle@broadinstitute.org.
² Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.
³ Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
⁴ Broad Institute of Harvard and MIT, 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 02115, USA.
⁵ Massachusetts Department of Public Health, Boston, MA 02199, USA.
⁶ Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA 02114, USA.
⁷ Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Faculty of Arts and Sciences, Harvard University, Cambridge, MA 02138, USA.
⁸ Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.
⁹ Department of Epidemiology, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA; Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T. H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA.
¹⁰ Massachusetts Department of Public Health, Boston, MA 02199, USA; Applied Epidemiology Fellowship, Council of State and Territorial Epidemiologists, Atlanta, GA 30345, USA.
¹¹ Barnstable County Department of Health and the Environment, Barnstable, MA 02630, USA.
¹² Barnstable County Department of Human Services, Barnstable, MA 02630, USA.
¹³ Community Tracing Collaborative, Commonwealth of Massachusetts, Boston, MA 02199, USA.
¹⁴ Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA; Massachusetts Consortium for Pathogen Readiness, Boston, MA 02115, USA. Electronic address: bronwyn@broadinstitute.org.
¹⁵ Broad Institute of Harvard and MIT, 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 02115, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; Massachusetts Consortium for Pathogen Readiness, Boston, MA 02115, USA.

Abstract

An outbreak of over 1,000 COVID-19 cases in Provincetown, Massachusetts (MA), in July 2021-the first large outbreak mostly in vaccinated individuals in the US-prompted a comprehensive public health response, motivating changes to national masking recommendations and raising questions about infection and transmission among vaccinated individuals. To address these questions, we combined viral genomic and epidemiological data from 467 individuals, including 40% of outbreak-associated cases. The Delta variant accounted for 99% of cases in this dataset; it was introduced from at least 40 sources, but 83% of cases derived from a single source, likely through transmission across multiple settings over a short time rather than a single event. Genomic and epidemiological data supported multiple transmissions of Delta from and between fully vaccinated individuals. However, despite its magnitude, the outbreak had limited onward impact in MA and the US overall, likely due to high vaccination rates and a robust public health response.

Keywords: Delta; SARS-CoV-2; contact tracing; genomics; transmission; vaccination.

Publication types

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

MeSH terms

Adolescent
Adult
Aged
Aged, 80 and over
COVID-19 / epidemiology*
COVID-19 / immunology*
COVID-19 / transmission*
COVID-19 / virology
Child
Child, Preschool
Contact Tracing / methods
Disease Outbreaks
Female
Genome, Viral
Humans
Infant
Infant, Newborn
Male
Massachusetts / epidemiology
Middle Aged
Molecular Epidemiology
Phylogeny
SARS-CoV-2 / classification
SARS-CoV-2 / genetics*
SARS-CoV-2 / immunology*
Vaccination
Whole Genome Sequencing
Young Adult

Supplementary concepts

SARS-CoV-2 variants

Abstract

Publication types

MeSH terms

Supplementary concepts

Grants and funding