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

Author:

Lemieux Jacob E.ORCID,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.ORCID,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,Sabeti Pardis C.,Park Daniel J.,Maclnnis Bronwyn L.

Abstract

AbstractSARS-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.

Publisher

Cold Spring Harbor Laboratory

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