Program in Molecular Medicine; Department of Medicine, Division of Infectious Diseases and Immunology
Epidemiology | Genetics and Genomics | Immunology and Infectious Disease | Infectious Disease | Virology | Virus Diseases
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.
SARS-CoV-2, COVID-19, outbreak, Massachusetts, Boston area, genomic epidemiology, superspreading events, mutations
Rights and Permissions
The copyright holder for this preprint is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-ND 4.0 International license.
DOI of Published Version
medRxiv 2020.08.23.20178236; doi: https://doi.org/10.1101/2020.08.23.20178236. Link to preprint on medRxiv
Lemieux J, Siddle KJ, Luban J, Gallagher GR, Madoff LC, Smole S, Pierce VM, Rosenberg E, Sabeti PC, Park DJ, MacInnis BL. (2020). Phylogenetic analysis of SARS-CoV-2 in the Boston area highlights the role of recurrent importation and superspreading events. COVID-19 Publications by UMMS Authors. https://doi.org/10.1101/2020.08.23.20178236. Retrieved from https://escholarship.umassmed.edu/covid19/98
Creative Commons License
This work is licensed under a Creative Commons Attribution-Noncommercial 4.0 License