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

Our take —

This study, available as a preprint and thus not yet peer reviewed, describes the early wave of SARS-CoV-2 in Boston using phylogenetic analysis of over 700 patient sequences from the first few months of the epidemic. At least eighty distinct introductions into the Boston area were identified, and rapid spread of the virus was associated with superspreading events that resulted in sustained local transmission as well as subsequent exported transmission outside of Boston. The study demonstrates that limiting international travel was not enough to curb COVID-19 transmission in the region and therefore highlights the importance of local interventions in preventing SARS-CoV-2 spread. As sampling during the early part of the epidemic was focused on capturing superspreading events, their role may be over-represented, and transmission dynamics on lower prevalence communities may differ from those presented.

Study design

Case Series

Study population and setting

The study investigates the introduction, spread, and epidemiology of COVID-19 in the Boston, Massachusetts area. The study includes 778 SARS-CoV-2 genomes collected from 772 individuals between January 29 and April 18, 2020. These 772 patients represent almost all of the confirmed cases in Massachusetts between the beginning of the outbreak and March 8, 2020, and also includes patients from some of the highest-prevalence communities in Boston during this first wave. This dataset also includes patients from suspected superspreading events, including an international conference, a homeless shelter, and staff within a skilled nursing facility.

Summary of Main Findings

The researchers identified a total of 80 introductions of SARS-CoV-2 into the Boston area, from Asia, Europe and from the within the United States. Phylogenetic analysis also revealed that the first known COVID-19 case in Boston—a traveler returning from Wuhan, China—clustered with other sequences from China but no other sequences from Massachusetts. They concluded that this suggests that rapid detection and contact tracing were able to prevent this first case from spreading within the community. The study also shows that the majority of cases in the Boston area resulted from local transmissions associated with superspreading events including an international business conference, a homeless shelter, and a skilled nursing facility. A viral lineage associated with the conference was subsequently exported to several US states and several other countries. The viral lineage from the conference was also associated with the majority of sustained local transmission in Boston, as well as some community spread in Virginia, Michigan, and Australia.

Study Strengths

The authors used full genome sequences to show that the superspreading events at conferences and congregate facilities (including nursing homes and shelters) were responsible for the majority of SARS-CoV-2 cases in Boston. The sequences had a strong phylogenetic signal, which allowed the authors to have high confidence in the transmission analyses based on phylogenetic data.


Sampling for this study was non-random, and instead focused on capturing suspected superspreading events and patients from known high-prevalence communities. Therefore, the role of superspreading events may be over-represented, and transmission dynamics in lower-prevalence communities may differ from the conclusions presented.

Value added

The study provides evidence for the role of superspreading events in the transmission of SARS-CoV-2 in Boston, and the subsequent spread of the virus to other US states and abroad. The researchers demonstrate that closing down international travel was not enough to stop the spread of the virus as most of the transmissions were from domestic travel and community transmissions.

This review was posted on: 7 December 2020