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A Boston-based research team has used genomic epidemiology to investigate the introduction and spread of SARS-CoV-2 in the Boston, Massachusetts area. Data came from nearly all confirmed early cases in the Boston area, as well as putative superspreading events involving an international conference held locally from February 26–27 and from close-quarters living environments.

Analysis of 772 complete 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. The two events differed significantly in the genetic variation they generated, suggesting varying transmission dynamics in superspreading events.

The work is published in Science in the article, “Phylogenetic analysis of SARS-CoV-2 in Boston highlights the impact of superspreading events.”

Using SARS-CoV-2-positive samples collected in the state from March to May 2020, the team generated 778 complete virus genomes and reconstructed phylogenetic relationships among them. Using ancestral trait inference, they identified 122 putative importation events into Massachusetts, from four continents.

SARS-CoV-2 was introduced to the Boston area of Massachusetts many times in early 2020, according to a new analysis of virus genomes, but only a small number of importations—including one related to an international business conference—led to most cases there.

Because viruses circulating at the conference happened to be marked by distinct genomic signatures, the study’s authors were able to track its downstream effects far beyond the superspreading event itself.

Their work “provides powerful evidence of the importance of superspreading events in shaping the course of this pandemic,” they wrote. As the COVID-19 pandemic continues, countries around the world seek to improve their control of the spread of the virus. A better understanding of transmission dynamics—including superspreading events—could help.

Through further analysis, they confirmed two presumed superspreading events in the Boston area, including at the business conference and at a skilled nursing facility.

One variant associated with the conference spread extensively through Boston, the analysis shows. It began to appear in multiple other U.S. states by March, and by November, viruses containing this variant could be found in 29 states. The cluster of cases that proved to be a superspreading event at the skilled nursing facility led to significant mortality in the vulnerable population, but little broader spread, the authors reported.

The study “illustrates the role of chance in the trajectory of an epidemic,” said the authors. “[A] single introduction had an outsized effect on subsequent transmission because it was amplified by superspreading in a highly mobile population very early in the outbreak,” they added. By contrast, other early introductions led to very little onward transmission. The authors concluded: “This study provides clear evidence that superspreading events may profoundly alter the course of an epidemic and implies that prevention, detection, and mitigation of such events should be priority for public health efforts.”

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