A study of nearly 800 coronavirus genomes, conducted by no less than 54 researchers at the Broad Institute, Massachusetts General Hospital, the Massachusetts Department of Public Health and several other institutions in the state, has found that viruses carrying the conference’s characteristic mutation infected hundreds of people in the Boston area, as well as victims from Alaska to Senegal to Luxembourg. As of mid-July, the variant had been found in about one-third of the cases sequenced in Massachusetts and 3 percent of all genomes studied thus far in the United States.

The study, which was added Tuesday to the preprint website MedRxiv, is probably the largest genomic analysis of any U.S. outbreak so far and is among the most detailed looks at how coronavirus cases exploded in the pandemic’s first wave.AD

It documents the cost of the world’s naivete this spring, when people traveling for events like the Biogen conference unwittingly imported the virus into Massachusetts dozens of times. It reveals the connections between seemingly disparate communities, showing how an outbreak at a gathering of wealthy executives was only a few infections removed from sickening some of Boston’s most vulnerable residents. It highlights the outsize role of indoor “superspreading events” in accelerating and sustaining transmission. With genetic data, said co-author Bronwyn MacInnis, “a record of our poor decisions is being captured in a whole new way.”

Although the study must undergo the rigors of peer review before it is published in a scientific journal, both outside experts and the scientists involved say it shows the power and promise of an emerging field of research known as genomic epidemiology. The small mutations that accumulate in a virus’s genome are like genetic bar codes; by tracking them, researchers can trace infections to their sources and develop more effective interventions to stop the disease.

“This is the kind of study that … defines why genomics can be so useful in outbreak reconstruction,” said Vaughn Cooper, a microbiologist at the University of Pittsburgh who was not involved in the Boston research. “It reflects a great deal of coordinating work, and that’s what in part makes this so powerful.”

In the current study, the authors were able to rule out linked nosocomial spread in two episodes, reassuring hospital management that a failure of
infection control practice in these wards had not led to a nosocomial cluster, and showed that despite multiple introductions of SARS-CoV-2 into a SNF, one introduction was responsible for 90% of cases. Real-time genomic epidemiology may be increasingly valuable as schools and
workplaces navigate the challenges of reopening, as it can help distinguish between local outbreaks within institutions and introductions from outside.
The relatively narrow surveillance definition for SARS-CoV-2 in MA until March 4 may have limited identification of other early introductions or delayed detection of some individuals who did not meet testing criteria.

These findings repeatedly highlight the close relationships between seemingly disconnected groups and populations: viruses from international business travel seeded major outbreaks among individuals experiencing homelessness, spread throughout the Boston area, and were exported to other domestic and international sites. It also illustrates the role of chance in the trajectory of an epidemic: a single introduction had an outsize effect on subsequent transmission because it was unfortunately amplified by superspreading in a highly mobile population very early in the outbreak, before many precautions were put in place and when its effects would be further amplified by exponential growth. By contrast, other early introductions led to very little onward transmission and another superspreading event in a SNF, while devastating to the residents, had little large-scale effect because it occurred later and in a more isolated population.

This study provides direct evidence that superspreading events may
profoundly alter the course of an epidemic and implies that prevention, detection, and mitigation of such events should be a priority for public health efforts.

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