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Mass. health department to lead regional effort to improve outbreak response

Program aims to deploy genomic science in public health

A machine at the Broad Institute, which scrutinizes COVID-19 samples for signs of worrisome variants.Jessica Rinaldi/Globe Staff

The Massachusetts Department of Public Health has received a $25 million federal grant intended to help health officials address infectious disease outbreaks by deploying the burgeoning science of genomics.

Part of a federal initiative involving five state health departments and numerous private research centers, the program will enable health officials to reach beyond the traditional methods of investigating an outbreak — interviewing sick people, identifying the illness, and notifying their contacts. They will also be able to examine the very genes of the illness-causing microbes to more fully understand their spread and respond quickly to contain them.

The COVID-19 pandemic has exemplified the importance of this genomic sequencing; identifying and describing the coronavirus’s evolving variants has provided an early warning system about the virus’s ability to evade immunity. Indeed, early in the pandemic, the United States was criticized for its slow pace at completing such studies.


But the American Rescue Plan included $1.7 billion for genomic surveillance, including $90 million over five years for this new Pathogen Genomics Center of Excellence network.

The five centers will focus on all kinds of microbial threats, not just pandemics and emerging infections, but also commonplace hazards like food-borne illnesses and antibiotic-resistant bacteria.

“This new funding and collaboration will help us build on what we’ve learned responding to COVID-19, as well as to Zika, mumps, hepatitis A, and other infections of public health importance,” said Massachusetts Public Health Commissioner Margret Cooke in a statement.

The state health department will lead the New England Pathogen Genomics Center of Excellence, encompassing the Broad Institute of MIT and Harvard, Boston University, Yale University, Fathom Information Design, Mass General Brigham, and Theiagen Genomics. Additionally, Harvard Medical School, the Broad, and the Massachusetts Consortium on Pathogen Readiness will lead the efforts to educate and train the health departments in the national network.


The Centers for Disease Control and Prevention has also designated the state health departments in Georgia, Minnesota, Virginia, and Washington as regional centers.

Significantly, while many private universities and institutes have led the way in genomics research, this program puts state public health officials in the driver’s seat. Under the plan, state laboratories will increase their capacity for genomic analysis, public health officials will receive training in genomics, and knowledge developed at academic institutions will be quickly put to use for public health.

The grant will solidify collaborations between academic research centers and the state health department that already have flourished during the pandemic, said Bronwyn MacInnis, the Broad’s director of pathogen genomic surveillance. Health officials will learn to do more of the work themselves and apply up-to-date scientific knowledge to their outbreak response, she said.

“The best way to be prepared for the next pandemic will be to be doing this type of work routinely day in and day out,” MacInnis said.

The state already has some experience with genomics. For example, a 2016 mumps outbreak at Harvard College puzzled health officials because students were highly vaccinated. They worried that a new strain of mumps had evolved to evade the vaccine. But genomic sequencing at the Broad put that worry to rest and health officials traced the infection to non-students in East Boston, who were not fully vaccinated and possibly had worked at Harvard. The finding also informed the public health response — a vaccine campaign in East Boston.


Going forward, genomics could help with such endeavors as tracking the evolution of Eastern equine encephalitis, a rare but deadly mosquito-borne illness that comes and goes in little-understood patterns; developing faster and better flu vaccines; watching for and responding to the emergence of new drug-resistant infections; and faster identification of the sources of food-borne illnesses.

Felice J. Freyer can be reached at Follow her @felicejfreyer.