The 2016 Greater Boston mumps outbreaks occurred even though 65% of the patients had been vaccinated.

A newly published report details how scientists used gene sequencing technology to tie together what appeared to be unrelated mumps outbreaks in the 2010s in the Boston area, helping to rule out the possibility that the virus had mutated to evade vaccine protection.

The report, published in PLoS Biology on Feb. 11, which studied samples taken from 2014 through 2017, is the latest to show how gene sequencing helps public health officials solve infectious disease outbreaks.

The work was done in the lab of biologist and geneticist Pardis Sabeti, of Harvard University and the Broad Institute.

For the study, Sabeti and colleagues collaborated with epidemiologists from the Massachusetts Department of Public Health and from local university health services who were tracking an unusually large number of cases of mumps.

In a typical year, Massachusetts has fewer than 10 cases of mumps. In 2016, that number jumped to more than 250 cases. That was followed by 170 cases a year later.

These outbreaks occurred even though 65% of the patients had been vaccinated, raising concern the virus may have mutated in a way that made conventional vaccines no longer protective.

Many of the cases arose from 18 colleges and universities in the state. The virus had also sparked outbreaks in other parts of Boston and in communities across the United States.

Members of Sabeti’s lab were deputized by the health department and granted permission to sequence the genetic code of the virus taken from 201 individuals, mostly from university campuses. This information would help the researchers see if the infections were genetically related or imported from other parts of the country or outside the U.S.

Initially, the health department had considered an outbreak in East Boston to be distinct from one occurring in Boston universities. “When we looked at the sequences, they matched Harvard cases,” Sabeti said.

That led a Harvard public health team to discover that some Harvard employees lived in East Boston. They traced the infection back to a commencement event, Sabeti said.

“The public health teams could determine that they were essentially dealing with one problem, not two,” study co-author Bronwyn MacInnis, a viral genomics and infectious disease expert at the Broad Institute, said in a statement.

Ultimately, the researchers determined that the Massachusetts mumps cases were closely related to a 2006 mumps outbreak and that the virus was largely domestic rather than imported from other countries.

Because nearly two-thirds of the infected individuals had received the two recommended doses of the MMR vaccine, local teams worried that the virus had acquired enough mutations to make it impervious to the vaccine.

An analysis of the virus genome, however, found no evidence that the virus had mutated in a way that could increase its spread or cause it to escape the immune defenses produced by the vaccine.

“What it seems to suggest is this is waning immunity, and not vaccine escape,” Sabeti said.

She said the investigation showed the value of using genetic data to help track infectious disease outbreaks. Her team hopes to help build this capacity in many parts of the world, to help public health officials rapidly respond to outbreaks.

“Genetic sequence data is becoming a crucial tool in understanding outbreaks,” said Dr. Amesh Adalja, an infectious disease expert at the Johns Hopkins Center for Health Security who was not involved in the study.

He said the data bring insight that might not be detected using traditional epidemiological tools.

“By integrating sophisticated genetic tools into outbreak investigation, it will become possible to more precisely target interventions and alter the course of outbreaks more quickly,” he said in an email.