Combining viral genomics and public health data revealed new details about mumps outbreaks

February 11, 2020

In 2016 and 2017, a surge of mumps cases at Boston-area universities prompted researchers to study mumps virus transmission using genomic data, in collaboration with the Massachusetts Department of Public Health and local university health services. As the outbreaks unfolded, the teams analyzed mumps virus genomes collected from patients, revealing new links between cases that first appeared unrelated and other details about how the disease was spreading that weren't apparent from the epidemiological investigation.

The teams shared their sequencing data and findings in real-time during the outbreaks, with both each other and the broader scientific community, and now report their conclusions in PLOS Biology.

Analyzing viral genomes from an outbreak can show how a virus is evolving and being transmitted -- data that can help public health officials slow and stop the spread of disease.

"High-resolution genomic data about a virus, gathered from patient samples, allows us to reconstruct parts of an outbreak that aren't evident at first," said co-senior author Pardis Sabeti, institute member at the Broad Institute, professor at Harvard University, and Howard Hughes Medical Institute investigator. "The better we understand transmission chains in situations like this, the better we can inform efforts to control outbreaks and devise strategies to predict and stop them in the future."

In Massachusetts, the typical rate of mumps is less than 10 cases per year -- but more than 250 cases were reported in 2016 and more than 170 in 2017, despite high rates of vaccination. Many of the cases were from 18 colleges and universities in the state, including Harvard University, University of Massachusetts Amherst, and Boston University (these three universities met certain criteria to ensure patient privacy protection in this study and agreed to be named in the paper). Other outbreaks flared elsewhere in Boston and across the country around the same time.

These patterns of cases raised questions about how much the virus was circulating in the Massachusetts and US populations. To learn more, the research teams paired traditional epidemiological data with analysis of mumps virus whole genome sequences from 201 infected individuals, focusing primarily on the Massachusetts university communities.

Mumps insight

The viral genomic data revealed details about the Boston-area outbreaks that could not be reconstructed by relying solely on more traditional approaches. For example, the researchers found a clear link between cases at Harvard and an outbreak in East Boston, which were classified as distinct outbreaks during the initial public health investigation.

Public health officials first thought the cases in these two communities were unrelated based on several pieces of evidence: epidemiological data, the different demographic makeup of the two populations (older adults with no obvious university connection versus mostly college-aged students), and a long gap between the apparent end of the outbreak at Harvard and the cases in the local community.

However, the genomic data indicated that the mumps viruses in the East Boston cases were genetically similar to those in the Harvard virus samples. This finding enabled the teams to identify contacts and transmission links between the university and the wider community.

"Even though the two outbreaks were occurring at different places and different times, we were able to show connections between these outbreaks that were operationally informative," explained senior co-author Bronwyn MacInnis, associate director of malaria and viral genomics in the Infectious Disease and Microbiome Program and co-lead of the Global Health Initiative at Broad. "The public health teams could determine that they were essentially dealing with one problem, not two."

Understanding such transmission routes can help guide the outbreak response -- for example, by determining whether efforts should be focused more on controlling transmission within a single community or between different ones.

"Whole-genome sequencing of patient samples helps us reconstruct the progression of an outbreak," said co-first author Shirlee Wohl, formerly a Harvard graduate student in the Sabeti lab and now a postdoctoral fellow at Johns Hopkins University. "Traditional outbreak surveillance efforts can help identify possible sources of infection, but whole-genome sequencing can confirm these links and even suggest new, unexplored connections."

The team emphasized that this study was made possible by the close partnerships it had with the Massachusetts Department of Health and the health services teams at several universities. "I am proud to be part of the Massachusetts higher education community," Sabeti added. "They worked together and demonstrated the necessity of transparency in outbreak response. This is not a story of mumps at these universities, but of outstanding mumps reporting."

Mutating mumps?

Another question of particular interest to the local teams was whether a new mutation in the mumps virus -- for example, one that allows it to evade the immune system in a vaccinated individual -- might have sparked the outbreak. Of the infected individuals, 65 percent had received the recommended two doses of the MMR vaccine. However, given the available data, the researchers found no evidence that genetic variants arising specifically during this outbreak contributed to the disease spread. This finding suggests that, in the Boston area, the virus wasn't evolving into one that could dodge vaccine-induced immunity.

In addition to the findings related to the Boston-area outbreaks, the study's broader geographic analysis suggested that the mumps virus has been circulating continuously at a low rate around the US, only rarely flaring up into notable outbreaks as in 2016 and 2017.

"This whole endeavor demonstrated the value of genetic data to the epidemiological health response, and of data-sharing among collaborating teams," Sabeti said. "One of our goals is to build this capacity in many areas around the world so that public health officials can rapidly mobilize and do this type of analysis whenever they need to."
Co-first authors on this study include Hayden Metsky (Broad Institute, MIT) and Steve Schaffner (Broad Institute, Harvard University, Harvard T.H. Chan School of Public Health). Co-senior authors on this study are Paul Rota (CDC), Larry Madoff (MA DPH, University of Massachusetts Medical School), Nathan Yozwiak (formerly Broad Institute/Sabeti lab), Bronwyn MacInnis, Sandra Smole (MA DPH), Yonatan Grad (Broad Institute, Harvard T.H. Chan School of Public Health), and Pardis Sabeti.

Support for this study was provided by the National Institute of Allergy and Infectious Diseases (U19AI110818, U54GM088558), Howard Hughes Medical Institute, a Harvard University Burke Global Health Fellowship, Amazon Web Services Cloud Credits for Research, and the National Institute of General Medical Sciences (T32GM007753).

Paper cited:

Wohl S, Metsky HC, Schaffner SF, et al. Combining genomics and epidemiology to track mumps virus transmission in the United States. PLOS Biology. Online February 11, 2020. DOI: 10.1371/journal.pbio.3000611

About the Broad Institute of MIT and Harvard

Broad Institute of MIT and Harvard was launched in 2004 to empower this generation of creative scientists to transform medicine. The Broad Institute seeks to describe the molecular components of life and their connections; discover the molecular basis of major human diseases; develop effective new approaches to diagnostics and therapeutics; and disseminate discoveries, tools, methods, and data openly to the entire scientific community.

Founded by MIT, Harvard, Harvard-affiliated hospitals, and the visionary Los Angeles philanthropists Eli and Edythe L. Broad, the Broad Institute includes faculty, professional staff, and students from throughout the MIT and Harvard biomedical research communities and beyond, with collaborations spanning over a hundred private and public institutions in more than 40 countries worldwide. For further information about the Broad Institute, go to

Broad Institute of MIT and Harvard

Related Public Health Articles from Brightsurf:

COVID-19 and the decolonization of Indigenous public health
Indigenous self-determination, leadership and knowledge have helped protect Indigenous communities in Canada during the coronavirus disease 2019 (COVID-19) pandemic, and these principles should be incorporated into public health in future, argue the authors of a commentary in CMAJ (Canadian Medical Association Journal)

Public health consequences of policing homelessness
In a new study examining homelessness, researchers find that policy such a lifestyle has massive public health implications, making sleeping on the street even MORE unhealthy.

Electronic health information exchange improves public health disease reporting
Disease tracking is an important area of focus for health departments in the midst of the COVID-19 pandemic.

Pandemic likely to cause long-term health problems, Yale School of Public Health finds
The coronavirus pandemic's life-altering effects are likely to result in lasting physical and mental health consequences for many people--particularly those from vulnerable populations--a new study led by the Yale School of Public Health finds.

The Lancet Public Health: US modelling study estimates impact of school closures for COVID-19 on US health-care workforce and associated mortality
US policymakers considering physical distancing measures to slow the spread of COVID-19 face a difficult trade-off between closing schools to reduce transmission and new cases, and potential health-care worker absenteeism due to additional childcare needs that could ultimately increase mortality from COVID-19, according to new modelling research published in The Lancet Public Health journal.

The Lancet Public Health: Access to identification documents reflecting gender identity may improve trans mental health
Results from a survey of over 20,000 American trans adults suggest that having access to identification documents which reflect their identified gender helps to improve their mental health and may reduce suicidal thoughts, according to a study published in The Lancet Public Health journal.

The Lancet Public Health: Study estimates mental health impact of welfare reform, Universal Credit, in Great Britain
The 2013 Universal Credit welfare reform appears to have led to an increase in the prevalence of psychological distress among unemployed recipients, according to a nationally representative study following more than 52,000 working-age individuals from England, Wales, and Scotland over nine years between 2009-2018, published as part of an issue of The Lancet Public Health journal on income and health.

BU researchers: Pornography is not a 'public health crisis'
Researchers from the Boston University School of Public Health (BUSPH) have written an editorial in the American Journal of Public Health special February issue arguing against the claim that pornography is a public health crisis, and explaining why such a claim actually endangers the health of the public.

The Lancet Public Health: Ageism linked to poorer health in older people in England
Ageism may be linked with poorer health in older people in England, according to an observational study of over 7,500 people aged over 50 published in The Lancet Public Health journal.

Study: Public transportation use linked to better public health
Promoting robust public transportation systems may come with a bonus for public health -- lower obesity rates.

Read More: Public Health News and Public Health Current Events is a participant in the Amazon Services LLC Associates Program, an affiliate advertising program designed to provide a means for sites to earn advertising fees by advertising and linking to