From lemur gut health to COVID-19, Amanda Perofsky studies infectious diseases
Amanda Perofsky, a computational biologist, wants to track, understand and predict future outbreaks of infectious diseases and respiratory viruses.
What do Madagascar’s lemurs and the COVID-19 pandemic have in common? The answer is Amanda Perofsky.
A research assistant professor in public health and health sciences at Northeastern University’s Network Science Institute and the Portland, Maine-based Roux Institute, Perofsky focuses on understanding and predicting how infectious diseases like flu, COVID-19 and respiratory syncytial virus (RSV) spread and evolve.
Her path to becoming an infectious disease expert has been far from straightforward, taking her to Madagascar, Seattle and, now, Portland to study how the connections between people impact how diseases spread. Perofsky, who is also affiliated with Northeastern’s globe-spanning Network Science Institute, uses everything from statistics to machine learning to ensure there is no surprise with future viral outbreaks.
“There’s so much complexity to flu and so many different moving parts,” said Perofsky, whose appreciation for disease surveillance was shaped by the recent COVID-19 pandemic, when the world had a front row seat to the infectious disease and the viral strains that cause it.
“I’m hoping I can contribute, in some way, to better understand the drivers of flu outbreaks and how we can translate that into making better forecast models,” she said.
Perofsky began her academic career studying frogs in the University of Georgia’s herpetology lab, but her first course in disease ecology triggered a deep, longlasting love for public health. It combined all of her interests.
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“It goes back to my original interest in medicine. I was inspired by the public health, global health aspect of it, and it involved very rigorous math and statistical modeling,” Perofsky said. “Not that it’s not important to study frogs and salamanders!”
After graduating in 2009 with a bachelor’s degree in ecology, Perofsky began a virology fellowship at the National Institutes of Health. She followed that with a Ph.D. at the University of Texas at Austin, where her research on infectious diseases took her across the world to Madagascar. There, she set out to better understand how the social networks and relationships of lemurs, which are native to the African island, influenced the transmission of gut bacteria within a specific lemur colony. The goal was to create a map of these relationships, how their specific interactions spread bacteria and how that could inform disease response.
She also still found time to co-host her weekly college radio talk show, “They Blinded Me with Science,” on which she gave researchers a chance to share their work with the public.
“Part of the joy of being an academic is being able to pursue things that interest you, and I’m interested in a lot of different things,” Perofsky said.
In 2018, during a post-doctoral fellowship at the Fogarty International Center, NIH’s American health research hub, Perofsky started the work that would eventually bring her to Northeastern. As a member of a small team studying infectious diseases, Perofsky explored how the evolution of the flu virus impacts its intensity from season to season.
As part of that work, and through a collaboration with the Department of Defense, she created forecasts of flu and COVID-19 outbreaks for U.S. military bases. For the National Institute for Communicable Diseases, South Africa’s public health organization, she later tracked how the severity of COVID-19 varied across the country’s provinces and different age groups.
In 2021, she joined the Seattle Flu Study, a community-wide pandemic surveillance platform, and started investigating one of her most pressing research questions: the ways human behavior impacts how infectious diseases and respiratory viruses travel. The COVID-19 pandemic provided a real-time case study.
“When stay-at-home [orders] lifted, some pathogens came back right away,” Perofsky said. “Those were the non-enveloped viruses like rhinovirus, adenovirus, common cold type viruses. Others took a lot longer to return. Some of the viruses even had off season outbreaks.”
Perofksy joined the Roux Institute in 2025 with the intent of continuing this work, while focusing on the still-unanswered questions around how different diseases impact the spread of one another. In Maine, she also found a fresh twist on work she’d been doing for over a decade.
Populations like Maine’s, which are older and more rural, are significantly underrepresented in studies of how diseases evolve and spread, Perofsky said. But by working with EPISTORM, a Northeastern-led, federally-funded early disease detection center, and its healthcare partner Maine Health, Perofsky has access to information on health statistics, contact patterns for the entire U.S. population and flu forecasts, a level of data that is “unusual” for a community like Maine, she explained.
“I don’t want to just be publishing papers and that’s my contribution to the field,” Perofsky said. “I really hope I could help in translating mechanistic insights into the drivers of these pathogen outbreaks into forecasting or public health response in general.”
