The Massachusetts Department of Public Health has selected the Yale School of Public Health (YSPH) and five other partners to make up its new Pathogen Genomics Center of Excellence, one of five such centers recently launched by the U.S. Centers for Disease Control and Prevention. With $25 million in funding over five years, the center’s goal will be to improve technologies and coordinated processes for systematically monitoring infectious diseases and emerging variants, enabling the U.S. to better prevent and respond to outbreaks.
Other partners supporting the Massachusetts center are: The Broad Institute of MIT and Harvard University, which will be the center’s lead academic partner, as well as Boston University, Fathom Information Design, Massachusetts General Hospital, and Theiagen Genomics. Together, they will build on experience honed during the COVID-19 pandemic, when YSPH and similarly capable institutions across the U.S. jumped into action, organizing efforts to genetically sequence COVID-19 samples from hospitals and testing sites. Public health agencies relied on that data, which was relayed to them in near real-time, to guide their decision-making. Such a distributed alliance and infrastructure for responding to an outbreak—let alone a pandemic—had never formally existed.
“This network was critical for providing information about circulating variants, but it took a lot of time and effort to establish,” said Nathan Grubaugh, YSPH associate professor of epidemiology (microbial diseases). “The Yale SARS-CoV-2 Genomic Surveillance Program routinely provided our state, university, and [Yale-New Haven Hospital] with timely information about circulating variants, and the new center in Massachusetts will allow us to establish similar efforts if the needs arise.”
“We have learned a lot about the power of genomics, particularly the role of viral variants in disease outbreaks,” said Massachusetts Public Health Commissioner Margret Cooke in a press release. “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.”
The Yale team has already pivoted to monitor other infectious diseases, including some insect-borne illnesses found in Connecticut and the Northeast—such as the Powassan and West Nile viruses—as well as monkeypox, an animal-borne illness that has been spreading among people in the U.S. in 2022.
“With the workflow and infrastructure, we put in place to sequence SARS-CoV-2, it took us mere days to get involved with sequencing monkeypox,” said Chantal Vogels, a YSPH associate research scientist of epidemiology (microbial diseases). Monkeypox is a DNA-based virus, whereas SARS-CoV-2 is made of genetic material called RNA. “Whatever virus is of interest, we can adapt our surveillance program to detect genetic changes and new variants.”
“We use software and algorithms to analyze publicly available genomic information about pathogens to determine the best targets for testing and sequencing,” said Anne Hahn, a postdoctoral research associate in Grubaugh’s lab. “As new virus variants come in, we constantly monitor if we have to adapt our testing strategies, especially tools called ‘primers’”—small stretches of genetic material designed to bind to and signal the presence of certain genes, like matching a set of fingerprints on the genetic level — “so that they don’t fail to detect the virus in a sample, even if it’s an emerging variant.”
This network was critical for providing information about circulating variants.
Nathan Grubaugh
That has helped Yale become a leader in pathogen genomic epidemiology, a field that studies the genomes of viruses to understand how they’ve spread across a specific population. The CDC recently awarded $2 million in funding to Grubaugh, Hahn, and collaborators from YSPH and Yale’s School of Medicine to investigate new SARS-CoV-2 variants as they arise.
As part of its partnership with the new Massachusetts-led Pathogen Genomics Center, the Yale team will spend the next year “developing sequencing protocols, validating them with clinical samples, and transferring the protocols to public health labs,” Grubaugh said. “Our goal is to unify protocols across different pathogens to make it easy to switch focus depending on the public health needs, without having to conduct extensive training or change [the testing process] each time.”
The four other CDC-funded Pathogen Genomic Centers of Excellence are led by the Georgia Department of Public Health, Minnesota Department of Health, Virginia Division of Consolidated Laboratory Services, and the Washington State Department of Health.