Forecasting the Next Pandemic

In the summer of 2019, before most of the world had heard the word “coronavirus,” two postdoctoral researchers at Georgetown University were thinking about the next pandemic.

“We were building models of cross-species transmission using math and machine learning. What people would now call AI,” recalled Colin Carlson, now an assistant professor of epidemiology (microbial diseases) at the Yale School of Public Health (YSPH).

As their research progressed, Carlson and his colleagues would hold what he jokingly described as scientific “bake-offs,” testing whose models best predicted how viruses move among wildlife and into humans.

Then a novel coronavirus emerged in Wuhan.

“It wasn’t one of those moments where COVID happened and we said, ‘Oh, we need to figure out what to do,’” Carlson said. “It was more like we already had these tools. And suddenly the world exploded.”

Out of that moment grew the Viral Emergence Research Initiative (Verena). Now headquartered in Yale University’s Public Health Modeling Unit, it is one of the largest pandemic prevention research and training programs in the United States. Supported by a five-year $12.5 million grant from the National Science Foundation Biology Integration Institute (2022–2027), Verena has produced more than 100 publications and preprints and trained more than 60 postdoctoral fellows, graduate students, and undergraduates.

What began as a scrappy collaboration among postdocs has evolved into an eight-institution network spanning Yale, the University of Oklahoma, Washington State University, Colorado State University, Tulane University and others. In 2024 — in an unusual move for a federally funded center — Verena relocated from Georgetown to Yale, an acknowledgement of both Carlson’s research leadership and Yale’s growing prominence in pandemic science.

Verena’s mission is sweeping: to understand viral emergence across scales, from the molecular handshake between a viral protein and a host cell to the global forces of climate change reshaping disease risk.

“If we want to forecast pandemics, if we want to predict spillover, we have to start at the molecular scale,” Carlson explained. “Viruses and hosts interact at the scale of proteins and atoms, and everything emerges up from there.”

Team science and researching across scales is central to Verena’s design. Virologists use tools like AlphaFold to study how viral proteins bind to host cells. Ecologists track stressed bats and migratory birds across landscapes. Climate scientists model how warming temperatures alter species ranges. Epidemiologists and AI specialists like Carlson translate those patterns into predictive algorithms.

“No one has to know everything,” said Carlson, who is co-PI of the Verena project and Verena’s executive director. “One of us is thinking about molecules and proteins. Another is focused on organisms and stress responses. I’m thinking about how movement patterns change with climate change. Ultimately, our work comes together to create a more complete picture of a disease.”

Verena’s research network is broad, built over years of collaboration and partnership. At the University of Oklahoma, co–principal investigator Daniel Becker leads field teams sampling bats and tracking bird migration with radar towers across the heart of North America. In Colorado, Washington, and Connecticut, labs conduct pathogen genomics and outbreak investigations.

Together, the network represents what Carlson calls a “planetary defense” approach to health security.

For all of the work that it does, Verena is committed to open science. Its ‘dataverse’ has become a definitive source of One Health disease surveillance data, supporting 139 researchers in 21 countries to date.

Verena has a robust infrastructure for data management and information sharing. Two of its most widely used platforms are the Pathogen Harmonized Observatory (PHAROS) — an open-access database of wildlife disease surveillance — and the global Virome in One Network (VIRION) — an open atlas of more than 9,000 vertebrate viruses.

The team has worked closely with federal agencies to facilitate data sharing across state and local partners and can mobilize quickly in response to an emerging outbreak.

Before initiatives like Verena, Carlson said, much of the conversation about emerging zoonotic disease was driven by anecdotes rather than comprehensive data.

Verena’s research is filling that gap. Scientists like Carlson — a self-described “AI nerd before AI was ‘AI’” — have developed risk assessment algorithms for wildlife and livestock viruses; diagnostic algorithms for dengue, Ebola and Zika; and produced what the team describes as “the most systematic evidence base to date of the drivers of zoonotic spillover.”

Verena’s accomplishments include the discovery of a previously unknown form of antiviral immunity in vesper bats — a finding that could reshape how scientists understand viral tolerance in mammals. In the United States, Verena researchers have traced the proposed origins of borealpox virus in Alaska, assessed whether local mosquitoes could spread Oropouche virus, and tracked migration paths of birds and bats carrying influenza, rabies, and West Nile virus.

A paper Carlson wrote with his former Georgetown classmate Gregory Albery entitled Climate change increases cross-species viral transmission risk was rated by Carbon Brief as the top climate paper of 2022 in terms of news and social media attention.

At Yale, Carlson’s research focuses on how climate change and global environmental disruptions heighten pandemic risk and contribute to viral emergence.

“Every year, there are 5% more spillover events and 8% more deaths from these viruses,” he said. “That's humans at work — wildlife trade, deforestation, climate change. It’s all moving animals around. It’s moving mosquitoes around. It’s creating new problems for health systems.”

The global health security architecture, Carlson said, was built in the mid-20th century for a world where pandemics were once-in-a-century events. “We didn’t build the World Health Organization for a world where pandemics are a once-in-a-decade risk.”

Carlson’s lab examines everything from sea-level rise threatening coastal hospitals in countries like Bangladesh and Haiti to how warming temperatures may intensify viral transmission in species that don’t migrate.

“My goal,” he said, “is to understand what pandemic risk will look like in our lifetimes.”

Beyond its research endeavors, Verena is committed to teaching and community. The program has become a pipeline for early-career scientists in fields such as biology, epidemiology, computational modeling, genomics, and policy translation.

“We’re not postdocs in a garage anymore,” Carlson said, recalling the project’s early days. “Now the exciting work is happening with Ph.D. students. We get to watch the project grow up.”

With its research, training, and commitment to community outreach, Verena epitomizes Yale University’s role as a hub for interdisciplinary public health research and underscores Yale’s research impact across the country. Its collaborations with higher education institutions in Oklahoma, Colorado, Washington, and Louisiana have established a vital national network capable of responding to emerging infectious threats.

Ultimately, Carlson said, Verena’s mission is to identify those threats before catastrophe strikes.

“We’re not just doing fundamental science. We’re trying to inform prevention.”