Category: News

Researchers at the University of Georgia have added a key tool for epidemiologists to track and potentially control the spread of infectious diseases such as COVID-19.

A multidisciplinary team uniting the Colleges of Veterinary Medicine and Public Health, the Center for Ecology of Infectious Diseases, and the Institute of Bioinformatics applied a novel computer algorithm to the genomic sequence data from thousands of samples of SARS-CoV-2 viruses collected in 2021. They were able to trace the timing and number of viral introductions of the Delta strain of COVID in a defined geographical area, learning that most were domestic in origin and driven primarily by young and middle-aged adults.

Their findings were described in a paper titled Tracing SARS-CoV-2 Clusters Across Local Scales Using Genomic Data that was published in the August 2025 issue of The Proceedings of the National Academy of Sciences.

Leke Lyu, PhD, primary author of the paper, said the algorithm addresses a computational challenge presented by the unprecedented amount of genomic data gathered during the COVID-19 pandemic.

“In our paper, we introduce an analytical pipeline that decodes transmission dynamics from viral genome data to answer key public health questions: When and where did viral introductions occur? Once introduced, which populations acted as sources of local spread, and how do transmission patterns vary across regions?” Lyu said.

“Our study provides a high-resolution view of how SARS-CoV-2 spread within Houston, a large and demographically diverse metropolitan area. By analyzing over 26,000 viral genomes, we identified 1,479 independent introductions into Houston – most of them from domestic sources – indicating that Houston was unlikely to be a primary entry point for SARS-CoV-2 into the U.S.”

Houston was selected because of its diversity, including a large population of non-English speakers, and its population density. The researchers note that these factors strain the city’s public health system, making Houston more vulnerable than other U.S. metropolitan areas to a SARS-CoV-2 outbreak.

With the ability to deep-dive into the DNA profiles of virus samples, public health officials can fine-tune prevention efforts ahead of future outbreaks. The Houston samples included metadata identifying the zip code, age group and gender of each individual donor.

“This kind of fine-scale genomic analysis strengthens public health response efforts by identifying introduction hotspots, highlighting communities at greater risk of viral export or import, and guiding targeted interventions,” Lyu said. “It can ultimately help health departments prioritize resources, design localized containment strategies and respond more effectively to future outbreaks.”

Justin Bahl, PhD, senior author of the paper and co-director of the Georgia Pathogen Genomics Center of Excellence, said the study helps to bridge the gap between knowledge and action. The scientific community has done an impressive job of characterizing emerging pathogens, identifying epidemic sources, understanding how viruses move between continents, and tracking and tracing variants of concern, he said.

“Despite the power of these approaches, they are limited in that few methods enable detailed information that could inform public health responses to better control outbreaks,” Bahl said. “We’ve teamed with public health partners to form the Georgia Pathogen Genomics Center of Excellence and develop new approaches to understand local-scale determinants of disease transmission. The goal is to provide tools and pipelines that allow public health partners to better understand how outbreaks may spread within a community and control epidemics more effectively. The current work directly addresses this challenge.”

The Delta variant of COVID-19 spread rapidly and resulted in more hospitalizations than prior strains. Using the virus’s DNA to classify strains by domestic or international origin, the researchers were able to trace the progression of Delta’s introduction to Houston. At the onset of the outbreak in early 2021, infections caused by both international and domestic sources were found. By late April, however, local transmissions of Delta outnumbered outside introductions to the community.

“The scale of genome sequencing during this pandemic is unprecedented, enabling researchers to track viral introductions and spread in real time,” Lyu said. “That said, this volume of data also brings computational challenges, which our study helps address through a scalable, high-resolution workflow.”

The Houston Health Department and the Department of Health Promotion and Behavioral Sciences at The University of Texas Health Science Center collaborated with UGA researchers to produce this study.

The research was a major chapter of Lyu’s doctoral dissertation. He graduated from UGA’s Institute of Bioinformatics in May and recently began his postdoctoral work at Emory University. Bahl is jointly appointed to the faculty of the College of Veterinary Medicine’s Department of Infectious Diseases and the College of Public Health’s Department of Epidemiology and Biostatistics and the Office of Research’s Institute of Bioinformatics.