U.S. flag

An official website of the United States government

NIH: Fogarty International Center NIH: Fogarty International Center
Advancing Science for Global Health
Advancing Science for Global Health
Home > International Epidemiology & Population Studies > Evolutionary and Computational Virology Print

Evolutionary and Computational Virology

Illustration showing recombination between human CoVs, both within and between sHCoV species Viral infections continue to appear in human and wildlife populations, causing frequent epidemics and occasional pandemics. The Section of Genomic Epidemiology and Evolution of Pathogens (GEEP) at DIEPS, FIC, NIH aims to answer critical questions about pathogen emergence and establishment in animal and human populations using evolutionary and epidemiological information extracted from viral genomes. Specifically, our Evolutionary and Computational Virology project seeks to unravel viral host origins, the molecular signatures that promote pathogen transmission between hosts, the mechanisms of pathogen evolution within hosts, and the dynamics of spatiotemporal spread. We utilize integrated molecular biology, computational, and Bayesian statistical approaches to uncover the viral phylodynamic processes and better inform public health responses.

Current projects include investigations into the origins, evolution, and epidemiology of influenza A virus, seasonal coronaviruses, SARS-CoV-2, RSV, HIV, and rabies virus.


Origins and Evolution of Seasonal Human Coronaviruses

The 229E, NL63, OC43, and HKU1 seasonal human coronaviruses (sHCoVs) are endemic globally, however, little is known about their evolutionary history. Using a multigene and complete genomes analysis approach, we find the evolutionary histories of sHCoVs to be more complex than previously recognized, owing to frequent recombination of CoVs, including within and between sHCoVs. Depending on the gene studied, we observed a variety of potential ancestors for OC43 and 229E. HKU1 comprised two genetically divergent genotypes (A and B), possibly representing two independent transmission events from murine CoVs, with genotype B being genetically more diverse than all the other sHCoVs.

The Evolutionary History and Spatiotemporal Patterns of Respiratory Syncytial Virus

Phylodynamic analysis of the local and global patterns of spread of the respiratory syncytial virus (RSV) and identification of the factors affecting the spatial dynamics at different scales.

COVID-19 Breakthrough Infections in Vaccinated Health Care Workers

The evolutionary dynamics of SARS-CoV-2 breakthrough infections in Mexican healthcare workers and patients immunized with various vaccines. Molecular evolutionary analysis of 400+ SARS-CoV-2 sequences from Yucatan, Mexico sequenced in partnership with the Autonomous University of Yucatan and the COVID-19 International Research Team (COV-IRT) partners at the New York Genomics Center (NYGC).

The Early Dynamics of SARS-CoV-2 in Côte d’Ivoire - An Epidemic Seeded by Travel Fluxes

Investigate SARS-CoV-2 transmission and evolution in the early stages of the COVID-19 pandemic in Côte d’Ivoire, using viral genomes collected from patients with detailed travel history information. We aim to reconstruct the routes and timeliness of viral introductions into the country and assess the relative contribution of each introduction in terms of how the epidemic evolved over time.




  • Nídia S. Trovão
  • Joshua L. Cherry
  • Sana Tamim
  • Erin Yuan