Genomic Epidemiology and Evolution of Pathogens

The Section of Genomic Epidemiology and Evolution of Pathogens (GEEP) at DIEPS, FIC, NIH focuses on uncovering the molecular signatures, emergence and evolutionary history, cryptic circulation, and transmission dynamics of pathogens causing epidemics at the human-animal interface. We mine genomic and epidemiological data using molecular and computational biology approaches to improve outbreak preparedness and response. Current projects include investigating the origins and phylodynamic processes of influenza A virus, seasonal coronaviruses, SARS-CoV-2, Salmonella, and E. coli epidemics.

Staff

• Nídia Sequeira Trovão, M.Sc, Ph.D, Lead
  
• Joshua L. Cherry, Ph.D.
  
• Sana Tamim, Ph.D.
• Erin Yuan

Alumni:

• James R. Otieno, Ph.D.
• Jerry Dulluog
  
• Vincent Pan
  

Programs

Evolutionary and Computational Virology
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.

Bacterial Molecular Evolution
For several bacterial species, available whole-genome DNA sequences number in the tens or hundreds of thousands. Such datasets allow reconstruction of evolutionary history that includes thousands of sequence changes that have occurred fairly recently.

Capacity-Building in Genomic Surveillance and Epidemiology
The Section of Genomic Epidemiology and Evolution of Pathogens (GEEP) at DIEPS, FIC, NIH leads a capacity-building program toward real-time genomic surveillance and phylodynamic analysis of emerging infectious diseases for low-resource settings.