Project Details
Centers for Disease Control and Prevention
The Pathogen Genomics Center of Excellence (PGCOE) mission is to establish a sustainable public health infrastructure that translates genomic data into actionable insights for disease prevention and control. Through this work, the network will create a more predictive and responsive national surveillance system, ensuring the nation is better prepared for future infectious disease threats.
As a key part of this national network, the Virginia PGCoE unites the Division of Consolidated Laboratory Services (DCLS), the Virginia Department of Health (VDH), Virginia Commonwealth University (VCU), and the University of Virginia (UVA). Drawing on their collective pandemic response experience, the Virginia PGCoE will apply expertise in public health, clinical microbiology, genomics, and modeling to advance the translation of genomic epidemiology. A central goal is to develop tools and protocols that expand this collaboration beyond SARS-CoV-2, building a broader and more robust public health response capability.
Wet lab projects will include protocol development for viral sequencing beyond SARS-CoV-2, including Hepatitis A Virus (HAV) and Adenovirus (AV), and sequencing techniques for unknown pathogens. In addition, a cross-laboratory validation of long-read sequencing for antimicrobial resistance (AMR) pathogens will be conducted. These projects will lead to the development of high-quality, scalable, and standardized methods that can be adopted for public health use. Bioinformatics projects will include developing software to analyze common viral pathogens, beginning with HAV and AV, and the development of new approaches for the analysis of healthcare-associated infection (HAI) outbreak data. These projects will lead to bioinformatic tools for the analysis of relevant public health pathogens and will allow for the distribution of software to the wider public health network. Data projects will include the implementation of standardized analysis measures, relevant public health visualizations, and the utilization of real-world data to inform predictive models of disease spread for more accurate and timely threat response. This will all be accomplished through the development of a platform that combines secured patient-level metadata with sequencing data and incorporates standard analysis pipelines and infectious disease models. Genomic surveillance projects will include the prospective surveillance of HAIs to assess the effect of improved surveillance tactics on the practices to control pathogens in healthcare settings. Additionally, we will refine methods for tracking genomic evolution across species and measuring disease burden, using SARS-CoV-2 as a use case. This will be accomplished by developing better modeling that can account for pathogen and population nuances. Field Applications projects will use plasmid detection and wastewater characterization methods to assess the spread of AMR genes. Applying genomic data to respond to the spread of resistant organisms or other threats will lead to further refinement of tools used to predict and prevent disease. Additionally, VCU proposes to be the Lead PGCoE for Education and will utilize instructional skill, expertise in microbial genomics, and learning management systems to provide training content to the US public health workforce.