Virginia pathogen genomics center of excellence - this application is for the mandatory components (core, response implementation) and also includes the optional component (lead pgcoe for education)

The virginia department of general services, division of consolidated laboratory services (dcls), is applying to serve as a pathogen genomics center of excellence (pgcoe) in collaboration with the virginia department of health (VDH), virginia commonwealth university (VCU), and the university of virginia (UVA). Together, this pgcoe will bring expertise in public health, clinical microbiology, genomics, genomic epidemiology, computing, and infectious disease modeling to advance the translation of pathogen genomics into public health action. During the sars-COV-2 pandemic, dcls and VDH formed a partnership with VCU and UVA to expand variant surveillance and modeling efforts. The pgcoe will develop agreements and protocols to expand collaboration beyond sars-COV-2 for a broader infectious threat response base, and will use the information gained through proposed projects and existing network experience for response implementation against an emerging pathogen threat. Projects proposed were selected to expand genomic sequencing and genomic epidemiology applications to improve the health of our communities. A landscape analysis will be performed across five scientific areas (wet lab, bioinformatics, data, genomic surveillance, and field applications) to better understand the needs and challenges to expand the use of pathogen genomics in public health and to design a roadmap that will guide the future work of the pgcoes. Wet lab projects will include protocol development for viral sequencing beyond sars-COV-2, to include 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 development of new approaches for analysis of healthcare-associated infection (HAI) outbreak data. These projects will lead to bioinformatic tools for analysis of relevant public health pathogens and will allow for 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.