The VA PGCoE develops educational materials and holds outreach events to promote the use of genomics in public health. The following have been developed as part of the work done in the Center, or are of relevance to genomics in public health.
Education
Introduction to Advanced Genomic Epidemiology: This video series presents critical concepts in genomic epidemiology for public health investigators with various backgrounds. We build on our previous fundamental skill training to describe public health applications of pathogen genomics. We also discuss theories of pathogen evolutionary rates and how this affects genetic diversity. Laboratory workflows are covered to assist with communication between the laboratorians, bioinformaticians, and epidemiologists. Finally, the series provides advantages and disadvantages of using sequencing for disease transmission elucidation, as well as addressing the limitations of interpreting genomic results.
Playlist page
Genomic Applications in Public Health (Infectious Diseases)
Pathogen Diversity
Inferring Genomic Relatedness
Pathogen Murder Mystery: This video series demonstrates an example of identifying a pathogen during an outbreak. We will explore the identification of an isolate from the 2011 European outbreak of Escherichia coli in our analysis, demonstrating how to identify the organism and its serotype from reads and contigs. We will also step through assembly and annotation, and then do a deeper dive on phylogenetic trees and their interpretation.
Link
Metagenomic Analysis: This set of video series demonstrates the use of three tools for metagenomic analysis: Taxonomic Classification, Metagenomic Binning, and Metagenomic Read Mapping. As an example, the series features analysis of sequence reads from a metagenomic sample isolated from an immunocompromised patient who had a kidney transplant.
Taxonomic Classification
Metagenomic Binning
Metagenomic Read Mapping
Outreach
Researchers from UVA Biocomplexity Institute (UVA-BI) hosted a two-day working meeting in July 2024 on the current state-of-the-art in wastewater-based epidemiology (WBE) with an aim of creating a roadmap of collaborative activities between academics and public health agencies. The workshop was jointly supported by the Council of State and Territorial Epidemiologists (CSTE) and the Virginia Pathogen Genomics Center of Excellence (VA-PGCoE). It was attended by public health epidemiologists from the states of Washington, Delaware, and Tennessee, and researchers at UVA-BI and UVA School of Medicine (UVA-SoM).
Working Meeting on Applications and Methods for Processing Wastewater Surveillance
