The VA PGCoE provides resources to support use of genomics public health. These include data, tools, guidance on best practices, and other relevant information.
Data
Virginia Digital Similar: The Biocomplexity Institute (BI) has constructed a synthetic population ("digital similar" or "digital twin") for the state of Virginia. It represents each individual person in Virginia, their household structures, demographic attributes, representative daily activities, locations where activities occur, and estimated contacts that arise as they execute their itineraries. Highlights for this Digital Twin of Virginia (DP-VA-2.4.0) include:
- A statistically accurate description of VA population matching US Census data at the resolution of Census block groups.
- For each person there are key attributes such as age, gender, household income, race/ethnicity, and a precise residence location. The race and ethnicity attributes constitute a new, major addition to BI’s synthetic population for Virginia.
- The addition was accomplished by extending existing computational tools and data sources. With these attributes, DP-VA-2.4.0 will now support a range of policy and equity analyses involving race.
- The synthetic population is statistically indistinguishable from the real population (as per Census), but it preserves privacy: only publicly available information was used in the synthesis.
- The detailed mapping connecting synthetic individuals and their attributes to their residence locations supports a wide range of policy impact analyses
Link to Digital Similar data files
More information on Digital Similars
Synthetic Pandemic: In this work, we add another data layer to the digital similar using an agent-based epidemiological model, to represent an infectious disease outbreak. We use COVID-19 as a specific example of an infectious disease here; extensions to other airborne viral diseases can be undertaken by extending these basic techniques. We provide several sets of pandemic data to allow the study of various problems such as bio-surveillance, optimal resource allocation, intervention assessment, and cascade reconstruction. The synthetic outbreak data represents instances of realistic epidemic outbreak over the synthetic social contact network based on realistic COVID-19 models of within-host disease progression and between-host disease transmission.
A Digital Twin of an Evolving Pandemic for Genomic Epidemiology
Link to Synthetic Pandemic data files
Tools
MicrobeTrace (CDC): MicrobeTrace is an interactive web application that renders existing data from high-risk contact networks in an easy-to-use Graphical User Interface (GUI). Introductory videos are available from the links below:
Guidance and Reports
Sensitivity of Wastewater Viral Loads for Detection Based on Technology Limits - Correlation Analysis: Examines the correlation of SARS-COV2 viral loads in wastewater and the COVID-19 surveillance signals like hospitalizations. We also investigate the leading indicator characteristics of the viral load to cases and hospitalizations.
Link to Report
Baseline COVID-19 Strain Severity Metrics, US: This analysis uses data from the National COVID Cohort Collaborative (N3C) to calculate baseline severity metrics for the US per 8 distinct epochs of time during the COVID pandemic.
Link to Report
Pathogen Genomics Centers of Excellence
CDC Pathogen Genomics Centers of Excellence: The PGCoE network is meant to foster and improve innovation and technical capacity in pathogen genomics, molecular epidemiology, and bioinformatics to better prevent, control, and respond to microbial threats of public health importance. The network also represents an unprecedented opportunity to expand and deepen collaboration between U.S. public health agencies and academic institutions to form a national resource to better prevent, control, and respond to microbial threats of public health importance. Each center of excellence consists of a health department and one or more academic institutions. The five recipients are the Georgia Department of Public Health, the Massachusetts Department of Public Health, the Minnesota Department of Health, the Virginia Division of Consolidated Laboratory Services, and the Washington State Department of Health.
Link with map
Other Centers of Excellence (non-PGCoE)
Integrated Food Safety Centers of Excellence: The Integrated Food Safety Centers of Excellence (Food Safety CoEs) is a CDC program started in 2012 under the authority of the Food Safety Modernization Act. The Food Safety CoEs provide peer assistance and training to support state and local health departments in building their capacity to track and investigate enteric diseases. The Food Safety CoEs are Colorado, Minnesota, New York, Tennessee, and Washington state health departments and their partner academic institutions. Each Food Safety CoE serves a region of the country to help guide jurisdictions to the resources that best meet their needs.
Link
Other Resources (non-PGCoE)
An applied genomic epidemiological handbook: This handbook provides a short guide to the theory and practice of viral genomic epidemiology for public health purposes. It is intended to be an open resource - if you feel that this book would be useful to someone, please share it with them. This handbook is almost meant to be “living”. If you would like to recommend changes, or if you find errors that should be corrected, or if you’d like to see a topic added, please open an issue in the git repo.
Link
Gen Epi Learning Center: These modules, handbook, practical exercises, and seminars cover the basics for understanding infectious disease dynamics through genomic epidemiology.
Link
State Public Health Bioinformatics Group (StaPH-B): The State Public Health Bioinformatics Group (StaPH-B) is a consortium of public health scientists interested in addressing the common barriers impeding bioinformatics implementation in state public health laboratories.
Link
R for applied epidemiology and health: This handbook serves as a quick R code reference manual (online and offline) with task-centered examples that address common epidemiological problems.
Link
How to read a phylogenetic tree: Phylogenetic trees contain a lot of information about the inferred evolutionary relationships between a set of viruses. Decoding that information is not always straightforward and requires some understanding of the elements of a phylogeny and what they represent. This is a tutorial on how to read a phylogenetic tree.
Link
VDH Weekly Briefings: Since early 2020, the University of Virginia (UVA) Biocomplexity Institute (BI) COVID-19 response team has been directly consulting with the Commonwealth of Virginia, including the Virginia Department of Health (VDH) and the Virginia Department of Emergency Management (VDEM) to support government officials in providing guidance to the public. The UVA BI COVID-19 response team provides a weekly report with disease projections and analyses to help government officials, healthcare providers, and the general public better evaluate the impact of the pandemic. The VDH Office of Emergency Preparedness (OEP) uses these briefings to produce the VDH OEP Weekly Situation Update, which covers ongoing or potential public health and emergency preparedness issues, including COVID-19.
Link
