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Principal Investigator: Alison Motsinger-Reif
Organization: NATIONAL INSTITUTE OF ENVIRONMENTAL HEALTH SCIENCES
Fiscal Year: 2022
Award: $999,804
Funding agency: National Institute of Environmental Health Sciences
There have been major efforts in this project in both the public health applications of PVI, and in the building and dissemination of the software tools that enable expanded impact of the visualization and contextualization tools.
Public health efforts:
The Centers for Disease Control and Prevention uses 3 indices for the COVID-19 response: the CDC Social Vulnerability Index , the US COVID-19 Community Vulnerability Index , and the Pandemic Vulnerability Index. In a collaboration between NIEHS and CDC, we conducted a review to describe these tools and explain the similarities and differences between them. We described the 3 indices, outlined the underlying data sources and metrics for each, and discussed their use by CDC for the COVID-19 response. To address risk specific to the COVID-19 pandemic, the CCVI and PVI build on the CDC-SVI and include additional variables. Spearman for comparisons between the CDC-SVI score and the CCVI and between the CCVI and the PVI score was 0.83. Spearman for the comparison between the CDC-SVI score and PVI score was 0.73.
Additionally, we worked with with multiple federal partners as they began implementing national testing programs for epidemiologic surveillance, monitoring of frontline workers and populations at higher risk for acquiring COVID-19, and identifying and allocating limited testing resources. Effective testing supports identification of COVID-19 cases; facilitates isolation, quarantine, and timely treatment measures that limit the spread of SARS-CoV-2 ; and guides public health officials about the incidence of COVID-19 in a community. A White House Joint Task Force, co-led by the Department of Health and Human Services and the Federal Emergency Management Agency , created the Community-Based Testing Sites program working with state and local partners. We developed a report that describes the timeline, services delivered, and scope of the CBTS program. In April 2021, the CBTS Pharmacies+ Testing and Surge Testing programs were expanded into the Increasing Community Access to Testing program. As of November 12, 2021, the CBTS and ICATT programs conducted approximately 26. SARS-CoV-2 testing, with its successful partnerships and adaptability, the CBTS program serves as a model to guide current community-based screening, surveillance, and disease control programs, and responses to future public health emergencies.
Software development:
ArcGIS is a predominant geospatial software available for presenting and communicating geographic data, yet to our knowledge there is no methodology for integrating ToxPi profiles into ArcGIS maps. Led by a trainee supported by this project, we developed a suite of software, the ToxPi*GIS Toolkit, for creating, viewing, sharing, and analyzing interactive ToxPi profiles in ArcGIS to allow for new GIS analysis and an avenue for providing geospatial results to the public. The ToxPi*GIS Toolkit is a collection of methods for creating interactive feature layers that contain ToxPi profiles. It currently includes an ArcGIS Toolbox for drawing location-specific ToxPi profiles in a single feature layer, a collection of modular Python scripts that create predesigned layer files containing ToxPi feature layers from the command line, and a collection of Python routines for useful data manipulation and preprocessing. The ArcGIS Toolbox provides a simple means for generating ToxPi feature layers. The integration of ToxPi profiles with ArcGIS provides new avenues for geospatial analysis, visualization, and public sharing of multi-factor data.
Additionally, we have developed an R package implementation of the tools. toxpiR is an open-source R package for the Toxicological Priority Index (ToxPi) framework, which is a generalized method for combining and visualizing diverse data types. ToxPi was originally created to prioritize toxicological contaminants for intervention. More recently, it has been applied to a large variety of problems and data types. One application has been the pandemic vulnerability index (PVI) that examines COVID-19 risk factors on a census tract level. This has been used to help understand what factors are most important when looking at COVID-19 risk. ToxPi was built to handle and combine a variety of assays that on the surface have little to do with each other and create easily digestible visualizations for analysis. The toxpiR packages adds new functionality for data handling, recombination, and customization. The internal data structures allow automated, flexible model creation, customizable graphical output, and handling of larger datasets than previously possible. The compatibility of toxpiR input/output files with other ToxPi applications and the open-source code facilitates methodological extensions and expands application domains. toxpiR is freely available on CRAN at https://CRAN.R-project.org/package=toxpiR and details, vignettes, code, and sample data are maintained at https://github.com/ToxPi/toxpiR.
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