Location: Geospatial and Environmental Epidemiology Research Unit
2023 Annual Report
Objectives
1. Develop the data sets and analysis pipelines needed for predicting and modeling the emergence of new pathogens.
1.A. Integrated predictive modeling capability for emerging infectious diseases of animals and the collection of data to support these models.
1.B. Comprehensive maps of virus-host interactions required for pathogens to adapt to new hosts.
1.C. Identification of molecular determinants that enable emerging pathogens to infect new animal hosts, including humans.
1.D. Three-dimensional epidemiological information, integrating metagenomics with climatic and ecological data.
1.E. Multi-scale big-data integration models for predicting the emergence of new pandemic pathogens.
1.F. Determine quantifiable species-specific transmission parameters of emerging pathogens for modeling and outbreak preparedness.
1.G. Methods to rapidly detect and characterize the etiology of new and emerging diseases.
1.H. Develop standardized systems for data collection and integrative analysis.
1.I. Conduct the molecular characterization of emerging pathogens including phylogenetic analysis and network analysis.
1.J. Conduct large-scale genomic sequencing to improve the surveillance of mutations that lead to new pathogenic variants.
1.K. Develop integrated techniques from spatiotemporal epidemiology, ecophylogenetics, and distributional ecology.
Approach
Our capability to rapidly identify, characterize, control, and eradicate new emerging animal pathogens is not well developed. Accordingly, emphasis will be given to filling gaps in our toolbox for predicting the emergence of new pathogens. For example, the inclusion of climatic and ecological information during disease outbreaks is nascent or rarely included in predictive models as it requires access to supercomputing capability for analysis of large data sets. The pathogen-host molecular interactome, consisting in part of protein-protein or nucleic acid-protein interactions, have yet to be deciphered. Environmental parameters that may affect virus-host molecular interactions and/or contribute to epigenetic effects is another significant gap in our knowledge base. Research will be conducted to identify mechanisms of disease, disease transmission, and host range specificity to determine the prevalence and emerging potential of new diseases. Ultimately, this research will lead to predictors of disease emergence and disease outbreaks and the development of the appropriate intervention strategies.
Progress Report
The Unit was established this fiscal year and planning operations began in January 2023. This initial report focuses primarily on the administrative efforts of the unit.
Physical space allocation: The unit has secured a single co-located space in the HPCC building at Mississippi State.
Internship program: Initiated a multiyear internship program with Mississippi State University (MSU). The program paired ARS researchers with MSU faculty mentors and students. The students are spending the summer analyzing ARS datasets under the guidance of their faculty mentors. Twenty-one students are working with ARS researchers on a diverse range of projects related to plant and animal health. The program is building relationships that will strengthen collaboration with MSU.
Unit Staffing: The unit has completed human resource actions for a Research Leader (RL) and a Program Support Assistant. Both actions are awaiting advertisement.
Scoping workshop: The Unit is planning a workshop to identify potential program areas for the future RL of the unit. The Meeting is scheduled for 11/14-11/15 Fiscal Year 2024.
Accomplishments
