Grantee Research Project Results
2023 Progress Report: Development of a Wastewater Hierarchical Sentinel Site Identification for Future Pandemic Surveillance Systems
EPA Grant Number: R840487Title: Development of a Wastewater Hierarchical Sentinel Site Identification for Future Pandemic Surveillance Systems
Investigators: Nguyen, Thanh (Helen) H. , Jutla, Antarpreet , Smith, Rebecca , Schmidt, Arthur , Keefer, Laura , Unnikrishnan, Avinash , Galan, Deise
Institution: University of Illinois Urbana-Champaign , Portland State University , University of Florida , National Association of County and City Health Officials
EPA Project Officer: Callan, Richard
Project Period: September 1, 2022 through August 31, 2025
Project Period Covered by this Report: September 1, 2022 through August 31,2023
Project Amount: $1,000,000
RFA: National Priorities: Innovative Sampling Designs for Public Health Surveillance of Coronaviruses and Other Pathogens in Wastewater Request for Applications (RFA) (2022) RFA Text | Recipients Lists
Research Category: Environmental Engineering , Water
Objective:
Working closely with local departments of public health partners, we plan to achieve the following. Objective 1: Develop optimal sampling strategies for wastewater monitoring networks for the detection of emerging pandemic pathogens; Objective 2: Develop and test a framework for adapting the wastewater monitoring strategies based on characteristics of the pathogen, its infection, transmission processes, and target populations; Objective 3: Develop a secure data management platform to provide actionable wastewater monitoring information to public health officials and utilities for pandemic control.
Progress Summary:
The first year of the project has been devoted to the first two objectives and the outputs and outcomes are documented below:
- In objective 1, we completed an analysis of COVID-19 cases in the US. We found that on county scales primarily in the USA, most of the cases were observed during winter season. However, warmer regions in the USA had a significant number of cases during summer season. The temperate countries experienced many more cases in winter when compared to other seasons, while the subtropics and tropics had the most significant caseloads in winter and summer seasons. Based on these findings and preliminary analysis, we determined six variables to develop the predictive system: ambient air temperature, dew point temperature, population density, ethnicity, human mobility, and household income. This predictive system will guide the selection of sentinel sites for wastewater surveillance.
- In objective 2, we developed better nucleic acid-based assays, such as polymerase chain reaction (PCR), to capture viral genetic diversity. For example, we found that endemic viruses exhibit a high percentage of variable nucleotides (e.g., 51.4% for norovirus genogroup II). This genetic diversity led to the variable probability of detection of PCR assays (the proportion of viral sequences that contain the assay’s target sequences divided by the total number of viral sequences). We then experimentally confirmed that the probability of the target sequence detection is indicative of the number of mismatches between PCR assays and norovirus genomes. Next, we developed a degenerate PCR assay that detects 97% of known norovirus genogroup II genome sequences and recognized norovirus in eight clinical samples. By contrast, previously developed assays with 31% and 16% probability of detection had 1.1 and 2.5 mismatches on average, respectively, which negatively impacted RNA quantification. In addition, the two PCR assays with a lower probability of detection also resulted in false negatives for wastewater-based epidemiology. Our findings suggest that the probability of detection serves as a simple metric for evaluating nucleic acid-based assays for genetically diverse virus surveillance.
Future Activities:
- Objective 1: we have developed the predictive system through socio-environmental factors and have modeled human mobility through the inverse distance method. Now we will be working with mobility ecosystem (traffic movement) companies for validation. Along with the validation of the existing framework, the mobility ecosystem data will be used to incorporate the impact of long-distance travel; therefore, if a county or a nearby county has a major international airport, the risk of COVID-19 infection being transmitted from an international destination to that county will be higher.
- Objective 2: we have been sampling three schools serving rural communities, mostly on septic systems, in Central Illinois for the whole academic year 2022 and 2023. During the project's first year, we also surveyed interests from the rural public health departments. The response has been extensive across the country, from CA to MA. We have identified four departments in the Midwest that have connected us with schools serving their communities. Based on the discussion with these partners, we decided to design low-cost composite samplers, which are also simple to use, so that the custodial staff at the school can install and use them starting in fall 2023. We have also installed a sampling network along highways in IL. The sampling sites are the rest stations along the highways. Due to the low flow characteristics of these sites, we designed and tested low-cost passive samplers. In addition to sampling, we have developed analytical methods to detect and quantify norovirus. Assays for other viruses under development include those for rotavirus and influenza viruses. In addition, we will start testing the MCS at schools identified by NACCHO.
- Objective 3: as soon as we receive the data, we will start working on the data dashboard. Currently, we are working on a literature review to design the dashboard.
Journal Articles on this Report : 3 Displayed | Download in RIS Format
Other project views: | All 3 publications | 3 publications in selected types | All 3 journal articles |
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Magers B, Usmani M, Wu CY, Jutla A. Geographical quantification of the seasonality of transmission of COVID-19 in human populations as a function of the variability of temperatures. Environmental Research:Health 2023;1(4):045006. |
R840487 (2023) |
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Oh C, Zhou A, O'Brien K, Schmidt IV AR, Geltz J, Shisler JL, Schmidt AR, Keefer L, Brown WM, Nguyen TH. Improved performance of nucleic acid-based assays for genetically diverse norovirus surveillance. Applied and environmental microbiology 2023;89(10):e00331-23. |
R840487 (2023) |
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Usmani M, Brumfield KD, Magers B, Zhou A, Oh C, Mao Y, Brown W, Schmidt A, Wu CY, Shisler JL, Nguyen TH. Building Environmental and Sociological Predictive Intelligence to Understand the Seasonal Threat of SARS-CoV-2 in Human Populations. The American journal of tropical medicine and hygiene 2024:tpmd230077-. |
R840487 (2023) |
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Supplemental Keywords:
wastewater, virus, pathogen, infection, risk, secured data platformThe perspectives, information and conclusions conveyed in research project abstracts, progress reports, final reports, journal abstracts and journal publications convey the viewpoints of the principal investigator and may not represent the views and policies of ORD and EPA. Conclusions drawn by the principal investigators have not been reviewed by the Agency.