Using probe hybridization panels to enrich wastewater samples for pathogen detection: Wastewater contains a diverse array of genetic material (DNA and RNA), much of which originates from the microbial and viral communities associated with the local human population. By sequencing this material, researchers can infer the presence of human pathogens circulating within the community. However, the majority of sequences recovered from wastewater are not from human pathogens (such as plant viruses or bacteria native to the sewer system). To enhance the detection of clinically relevant viral signals, I am applying targeted sample processing techniques designed to enrich for genetic sequences associated with human-pathogenic viruses.

Spatiotemporal analysis of SARS-CoV-2 sequences from wastewater: targeted full-genome sequencing of SARS-CoV-2 in wastewater samples can identify which variants currently infect the surrounding population. Using a set of over 12,000 samples collected from over 80 wastewater treatment plants across Illinois between 2022 and 2025, I am examining  the evolution and spatial distribution patterns of mutations in the SARS-CoV-2 genome at a large scale.

Quantifying the removal of SARS-CoV-2 RNA during wastewater treatment: early on in the COVID-19 pandemic, it was discovered that SARS-CoV-2 RNA could be detected in untreated wastewater, and that concentrations of SARS-CoV-2 RNA reflected infection rates in the surrounding population. Many laboratories around the world began quantifying SARS-CoV-2 RNA in raw wastewater to aid in characterizing and predicting local disease burden. However, few labs also tested treated wastewater, so the impact of wastewater treatment on SARS-CoV-2 RNA concentrations, and potential discharge into the environment, was not well understood. I analyzed SARS-CoV-2 RNA concentration data from the raw sewage entering WWTPs along with fully treated outflow water from seven WWTPs in the Greater Chicago Area. Two of the WWTPs utilized seasonal disinfection, allowing me to additionally evaluate the impact of chlorination and UV treatment on SARS-CoV-2 RNA removal. Although SARS-CoV-2 RNA was regularly detected in both raw sewage and treated outflow, concentrations were generally much lower post-treatment. Interestingly, the difference in raw and treated concentrations was not altered by adding a chlorination or UV disinfection step to the wastewater treatment process. The results of this project are published in FEMS Microbes. See the paper at https://doi.org/10.1093/femsmc/xtac015.