The recent COVID-19 pandemic has highlighted the importance of wastewater-based-epidemiology (WBE) methods to effectively monitor and predict infectious viral disease outbreaks. Traditional disease detection systems rely on identification of outbreaks by diagnostic analysis of clinical samples. Since it is impossible to test every individual in a community for all potential viral infections those systems are lacking in their ability to predict outbreaks. Environmental based surveillance that includes WBE can help reduce the load of medical systems, guide clinical testing, and provide early warnings. Untreated wastewater can serve as a community-based excrement sample that can be tested to identify the diversity of human viruses prevalent in the community. This dissertation presents innovative screening tools based on molecular methods, high throughput sequencing, and bioinformatics analysis that can be applied in the analysis of wastewater samples to identify viral diversity in the corresponding catchment community. Confirmation of this method was done using traditional PCR methods and all results were correlated with clinical samples. Further, population biomarker methods were developed to normalize the signals. The proposed methods were applied to identify endemic and emerging viral infections in a major metropolitan city in US (Detroit-MI) and Latin America (Trujillo-Peru) using wastewater-based-epidemiology methods. The first chapter of the dissertation focuses on an application of bioinformatics-based screening tool to reveal high abundance of rare human herpesvirus 8 in Detroit wastewater. The second chapter focuses on early warning of COVID-19 second wave in Detroit MI. The third chapter focuses on surveillance of SARS-CoV-2 in nine neighborhood sewersheds in Detroit Tri-County area, United States and assessing per capita SARS-CoV-2 estimations and COVID-19 incidence. The fourth chapter uses the bioinformatics-based screening tool identify a wide variety of human viruses in Trujillo-Peru wastewater and confirms Covid-19, monkeypox, and diarrheal disease outbreaks.
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