Title : Identification and characterization of bioterrorism agents through the genomic and bioinformatic analyses of wastewater
Abstract:
The COVID-19 pandemic in the United States was exacerbated by the inability to track infections in a timely manner. Testing of humans revealed new public health challenges due to the lack of test kits and perhaps equally important, the lack of symptoms in up to 70% of infected communities. To address the testing challenge, we and others utilized wastewater monitoring programs to provide a cost-effective and scalable method to track the transmission of SAR-CoV-2 at the community (wastewater treatment plants and interceptor lines) and facility (dormitories, elementary schools, airports, homeless shelters, and senior living homes) level. Over the last three years, we have demonstrated that we can sequence microbial genomes (SARS-CoV-2, Influenza, and Monkeypox) from sewage with a genome coverage of more than 80% and more than 100X depth using tiled-amplicon library preparation kits. These metrics have enabled our team to use whole genome sequencing to track every SARS-CoV-2 variant including Alpha, Epsilon, Lambda, Delta, and Omicron in Nevada. Interestingly, viral genomes are not restricted to wastewater and we and others can also show that such genomes are present in stormwater due to a contribution from homeless populations living in tunnels and wildlife (primarily feral cats) in the area. These findings also revealed the identification of ultra-rare SARS-CoV-2 mutations in the spike protein that have never been identified in humans. Taken together, wastewater monitoring programs can be leveraged to complement public health efforts to track new and emerging pandemics.
