ITCA ASU-Sequencing of Tribal Wastewater to Assess Coronavirus Variants

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PROJECT SUMMARY The COVID pandemic has been particularly detrimental for Tribal communities across the U.S., who have experienced mortality rates greater than any other race: American Indians have 256 deaths per 100,000 people compared to 150/100,000 for white Americans. Several factors have been suggested as contributors to elevated infectivity, including inadequate infrastructure and underlying health conditions. An additional consideration is the presence of SARS-CoV-2 variants within Tribal communities, of which little is known as COVID testing and vaccine distribution have been the priorities of Tribal Health Departments and COVID Response Teams. To determine if variants are present in Tribal communities, we propose to assess wastewater for excreted coronavirus variants, a non-invasive approach that will capture community-wide mutations more efficiently than sequencing clinical samples. Untreated wastewater samples (24-hour composites) will be processed and quantified for coronavirus using RT-qPCR for the E-gene of SARS-CoV-2. After confirmation of the presence of coronavirus, extracted RNA will be converted to cDNA and sequenced with primers that cover the entire 30kb genome. While we are particularly interested in the U.K., South African, and Brazil strains, we will also report if other U.S. and novel variants are detected in the selected Tribal communities. Nucleotide mutations will be translated and modelled in silico to determine if the polymorphism(s) result in amino acid mutagenesis and/or are mapped to key protein regions. Results will be returned to Tribal health administrators to determine if additional testing of clinical biospecimens is necessary. This NARCH project will provide critical and timely pandemic information to sensitive populations through scientific translation and collaboration with Tribal communities.