Idaho INBRE SARS-CoV-2 variant surveillance using viral genome sequencing and analyses

PROJECT SUMMARY (30-lines) This Idaho INBRE Program Administrative Supplement will fund a surveillance study of severe acute respiratory syndrome corona virus-2 (SARS-CoV-2) in a unique study population. It will leverage the IDeA-built advanced-level bioinformatics infrastructure at the University of Idaho to sequence and analyze the genomes of SARS-CoV-2 circulating in the state. Idaho is primarily rural, poor, and geographically remote. The state ranks at or near the bottom among all states in the U.S. in health, education, socioeconomic status, and the number of primary-care physicians per capita. The study population will include the University of Idaho and the surrounding region. The University of Idaho has the only repository of SARS-CoV-2 clinical isolates in northern Idaho. Currently, there are 1,782 SARS-CoV-2 positive samples and based on projections, this number will increase to >2,400 over the next months; 2,100 viral genomes will be sequenced, assembled, and coupled with metadata to determine associations with specific times (travel/holidays), gender, and age groups. This data will be used in collaboration with the Idaho Department of Health & Welfare and the COBRE in Matrix in Biology to track the pandemic in rural communities. The entire northern Idaho region is critically missing from the state's sequencing strategy as almost no commercial labs or hospitals testing for SARS-CoV-2 have saved positive samples. The proposal has three specific aims. Specific Aim 1 will sequence SARS-CoV-2 genomes from the unique Idaho study population and identify variants present over time. Specific Aim 2 will determine if SARS-CoV-2 variants are associated with outbreak events, specific times, and/or statewide travel by a highly mobile university student sub- population undergoing mandatory testing. Specific Aim 3 will determine how SARS-CoV-2 variants in the unique Idaho study population are distributed by gender and age groups. The mandatory university testing removes bias from a large subset of the positive samples and represents a unique opportunity to monitor the appearance and spread of new variants. Previous and ongoing positive viral isolates are or will be appropriately stored and cataloged. CDC/NIH-recommended protocols, standards, and resources for SARS-CoV-2 sequencing and data processing will be used. These analyses will contribute to our understanding of the dynamics of SARS-CoV-2 transmission, mutation, and the emergence of variants. SARS-CoV-2 variants are a major public health concern as they may increase infection rate, increase disease severity, and/or undermine immunization strategies. This work will advance and improve SARS- CoV-2 variant surveillance in Idaho.