Epidemiological and clinical characterization of genomic variation in SARS-CoV-2

Preliminary analysis of SARS-CoV-2 isolates in the Chicago area by researchers at Northwestern University have revealed three distinct clades, one of which appears to be unique to Chicago, but these results are limited to the patients and parts of the city covered by affiliates of Northwestern Memorial Hospital (NMH). To expand the scale and scope of this work, we propose to sequence viral genomes from COVID-19 patient samples collected in the University of Chicago Medical Center (UCMC) and merge these data into a unified database. Sequencing data will be merged with socioeconomic and clinical records to build a temporal model of COVID-19 in the Chicago area in context of the global information of disease spread. Hypothesis: We hypothesize that genomic sequencing of novel SARS-CoV-2 strains circulating in the Chicago area will reveal multiple origins of viral infection and will support the emergence of a region-specific clade. We furthermore hypothesize that novel SARS-CoV-2 isolates arising in COVID-19 patients together with patient demographics and/or clinical outcomes are highly predictive of disease trajectory. Practical Significance: By comparing numerous sequences of the viral genome, we hope to identify sequence fragments that can be used for high-specificity testing for COVID-19.