Longitudinal host transcriptional responses to SARS-CoV-2 infection in adults with extremely high viral load

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is the etiologic agent of the coronavirus disease 2019 (COVID-19) pandemic. We conducted a longitudinal study to investigate gene expression patterns during the acute SARS-CoV-2 illness. The cases included SARS-CoV-2 infected individuals with an extremely high viral load early in their illness matched to individuals who either had a low SARS-CoV-2 viral load early in their infection or were otherwise stable patients who tested negative for SARS-CoV-2 prior to their outpatient surgical or aerosol generating procedure. We detected hundreds of up-regulated genes that were highly correlated to the SARS-CoV-2 viral load. Many of these up-regulated genes were enriched in cellular pathways involved in the innate immune response, antiviral interferon and cytokine signaling, and cell death. Of 73 mid-turbinate (MT) swab samples originally collected from SARS-CoV-2 cases with longitudinal follow-up, 44 (60.3%) MT swab samples from 20 (66.7%) individuals were of good quality to generate RNA-sequence data to study the host response to SARS-CoV-2 infection over time. Widespread gene expression changes attributable to transcriptional host responses to SARS-CoV-2 infection were determined by correlating the expression of each gene with sample viral load (representing the inverse correlation with Ct value) across the 44 MT swab samples. **RAW DATA NOT PROVIDED DUE TO PATIENT PRIVACY CONCERNS**