Comparative transcriptomic analysis of nasopharyngeal swabs from individuals with and without COVID-19

This dataset contains the results of a transcriptomic (RNA-seq) analysis of nasopharyngeal swabs collected from 50 individuals with COVID-19 and 13 individuals without COVID-19 based on clinical qPCR testing. COVID-19 positive individuals included 16 outpatients, 16 hospitalized, non-ICU patients, and 18 hospitalized ICU patients. Samples were collected from a clinical cohort in Greater Toronto Area hospitals and outpatient assessment centres between October 2020 and October 2021. Four comparative analyses were performed using DESeq2: all COVID-19 positive individual versus negatives, COVID-19 ICU individuals versus negatives, non-ICU COVID-19 positive individuals versus negatives, and COVID-19 positive outpatients versus negatives. The analysis was performed with DESeq2 v1.30.1 using the Gencode human reference transcriptome v37.