Comprehensive RNA-seq profiling of COVID-19 patients: combining microbial diagnostics with host genetic determinants of disease severity

Nasopharyngeal swabs have become commonplace throughout the COVID-19 pandemic. In order to assess the breadth of information possible from such swabs, a national team of researchers has gathered 66 swabs sequenced with RNA-seq from different patient types (ICU, non-ICU, outpatient, and COVID-19 negative-testing hospital visitors), with more samples currently being collected. I have already incorporated SARS-CoV-2 variant classification, within-host variation in the SARS-CoV-2 population, host gene expression, and microbial coinfections differentiated by patient type into an analysis pipeline (manuscript in preparation). I propose determining host genetic variants from these samples, assessing their importance to COVID-19 disease severity using the many COVID-19 genome-wide association studies already published, and using the unique Canadian HostSeq database to uncover the Canada-wide variant frequencies associated with our samples. This multifaceted approach to data analysis will provide a comprehensive overview of the impact of the COVID-19 pandemic on Canadians, and profile the richness of data attainable from nasopharyngeal swabs.