RNA-Seq of Nasopharyngeal Swabs from ICU Patients Infected with SARS-CoV-2 Omicron Sublineages in Adelaide, Australia, 2022–2023

COVID-19 diagnostic testing generally involves collection of patient samples via nasopharyngeal swabs. Herein we describe viral and human gene expression data available from such samples using RNA-Seq and bioinformatics. Swabs were collected from 38 patients admitted to an Australian intensive care unit (ICU) from October 2022 to August 2023. During this time the omicron sublineages changed from BA.5, BA.2-like, XBB-like to XBC. RNA-Seq viral read data correlating well with RTPCR-based quantitation and sublineage identification. High viral loads were associated with patients >64 years of age. Treatment with corticosteroids or baricitinib did not significantly influence viral loads. Viral loads did not correlate with length of stay in hospital or ICU, or with vaccination status. Analyses of human gene expression data were complicated by the very large range (>5 log) and variability in viral reads. Nevertheless, comparison of XBC and BA.5 samples that had comparable viral read counts, revealed differentially expressed genes and a cellular deconvolution signature that indicated increased infection of ciliated epithelial cells by XBC. A key feature that differentiated the omicron lineage from previous lineages was the increased targeting of ciliated epithelia in the upper respiratory track. The data presented herein argue that this evolutionary trend continued in the omicron sublineages.