RNA-Seq investigating the global landscape of the host molecular response to infection by SARS-CoV-2 variants of concern

Purpose: RNA-Seq was performed for gene expression analysis following infection of human cells with different VOC depending on the experiment group to investigate changes in the host and viral molecular response. Methods: RNA was extracted from 10^6 cells using the Qiagen RNeasy extraction kit according to the manufacturer's protocol and quantified by nanodrop. Samples were submitted for RNA-Seq to Genewiz (Azenta) for library preparation and subsequent steps. Results: We have identified SARS-CoV-2 VOC-specific differences in RNA expression, including for N, Orf9b, and Orf6. We have also measured ISG expression and proinflammatory gene suppression across the VOC, determining changes in ISG expression and proinflammatory gene suppression during amongst VOC during SARS-CoV-2 evolution. Conclusions: Our study examines changes in the host molecular response to VOC infection to identify changes in gene expression, especially those related to the innate immune response, that have occurred during SARS-CoV-2 evolution. A total of 340 samples consisting of triplicates across six experiment groups were submitted for RNA-Seq. Mock and early-lineage VOC infection samples were used as controls throughout the experiments.