Quantitative proteomic analysis of SARS-CoV-2 infection of primary human airway ciliated cells and lung epithelial cells demonstrates the effectiveness of SARS-Cov-2 innate immune evasion

We used two model systems to characterise the changes caused by SARS-CoV-2 using quantitative proteomics. We used primary human epithelial cells differentiated at the air-liquid interface, first describing the relative abundance of proteins found in each major cell type of the epithelium, and then characterised the infection of ciliated cells specifically as these showed the greatest susceptibility to SARS-CoV-2 infection. We also used a lung epithelial cell line, CaLu-3, and compared the infection with B.29 and B.1.1.7 (Alpha) variant over a time-course of infection. In each case, immunostaining for nucleoprotein combined with FACS allowed for the purification of infected cells from uninfected ‘bystander’ cells.