Abstract
Genomic and proteomic screens have identified numerous host factors of SARS-CoV-2, but efficient delineation of their molecular roles during infection remains a challenge. Here we use Perturb-seq, combining genetic perturbations with a single-cell readout, to investigate how inactivation of host factors changes the course of SARS-CoV-2 infection and the host response in human lung epithelial cells. Our high-dimensional data resolve complex phenotypes such as shifts in the stages of infection and modulations of the interferon response. However, only a small percentage of host factors showed such phenotypes upon perturbation. We further identified the NF-κB inhibitor IκBα (NFKBIA), as well as the translation factors EIF4E2 and EIF4H as strong host dependency factors acting early in infection. Overall, our study provides massively parallel functional characterization of host factors of SARS-CoV-2 and quantitatively defines their roles both in virus-infected and bystander cells.
Competing Interest Statement
The authors have declared no competing interest.
Footnotes
Our revised manuscript includes new BSL-3 experiments to orthogonally validate findings for host factors of interest. Specifically, we measured SARS-CoV-2 infectious virus production in cells where host factors of interest (NFKBIA, EIF4E2, EIF4H, and ACE2 as positive control) were knocked out, and show that perturbation of these host factors reduces the ability of these cells to produce infectious virus. The new data are included in Fig. 3E. Our new measurements of viral titers are in excellent agreement with the levels of protection measured by our orthogonal approaches (scRNAseq and fluorescence microscopy), described in the initial version of our manuscript. Additionally, there are several new supplemental panels and textual revisions to improve the clarity of our manuscript.
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE208240