RNA interference screen against SARS-CoV-2 identifies proviral vesicular transport factors involved in release

Identifying host factors of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is paramount to understanding the replication cycle and developing host-targeting antivirals. However, most host factor screens are significantly biassed towards early replication factors and miss the important steps of assembly and release. Here, we present an arrayed, druggable genome RNAi knockdown screen interrogating SARS-CoV-2 replication in human cells using reverse transcription-quantitative polymerase chain reaction quantification of virus production at two timepoints for comprehensive analysis of pro- and antiviral factors across the entire replication and reinfection cycle. Comparative meta-analysis with other screens and genome-wide association studies demonstrated overlap. Pathway analysis and validation confirmed the identification of known and novel key pathways in SARS-CoV-2 infection. A cluster of proviral factors involved in vesicle-mediated exocytic transport was confirmed to be involved in virus production in the 'European original' and variants Delta and Omicron. Inhibiting proviral Rab11a-mediated cargo delivery with cyclin-dependent kinase 9 inhibitor-73 prevented SARS-CoV-2 release, highlighting potential new mechanisms of action for host-targeting antivirals.