Identification of Required Host Factors for SARS-CoV-2 Infection in Human Cells

Cell. 2021 Jan 7;184(1):92-105.e16. doi: 10.1016/j.cell.2020.10.030. Epub 2020 Oct 24.


To better understand host-virus genetic dependencies and find potential therapeutic targets for COVID-19, we performed a genome-scale CRISPR loss-of-function screen to identify host factors required for SARS-CoV-2 viral infection of human alveolar epithelial cells. Top-ranked genes cluster into distinct pathways, including the vacuolar ATPase proton pump, Retromer, and Commander complexes. We validate these gene targets using several orthogonal methods such as CRISPR knockout, RNA interference knockdown, and small-molecule inhibitors. Using single-cell RNA-sequencing, we identify shared transcriptional changes in cholesterol biosynthesis upon loss of top-ranked genes. In addition, given the key role of the ACE2 receptor in the early stages of viral entry, we show that loss of RAB7A reduces viral entry by sequestering the ACE2 receptor inside cells. Overall, this work provides a genome-scale, quantitative resource of the impact of the loss of each host gene on fitness/response to viral infection.

Keywords: COVID-19; CRISPR; Cas9; ECCITE-seq; SARS-CoV-2; cholesterol; endosome; genome-wide screen; human lung; loss of function.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • A549 Cells
  • Alveolar Epithelial Cells / metabolism
  • Alveolar Epithelial Cells / virology
  • Angiotensin-Converting Enzyme 2 / metabolism
  • Biosynthetic Pathways
  • COVID-19 / genetics*
  • COVID-19 / metabolism
  • COVID-19 / virology*
  • Cholesterol / biosynthesis
  • Clustered Regularly Interspaced Short Palindromic Repeats
  • Endosomes / metabolism
  • Gene Expression Profiling
  • Gene Knockdown Techniques
  • Gene Knockout Techniques / methods
  • Genome-Wide Association Study
  • Host-Pathogen Interactions* / drug effects
  • Humans
  • RNA Interference
  • SARS-CoV-2 / growth & development
  • SARS-CoV-2 / physiology*
  • Single-Cell Analysis
  • Viral Load / drug effects
  • rab GTP-Binding Proteins / genetics
  • rab7 GTP-Binding Proteins


  • rab7 GTP-Binding Proteins
  • Cholesterol
  • ACE2 protein, human
  • Angiotensin-Converting Enzyme 2
  • rab GTP-Binding Proteins