Genetic dissection of Flaviviridae host factors through genome-scale CRISPR screens

Nature. 2016 Jul 7;535(7610):159-63. doi: 10.1038/nature18631. Epub 2016 Jun 17.


The Flaviviridae are a family of viruses that cause severe human diseases. For example, dengue virus (DENV) is a rapidly emerging pathogen causing an estimated 100 million symptomatic infections annually worldwide. No approved antivirals are available to date and clinical trials with a tetravalent dengue vaccine showed disappointingly low protection rates. Hepatitis C virus (HCV) also remains a major medical problem, with 160 million chronically infected patients worldwide and only expensive treatments available. Despite distinct differences in their pathogenesis and modes of transmission, the two viruses share common replication strategies. A detailed understanding of the host functions that determine viral infection is lacking. Here we use a pooled CRISPR genetic screening strategy to comprehensively dissect host factors required for these two highly important Flaviviridae members. For DENV, we identified endoplasmic-reticulum (ER)-associated multi-protein complexes involved in signal sequence recognition, N-linked glycosylation and ER-associated degradation. DENV replication was nearly completely abrogated in cells deficient in the oligosaccharyltransferase (OST) complex. Mechanistic studies pinpointed viral RNA replication and not entry or translation as the crucial step requiring the OST complex. Moreover, we show that viral non-structural proteins bind to the OST complex. The identified ER-associated protein complexes were also important for infection by other mosquito-borne flaviviruses including Zika virus, an emerging pathogen causing severe birth defects. By contrast, the most significant genes identified in the HCV screen were distinct and included viral receptors, RNA-binding proteins and enzymes involved in metabolism. We found an unexpected link between intracellular flavin adenine dinucleotide (FAD) levels and HCV replication. This study shows notable divergence in host-depenency factors between DENV and HCV, and illuminates new host targets for antiviral therapy.

Publication types

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

MeSH terms

  • CRISPR-Cas Systems / genetics*
  • Dengue Virus / genetics
  • Dengue Virus / growth & development
  • Dengue Virus / physiology*
  • Drug Discovery
  • Endoplasmic Reticulum / metabolism
  • Endoplasmic Reticulum-Associated Degradation
  • Flavin-Adenine Dinucleotide / biosynthesis
  • Flavin-Adenine Dinucleotide / metabolism
  • Flavivirus Infections / genetics
  • Flavivirus Infections / virology
  • Genome, Human / genetics*
  • Glycosylation
  • Hepacivirus / physiology*
  • Hexosyltransferases / deficiency
  • Hexosyltransferases / genetics
  • Hexosyltransferases / metabolism
  • Host-Derived Cellular Factors / genetics*
  • Host-Pathogen Interactions / genetics*
  • Humans
  • Membrane Proteins / deficiency
  • Membrane Proteins / genetics
  • Membrane Proteins / metabolism
  • Molecular Targeted Therapy
  • Protein Binding
  • Protein Sorting Signals
  • RNA-Binding Proteins / genetics
  • Receptors, Virus / genetics
  • Viral Nonstructural Proteins / metabolism
  • Virus Replication
  • Zika Virus / metabolism


  • Host-Derived Cellular Factors
  • Membrane Proteins
  • Protein Sorting Signals
  • RNA-Binding Proteins
  • Receptors, Virus
  • Viral Nonstructural Proteins
  • Flavin-Adenine Dinucleotide
  • Hexosyltransferases
  • dolichyl-diphosphooligosaccharide - protein glycotransferase