Table 3.

Genome-wide CRISPR screens of pathways and processes involved in SARS-CoV-2 infection

Screened pathways & process	Screened cell line	Top-ranked gene clusters in pathway		Highlights	Similar small molecule	References
		Resistant genes	Sensitize genes
Cholesterol biosynthesis pathway (part of the endosomal entry pathway from the vacuolar ATPase proton pump, Retromer, and Commander complexes)	A549	ATP6AP1 ATP6V1A NPC1 RAB7A CCDC22 PIK3C3		Loss of resistant genes such as RAB7A reduces viral entry by sequestering the ACE2 receptor inside cell	RNA-sequencing of cells treated with amlodipine small molecule shows a similar differential gene expression profile as seen in CRISPR knock-out of genes in cholesterol biosynthesis pathway	[84]
Rab-GTPase requirements Glycosylphosphatidylinositol-anchored biosynthesis Cholesterol biosynthesis	HAP1 Huh-7.5-Cas9	SREBP/SCAP HS2ST1 EIF4E2 RAB2A RAB10 RAB14	MRPS2 MRPS5 MRPS25 MRPS27	SCAP regulates lipid and cholesterol homeostasis by sequestering SREBPs in the ER in the presence of sterols	Fatostatin molecule as SCAP inhibitors shows anti-viral properties 27-Hydroxycholesterol (27OHC) and 25OHC have SARS-CoV-2 anti-viral activity in VeroE6 cells	[83]
Replication cycle	A549	TMEM41B		SARS-CoV-2 require TMEM41B for replication cycles in cell	None	[85]
Chromatin remodeling Histone modification Cellular signaling RNA regulation	Huh7.5 VeroE6	ARID1A DYRK1A KDM6A CTSL ACE2 SMARCA4 DYRK1A KDM6A HMGB1 HIRA CABIN1 TRIP12 BPTF PIAS2	TARDBP	Viral RNA-RNA and RNA–protein interactions reveal specific SARS-CoV-2-mediated mitochondrial dysfunction during infection pro-viral genes and pathways, including HMGB1, and the SWI/SNF chromatin remodeling complex are SARS-CoV-2 lineage HMGB1 is critical for SARS lineage viral entry with critical role in ACE2 expression	PFI-3, which targets the bromodomains of the SWI/SNF proteins SMARCA4 and SMARCA2 SIS3, which targets the pro-viral gene SMAD3 identified in the screen	[80, 81]
Glycosaminoglycan biosynthesis SREBP signaling Glycosylphosphatidylinositol biosynthesis Cholesterol biosynthesis	Huh-7.5 hepatoma cells (Huh-7.5-Cas9)	SCAP TMEM106B TMEM41B VAC14 ACE2 HMGCS1 MVK PMVK RAB6A RAB10		Absolute requirement for the VTT-domain containing protein TMEM41B for infection by SARS-CoV-2	None	[86]
Phosphatidylinositol phosphate biosynthesis Cholesterol homeostasis Heparan sulfate biosynthetic genes	Huh7.5.1 hepatoma cells	TMEM106B B3GALT6 B3GAT3 B4GALT7 EXT1 EXT2 EXTL3 FAM20B NDST1 SLC35B2 UGDH XYLT2 SREBP/SCAP		Deletions in TMEM106B caused defects in lysosome trafficking, impaired acidification, and reduced levels of lysosomal enzymes but its precise molecular function remains enigmatic	None	[87, 88]
O-glycan biosynthesis N-glycan biosynthesis	HEK293T	C1GalT1 MGAT1		Knocking-out N-glycan biosynthesis on Spike-abrogated viral entry	Kifunensine small molecule inhibits N-linked glycosylation to reduce viral entry	[89]
Cholesterol biosynthesis pathway (part of the endosomal entry pathway from the vacuolar ATPase proton pump, Retromer, and Commander complexes)	A549	ATP6AP1 ATP6V1A NPC1 RAB7A CCDC22 PIK3C3		Loss of resistant genes such as RAB7A reduces viral entry by sequestering the ACE2 receptor inside cell	RNA-sequencing of cells treated with amlodipine small molecule shows a similar differential gene expression profile as seen in CRISPR knock-out of genes in cholesterol biosynthesis pathway	[84]
Rab-GTPase requirements Glycosylphosphatidylinositol-anchored biosynthesis Cholesterol biosynthesis	HAP1 Huh-7.5-Cas9	SREBP/SCAP HS2ST1 EIF4E2 RAB2A RAB10 RAB14	MRPS2 MRPS5 MRPS25 MRPS27	SCAP regulates lipid and cholesterol homeostasis by sequestering SREBPs in the ER in the presence of sterols	Fatostatin molecule as SCAP inhibitors shows anti-viral properties 27-hydroxycholesterol (27OHC) and 25OHC have SARS-CoV-2 anti-viral activity in VeroE6 cells	[83]
Replication cycle	A549	TMEM41B		SARS-CoV-2 require TMEM41B for replication cycles in cell	None	[85]
Chromatin remodeling Histone modification Cellular signaling RNA regulation	Huh7.5 VeroE6	ARID1A DYRK1A KDM6A CTSL ACE2 SMARCA4 DYRK1A KDM6A HMGB1 HIRA CABIN1 TRIP12 BPTF PIAS2	TARDBP	Viral RNA-RNA and RNA–protein interactions reveal specific SARS-CoV-2-mediated mitochondrial dysfunction during infection pro-viral genes and pathways, including HMGB1, and the SWI/SNF chromatin remodeling complex are SARS-CoV-2 lineage HMGB1 is critical for SARS lineage viral entry with critical role in ACE2 expression	PFI-3, which targets the bromodomains of the SWI/SNF proteins SMARCA4 and SMARCA2 SIS3, which targets the pro-viral gene SMAD3 identified in the screen	[80, 81]
Glycosaminoglycan biosynthesis SREBP signaling Glycosylphosphatidylinositol biosynthesis Cholesterol biosynthesis	Huh-7.5 hepatoma cells (Huh-7.5-Cas9)	SCAP TMEM106B TMEM41B VAC14 ACE2 HMGCS1 MVK PMVK RAB6A RAB10		Absolute requirement for the VTT-domain containing protein TMEM41B for infection by SARS-CoV-2	None	[86]
Phosphatidylinositol phosphate biosynthesis Cholesterol homeostasis Heparan sulfate biosynthetic genes	Huh7.5.1 hepatoma cells	TMEM106B B3GALT6 B3GAT3 B4GALT7 EXT1 EXT2 EXTL3 FAM20B NDST1 SLC35B2 UGDH XYLT2 SREBP/SCAP		Deletions in TMEM106B caused defects in lysosome trafficking, impaired acidification, and reduced levels of lysosomal enzymes but its precise molecular function remains enigmatic	None	[87, 88]
O-glycan biosynthesis N-glycan biosynthesis	HEK293T	C1GalT1 MGAT1		Knocking-out N-glycan biosynthesis on Spike-abrogated viral entry	Kifunensine small molecule inhibits N-linked glycosylation to reduce viral entry	[89]