Table 2.

CRISPR screens for studying viral infections.

Virus	Screen Type	gRNA Library	Cells	Top Screening Hits	Ref.
HIV	CRISPR-ko	Custom library of 187,536 gRNAs targeting 18,543 genes	GXR cell line	TPST2, SLC35B2, ALCAM, CCR5, CD4	[34]
	CRISPRi	CRISPRi-v2	Jurkat	TMEM178A, FTSJ3, INTS2, INTS5, INTS8, NICN1	[88]
	CRISPR-ko	GeCKO	C11 cell line	PEPB1, BRD2, BRD4	[89]
	CRISPR-ko	GeCKO	Jurkat	ZNF304	[90]
	CRISPR-ko	GeCKO v2	Jurkat (J-Lat 10.6 cell line)	52 genes including IWS1, POLE3, POLR1B, PSMD1, TGM2	[91]
	CRISPR-ko	GeCKO v2	Jurkat (HIV-1 latent infection cell line [C11])	TCS1, DEPDC5, SUV39H1, SPATA6L, NFKB2, and other genes	[92]
Coronaviruses (SARS-CoV-2, MERS)	CRISPR-ko	Brunello	Huh-7.5	146 (37 °C) and 171 (33 °C) genes, including TMEM41B for all of investigated viruses	[93]
	CRISPR-ko	Custom library of 83,963 gRNAs	Vero-E6	Genes of SWI/SNF complex, ACE2, DPP4, CTSL, PCBD1, KMT2D, SMAD3, HMGB1, and others	[94]
	CRISPR-ko	GeCKO v2	A549ACE2	RAB7A, CCDC22, VPS35, ACE2, CTSL, and others	[95]
	CRISPR-ko	GeCKO v2	Huh7.5.1	TMEM106B and other genes	[96]
Dengue virus (DENV)	CRISPR-ko	GeCKO v2	Haploid HAP1 cells	17 genes including DPM1 and DPM3	[97]
	CRISPR-ko	GeCKOv2	Huh7.5.1	STT3A, STT3B, DC2, MAGT, RPN2, OST4	[98]
Zika virus (ZIKV), yellow fever virus	CRISPR-ko	GeCKO	HAP1	TMEM41B and VMP1 (overlap between the two viruses)	[99]
ZIKV	CRISPR-ko	Brunello	TS576	CENPH, ITGB5, MYLPH, HOMER1, BAALC, GABBR2, EPHA10, PTNP2, GCNT7, TRAM1, TMEM41B	[100]
	CRISPRa	LentiSAMv2	Huh7	IFI6, IFNL2, ISG20, HELZ2	[101]
	CRISPR-ko	LentiCRISPRv1; custom library	Human neural progenitors cells	TM9SF2, ATP6V1C1, ATP6V1F, SSR2, SSR3, EMC2, EMC6, C3orf58, ISG15, SOCS3, STAT3	[102]
Hepatitis A virus (HAV)	CRISPR-ko	Brunello	HeLa	39 genes including UGCG, GALE, and SLC35A2	[103]
Hepatis B virus (HBV)	CRISPR-ko	Custom library of 19,050 genes, with 5 gRNAs/gene	HepG2	22 pro-HBsAg genes, including ZCCHC14, NXT1, and ENY2; 38 anti-HBsAg genes, including DCAF7, UBE2J1, RNF139, and UBE2J2	[104]
Epstein-Barr virus	CRISPR-ko	AVANA	P3HR-1	MYC, EP300, STAGA, FACT, cohesin subunits	[105]
	CRISPR-ko	Brunello	Lymphoblastoid cell lines (LCL)	TAF family proteins, MEF2C	[106]
	CRISPR-ko	Avana	P3HR-1, GM12878	57 genes for P3HR1 and 87 genes for GM12878	[107]
Human cytomegalovirus (HCMV)	CRISPR-ko	GeCKO v2	ARPE-19; HEL fibroblasts	OR14I1, PDGFRA	[108]
	CRISPR-ko	GeCKO v2	Human foreskin fibroblasts (HFF)	PDGFRA	[109]
Influenza A virus (IAV)	CRISPR-ko	AVANA-4	A549	WDR7, CCDC115, TMEM199, CMTR1	[110]
	CRISPR-ko	GeCKO	A549	SLC35A1 and other genes	[111]
Adeno-associated virus	CRISPR-ko	GeCKO	Huh7	GPR108, NEU1, GCNT4, CTSA	[112]
	CRISPR-ko	GeCKO v2	Huh7	Crb3, CLDN15	[113]
Ebola virus (EBOV)	CRISPR-ko	GeCKO v2	Huh7.5.1	GNPTAB, NPC1, SPNS1, SLC30A1, HOPS complex, UVRAG	[114]
Enteroviruses (RV-C15 and non-polio EV-D68)	CRISPR-ko	GeCKO v2	H1-HeLa cells	SETD3, CSDE1, PLA2G16	[115]
Severe fever with thrombocytopenia syndrome virus	CRISPR-ko	GeCKO v2	HeLa	SNX11	[116]
Norovirus restriction factors	CRISPRa	Calabrese	Hela	TRIM7, PITX1, HOXC11, DDX60, MX1, PLSCR1	[117]
Flaviviruses	CRISPR-ko	Brunello	Huh7.5	IFI6, STAT2, IRF9	[118]
	CRISPR-ko	GeCKO v2	293T	STT3A, SEC63, SPCS1, SPCS3	[119]
West Nile virus	CRISPR-ko	Custom library of 77,406 gRNAs covering 20,121 genes	293FT	EMC2, EMC3, SEL1L, DERL2, UBE2G2, UBE2J1, HRD1	[120]
Arthritogenic alphaviruses (chikungunya, Ross River, Mayaro, O’nyong nyong)	CRISPR-ko	GeCKO v2	3T3	MXRA8	[121]
Rotavirus	CRISPR-ko	GeCKO	H1-Hela	SLC35A1, GNE, CMAS, UGCG, FA2H, LATS2, STAG2	[122]