Table 1.

Autoantigens identified by DS-affinity and their alterations in SARS-CoV-2 infection

P	Gene	Protein	Cell line						SARS-Cov-2 infection			DS affinity		Ref.
			HFL1	HS-Sultan	Wil2	A549	Jurkat	HEp-2	u	d	interact.	hi	low
5	A2M	Alpha-2-macroglobulin	+			+				d			+	[1]
6	AARS	Alanine-tRNA ligase, AARS1	+	+					u	d			+	[2]
15	ACLY	ATP-citrate synthase		+		+			u	d			+	[3]
4	ACTA1	Actin, alpha skeletal muscle			+				u	d		+		[4]
10	ACTA2	Actin, aortic smooth muscle	+	+		+		+	u	d		+	+	[5]
8	ACTB	Actin, cytoplasmic 1	+	+		+		+	u	d		+	+	[6]
7	ACTBL2	Beta-actin-like protein	+	+		+		+	u	d		+	+	[6]
2	ACTBL3	Putative beta-actin-like protein 3, kappa actin, POTEKP			+		+		u				+
6	ACTC1	Actin, alpha cardiac muscle					+		u	d		+	+	[7]
4	ACTG1	Actin, cytoplasmic 2			+		+		u	d		+	+	[8]
28	ACTN1	Alpha-actinin-1	+	+	+	+	+	+	u	d			+	[9]
22	ACTN4	Alpha-actinin-4	+	+	+	+		+	u	d			+	[5]
2	ACTR2	Actin-related protein 2		+					u	d			+	[10]
2	ACTR3	Actin-related protein 3		+					u				+	[11]
2	ADSS2	Adenylosuccinate synthetase isozyme 2, ADSS				+			u				+
3	AFP	Alpha-fetoprotein	+	+		+				d			+	[12]
2	AGRN	Agrin				+			u		Nsp6 Nsp13 Orf8 Orf10	+		[13]
15	AHCY	Adenosylhomocysteinase, SAHH		+		+				d			+	[14]
5	AHNAK	Neuroblast differentiation-associated protein	+						u	d			+	[15]
4	AHSA1	Activator of 90 kDa heat shock protein ATPase homolog 1		+						d			+
2	AHSG	Alpha-2-HS-glycoprotein, FETUA						+		d			+	[16]
5	AKR1B1	Aldo-keto reductase family 1 member B1				+			u	d	Orf3		+	[17]
10	ALB	Albumin	+			+			u	d		+	+	[18]
5	ALDH18A1	Delta-1-pyrroline-5-carboxylate synthetase		+			+			d			+
23	ALDH1A1	Retinal dehydrogenase 1				+			u	d			+	[19]
5	ALDH2	Aldehyde dehydrogenase, mitochondrial				+			u	d	E Nsp5 Nsp12 Nsp16		+	[20]
5	ALDH3A1	Aldehyde dehydrogenase 3, ALDH3				+			u	d			+
9	ALDOA	Fructose-bisphosphate aldolase A		+		+			u	d			+	[21]
4	ALDOC	Fructose-bisphosphate aldolase C		+					u	d			+	[22]
3	ALPP	Alkaline phosphatase, placental type precursor	+									+		[23]
10	ANP32A	Acidic leucine-rich nuclear phosphoprotein 32 member A	+	+	+	+	+	+	u	d		+	+
13	ANP32B	ANP 32 family member B	+	+	+	+	+	+		d	N	+	+	[24]
3	ANP32C	ANP 32 family member C, PP32R1	+	+		+						+	+
4	ANP32E	ANP 32 family member E	+		+	+			u	d	Orf9c	+	+
4	ANXA2	Annexin A2	+			+			u	d		+	+	[25]
13	ANXA2P2	Putative annexin A2-like protein, ANX2L2, LPC2B	+			+			u	d			+	[26]
10	ANXA3	Annexin A3				+			u	d			+	[25]
5	ANXA4	Annexin IV				+			u	d			+	[27]
15	ANXA5	Annexin A5	+	+		+			u	d	Orf3		+	[28]
33	ANXA6	Annexin VI	+	+	+	+	+		u	d			+	[29]
2	AP1B1	AP-1 complex subunit beta-1	+										+
8	AP3B1	AP-3 complex subunit beta-1	+			+			u		E	+
2	AP3B2	AP-3 complex subunit beta-2	+			+						+		[30]
8	AP3D1	AP-3 complex subunit delta-1	+			+			u	d		+
4	APEH	Acylamino-acid-releasing enzyme		+									+
4	APEX1	DNA-(apurinic or apyrimidinic site) lyase		+		+			u	d			+	[31]
2	API5	Apoptosis inhibitor 5		+	+					d			+
3	APOA1	Apolipoprotein A-I	+							d			+	[32]
2	APOD	Apolipoprotein D	+						u	d			+
8	ARF1	ADP-ribosylation factor	+	+							Nsp6		+
2	ARHGAP1	Rho-GTPase-activating protein 1	+						u		Orf3a Orf3b Orf6 Orf7a Orf7b Orf8 Orf9c S		+
6	ARHGDIA	Rho GDP-dissociation inhibitor 1	+	+					u	d			+
8	ARHGDIB	Rho GDP-dissociation inhibitor 2		+						d			+	[33]
3	ARPC2	Actin-related protein 2/3 complex subunit 2		+						d			+
7	ASMTL	N-Acetylserotonin O-methyltransferase-like protein			+								+
2	ASNS	Glutamine-dependent asparagine synthetase		+					u				+
4	ASPH	Aspartyl/asparaginyl beta-hydroxylase				+			u	d	Orf9c	+
14	ATIC	Bifunctional purine biosynthesis protein, PURH		+	+	+							+	[34]
2	ATP2A2	Sarcoplasmic/ER calcium ATPase 2				+			u		Nsp4	+		[35]
13	ATP5F1B	ATP synthase subunit beta, mitochondrial, ATP5B	+	+	+	+	+		u	d	Nsp6 Orf9b	+	+	[36]
3	ATXN10	Ataxin-10, Spinocerebellar ataxia type 10 protein		+					u	d			+
3	BASP1	Brain acid soluble protein 1 (Neuronal axonal membrane protein NAP22)						+	u	d	M Orf3a Orf7b S		+
3	BCAT1	Branched chain amino acid aminotransferase	+						u				+
2	BCCIP	BRCA2 and CDKN1A-interacting protein	+										+
2	BGN	Biglycan	+									+		[37]
3	BRIX1	Ribosome biogenesis protein BRX1 homolog				+						+
2	BSG	Basigin, CD147	+							d		+		[38]
3	BTF3	Transcription factor BTF3, NACB			+				u	d			+
2	BZW1	Basic leucine zipper and W2 domain-containing protein 1		+					u				+
3	BZW2	Basic leucine zipper and W2 domain-containing protein 2	+	+			+				M		+
7	C1QBP	Complement C1q-binding protein	+	+	+	+	+	+		d		+	+	[39]
7	CALD1	Caldesmon	+							d			+	[40]
8	CALM1	Calmodulin-1	+	+			+	+	u	d			+	[41]
5	CALM2	Calmodulin-2			+					d			+
2	CALM3	Calmodulin-3			+		+		u				+	[42]
19	CALR	Calreticulin	+	+	+	+	+	+	u	d			+	[43]
2	CALU	Calumenin	+						u	d	E M Nsp6 Nsp7 Orf3a Orf3b Orf6 Orf7a Orf7b Orf9c S		+	[44]
15	CAND1	Cullin-associated NEDD8-dissociated protein 1		+	+		+						+
7	CANX	Calnexin	+			+		+	u	d	Nsp4 Orf8	+		[45]
9	CAP1	Adenylyl cyclase-associated protein 1	+	+		+			u	d	Orf3		+
7	CAPN1	Calpain-1 catalytic subunit	+	+		+							+
5	CAPN2	Calpain-2 catalytic subunit	+					+	u	d	Nsp16		+	[41]
3	CAPNS1	Calpain small subunit 1	+										+
3	CAPRIN1	Caprin-1		+	+		+			d			+
3	CAPZA1	F-actin-capping protein subunit alpha-1	+	+			+			d		+	+	[46]
3	CAPZB	F-actin-capping protein subunit beta	+	+		+				d			+	[47]
8	CAVIN1	Caveolae-associated protein 1, PTRF	+						u	d	N S		+	[48]
3	CBX1	Chromobox protein homolog 1	+		+				u				+	[49]
3	CBX3	Chromobox protein homolog 3			+				u	d			+
3	CCDC6	Coiled-coil domain-containing protein 6	+						u	d			+	[50]
12	CCT2	T-complex protein 1 subunit beta	+	+	+		+			d	Nsp12 Orf8 Orf9b Orf10		+	[51]
12	CCT3	T-complex protein 1 subunit gamma		+	+		+		u		Orf8 Orf10		+	[52]
6	CCT4	T-complex protein 1 subunit delta		+	+		+		u				+	[52]
10	CCT5	T-complex protein 1 subunit epsilon		+	+		+		u	d	Nsp1 Nsp12 Orf8 Orf10		+	[51]
7	CCT6A	T-complex protein 1 subunit zeta		+	+		+		u	d	Nsp1 Nsp12 Orf10		+	[51]
9	CCT7	T-complex protein 1 subunit eta		+	+		+				Orf10		+	[51]
20	CCT8	T-complex protein 1 subunit theta	+	+	+	+	+		u	d	Nsp1 Nsp12 Nsp14 Nsp15		+	[52]
4	CD248	Endosialin	+							d			+
7	CDC37	Hsp90 co-chaperone Cdc37	+	+	+		+		u	d	Nsp16		+
3	CDK11A	Cyclin-dependent kinase 11A, CDC2L2				+			u			+
3	CEBPZ	CCAAT/enhancer-binding protein zeta				+			u			+
2	CFL1	Cofilin-1, CFL			+				u	d			+	[53]
4	CKAP4	Cytoskeleton-associated protein 4, P63	+						u	d	Nsp2 Orf7b	+		[54]
8	CKB	Creatine kinase B-type							u	d			+	[55]
7	CLIC1	Chloride intracellular channel protein 1	+	+	+	+			u	d	Nsp16		+	[56]
2	CLIC4	Chloride intracellular channel protein 4	+						u	d			+
51	CLTC	Clathrin heavy chain 1	+	+		+		+	u	d		+	+	[57]
4	CLTCL1	Clathrin heavy chain 2	+	+		+		+				+	+
4	CLUH	Clustered mitochondria protein homolog (mRNA-binding)		+						d	Nsp7 Nsp16		+
2	CMPK1	UMP-CMP kinase		+						d			+
3	CNDP2	Cytosolic non-specific dipeptidase		+					u		Orf3 Orf10		+
3	CNPY2	Protein canopy homolog	+	+	+					d	Orf3a		+
13	COL12A1	Collagen type XII alpha-1 chain	+						u	d			+
45	COL1A1	Collagen type I alpha-1 chain	+						u	d			+	[58]
37	COL1A2	Collagen type I alpha-2 chain	+							d			+	[59]
2	COL2A1	Collagen type II alpha-1 chain	+						u				+	[60]
12	COL3A1	Collagen type III alpha-1 chain	+										+	[61]
3	COL5A1	Collagen type V alpha 1	+						u				+	[62]
6	COL6A1	Collagen type VI alpha-1 chain	+							d	Orf8		+	[63]
4	COL6A2	Collagen type VI alpha-2 chain	+							d			+
29	COL6A3	Collagen type VI alpha-3 chain	+							d			+
2	COPA	Coatomer subunit alpha	+			+			u	d		+		[64]
2	COPB1	Coatomer subunit beta	+							d	Nsp7	+		[65]
5	COPB2	Coatomer subunit beta’	+					+	u			+		[66]
2	COPD	Coatomer subunit delta, ARCN1	+							d	Orf3b Orf6		+
2	COPG1	Coatomer subunit gamma-1						+			E M Nsp4 Nsp6 Orf3b Orf6 Orf7a Orf7b		+	[39]
2	COPZ1	Coatomer subunit zeta-1	+	+						d			+
12	CORO1A	Coronin-1A		+					u				+	[67]
3	CORO1C	Coronin-1C	+										+
3	CPNE1	Copine-1		+									+
4	CPNE3	Copine-3		+		+			u	d			+
4	CRK	Proto-oncogene c-Crk	+						u	d	Nsp12 Nsp14 Nsp15		+
5	CRTAP	Cartilage-associated protein, P3H5	+							d		+
3	CS	Citrate synthase, mitochondrial		+					u	d	E		+	[3]
4	CSK	Tyrosine-protein kinase CSK		+						d			+	[68]
3	CSNK2A1	Casein kinase 2, alpha 1			+								+
4	CSPG4	Chondroitin sulfate proteoglycan 4	+							d	Orf7b S	+		[69]
4	CTCFL	High mobility group box 1 pseudogene 1, HMGB1P1, HMGB1L1	+										+	[136]
2	CTR9	RNA polymerase-associated protein CTR9 homolog				+			u	d	Orf9c	+
3	CTSB	Cathepsin B, APP secretase	+						u	d	M Nsp12		+
2	CTSD	Cathepsin D	+						u	d			+	[70]
2	CUTA	Protein CutA	+						u	d			+
6	DAP3	28S ribosomal protein S29, mitochondrial, MRPS29				+						+
6	DARS	Aspartate-tRNA ligase, DARS1		+									+	[71]
2	DBN1	Drebrin 1	+						u	d			+	[72]
4	DCAF1	DDB1- and CUL4-associated factor 1, VPRBP				+			u	d		+
3	DCK	Deoxycytidine kinase		+					u				+
3	DCN	Decorin	+							d		+		[73]
2	DCTN1	Dynactin subunit 1, 150 KDa Dynein-associated protein	+							d		+		[74]
5	DCTN2	Dynactin subunit 2	+	+							Orf6		+
3	DCTPP1	dCTP pyrophosphatase 1		+						d	Orf9b		+
28	DDB1	DNA damage-binding protein 1	+	+		+	+	+	u	d		+	+	[57]
3	DDX17	ATP-dependent RNA helicase DDX17				+			u	d		+		[53]
7	DDX18	ATP-dependent RNA helicase DDX18				+			u			+
5	DDX21	Nucleolar RNA helicase 2			+	+			u	d	N	+		[75]
4	DDX27	ATP-dependent RNA helicase DDX27				+			u			+
3	DDX30	ATP-dependent RNA helicase DHX30				+				d		+
7	DDX39A	ATP-dependent RNA helicase DDX39A	+	+	+		+		u	d			+	[39]
5	DDX39B	Spliceosome RNA helicase BAT1	+	+	+		+			d			+
4	DDX5	ATP-dependent RNA helicase, p68		+		+			u	d		+	+	[76]
16	DDX9	ATP-dependent RNA helicase A, DHX9	+	+	+	+		+				+	+	[77]
2	DEK	Protein DEK			+				u	d			+	[53]
12	DHX15	Pre-mRNA-splicing factor ATP-dependent RNA helicase	+	+		+	+			d		+	+
4	DHX36	ATP-dependent RNA helicase DHX36				+			u			+
5	DIABLO	Second mitochondria-derived activator of caspase	+	+	+				u	d	Nsp6 Nsp15		+
4	DKC1	H/ACA ribonucleoprotein complex subunit B	+			+			u	d		+
4	DLD	Dihydrolipoyl dehydrogenase, mitochondrial		+									+	[79]
2	DLST	Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex	+							d			+	[80]
2	DNAJB11	DnaJ (Hsp40) homolog subfamily B member 11	+						u				+	[81]
2	DNAJC8	DnaJ homolog subfamily C member 8		+					u				+
4	DNPH1	2’-deoxynucleoside 5’-phosphate N-hydrolase 1		+					u				+
6	DPP3	Dipeptidyl-peptidase 3	+	+		+				d			+
3	DPYSL2	Dihydropyrimidinase-related protein	+						u	d			+	[82]
3	DRG1	Developmentally-regulated GTP-binding protein	+							d			+
5	DUT	Deoxyuridine 5’-triphosphate nucleotidohydrolase, mitochondrial		+					u	d			+
5	DYNC1H1	Dynein cytoplasmic 1 heavy chain 1	+									+
3	DYNC1I2	Dynein cytoplasmic 1 intermediate chain 2	+			+						+
3	EBP2	Probable rRNA-processing protein, EBNA1BP2				+						+
4	ECH1	Delta(3,5)-delta(2,4)-dienoyl-CoA isomerase, mitochondrial				+			u	d			+	[83]
2	EEF1A1	Elongation factor 1-alph 1	+	+		+			u	d			+	[84]
4	EEF1A2	Elongation factor 1-alpha 2	+	+		+			u		Orf3		+	[85]
2	EEF1B2	Elongation factor 1-beta 2	+	+	+		+			d			+
5	EEF1D	Elongation factor 1-delta	+	+	+					d			+	[86]
10	EEF1G	Elongation factor 1-gamma	+	+	+	+	+		u	d			+
17	EEF2	Elongation factor 2	+	+	+	+			u	d		+	+	[87]
16	EFTUD2	116 kDa U5 snRNP component, SNRP116	+	+	+	+		+		d		+	+	[88]
4	EHD2	EH domain-containing protein 2	+						u	d			+
3	EIF2A	Eukaryotic translation initiation factor 2 subunit 1, EIF2S1	+	+	+	+							+	[89]
10	EIF3A	Eukaryotic translation initiation factor 3 subunit A	+	+		+			u	d	Nsp1	+	+	[90]
9	EIF3B	Eukaryotic translation initiation factor 3 subunit B	+	+		+			u	d	Nsp1	+	+	[39]
2	EIF3C	Eukaryotic translation initiation factor 3 subunit C		+	+					d	Nsp1		+	[91]
3	EIF3CL	Eukaryotic translation initiation factor 3 subunit C-like protein	+			+				d		+
5	EIF3E	Eukaryotic translation initiation factor 3 subunit E	+	+	+	+			u	d	Nsp1	+	+	[92]
4	EIF3F	Eukaryotic translation initiation factor 3 subunit F	+	+					u	d	Nsp1	+	+	[93]
2	EIF3G	Eukaryotic translation initiation factor 3 subunit G	+								Nsp1		+	[93]
2	EIF3I	Eukaryotic translation initiation factor 3 subunit I		+						d	Nsp1		+	[91]
10	EIF3L	EIF3, subunit E interacting protein	+	+	+	+				d	Nsp1	+	+	[39]
19	EIF4A1	Eukaryotic initiation factor 4A-1, DDX2A	+	+		+	+		u	d			+
8	EIF4A3	Eukaryotic initiation factor 4A-III, DDX48	+	+		+						+	+	[94]
4	EIF4G1	Eukaryotic translation initiation factor 4 gamma 1	+		+				u	d			+	[93]
2	EIF4G2	Eukaryotic translation initiation factor 4 gamma 2	+							d	Nsp1		+	[93]
2	EIF5	Eukaryotic translation initiation factor 5		+					u	d			+	[95]
5	EIF5A	Eukaryotic translation initiation factor 5A-1	+	+		+			u	d			+	[95]
2	EIF5A2	Eukaryotic translation initiation factor 5A-2	+		+		+			d			+	[95]
2	EIF5B	Eukaryotic translation initiation factor 5b (eif-5b) (translation initiation factor if-2)			+				u				+
3	EIF6	Eukaryotic translation initiation factor 6	+	+	+				u				+
4	ELAVL1	ELAV-like protein	+	+						d			+	[96]
2	ELOB	Transcription elongation factor B, TCEB2	+						u	d	Nsp16 Orf10		+
2	EMG1	Ribosomal RNA small subunit methyltransferase NEP1				+			u	d			+
12	ENO1	Alpha-enolase	+		+	+		+	u	d			+	[97]
7	ENO2	Gamma-enolase	+	+					u	d			+	[98]
2	ENOPH1	Enolase-phosphatase E1	+						u				+
6	EPHX1	Epoxide hydrolase				+				d		+		[99]
4	ERO1A	Endoplasmic oxidoreductin-1-like protein, ERO1L		+				+		d	Orf3a		+
6	ERP44	Endoplasmic reticulum resident protein ERp44	+								Orf8		+	[101]
4	ESYT1	Extended synaptotagmin-1, FAM62A	+			+					E M Nsp3 Nsp4 Nsp6 Orf3a Orf6 Orf7a Orf7b Orf8 Orf9c S	+		[102]
4	ETF1	Eukaryotic peptide chain release factor subunit 1		+					u				+
2	EWSR1	EWS RNA-binding protein	+						u	d			+
14	EZR	Ezrin		+		+			u	d	S		+	[103]
2	FAF1	FAS-associated factor 1	+						u				+
3	FARSB	Phenylalanine-tRNA ligase beta subunit		+									+	[104]
19	FASN	Fatty acid synthase	+	+	+		+		u	d			+	[105]
3	FBLN1	Fibulin 1	+						u	d			+	[106]
2	FDPS	Farnesyl pyrophosphate synthetase like-4 protein		+						d			+
2	FEN1	Flap endonuclease 1		+					u	d			+
2	FERMT3	Fermitin family homolog 3		+					u				+
8	FKBP10	FK506-binding protein 10	+								Orf8		+
11	FKBP4	Peptidyl-prolyl cis-trans isomerase FKBP4, FKBP-52		+		+					Nsp12		+	[107]
2	FKBP5	Peptidyl-prolyl cis-trans isomerase FKBP5 (FK506-binding protein)		+					u				+
4	FKBP9	FK506-binding protein 9	+							d			+
43	FLNA	Filamin-A	+			+		+	u	d		+	+	[108]
25	FLNB	Filamin-B	+			+		+	u				+	[57]
24	FLNC	Filamin-C	+			+			u	d		+	+	[109]
23	FN1	Fibronectin	+						u	d			+	[110]
3	FSTL1	Follistatin-related protein	+						u	d			+	[111]
2	FTH1	Ferritin heavy chain	+			+			u	d			+	[111]
2	FUBP1	Far upstream element-binding protein 1		+					u	d			+	[112]
10	G6PD	Glucose-6-phosphate 1-dehydrogenase	+	+		+			u	d		+	+	[44]
15	GANAB	Neutral alpha-glucosidase AB	+	+		+				d	Orf6 Orf8 Orf9c		+	[113]
6	GAPDH	Glyceraldehyde-3-phosphate dehydrogenase	+	+	+	+			u	d	Orf8	+	+	[114]
2	GAR1	H/ACA ribonucleoprotein complex subunit 1	+			+						+
4	GARS	Glycine-tRNA ligase, GARS1		+					u				+	[115]
2	GART	Trifunctional purine biosynthetic protein adenosine-3		+						d	Nsp15		+
2	GBE1	1,4-alpha-glucan-branching enzyme		+		+			u				+
4	GCLC	Glutamate-cysteine ligase catalytic subunit				+					Orf3		+
8	GDI1	Rab GDP dissociation inhibitor alpha	+	+		+			u	d			+	[116]
10	GDI2	Rab GDP dissociation inhibitor beta	+	+		+			u	d	Nsp12 Orf9b		+	[117]
2	GGCT	Gamma-glutamylcyclotransferase, cytochrome c-releasing factor 21		+					u				+
3	GLO1	Lactoylglutathione lyase		+		+				d	Orf3		+	[118]
3	GLRX3	Glutaredoxin 3, Thioredoxin-like 2	+	+						d			+	[119]
10	GLUD1	Glutamate dehydrogenase 1, mitochondrial		+									+	[120]
2	GMFB	Glia maturation factor, beta	+	+					u				+
2	GPALPP1	Lipopolysaccharide-specific response protein 7			+								+
5	GPC1	Glypican-1	+			+				d		+
2	GPI	Glucose-6-phosphate isomerase				+			u	d	E Nsp6 Orf3 Orf3b Orf6		+	[121]
4	GRWD1	Glutamate-rich WD repeat-containing protein 1				+						+
16	GSN	Gelsolin	+						u	d			+	[16]
3	GSPT1	Eukaryotic peptide chain release factor GTP-binding subunit ERF3A		+									+
3	GSS	Glutathione synthetase		+						d			+
6	GSTP1	Glutathione S-transferase				+			u	d			+	[122]
4	GTF2I	General transcription factor II-I	+	+					u	d			+	[25]
3	H1-1	Histone H1.1, H1F1, HIST1H1A, H1FNT			+		+		u	d		+	+	[123]
2	H1F0	Histone H1.0, H1FV, H1-0						+	u	d	Nsp3 Nsp8 Orf3b Orf10		+
3	H2AFV	Histone H2A.V, H2AZ2	+	+		+		+	u	d		+	+	[127]
11	H2AFY	Core histone macro-H2A.1, MACROH2A1				+		+	u			+		[128]
4	H2AFY2	Cor2 histone macro-H2A.2, MACROH2A2	+	+		+			u			+		[128]
4	HADHA	Trifunctional enzyme subunit alpha, mitochondrial				+						+
3	HARS	Histidyl-tRNA synthetase, cytoplasmic	+	+		+							+	[41]
5	HDGF	Hepatoma-derived growth factor, HMG1L2	+	+	+		+	+	u	d			+	[134]
2	HDLBP	Vigilin, High density lipoprotein binding protein	+						u	d	N Nsp2		+
4	HEATR1	HEAT repeat-containing protein 1				+			u	d		+
2	HEBP2	Heme-binding protein 2	+						u				+
5	HEXB	Beta-hexosaminidase subunit beta	+							d			+
6	HIST1H1B	Histone H1.5, H1F5, H1-5	+		+	+	+	+	u	d		+	+	[124]
6	HIST1H1C	Histone H1.2, H1F2, H1-2	+	+	+	+	+	+	u	d	Nsp8	+	+	[124]
4	HIST1H2A A	Histone H2A type 1-A, H2AFR, H2AC1			+	+	+					+	+	[125]
2	HIST1H2AB	Histone H2A type 1-B/E, H2AFM, H2AC4		+						d		+		[126]
5	HIST1H2BA	Histone H2B type 1-A, H2BC1			+		+					+	+	[123]
5	HIST1H2BB	Histone H2B type 1-B, H2BFF, H2BC3			+		+					+		[131]
2	HIST1H2BL	Histone H2B type 1-L, H2BFC, H2BC13	+	+		+			u	d		+		[129]
12	HIST2H2BE	Histone H2B type 2-E, H2BC21	+	+		+		+	u	d		+		[130]
5	HIST2H3A	Histone H3.2, H3C15	+	+		+		+	u	d		+	+	[132]
4	HIST3H3	Histone H3.1t, H3FT, H3-4			+		+					+	+	[123]
14	HIST4H4	Histone H4, H4C1	+	+	+	+	+	+	u	d		+	+	[133]
10	HMGB1	High mobility group protein 1		+	+		+			d			+	[135]
3	HMGCS1	Hydroxymethylglutaryl-CoA synthase, cytoplasmic		+	+		+		u	d			+
2	HMGN1	Non-histone chromosomal protein HMG14			+				u				+
4	HNRNPA1	Heterogeneous nuclear ribonucleoprotein A1	+	+	+		+	+	u	d			+	[137]
8	HNRNPA2 B1	hnRNP A2/B1	+	+	+	+		+	u	d			+	[138]
2	HNRNPA3	hnRNP A3	+	+				+	u	d			+	[139]
2	HNRNPAB	hnRNP A/B		+						d			+	[139]
3	HNRNPC	hnRNP C1/C2	+	+	+	+			u	d		+	+	[140]
7	HNRNPCL1	hnRNP C-like 1	+	+	+	+	+	+				+	+	[141]
5	HNRNPD	hnRNP D, AUF1	+	+	+								+	[142]
3	HNRNPDL	hnRNP D-like	+	+					u	d			+	[143]
5	HNRNPF	hnRNP F	+	+		+				d		+	+	[144]
2	HNRNPH1	hnRNP H1	+	+	+	+			u	d			+
2	HNRNPH3	hnRNP H3	+						u	d			+	[145]
9	HNRNPK	hnRNP K	+	+	+	+	+		u				+	[146]
3	HNRNPM	hnRNP M				+			u	d		+
6	HNRNPQ	hnRNP Q, SYNCRIP	+	+	+	+	+	+		d			+
7	HNRNPR	hnRNP R	+	+	+	+		+	u	d			+	[147]
5	HNRNPU	hnRNP U (scaffold attachment factor A)	+	+	+	+	+	+	u	d		+	+	[148]
6	HNRNPUL1	hnRNP U-like protein 1	+			+			u	d		+
4	HNRNPUL 2	hnRNP U-like protein 2				+			u	d		+
6	HPRT1	Hypoxanthine-guanine phosphoribosyltransferase		+									+
2	HSP70B	Putative heat shock 70 kDa protein, HSPA7				+			u	d		+
38	HSP90AA1	Heat shock protein 90-alpha	+	+	+	+	+	+	u	d		+	+	[149]
6	HSP90AA2	Heat shock protein 90-alpha A2	+	+		+		+	u			+	+	[150]
16	HSP90AB1	Heat shock protein HSP 90-beta	+	+	+	+	+	+	u	d	Nsp12		+	[151]
31	HSP90B1	Endoplasmin, GRP94	+	+	+	+	+	+	u	d	Orf3a Orf9c	+	+	[152]
7	HSPA1A	Heat shock 70 kDa protein 1A	+			+			u	d	N Orf9b		+
4	HSPA1L	Heat shock 70 kDa protein 1-like, HSP70T	+			+							+	[153]
2	HSPA2	Heat shock 70 kda protein 2			+				u		Nsp3	+
14	HSPA4	Heat shock 70 kDa protein 4	+	+	+		+		u	d			+	[154]
35	HSPA5	Endoplasmic reticulum chaperone BiP, GRP78	+	+	+	+	+	+	u	d	E M Nsp2 Nsp4 Nsp6 Orf3a Orf7a Orf7b S		+	[155]
27	HSPA8	Heat shock cognate 71 kDa protein	+	+	+	+		+	u	d	Nsp2 Nsp12		+	[156]
25	HSPA9	Stress-70 protein, mitochondrial (GRP75)	+	+	+	+		+	u	d	N		+	[156]
7	HSPB1	Heat shock protein beta-1	+						u	d			+	[157]
2	HSPBP1	Hsp70-binding protein 1				+			u	d	S		+
30	HSPD1	60 kDa heat shock protein, mitochondrial	+	+	+		+		u	d			+	[158]
3	HSPG2	Basement membrane heparan sulfate proteoglycan	+			+			u	d		+		[159]
13	HSPH1	Heat shock protein 105 kDa		+	+		+		u				+	[160]
4	HTATSF1	HIV Tat-specific factor 1	+			+				d		+
7	HYOU1	Hypoxia up-regulated protein	+		+		+		u		Nsp4 Orf3a Orf8		+	[161]
4	IDE	Insulin-degrading enzyme		+		+					Nsp4 Nsp12 Nsp14 Nsp15 Nsp16 Orf3b		+
2	IDH3A	Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial		+									+
2	IGBP1	Immunoglobulin-binding protein 1	+						u	d			+
2	IL18	Interleukin-18				+			u	d			+	[162]
7	ILF2	Interleukin enhancer-binding factor 2	+	+	+	+			u			+	+	[163]
6	ILF3	Interleukin enhancer-binding factor 3	+		+				u				+	[163]
2	IMPDH2	Inosine-5’-monophosphate dehydrogenase 2 (imp dehydrogenase 2) (impdh-ii)			+					d	Nsp14		+
7	IPO5	Importin-5, KPNB3, RANBP5		+	+		+						+	[164]
3	IPO7	Importin-7, RANBP7		+							Nsp6 Orf9c		+	[165]
13	IQGAP1	Ras GTPase-activating-like protein IQGAP1	+	+		+		+	u			+	+	[166]
2	IRGQ	Immunity-related GTPase family Q protein	+						u	d			+
4	ITGB1	Integrin beta-1	+			+			u	d	Nsp4 Of3b Orf6 Orf8 Orf9c	+		[167]
2	IWS1	Protein IWS1 homolog				+			u	d		+
4	KARS	Lysyl-tRNA synthetase	+	+		+					Nsp7	+	+	[100]
3	KHSRP	Far upstream element-binding protein 2 (KH-type splicing regulatory protein), FUBP2		+					u	d			+	[53]
2	KPNA2	Importin subunit alpha-1		+						d	Orf6		+
2	KPNA3	Importin subunit alpha-4	+		+							+	+
11	KPNB1	Importin subunit beta-1	+	+	+	+	+	+				+	+	[164]
2	KRR1	KRR1 small subunit processome component homolog, HIV-1 Rev-binding protein				+				d		+		[168]
10	KTN1	Kinectin	+						u		Orf6		+	[169]
2	KYNU	Kynureninase				+			u		Orf3		+
7	LAMB1	Laminin subunit beta-1	+							d			+	[170]
5	LAMC1	Laminin subunit gamma-1	+						u	d			+	[171]
2	LAMP2	Lysosome-associated membrane glycoprotein 2				+			u	d			+	[172]
2	LARS	Leucyl-tRNA synthetase, cytoplasmic				+						+		[100]
8	LDHA	L-lactate dehydrogenase A chain		+	+	+			u	d	Nsp12		+	[173]
10	LDHB	L-lactate dehydrogenase B chain		+	+	+			u	d	Nsp12 Nsp7		+	[174]
2	LEO1	RNA polymerase-associated protein LEO1				+			u			+
5	LGALS1	Galectin-1	+						u	d			+	[175]
23	LMNA	Prelamin-A/C	+			+		+	u	d	Nsp13 Orf3b Orf8 Orf10		+	[176]
8	LMNB1	Lamin-B1	+		+		+		u	d		+	+	[177]
7	LMNB2	Lamin-B2	+			+			u	d		+		[178]
16	LRPPRC	Leucine-rich PPR motif-containing protein	+	+	+	+		+		d			+	[179]
2	LSM2	U6 snRNA-associated Sm-like protein LSm2	+						u				+
2	LSM6	U6 snRNA-associated Sm-like protein LSm6	+						u				+
2	LSM8	U6 snRNA-associated Sm-like protein LSm8					+						+
2	MAGOHB	Protein mago nashi homolog	+						u	d			+
3	MANBA	Beta-mannosidase	+							d			+
3	MAP1B	Microtubule-associated protein 1B	+			+			u	d		+	+	[180]
6	MAPRE1	Microtubule-associated protein RP/EB family member	+		+		+				Orf3		+
2	MARCKS	Myristoylated alanine-rich c-kinase substrate (marcks) (protein kinase c substrate, 80 kda protein, light chain) (pkcsl)			+				u	d	M Nsp4 Nsp6 Orf3a Orf3b Orf7b S		+
2	MARS	Methionine-tRNA ligase, MARS1				+				d		+		[39]
9	MCM2	DNA replication licensing factor MCM2		+	+		+	+		d			+	[181]
7	MCM3	DNA replication licensing factor MCM3		+	+		+	+	u	d			+	[39]
5	MCM4	DNA replication licensing factor MCM4		+	+		+		u	d			+	[181]
3	MCM5	DNA replication licensing factor MCM5			+		+		u	d			+	[181]
9	MCM6	DNA replication licensing factor MCM6		+	+		+	+	u	d			+	[39]
2	MDH1	Malate dehydrogenase, cytoplasmic			+					d	E Orf3		+
3	MDH2	Malate dehydrogenase, mitochondrial				+			u	d			+	[25]
2	ME2	NAD-dependent malic enzyme, mitochondrial		+					u	d	Nsp15		+
10	MOV10	Putative helicase, Moloney leukemia virus 10 protein	+			+			u	d	E M N Nsp3 Nsp4 Nsp6 Orf3a Orf7a Orf7b Orf8 Orf9c S	+
5	MRPL1	39S ribosomal protein L1, mitochondrial				+						+
3	MRPL13	39S ribosomal protein L13, mitochondrial				+				d		+
2	MRPL15	39S ribosomal protein L15, mitochondrial				+			u	d		+
2	MRPL17	39S ribosomal protein L17, mitochondrial				+				d		+
2	MRPL18	39S ribosomal protein L18, mitochondrial				+				d		+
4	MRPL19	39S ribosomal protein L19, mitochondrial				+				d	Orf8	+
2	MRPL2	39S ribosomal protein L2, mitochondrial				+				d	Nsp6	+
2	MRPL23	39S ribosomal protein L23, mitochondrial				+				d		+
5	MRPL37	39S ribosomal protein L37, mitochondrial				+			u	d		+
5	MRPL38	39S ribosomal protein L38, mitochondrial				+				d		+
2	MRPL39	39S ribosomal protein L39, mitochondrial				+		+		d		+	+
3	MRPL45	39S ribosomal protein L45, mitochondrial				+				d		+
2	MRPL49	39S ribosomal protein L49, mitochondrial				+				d		+
4	MRPS22	28S ribosomal protein S22, mitochondrial				+						+
4	MRPS23	28S ribosomal protein S23, mitochondrial				+						+
6	MRPS27	28S ribosomal protein S27, mitochondrial				+					Nsp8	+
2	MRPS28	28S ribosomal protein S28, mitochondrial, MRPS35				+						+
2	MRPS30	28S ribosomal protein S30, mitochondrial				+				d		+
2	MRPS34	28S ribosomal protein S34, mitochondrial				+				d		+
3	MRPS9	28S ribosomal protein S9, mitochondrial				+						+
6	MSN	Moesin	+	+		+			u		Nsp6 Orf3 S		+	[182]
21	MVP	Major vault protein	+			+			u	d		+		[183]
4	MXRA5	Matrix-remodeling-associated protein 5	+							d		+		[183]
16	MYBBP1A	Myb-binding protein 1A			+	+		+	u	d		+	+
2	MYG1	UPF0160 protein MYG1, mitochondrial, C12orf10		+		+							+
2	MYH10	Myosin-10	+						u	d	Nsp9	+		[184]
43	MYH9	Myosin-9	+		+	+		+	u	d		+	+	[184]
3	MYL6	Myosin light chain 6	+				+		u				+	[185]
4	MYLK	Myosin light chain kinase, smooth muscle	+						u	d			+
3	MYO1C	Unconventional myosin-Ic, MYO1E	+			+			u	d		+		[186]
4	MZB1	Marginal zone B- and B1-cell-specifc protein (Proapoptotic caspase adapter protein, plasma cell-induced resident protein)		+					u				+
3	NAA15	N-alpha-acetyltransferase 15, NatA auxiliary subunit (NMDA receptor-regulated protein, NARG1)		+						d			+
2	NAA25	N-alpha-acetyltransferase 25, NatB auxiliary subunit (TPR repeat-containing protein C12orf30)		+									+
4	NACA	Nascent polypeptide associated complex subunit alpha	+	+	+		+		u	d			+	[187]
7	NAP1L1	Nucleosome assembly protein 1-like 1	+	+	+	+			u	d		+	+
7	NAP1L4	Nucleosome assembly protein 1-like 4	+	+	+				u	d		+	+
5	NARS	Asparagine-tRNA ligase, cytoplasmic, NARS1		+						d			+	[188]
6	NASP	Nuclear autoantigenic sperm protein	+	+	+		+		u	d			+	[189]
23	NCL	Nucleolin	+	+	+	+	+	+	u	d		+	+	[190]
2	NES	Nestin	+						u	d			+
2	NEU1	Sialidase-1	+						u	d	Orf8		+	[191]
3	NEXN	Nexilin F-actin binding protein	+						u	d			+
2	NFU1	HIRA interacting protein 5	+										+
8	NME1	Nucleoside diphosphate kinase A, RMRP	+	+		+			u	d			+	[192]
3	NME2	Nucleoside diphosphate kinase 2, NM23				+			u	d			+	[193]
2	NMT1	Glycylpeptide N-tetradecanoyltransferase 1	+										+	[194]
2	NMT2	Glycylpeptide N-tetradecanoyltransferase 2	+							d			+
2	NOC2L	Nucleolar complex protein 2 homolog				+				d		+
7	NOLC1	Nucleolar phosphoprotein p130 (nucleolar and coiled-body phosphoprotein 1)			+				u	d			+
9	NOP2	Probable 28S rRNA (cytosine(4447)-C(5)-methyltransferase				+			u			+
15	NPEPPS	Puromycin-sensitive aminopeptidase, metalloproteinase MP100	+	+		+							+
7	NPM1	Nucleophosmin (nucleolar phosphoprotein, numatrin)	+	+	+	+	+	+	u	d	Orf9c	+	+	[195]
2	NRCAM	Neuronal cell adhesion molecule				+			u	d			+	[196]
3	NSFL1C	NSFL1 cofactor p47		+					u				+
8	NUDC	Nuclear distribution C, Dynein complex regulator	+	+	+					d	Nsp12		+
4	NUDT21	Cleavage and polyadenylation specificity factor 5	+	+		+				d			+
2	NUDT3	Diphosphoinositol polyphosphate phosphohydrolase		+									+
4	NUDT5	Nudix hydrolase 5	+	+	+		+			d			+
3	NUMA1	Nuclear mitotic apparatus protein 1	+						u	d			+	[197]
2	OLA1	Obg-like ATPase 1				+			u				+
2	OTUB1	Ubiquitin thioesterase protein OTUB1		+									+
5	P3H1	Basement membrane chondroitin sulfate proteoglycan	+						u				+
2	P3H3	Prolyl 3-hydroxylase 3, LEPREL2	+							d		+
2	P3H4	ER protein SC65, nucleolar autoantigen No55	+								M	+		[198]
2	P4HA2	Prolyl 4-hydroxylase subunit alpha-2	+							d			+
18	P4HB	Protein disulfide-isomerase	+	+	+	+	+	+	u	d	Nsp7 Orf3b		+	[199]
14	PA2G4	Proliferation-associated protein 2G4	+	+					u	d			+
22	PABPC1	Poly(A)-binding protein 1	+	+		+				d	N	+		[200]
9	PABPC3	Poly(A)-binding protein 3			+		+	+		d		+	+
16	PABPC4	Poly(A)-binding protein 4, APP1	+		+	+		+		d	N	+	+	[201]
4	PAF1	RNA polymerase II-associated factor 1 homolog				+				d		+
2	PAFAH1B2	Platelet-activating factor acetylhydrolase IB subunit beta		+		+			u	d			+
3	PAFAH1B3	Platelet-activating factor acetylhydrolase IB subunit gamma		+		+			u		Nsp12 Nsp5 Orf3b		+
6	PAICS	Multifunctional protein ADE2		+						d			+
2	PARP1	Poly [ADP-ribose] polymerase 1		+					u	d			+
3	PARVA	Alpha-parvin	+						u				+
8	PCNA	Proliferating cell nuclear antigen	+	+	+	+	+	+	u	d			+	[202]
2	PDCD10	Programmed cell death protein 10		+									+
21	PDIA3	Protein disulfide-isomerase A3	+	+		+			u	d	M Orf3a Orf3b Orf8 Orf9c		+	[203]
34	PDIA4	Protein disulfide-isomerase A4	+	+	+	+	+	+	u	d	Nsp16 Nsp7 Orf3b		+	[204]
10	PDIA6	Protein disulfide-isomerase A6	+	+	+	+	+	+	u	d			+	[205]
6	PELP1	Proline-, glutamic acid-, leucine-rich protein 1				+				d		+
2	PES1	Pescadillo homolog				+				d		+
7	PFAS	Formylglycinamide ribonucleotide amidotransferase		+		+					Nsp7 Nsp12 Nsp15 Nsp16		+
3	PFDN2	Prefoldin subunit 2	+	+					u		Nsp12 Nsp15 Orf10		+	[206]
4	PFDN3	Prefoldin subunit 3, von hippel-lindau-binding protein 1, VBP1	+	+	+		+			d	Nsp12 Nsp15		+
2	PFKP	ATP-dependent 6-phofructokinase, platelet type				+			u	d	Orf7a		+	[207]
9	PFN1	Profilin-1	+	+	+				u	d			+	[208]
2	PFN2	Profilin-2	+						u				+	[181]
4	PGAM1	Phosphoglycerate mutase 1		+					u	d			+	[209]
4	PGAM2	Phosphoglycerate mutase 2		+		+							+
9	PGD	6-phosphogluconate dehydrogenase, decarboxylating				+			u	d			+
3	PGLS	6-phosphogluconolactonase		+					u				+
3	PHGDH	D-3-phosphoglycerate dehydrogenase		+					u	d			+	[210]
2	PLA2G4A	Cytosolic phospholipase a2			+								+
10	PLCG2	1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase gamma-2		+					u				+
2	PLD3	Phospholipase D3, 5’–3’ exonuclease PLD3				+			u	d	Nsp2 Nsp3 Nsp5 Orf6 Orf7b Orf8 Orf10		+
91	PLEC	Plectin-1, PLEC1	+			+			u	d		+	+	[211]
5	PLOD1	Procollagen-lysine, 2-oxoglutarate 5-dioxygenase 1	+							d			+
5	PLOD3	Multifunctional procollagen lysine hydroxylase and glycosyltransferase LH3	+										+
2	PLS1	Plastin-1				+				d			+
30	PLS2	Plastin-2, LCP1	+	+	+	+	+		u	d			+	[212]
6	PLS3	Plastin-3	+			+			u	d			+
2	PMPCB	Mitochondrial-processing peptidase subunit beta		+						d	M		+
2	POP1	Ribonucleases P/MRP protein subunit POP1				+			u			+		[213]
3	POR	NADPH--cytochrome P450 reductase				+			u	d	Nsp2 Orf6	+
8	PPA1	Inorganic pyrophosphatase		+		+			u		Orf3		+	[214]
3	PPAT	Amidophosphoribosyltransferase		+						d			+
10	PPIB	Peptidyl-prolyl cis-trans isomerase	+	+		+			u	d	Orf8		+	[215]
3	PPM1G	Protein phosphatase 1G (PPM1C)			+			+			Orf9b		+
2	PPP1R7	Protein phosphatase 1 regulatory subunit 7 (subunit 22)		+			+		u				+
7	PPP2R1A	Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform		+	+		+			d			+
6	PRDX1	Peroxiredoxin-1		+		+			u	d			+	[216]
5	PRDX3	Thioredoxin-dependent peroxide reductase	+	+		+			u	d			+	[217]
3	PRDX4	Peroxiredoxin-4	+			+			u	d	Orf3a		+	[218]
2	PRKAR2A	Protein kinase CAMP-dependent type II regulatory alpha	+						u		Nsp1 Orf9b		+	[48]
2	PRKCDBP	Protein kinase C delta-binding protein	+										+
11	PRKCSH	Protein kinase C substrate 80K-H	+	+	+		+	+		d	Nsp6 Orf3 Orf3a S		+
17	PRKDC	DNA-dependent protein kinase catalytic subunit (DNA-PKcs)	+		+	+		+	u	d	M Nsp4	+	+	[219]
5	PRMT1	Protein arginine N-methyltransferase 1 (Histone-arginine N-methyltransferase)	+	+	+	+	+	+		d			+	[220]
24	PRPF8	Pre-mRNA-processing-splicing factor 8 (U5 snRNP-specific protein 220 kDa)	+			+		+	u	d		+	+	[57]
2	PRPSAP2	Phosphoribosyl pyrophosphate synthetase-associated protein 2		+					u				+
2	PSAP	Proactivator polypeptide, Prosaposin	+						u	d			+
6	PSAT1	Phosphoserine aminotransferase 1				+			u	d	Orf3 Orf7a		+
3	PSMA1	Proteasome subunit alpha type-1		+	+		+			d	Orf3b		+	[25]
2	PSMA2	Proteasome subunit alpha type-2		+			+	+		d			+
6	PSMA3	Proteasome subunit alpha type-3, C8	+	+			+		u	d	Nsp2 Nsp4 Nsp7 Nsp10 Nsp12		+	[221]
5	PSMA4	Proteasome subunit alpha type-4, C9	+	+					u				+	[25]
5	PSMA5	Proteasome subunit alpha type-5	+	+	+		+	+	u		Orf3b		+	[222]
8	PSMA6	Proteasome subunit alpha type-6	+	+					u	d	Orf3b		+
6	PSMA7	Proteasome subunit alpha type-7	+	+	+		+	+	u	d			+	[223]
3	PSMA8	Proteasome subunit alpha type 7-like			+		+						+	[223]
5	PSMB1	Proteasome subunit beta type-1	+	+									+	[224]
3	PSMB3	Proteasome subunit beta type-3	+	+			+			d	Orf3b		+	[221]
7	PSMB4	Proteasome subunit beta type-4	+	+	+		+				Orf3b		+	[25]
3	PSMB6	Proteasome subunit beta type-6	+	+	+					d	Orf3b		+
5	PSMB7	Proteasome subunit beta type-7	+	+			+			d			+	[221]
3	PSMB8	Proteasome subunit beta type-8		+					u	d			+
4	PSMB9	Proteasome subunit beta type-9		+					u	d			+
2	PSMC1	26s Proteasome regulatory subunit 4					+			d	Orf6		+
2	PSMC3	26S protease regulatory subunit 6A		+						d	Orf6		+
5	PSMD1	26S proteasome non-ATPase regulatory subunit 1	+	+		+			u		Nsp7 Orf6 Orf8	+	+
9	PSMD11	Proteasome 26S non-ATPase regulatory subunit 11		+	+				u				+
3	PSMD12	26S proteasome non-ATPase regulatory subunit 12	+	+						d		+	+
3	PSMD13	Proteasome 26S non-ATPase subunit 13	+					+		d			+	[225]
2	PSMD14	26S proteasome non-ATPase regulatory subunit 14		+									+
8	PSMD3	26S proteasome non-ATPase regulatory subunit 3		+						d			+
9	PSMD6	26S proteasome non-ATPase regulatory subunit 6	+	+		+		+					+
2	PSMD7	26S proteasome non-ATPase regulatory subunit 7	+						u				+
11	PSME1	Proteasome activator complex subunit 1		+					u		Nsp15		+
8	PSME2	Proteasome activator complex subunit 2		+					u				+
4	PSME3	Proteasome activator complex subunit 3		+	+		+			d	Nsp16		+	[226]
2	PSPH	Phosphoserine phosphatase		+									+
6	PTBP1	Polypyrimidine tract-binding protein, hnRNP I	+	+					u	d			+	[227]
2	PTBP3	Polypyrimidine tract-binding protein, ROD1	+	+					u	d			+	[227]
16	PTCD3	Pentatricopeptide repeat-containing protein 3, mitochondrial, MRPS39	+			+						+
2	PTGES3	Prostaglandin E synthase 3 (telomerase-binding protein p23) (hsp90 co-chaperone) (progesterone rec)		+	+		+			d			+
4	PTMA	Prothymosin alpha			+		+	+	u	d			+	[228]
2	PTPN6	Tyrosine-protein phosphatase non-receptor type 6		+					u	d			+
2	PUF60	Poly(U)-binding-splicing factor PUF60	+						u				+	[229]
18	PUM1	Pumilio homolog 1				+				d		+
3	PURA	Transcriptional activator protein Pur-alpha				+			u	d		+
2	PUS1	tRNA pseudouridine synthase A		+									+
2	PZP	Pregnancy zone protein, alpha-2macroglobulin like	+							d			+	[230]
4	QARS	Bifunctional glutamate/proline-tRNA ligase, EPRS, EPRS1	+	+		+			u			+	+	[100]
3	RAB1A	Ras-related protein Rab-1A	+			+				d	Nsp7 Orf3 Orf7b	+
5	RAB7A	Ras-related protein Rab-7a	+	+					u	d	Nsp7 Orf3 Orf7b		+
3	RAD23A	UV excision repair protein RAD23 homolog A	+	+						d			+	[231]
5	RAD23B	UV excision repair protein RAD23 homolog B	+						u	d	Orf3a Orf3b Orf7a Orf9c		+	[231]
6	RALY	RNA binding protein, autoantigen p542	+			+			u	d	Orf9c	+		[232]
3	RANBP1	Ran-specific GTPase-activating protein		+					u	d			+
2	RANBP6	Ran-binding protein 6		+						d	Orf7a		+
2	RANGAP1	Ran GTPase-activating protein 1			+	+				d		+		[165]
3	RARS	Arginyl-tRNA synthetase, cytoplasmic, RARS1				+			u			+		[39]
5	RBBP4	Chromosome assembly factor 1 subunit C	+			+				d		+		[233]
3	RBBP7	Histone-binding protein rbbp7			+		+		u	d			+
2	RBM3	Putative RNA-binding protein 3	+						u	d	Orf8		+
3	RBM8A	RNA-binding protein 8A				+			u			+
2	RBMXL2	RNA-binding motif protein X-linked-like-2	+										+
2	RCN3	Reticulocalbin-3	+										+
8	RDX	Radixin	+	+	+	+			u	d	Nsp13		+	[234]
2	RMI2	RecQ-mediated genome instability protein 2			+							+
3	RNPEP	Arginine aminopeptidase, APB				+					Orf3		+
2	RNPS1	RNA-binding protein with serine-rich domain 1				+			u	d		+
4	RO52	E3 ubiquitin-protein ligase TRIM21 (Ro/SS-A), TRIM21						+	u	d		+
4	RO60	60 kDa SS-A/Ro ribonucleoprotein	+			+			u			+		[235]
2	RPA3	Replication protein A 14 kda subunit					+						+	[236]
3	RPF2	Ribosome production factor 2 homolog, BXDC1	+			+						+
2	RPL10A	60S ribosomal protein L10a		+		+						+
2	RPL11	60S ribosomal protein L11	+	+		+			u			+
4	RPL12	60S ribosomal protein L12	+		+	+			u	d		+		[237]
2	RPL15	60S ribosomal protein L15	+	+	+	+				d		+
3	RPL18	60S ribosomal protein L18	+		+	+				d		+
2	RPL22	60S ribosomal protein L22	+	+	+		+			d			+	[93]
2	RPL23A	Ribosomal protein L23a			+				u				+
2	RPL26L1	60S ribosomal protein L26-like 1, RPL26P1			+	+					Orf9b	+
3	RPL3	60s ribosomal protein L3 (hiv-1 tar rna-binding protein b)			+				u	d		+
2	RPL31	60S ribosomal protein L31			+				u	d			+
2	RPL35A	60S ribosomal protein L35a				+			u	d		+		[238]
2	RPL4	60S ribosomal protein L4				+			u	d		+
17	RPL5	60S ribosomal protein L5	+		+	+	+	+		d		+	+	[239]
11	RPL6	60S ribosomal protein L6	+		+	+	+	+	u	d		+		[181]
9	RPL7	60S ribosomal protein L7, RPL7P32	+		+	+	+	+	u	d		+		[93]
4	RPL7A	60S ribosomal protein L7A			+	+			u	d		+		[238]
2	RPL8	60S ribosomal protein L8			+	+			u	d		+		[165]
8	RPLP0	60S acidic ribosomal protein P0	+	+	+	+	+		u	d		+		[240]
2	RPLP1	60S acidic ribosomal protein P1				+			u	d		+		[241]
4	RPLP2	60S acidic ribosomal protein P2	+		+	+	+		u	d		+	+	[241]
2	RPS15A	40s ribosomal protein S15a		+	+	+			u			+
3	RPS18	40S ribosomal protein S18	+			+			u	d	Nsp13 Orf8 Orf10	+		[165]
3	RPS19	40S ribosomal protein S19	+							d	Orf9c		+	[238]
3	RPS2	40S ribosomal protein S2	+		+	+			u	d		+		[39]
2	RPS25	40S ribosomal protein S25		+	+				u	d	Orf8	+	+	[93]
3	RPS27A	Ubiquitin-40S ribosomal protein S27a, UBA80, UBCEP1		+		+			u	d	Nsp4 S	+		[93]
6	RPS3	40S ribosomal protein S3	+	+	+	+			u	d	Orf8	+	+	[242]
3	RPS3A	40S ribosomal protein S3a	+	+	+		+		u	d	Orf8	+	+
3	RPS4X	40S ribosomal protein S4, X isoform	+			+				d	Orf8	+		[25]
3	RPS6	40S ribosomal protein S6			+	+			u	d	Nsp6	+		[238]
3	RPS7	40S ribosomal protein S7		+	+		+		u	d			+	[93]
2	RPS8	40S ribosomal protein S8	+			+			u	d		+
8	RPS9	40S ribosomal protein S9	+		+	+		+		d		+		[238]
5	RPSA	40S ribosomal protein SA		+		+			u	d			+	[243]
13	RRBP1	Ribosome-binding protein 1	+			+			u	d	Orf8	+	+
11	RRP12	RRP12-like protein				+			u			+
4	RRP9	U3 small nucleolar RNA-interacting protein 2			+	+			u	d	N	+		[244]
4	RRS1	Ribosome biogenesis regulatory protein homolog				+			u			+
5	RSL1D1	Ribosomal L1 domain-containing protein 1				+			u	d		+
6	RUVBL1	RuvB-like 1, tata box-binding protein-interacting protein		+	+	+					Nsp1 Nsp7 Nsp12 Orf9b	+	+	[245]
5	RUVBL2	RuvB-like 2		+						d	Nsp1 Nsp7 Nsp12 Orf9b		+	[246]
2	SARS	Serine-tRNA ligase, cytoplasmic, SARS1		+					u		Nsp15		+
4	SEPHS1	Selenide, water dikinase	+							d			+	[247]
2	SEPT11	Septin-11		+						d			+	[25]
2	SEPT2	Septin-2, NEDD5, DIFF6	+	+					u	d			+	[248]
3	SEPT7	Septin-7		+						d			+	[249]
5	SERPINB1	Leukocyte elastase inhibitor				+			u				+
4	SERPINB6	Serpin B6, peptidase inhibitor 6				+							+
8	SERPINB9	Serpin B9		+					u	d			+
2	SERPINC1	Antithrombin-III		+		+			u				+
3	SERPINE1	Plasminogen activator inhibitor 1	+						u	d	Orf8		+	[250]
4	SERPINH1	Serpin H1, HSP47	+							d			+	[251]
6	SET	SET nuclear proto-oncogene (Inhibitor of granzyme A-activated DNase, HLA-DR-associated protein II)	+	+	+	+	+	+	u	d		+	+	[252]
2	SF3A1	Splicing factor 3 subunit 1 (spliceosome-associated protein 114) (sap 114) (sf3a120)			+				u				+
14	SF3B1	Splicing factor 3B subunit 1	+			+			u	d		+		[253]
13	SF3B3	Splicing factor 3B subunit 3, SAP130	+	+	+	+	+	+	u			+	+	[253]
8	SFN	14-3-3 protein sigma, Stratifin				+		+	u	d			+	[254]
3	SFPQ	Splicing factor, proline- and glutamine-rich	+	+					u	d			+	[255]
3	SGTA	Small glutamine-rich tetratricopeptide repeat-containing protein alpha		+					u	d	M		+
3	SH3BGRL3	SH3 domain-binding glutamic acid-rich-like protein 3	+							d			+
2	SHMT1	Serine hydroxymethyltransferase, cytosolic		+						d			+
9	SHMT2	Serine hydroxymethyltransferase, mitochondrial		+						d			+
2	SKP1	S-phase kinase-associated protein 1	+						u	d			+
2	SLC1A5	Neutral amino acid transporter B, Simian type D retrovirus receptor, Baboon M7 virus receptor				+			u	d	Orf3 S	+
2	SLC2A1	HepG2 glucose transporter, GLUT1				+				d	Nsp8	+		[256]
17	SLC3A2	4F2 cell-surface antigen heavy chain, CD98	+			+			u	d	Orf3b Orf9c	+
2	SLIRP	SRA stem-loop-interacting RNA-binding protein, mitochondrial		+					u	d			+
4	SMS	Spermine synthase	+						u	d	Orf3		+
9	SND1	Staphylococcal nuclease domain-containing protein 1	+	+		+			u	d			+
15	SNRNP200	U5 small nuclear ribonucleoprotein 200 kDa helicase	+			+				d		+		[257]
3	SNRNP70	U1 small nuclear ribonucleoprotein 70 kDa		+	+		+		u	d			+	[258]
3	SNRPA	U1 small nuclear ribonucleoprotein A	+	+		+			u				+	[259]
8	SNRPA1	U2 small nuclear ribonucleoprotein A’		+	+							+	+	[260]
3	SNRPB	SnRNP-associated proteins B and B’	+		+	+			u	d		+		[261]
2	SNRPD1	Small nuclear ribonucleoprotein Sm D1	+	+		+			u			+	+	[262]
4	SNRPD2	Small nuclear ribonucleoprotein Sm D2	+	+	+	+	+			d		+	+	[263]
2	SNRPD3	Small nuclear ribonucleoprotein Sm D3	+	+			+			d		+	+	[262]
2	SNRPE	Small nuclear ribonucleoprotein E	+	+	+					d		+	+	[264]
2	SNRPG	Small nuclear ribonucleoprotein G, PBSCG				+						+		[264]
2	SOD1	Superoxide dismutase [Cu-Zn]				+			u	d			+	[265]
46	SPTAN1	Spectrin alpha chain, brain (spectrin, non-erythroid alpha chain)	+	+	+	+		+	u	d		+	+	[266]
29	SPTBN1	Spectrin beta chain, brain	+		+	+			u	d		+		[267]
3	SRM	Spermidine synthase		+						d			+
3	SRP14	Signal recognition particle 14 kDa protein		+					u	d	Nsp13 Orf8		+
2	SRP68	Signal recognition particle 68 kda protein			+						N Nsp2		+
2	SRP72	Signal recognition particle 72 kDa protein				+				d	Nsp8	+		[268]
2	SRP9	Signal recognition particle 9 kda protein			+				u	d		+
2	SRRT	Arsenite-resistance protein 2					+			d			+
5	SRSF1	Serine/argine-rich splicing factor 1		+	+	+	+		u	d		+	+	[269]
2	SRSF11	Arginine/serine-rich splicing factor 11, SRSF11	+						u	d			+
3	SRSF2	Arginine/serine-rich splicing factor 2, SFRS2	+	+	+				u	d			+	[65]
2	SRSF3	Serine/arginine-rich splicing factor 3, SFRS3					+						+	[270]
4	SRSF4	Splicing factor, arginine/serine-rich 4 (srp75)			+								+
2	SRSF5	Serine/arginine-rich splicing factor 5, SRP40			+		+		u	d			+	[271]
2	SRSF6	Splicing factor, arginine/serine-rich 6			+				u	d			+
3	SRSF7	Serine /arginine-rich splicing factor 7, SRSF7	+		+		+	+	u			+	+	[271]
2	SRSF8	Serine/arginine-rich splicing factor 8			+		+			d			+
11	SSB	Lupus la protein (sjoegren syndrome type b antigen) (La/SSB)	+	+	+	+	+	+	u	d		+	+	[41]
9	SSBP1	Single-stranded DNA-binding protein, mitochondrial	+	+		+					N	+
8	SSRP1	Fact complex subunit ssrp1 (facilitates chromatin transcription complex subunit ssrp1) (factp80) (chromatin- specific transcription elongation factor 80 kda)	+		+	+			u	d		+		[272]
6	ST13	Hsc70-interacting protein (hip) (suppression of tumorigenicity protein 13) (putative tumor suppressor st13) (protein fam10a1) (progesterone receptor-associate)	+	+	+	+	+		u		Nsp12 Orf3b Orf6 Orf8 Orf10		+	[273]
3	STIP1	Stress-induced-phosphoprotein 1		+					u	d	E Nsp12 Orf3a Orf8		+	[14]
2	STRBP	Spermatid perinuclear RNA-binding protein	+								Nsp15		+
4	SUB1	Activated RNA polymerase II transcriptional coactivator p15 (PC4, RPO2TC1)	+		+			+	u	d		+	+
2	SUGT1	Protein SGT1 homolog (Suppressor of G2 allele of SKP1 homolog)		+					u		Nsp12 Nsp15		+
2	SUMO1	Small ubiquitin-related modifier	+							d			+	[274]
9	SUPT16H	FACT complex subunit SPT16	+		+	+				d		+
2	SUPT5H	Transcription elongation factor SPT5				+						+
2	SWAP70	Switch-associated protein 70		+						d	Nsp2		+
11	TALDO1	Transaldolase		+		+			u	d			+	[275]
3	TBCA	Tubulin-specific chaperone A		+							Nsp11		+
3	TCL1A	T-cell leukemia/lymphoma protein 1A		+					u	d			+
7	TCP1	T-complex protein 1 subunit alpha (tcp-1-alpha) (cct-alpha)		+	+		+			d	Orf10		+	[51]
4	TEX10	Testis-expressed protein 10				+						+
3	TFG	TRK-fused gene protein	+			+							+
4	TGM2	Protein-glutamine gamma-glutamyltransferase 2				+			u	d			+	[276]
9	THBS1	Thrombospondin-1	+						u	d			+	[277]
29	TLN1	Talin-1	+	+	+	+			u	d			+	[278]
4	TLN2	Talin-2	+						u				+
6	TNC	Tenascin C	+							d			+	[279]
5	TNPO1	Transportin-1, KPNB2		+									+
3	TOP1	DNA topoisomerase 1 (Scl 70)		+	+	+		+	u			+		[280]
5	TP53I3	Quinone oxidoreductase				+			u	d			+
3	TPD52L2	Tumor protein D54	+						u	d	Nsp4 Orf6		+
2	TPI1	Triosephosphate isomerase			+					d	Nsp15		+	[53]
16	TPM1	Tropomyosin 1 alpha chain	+	+	+	+	+	+	u	d	Nsp9		+	[281]
17	TPM2	Tropomyosin beta chain	+		+	+		+	u	d			+	[25]
6	TPM3	Tropomyosin alpha-3 chain	+	+	+	+	+	+	u	d			+	[282]
20	TPM4	Tropomyosin alpha-4 chain	+	+	+	+	+	+	u	d			+	[283]
2	TPP1	Tripeptidyl-peptidase 1	+						u	d		+
4	TPP2	Tripeptidyl-peptidase 2		+									+
4	TPR	Nucleoprotein TPR	+						u	d			+	[284]
4	TPT1	Tumor protein, translationally-controlled	+						u	d			+
3	TSN	Translin				+				d			+
3	TTLL12	Tubulin-tyrosine ligase-like protein 12		+	+					d			+	[285]
2	TTLL3	Tubulin monoglycylase TTLL3		+					u				+
4	TUBA1C	Tubulin alpha-1C, tubulin alpha-6	+	+	+	+	+	+	u	d		+	+	[286]
10	TUBA3C	Tubulin alpha-3C chain, TUBA2			+		+					+	+
12	TUBA4A	Tubulin alpha-4A chain, TUBA1	+	+		+			u	d		+	+	[287]
7	TUBB	Tubulin beta chain, TUBB5	+	+	+		+		u	d		+	+	[288]
4	TUBB1	Tubulin beta-1 chain	+	+	+							+	+	[289]
2	TUBB4A	Tubulin beta-4A chain, TUBB4, TUBB5		+					u	d			+	[290]
12	TUBB4B	Tubulin beta-4B chain, TUBB2C	+	+		+		+	u	d		+	+	[289]
2	TXN	Thioredoxin	+						u	d			+	[291]
2	TXNDC17	Thioredoxin domain-containing protein 17	+	+					u	d			+
4	TXNDC5	Thioredoxin domain-containing protein 5	+			+			u	d			+
2	TXNL1	Thioredoxin-like protein 1 (32 kda thioredoxin-related protein)			+				u				+
15	TXNRD1	Thioredoxin reductase 1, cytoplasmic	+	+		+			u	d			+	[291]
2	U2AF2	Splicing factor U2AF 65 kDa subunit		+						d			+	{Imai, 1993 #256}
15	UBA1	Ubiquitin-like modifier-activating enzyme 1	+	+	+	+	+	+	u	d			+	[292]
2	UBA2	Ubiquitin-like 1-activating enzyme e1b (sumo-1-activating enzyme subunit 2) (anthracycline-associated resistance arx)			+					d	Nsp7		+
2	UBA6	Ubiquitin-like modifier-activating enzyme 6		+							Nsp7		+
2	UBE2K	Ubiquitin-conjugating enzyme E2 K		+									+
2	UBLE1A	Ubiquitin-like 1-activating enzyme e1a (SUMO-1-activating enzyme subunit 1), SAE1	+		+				u	d			+	[274]
2	UBTF	Nucleolar transcription factor 1, autoantigen NOR-90				+				d		+		[293]
2	UCHL1	Ubiquitin carboxyl-terminal hydrolase isozyme L1	+			+			u	d	Nsp7 Orf3		+	[294]
5	UGDH	UDP-glucose 6-dehydrogenase				+			u	d			+
6	UGGT1	UDP-glucose:glycoprotein glucosyltransferase 1, UGCGL1	+							d	Orf3a Orf7a		+
18	UPF1	Regulator of nonsense transcripts 1	+			+				d	N	+
3	USP5	Ubiquitin carboxyl-terminal hydrolase 5 (ubiquitin thioesterase 5) (ubiquitin-specific-processing protease 5) (deubiquitinating enzyme 5) (isopeptidase T)	+	+	+				u	d			+
2	USP7	Ubiquitin carboxyl-terminal hydrolase (Herpes virus associated)				+			u		E M Nsp4 Orf7a Orf7b	+
2	USP9X	Ubiquitin specific protease 9, X chromosome	+						u	d		+
3	VARS1	Valine-tRNA ligase		+									+
4	VASN	Vasorin	+						u	d			+
4	VAT1	Synaptic vesicle membrane protein VAT-1 homolog	+						u	d	Orf3b Orf6		+
27	VCL	Vinculin	+			+			u	d	Nsp14		+	[295]
18	VCP	Transitional endoplasmic reticulum ATPase (Valosin-containing protein) (ER)	+	+	+	+	+	+	u	d			+	[296]
17	VIM	Vimentin	+	+	+	+	+	+	u	d		+	+	[297]
2	VPS35	Vacuolar protein sorting 35					+		u	d			+	[298]
6	WARS	Tryptophanyl-tRNA synthetase, cytoplasmic	+	+					u	d			+	[299]
5	WDR18	WD repeat-containing protein 18				+				d	Nsp15	+
2	XPNPEP1	Xaa-Pro aminopeptidase 1		+	+					d			+
4	XPO1	Exportin-1		+							Nsp4 Orf7a		+
10	XPO2	Exportin-2, CAS, CSE1L		+						d			+
5	XPOT	Exportin-T (trna exportin) (exportin(trna))		+	+				u		Orf7a		+
32	XRCC5	ATP-dependent DNA helicase 2 subunit 2, Ku80	+	+	+	+	+	+		d		+	+	[300]
30	XRCC6	ATP-dependent DNA helicase 2 subunit 1, Ku70	+	+	+	+	+	+	u	d		+	+	[300]
6	YARS	Tyrosine-tRNA ligase, cytoplasmic, YARS1		+					u	d			+	[301]
3	YBX1	Y-box-binding protein 1			+	+			u	d		+		[302]
6	YBX3	Y-box-binding protein 3	+		+	+		+	u	d		+		[303]
12	YWHAB	14-3-3 protein beta/alpha	+	+	+	+	+	+	u	d			+
15	YWHAE	14-3-3 protein epsilon	+	+	+	+	+	+	u	d			+	[254]
6	YWHAG	14-3-3 protein gamma	+	+	+	+	+	+	u	d			+	[254]
5	YWHAH	14-3-3 protein eta	+	+	+	+	+			d			+	[304]
7	YWHAQ	14-3-3 protein theta	+	+	+	+	+	+	u	d			+	[243]
7	YWHAZ	14-3-3 protein zeta/delta	+	+	+	+	+	+	u	d			+	[305]
2	ZPR1	Zinc finger protein ZPR1		+					u	d			+	[306]

Columns from left to right: P (the largest number of peptides identified for a protein by mass spectrometry for all cell lines), gene symbol, protein name, cell lines (HFL1 fetal lung fibroblast, HS-Sultan B lymphoblast, Wil2-NS B-lymphoblast, A549 lung epithelial cell, Jurkat T-lymphoblast, HEp-2 fibroblast), SARS-Cov-2 infection (up-regulated, down-regulated, interactome of specific viral protein), dermatan sulfate (DS) affinity (high affinity: eluted from DS-affinity resins with 1.0 M NaCl; low affinity: eluted with 0.4–0.6 M NaCl), Ref. (representive paper reporting autoantibodies specific for the autoAg protein). Highlighted in red: common (shared) autoAgs found in all 6 cell lines.