Extended Data Figure 1

a SARS-CoV2 PCR(+) (days from COVID-19 diagnosis) -14 -10 -6 -2 0 2 6 10 14 20 60 100 140 AP1 AP2 AP3 AP4 AP5 AP6 Adult AP7 COVID-19 AP8 AP9

AP10 symptom onset AP11 AP12 SARS-CoV2 PCR detection AP13 Nasal/Tracheal/Bronchi brush, AP14 blood BP1 BP2 Convalescent blood BP3 BP4

PP1 Paediatric PP2 COVID-19 PP3 PP4

PC2 Post PC6 COVID-19 PC9 PC11 PC12 PC21

b Neonate Infant Young Child Child Adolescent Adult Patient 0 1 0 1 0 6 Sample Nasal brush 0 1 0 1 0 5 Tracheal/bronchial brush 0 0 0 0 0 0 Blood 0 1 0 1 0 5 Severe Post COVID-19 Moderate severity Mild Age group Neonate Infant Young Child Child Adolescent Adult 0 30d 1y 2y 6y 12y 18y 30y 50y 70y 90y

Bronchial brush Tracheal brush Nasal brush Blood

East Asian

African

South Asian

PC2 PC3 PC1 European Extended Data Figure 2

c Extended Data Figure 3

a Healthy Children

Basal 1 Basal 2 Basal cycling Squamous Secretory Goblet 1 Fraction of cells in group (%) Goblet 2 Club Inflamm epi 5 10 15 20 25 Deuterosomal Ciliated 1 Ciliated 2 Ionocyte Brush Neuroendocrine Melanocyte T/NK/ILC B/Plasma Mean expression in group Myeloid Mast

0 1 2 3 BSG IFIT2 IFIT3 LY6E ST14 CTSL DPP4 ACE2 TFRC CTSB NRP1 RHOA TAPT1 FURIN AP2A2 CD209 IFITM1 IFITM2 IFITM3 RAB14 RAB10 TOP3B AP2M1 RAB1A ANPEP CDHR3 CLEC4G CLEC4M CHMP2A ST3GAL1 TMPRSS2 TMPRSS4

TMPRSS11D Lorem ipsum SARS-CoV-2 SARS-CoV, Protease Restriction factors Post-entry factors receptor HCoV-229E receptor MERS-CoV receptor Rhinovirus-C receptor

b (H1N1) receptor A Influenza Correlation between mean viral expression and mean expression of entry factors across cell types

0.4 p < 0.05 0 False True −0.4 Spreaman rho VCP BSG LY6E IFIT2 IFIT3 CTSL ST14 TFRC DPP4 CTSB ACE2 NRP1 RHOA FURIN TAPT1 AP2A2 ANPEP IFITM3 IFITM2 IFITM1 RAB14 RAB10 TOP3B RAB1A CD209 ZCRB1 AP2M1 DDX3X CDHR3 CLEC4G CLEC4M CHMP2A ST3GAL1 TMPRSS2 TMPRSS4 HNRNPA1 TMPRSS11D

c ACE2

0.100 Group 0.075 Adult_COVID+ Adult_Post-COVID 0.050 Ped_COVID+ 0.025 Ped_Healthy Ped_Post-COVID 0 Fraction of cells with expression Club Mast Brush Basal 1 Basal 2 Myeloid T/NK/ILC Goblet 1 Goblet 2 Ionocyte B/Plasma Ciliated 1 Ciliated 2 Secretory Squamous Melanocyte Inflamm epi Basal cycling Deuterosomal Neuroendocrine Cell type Extended Data Figure 4

a KRT14 KRT6A KRT13 KRT24

marker genes

“Hillock” associated

Tissue

Patient

COVID_status

Age_bin

Cell_viability

10x_kit

Ethnicity

Sex

Smoker

Date_of_process

residual

−0.5 0.0 0.5 1.0 1.5

Healthy nasal epithelial cells Neonate 0.3 Infant Young child Child 0.2 Adolescent

0.1 Proportion

0.0 Club Brush Basal 1 Basal 2 Goblet 1 Ionocyte Goblet 2 Ciliated 1 Ciliated 2 Secretory Squamous Melanocyte Inflamm epi Basal cycling Deuterosomal Neuroendocrine aExtended Data Figure 5 Expression signature scoring of cellular response to interferon a

1.0

0.5 Type 1

0.0

1.0

0.5 Gamma

0.0 LC NK ILC fDC Mac NKT pDC T gd Club Neut Mast T reg Mono Brush B mem T naive Basal 1 Basal 2 B naive Goblet 1 Goblet 2 Ionocyte B cycling Ciliated 1 Ciliated 2 Secretory Squamous Melanocyte Inflamm epi Plasma IGL Plasma IGK T CD4 mem T CD8 mem Basal cycling Mac activated cDC activated Deuterosomal Neuroendocrine Mono GPBAR1+ B mem activated T CD8 exhausted T CD4 FRMD4B+ B mem exhausted

response to interferon-alpha (GO:0035455)

response to interferon-gamma (GO:0034341)

all cells Monocytes

c Extended Data Figure 6

a Upper airway b Lower airway

CCNO CDC20B FOXN4 CCNO CDC20B FOXN4

Deu Deu

KRT4 KRT7 IF43 KRT4 KRT7 IF43

Ba-d Ba-d

ISG15 IFIT1 CXCL10 ISG15 IFIT1 CXCL10

IRC IRC

SAA1 S100A8 S100A9 SAA1 S100A8 S100A9

IETCs IETCs

c Chua et al. dataset

CCNO CDC20B FOXN4

Deu

KRT4 KRT7 IF43

Ba-d

ISG15 IFIT1 CXCL10

IRC

SAA1 S100A8 S100A9

IETCs Extended Data Figure 7 a log10 #genes log10 #proteins 5 detected 5 detected 4.0 2.5 0 0 3.5 2.0 1.5 −5 3.0 −5 1.0 −10WNN UMAP 2 −10WNN UMAP 2 2.5 0.5 −10 −5 0 5 10 2.0 −10 −5 0 5 10 0.0 WNN UMAP 1 WNN UMAP 1

log10 #UMIs log10 #UMIs from 5 from genes 5 antibody derived tags 5 5 0 4 0 4 −5 3 −5 3 2 2 WNN UMAP 2 −10 −10WNN UMAP 2 1 1 −10 −5 0 5 10 0 −10 −5 0 5 10 0 WNN UMAP 1 WNN UMAP 1 Sequencing library batch S1 S8 S15 S22 5 5 S2 S9 S16 S23 Sex 0 Female 0 S3 S10 S17 S24 S4 S11 S18 S25 −5 Male −5 S5 S12 S19 S26 −10WNN UMAP 2 −10WNN UMAP 2 S6 S13 S20 S27 S7 S14 S21 S28 −10 −5 0 5 10 −10 −5 0 5 10 WNN UMAP 1 WNN UMAP 1 Sample ID Percentage AP1 AP3 NP16 NP24 NP41 5 mitochondrial 5 10.0 AP1−post AP4 NP17 NP26 NP44 0 0 AP10 AP5 NP18 NP32 PC11 7.5 AP11 AP5−post NP19 NP35 PC2 −5 −5 5.0 AP12 AP6 NP20 NP36 PC21 WNN UMAP 2 WNN UMAP 2 −10 2.5 −10 AP13 AP9−post NP21 NP37 PC6 AP2 NP13 NP22 NP38 PC9 −10 −5 0 5 10 0.0 −10 −5 0 5 10 WNN UMAP 1 WNN UMAP 1 AP2−post NP15 NP23 NP39

b 100,000 30,000 10,000

genes 3,000

#UMIs from 1,000 ost p AP1 AP2 AP3 AP4 AP5 AP6 AP8 AP9 PP1 PP2 PP3 PP4 PC2 PC6 PC9 AP10 AP11 AP12 AP13 NP13 NP15 NP16 NP17 NP18 NP19 NP20 NP21 NP22 NP23 NP24 NP26 NP27 NP28 NP30 NP31 NP32 NP35 NP36 NP37 NP38 NP39 NP41 NP44 PC11 PC21 AP2− AP1−post AP5−post AP6−post AP7−post AP9−post 100,000

1,000

#UMIs from

ost

AP1

AP2

AP3 AP4 AP5

AP6

AP8 AP9

PP1 PP2 PP3 PP4

PC2

PC6 PC9

antibody derived tags

AP10 AP11 AP12 AP13

NP13 NP15 NP16 NP17 NP18 NP19 NP20 NP21 NP22 NP23 NP24 NP26 NP27 NP28 NP30 NP31 NP32 NP35 NP36 NP37 NP38 NP39 NP41 NP44 PC11

PC21

AP2−

AP1−post

AP5−post

AP6−post AP7−post

AP9−post c 15,000

10,000

5,000

after filtering

#cells detected 0

ost

AP1

AP2

AP3 AP4 AP5

AP6

AP8 AP9

PP1 PP2 PP3 PP4

PC2

PC6 PC9

AP10 AP11 AP12 AP13

NP13 NP15 NP16 NP17 NP18 NP19 NP20 NP21 NP22 NP23 NP24 NP26 NP27 NP28 NP30 NP31 NP32 NP35 NP36 NP37 NP38 NP39 NP41 NP44 PC11

PC21

AP2−

AP1−post

AP5−post

AP6−post AP7−post

AP9−post Extended Data Figure 8

a b

CD4 naive B exhausted CD4 Tcm Percent cells B naive CD4 Tem expressed B non−switched mem CD4 CTL B switched mem 0 CD14 monocytes T regs 25 CD16 monocytes CD8 naive 50 CD16+C1 monocytes CD8 Tcm CD4 CTL CD8 Tem 75 CD4 naive CD8 CTL CD4 Tcm CD4 Tem g/d T mRNA expression CD8 CTL MAIT (column z-score) CD8 naive Cycling T and NK CD8 Tcm NKT 2.5 CD8 Tem 2.0 cDC1 NK cDC2 NK CD56hi 1.5 Cycling T and NK cells ILC 1.0 g/d T CD14 monocytes 0.5 HSPCs CD16 monocytes ILC 0.0 MAIT CD16+C1 monocytes NK pDC Protein expression NK CD56hi cDC1 (column z-score) NKT cDC2 pDC 2.5 Plasma cells B naive 2.0 B non−switched mem Plasmablasts 1.5 Platelets B switched mem RBCs B exhausted 1.0 T regs

Plasmablasts 0.5 K Percentage N ILC dnT gdT

Plasma cells pDC

0.0 Treg Eryth

MAIT overlap (%) cDC1 cDC2 HSPCs ASDC HSPC B naive Platelet 100

Platelets CD4 CTL CD4 TEM CD8 TEM CD4 TCM CD8 TCM B memory CD8 Naive RBCs CD4 Naive CD14 Mono CD16 Mono Plasmablast 50 B intermediate NK Proliferating NK_CD56bright KIT CD8 Proliferating PF4 CD4 Proliferating CD4 HBB

IGHD 0 CD34 CD19 CD27 CD14 PPBP CD8A CCR6 C1QA CD3D CCR7 NCR1 IL3RA IL2RA MKI67 GZMH Azimuth annotation FXYD7 FCER2 MS4A1 TRDV2 FOXP3 TRGV9 NCAM1 CLEC9A ENTPD1 CD45RA FCER1A CLEC4C CD45RO FCGR3A SLC4A10 TRAV1−2 c TNFRSF13B Extended Data Figure 9

Nasal immune cells Nasal immune cells (with adult and paed PBMC samples (with adult and paed COVID19 effects considered seperately) COVID19 effects considered seperately) Residual Patient Patient Patient Age group Age group Residual Residual Age group COVID19 status COVID19 status COVID19 status Sex Sex Ethnicity Sequencing batch Sex

0.0 0.5 1.0 1.5 2.0 2.5 0.0 0.5 1.0 1.5 2.0 2.5 0.0 0.5 1.0 1.5 2.0 2.5

T naive T reg T CD4 FRMD4B+ T CD4 mem T CD8 mem T CD8 exhausted T gd NKT NK ILC B naive B mem Fraction of cells B mem exhausted in group (%) B mem activated B cycling Plasma IGK Plasma IGL 10 20 30 40 50 Mac Mac activated LC Mono Mono GPBAR1+ Mean expression Neut in group cDC activated pDC fDC 0.25 0.50 0.75 1.00 Mast CR2 SDS CD4 IGKC LEF1 LST1 GNLY CHPF CCR7 CCR4 CD27 CD8A CD1C C1QA VCAN CD3D IGLC2 GZMK MCM2 MKI67 KLRF1 KRT81 FCRL5 FCRL4 FCRL3 TPSB2 CTLA4 FOXP3 IGHG1 FCER2 TBX21 FDCSP LAMP3 CD207 PROK2 LILRA4 TRDV1 NR4A3 TRGV5 MS4A1 MS4A2 CAMK1 EOMES NCAM1 MARCO CLEC4C RNASE1 FCGR3B CD40LG GPBAR1 FRMD4B COL19A1

c Extended Data Figure 10 a combined_annot b chain_pairing c 100000 1 2 3 75000 4 5 6 50000 7 8 9 25000 >=10 UMAP2 UMAP2 Total # of T cell clones 0

Nasal PBMC 1.00 Tracheal 1 2 3 0.75 UMAP1 4 UMAP1 5 CD4 CTL CD8 Tem extra VDJ 6 extra VJ 0.50 7 CD4 Tcm CD8 naive 8 CD4 Tem Cycling T and NK cells no IR 9 >=10 CD4 naive MAIT orphan VDJ 0.25 fraction of TCR’s with CD8 CTL NKT orphan VJ differenting clone size CD8 T effect T regs single pair 0.00 two full chains CD8 Tcm Nasal PBMC Tracheal d patient_id tissue

AP1 AP12 NP28 AP1-post AP13 NP30 AP2 NP13 NP31 AP2-post NP15 NP32 AP3 NP16 NP35 AP4 NP17 NP36 AP5 NP18 NP37 Nasal AP5-post NP19 NP38 PBMC AP6 NP20 NP39 Tracheal AP6-post NP21 NP41 AP7-post NP22 NP44 AP8 NP23 PC11 clonotype_network2 clonotype_network2 AP9 NP24 PP1 AP9-post NP26 PP2 AP10 NP27 PP3 AP11 PP4 clonotype_network1 clonotype_network1 e receptor_subtype combined_annot chain_pairing

ambiguous B exhausted extra VDJ IGH B naive extra VJ IGH+IGK B non-switched mem no IR IGK+IGL B switched mem orphan VDJ UMAP2 ambiguous UMAP2 UMAP2 Plasma cells orphan VJ no IR Plasmablasts single pair two full chains

UMAP1 UMAP1 UMAP1 patient_id

f g AP1 AP13 NP30 1 AP1-post NP13 NP31 2 AP2 NP15 NP32 30000 3 AP2-post NP16 NP35 4 AP3 NP17 NP36 5 AP4 NP18 NP37 20000 6 AP5 NP19 NP38 7 AP5-post NP20 NP39 8 AP6 NP21 NP41 9 AP7-post NP22 NP44 10000 >=10 AP8 NP23 PC11

clonotype_network2 AP9 NP24 PP1 AP9-post NP26 PP2 0 AP10 NP27 PP3 AP11 NP28 PP4 AP12 Nasal PBMC Tracheal clonotype_network1 1.00 1 2 origin 3 h 0.75 4 5 6 0.50 7 8 9 0.25 >=10 Nasal PBMC Tracheal 0.00 clonotype_network2 Nasal PBMC Tracheal

clonotype_network1 Extended Data Table 1

SARS-CoV-2 negative children SARS-CoV-2 positive children SARS-CoV-2 positive adults Post-COVID19 (n = 30) (n = 4) (n = 18) (n = 6)

Median age 2.87 (3days - 16 yrs) 5.83 (21 days - 13 yrs) 66 (25 - 92 yrs) 35 (4 months - 47 yrs)

Sex Male (%) 13 (43.3) 3 (75) 10 (55.6) 3 (50) Female (%) 17 (56.7) 1 (25) 8 (44.4) 3 (50)

Ethnicity White (%) 20 (66.7) 3 (75) 7 (38.8) 2 (33.3) Black (%) 4 (13.3) 1 (25) 1 (5.6) 0 (0) Hispanic (%) 0 (0) 0 3 (16.7) 0 (0) South Asian (%) 1 (3.3) 0 5 (27.7) 1 (16.7) Other (%) 2 (6.7) 0 1 (5.6) 0 (0) Unspecified (%) 3 (10) 0 1 (5.6) 3 (50)

Peripheral blood test at sampling Lymphocyte count (cells/µl) 2,026 ± 684.6 2,370 ± 1,830 1,185 ± 504.1 2,160 ± 662.6

Viral infection symptoms Fever, Fatigue (%) 1 (3.3) 2 (50) 13 (72.2) 3 (50) Digestive symptom (%) 2 (6.7) 3 (75) 13 (72.2) 2 (33.3) Upper respiratory tract symptom (%) 3 (10) 2 (50) 9 (50) 3 (50) Respiratory failure (%) 6 (20) 4 (100) 12 (66.7) 6 (100)

Respiratory Support None (%) - 0 (0) 3 (16.7) 0 (0) Low flow oxygen (%) - 0 (0) 4 (22.2) 0 (0) HFNC / NIPPV (%) - 1 (25) 4 (22.2) 3 (50) IMV (%) - 3 (75) 7 (38.9) 3 (50)

COVID-19 severity Asymptomatic (%) NA 0 (0) 0 (0) 0 (0) Mild (%) NA 0 (0) 5 (27.8) 0 (0) Moderate (%) NA 0 (0) 3 (16.7) 0 (0) Severe (%) NA 4 (100) 10 (55.5) 6 (100)

Abbreviations: HFNC = high flow nasal canula, NIPPV = non-invasive positive pressure ventilation, IMV = invasive mechanical ventilation, NA = not assesed Extended Data Table 2

DNA_ID Clone Description Barcode DNA_ID Clone Description Barcode C0005 2D10 0005 anti-human CD80 ACGAATCAATCTGTG C0196 HIR2 0196 anti-human CD235ab GCTCCTTTACACGTA C0006 IT2.2 0006 anti-human CD86 GTCTTTGTCAGTGCA C0205 15-2 0205 anti-human CD206 (MMR) TCAGAACGTCTAACT C0007 29E.2A3 0007 anti-human CD274 (B7-H1, PD-L1) GTTGTCCGACAATAC C0206 7-239 0206 anti-human CD169 (Sialoadhesin, Siglec-1) TACTCAGCGTGTTTG C0008 24F.10C12 0008 anti-human CD273 (B7-DC, PD-L2) TCAACGCTTGGCTAG C0207 8F9 0207 anti-human CD370 (CLEC9A/DNGR1) CTGCATTTCAGTAAG C0009 2D3 0009 anti-human CD275 (B7-H2, ICOSL) GTGCATTCAACAGTA C0208 S15046E 0208 anti-human XCR1 AAGACGCATGTCAAC C0014 M1/70 0014 anti-mouse/human CD11b TGAAGGCTCATTTGT C0214 FIB504 0214 anti-human/mouse integrin β7 TCCTTGGATGTACCG C0021 11C3.1 0021 anti-human CD252 (OX40L) TTTAGTGATCCGACT C0215 11C1 0215 anti-human CD268 (BAFF-R) CGAAGTCGATCCGTA C0022 5F4 0022 anti-human CD137L (4-1BB Ligand) ATTCGCCTTACGCAA C0217 HA58 0217 anti-human CD54 CTGATAGACTTGAGT C0023 SKII.4 0023 anti-human CD155 (PVR) ATCACATCGTTGCCA C0218 AK4 0218 anti-human CD62P (P-Selectin) CCTTCCGTATCCCTT C0024 TX31 0024 anti-human CD112 (Nectin-2) AACCTTCCGTCTAAG C0224 IP26 0224 anti-human TCR α/β CGTAACGTAGAGCGA C0026 CC2C6 0026 anti-human CD47 GCATTCTGTCACCTA C0245 STA 0245 anti-human CD106 TCACAGTTCCTTGGA C0027 113-16 0027 anti-human CD70 CGCGAACATAAGAAG C0246 TU27 0246 anti-human CD122 (IL-2Rβ) TCATTTCCTCCGATT C0028 BY88 0028 anti-human CD30 TCAGGGTGTGCTGTA C0247 1A1 0247 anti-human CD267 (TACI) AGTGATGGAGCGAAC C0031 5C3 0031 anti-human CD40 CTCAGATGGAGTATG C0352 AER-37 (CRA-1) 0352 anti-human Fc εRlα CTCGTTTCCGTATCG C0032 24-31 0032 anti-human CD154 GCTAGATAGATGCAA C0353 HIP8 0353 anti-human CD41 ACGTTGTGGCCTTGT C0033 HI186 0033 anti-human CD52 CTTTGTACGAGCAAA C0355 4B4-1 0355 anti-human CD137 (4-1BB) CAGTAAGTTCGGGAC C0034 UCHT1 0034 anti-human CD3 CTCATTGTAACTCCT C0356 MIH24 0356 anti-human CD254 (TRANCE, RANKL) TCCGTGTTAGTTTGT C0046 SK1 0046 anti-human CD8 GCGCAACTTGATGAT C0358 GHI/61 0358 anti-human CD163 GCTTCTCCTTCCTTA C0047 5.1H11 0047 anti-human CD56 (NCAM) TCCTTTCCTGATAGG C0359 HB15e 0359 anti-human CD83 CCACTCATTTCCGGT C0050 HIB19 0050 anti-human CD19 CTGGGCAATTACTCG C0360 108-17 0360 anti-human CD357 (GITR) ACCTTTCGACACTCG C0052 P67.6 0052 anti-human CD33 TAACTCAGGGCCTAT C0362 7D4-6 0362 anti-human CD309 (VEGFR2) TTCACGCAGTAAGAT C0053 S-HCL-3 0053 anti-human CD11c TACGCCTATAACTTG C0363 G077F6 0363 anti-human CD124 (IL-4Rα ) CCGTCCTGATAGATG C0054 581 0054 anti-human CD34 GCAGAAATCTCCCTT C0366 12G5 0366 anti-human CD184 (CXCR4) TCAGGTCCTTTCAAC C0056 19F2 0056 anti-human CD269 (BCMA) CAGATGATCCACCAT C0367 TS1/8 0367 anti-human CD2 TACGATTTGTCAGGG C0058 W6/32 0058 anti-human HLA-A,B,C TATGCGAGGCTTATC C0368 11A8 0368 anti-human CD226 (DNAM-1) TCTCAGTGTTTGTGG C0060 5E10 0060 anti-human CD90 (Thy1) GCATTGTACGATTCA C0369 TS2/16 0369 anti-human CD29 GTATTCCCTCAGTCA C0061 104D2 0061 anti-human CD117 (c-kit) AGACTAATAGCTGAC C0370 201A 0370 anti-human CD303 (BDCA-2) GAGATGTCCGAATTT C0062 HI10a 0062 anti-human CD10 CAGCCATTCATTAGG C0371 P1E6-C5 0371 anti-human CD49b GCTTTCTTCAGTATG C0063 HI100 0063 anti-human CD45RA TCAATCCTTCCGCTT C0373 5A6 0373 anti-human CD81 (TAPA-1) GTATCCTTCCTTGGC C0064 6H6 0064 anti-human CD123 CTTCACTCTGTCAGG C0374 MEM-108 0374 anti-human CD98 GCACCAACAGCCATT C0066 CD7-6B7 0066 anti-human CD7 TGGATTCCCGGACTT C0375 M1310G05 0375 anti-human IgG Fc CTGGAGCGATTAGAA C0070 GoH3 0070 anti-human/mouse CD49f TTCCGAGGATGATCT C0384 IA6-2 0384 anti-human IgD CAGTCTCCGTAGAGT C0071 L291H4 0071 anti-human CD194 (CCR4) AGCTTACCTGCACGA C0385 TS1/18 0385 anti-human CD18 TATTGGGACACTTCT C0072 RPA-T4 0072 anti-human CD4 TGTTCCCGCTCAACT C0386 CD28.2 0386 anti-human CD28 TGAGAACGACCCTAA C0073 IM7 0073 anti-mouse/human CD44 TGGCTTCAGGTCCTA C0387 1D3 0387 anti-human TSLPR (TSLP-R) CAGTCCTCTCTGTCA C0081 M5E2 0081 anti-human CD14 TCTCAGACCTCCGTA C0389 HIT2 0389 anti-human CD38 TGTACCCGCTTGTGA C0083 3G8 0083 anti-human CD16 AAGTTCACTCTTTGC C0390 A019D5 0390 anti-human CD127 (IL-7Rα ) GTGTGTTGTCCTATG C0085 BC96 0085 anti-human CD25 TTTGTCCTGTACGCC C0391 HI30 0391 anti-human CD45 TGCAATTACCCGGAT C0087 UCHL1 0087 anti-human CD45RO CTCCGAATCATGTTG C0392 W6D3 0392 anti-human CD15 (SSEA-1) TCACCAGTACCTAGT C0088 EH12.2H7 0088 anti-human CD279 (PD-1) ACAGCGCCGTATTTA C0393 S-HCL-1 0393 anti-human CD22 GGGTTGTTGTCTTTG C0089 A15153G 0089 anti-human TIGIT (VSTM3) TTGCTTACCGCCAGA C0394 CY1G4 0394 anti-human CD71 CCGTGTTCCTCATTA C0090 MOPC-21 0090 Mouse IgG1, κ isotype Ctrl GCCGGACGACATTAA C0395 MIH43 0395 anti-human B7-H4 TGTATGTCTGCCTTG C0091 MOPC-173 0091 Mouse IgG2a, κ isotype Ctrl CTCCTACCTAAACTG C0396 BA5b 0396 anti-human CD26 GGTGGCTAGATAATG C0092 MPC-11 0092 Mouse IgG2b, κ isotype Ctrl ATATGTATCACGCGA C0397 5E8 0397 anti-human CD193 (CCR3) ACCAATCCTTTCGTC C0095 RTK4530 0095 Rat IgG2b, κ Isotype Ctrl GATTCTTGACGACCT C0399 7C9C20 0399 anti-human CD204 TAGCGAGCCAGATGT C0100 2H7 0100 anti-human CD20 TTCTGGGTCCCTAGA C0400 BV9 0400 anti-human CD144 (VE-Cadherin) TCCACTCATTCTGTA C0101 9E2 0101 anti-human CD335 (NKp46) ACAATTTGAACAGCG C0402 HI149 0402 anti-human CD1a GATCGTGTTGTGTTA C0102 BM16 0102 anti-human CD294 (CRTH2) TGTTTACGAGAGCCC C0406 12C2 0406 anti-human CD304 (Neuropilin-1) GGACTAAGTTTCGTT C0123 9C4 0123 anti-human CD326 (Ep-CAM) TTCCGAGCAAGTATC C0407 5-271 0407 anti-human CD36 TTCTTTGCCTTGCCA C0124 WM59 0124 anti-human CD31 ACCTTTATGCCACGG C0420 HP-MA4 0420 anti-human CD158 (KIR2DL1/S1/S3/S5) TATCAACCAACGCTT C0127 NC-08 0127 anti-Human Podoplanin GGTTACTCGTTGTGT C0437 4C7 0437 anti-mouse/human CD207 CGATTTGTATTCCCT C0134 P1H12 0134 anti-human CD146 CCTTGGATAACATCA C0576 9F10 0576 anti-human CD49d CCATTCAACTTCCGG C0135 67A4 0135 anti-human CD324 (E-Cadherin) ATCCTTCTCCCTTTC C0577 AD2 0577 anti-human CD73 (Ecto-5'-nucleotidase) CAGTTCCTCAGTTCG C0136 MHM-88 0136 anti-human IgM TAGCGAGCCCGTATA C0581 3C10 0581 anti-human TCR Vα7.2 TACGAGCAGTATTCA C0138 UCHT2 0138 anti-human CD5 CATTAACGGGATGCC C0582 B6 0582 anti-human TCR Vδ2 TCAGTCAGATGGTAT C0139 B1 0139 anti-human TCR γ/δ CTTCCGATTCATTCA C0583 B3 0583 anti-human TCR Vγ9 AAGTGATGGTATCTG C0140 G025H7 0140 anti-human CD183 (CXCR3) GCGATGGTAGATTAT C0584 6B11 0584 anti-human TCR Vα24-Jα18 (iNKT cell) AACTTCTGTGGTAGC C0141 J418F1 0141 anti-human CD195 (CCR5) CCAAAGTAAGAGCCA C0590 NKTA255 0590 anti-human CD305 (LAIR1) ATTTCCATTCCCTGT C0142 FUN-2 0142 anti-human CD32 GCTTCCGAATTACCG C0591 15C4 0591 anti-human LOX-1 ACCCTTTACCGAATA C0143 G034E3 0143 anti-human CD196 (CCR6) GATCCCTTTGTCACT C0592 DX27 0592 anti-human CD158b (KIR2DL2/L3, NKAT2) GACCCGTAGTTTGAT C0144 J252D4 0144 anti-human CD185 (CXCR5) AATTCAACCGTCGCC C0594 S16016B 0594 anti-human CD133 GTAAGACGCCTATGC C0145 Ber-ACT8 0145 anti-human CD103 (Integrin αE) GACCTCATTGTGAAT C0597 9E9A8 0597 anti-human CD209 (DC-SIGN) TCACTGGACACTTAA C0146 FN50 0146 anti-human CD69 GTCTCTTGGCTTAAA C0599 DX9 0599 anti-human CD158e1 (KIR3DL1, NKB1) GGACGCTTTCCTTGA C0147 DREG-56 0147 anti-human CD62L GTCCCTGCAACTTGA C0600 UP-R1 0600 anti-human CD158f (KIR2DL5) AAAGTGATGCCACTG C0148 G043H7 0148 anti-human CD197 (CCR7) AGTTCAGTCAACCGA C0801 P30-15 0801 anti-human CD337 (NKp30) AAAGTCACTCTGCCG C0149 HP-3G10 0149 anti-human CD161 GTACGCAGTCCTTCT C0802 P44-8 0802 anti-human CD336 (NKp44) GGGCAATTAGCGAGT C0151 BNI3 0151 anti-human CD152 (CTLA-4) ATGGTTCACGTAATC C0828 413D12 0828 anti-human CD307d (FcRL4) CGATTTGATCTGCCT C0152 11C3C65 0152 anti-human CD223 (LAG-3) CATTTGTCTGCCGGT C0829 509f6 0829 anti-human CD307e (FcRL5) TCACGCAGTCCTCAA C0153 SA231A2 0153 anti-human KLRG1 (MAFA) CTTATTTCCTGCCCT C0830 162.1 0830 anti-human CD319 (CRACC) AGTATGCCATGTCTT C0154 O323 0154 anti-human CD27 GCACTCCTGCATGTA C0831 DL-101 0831 anti-human CD138 (Syndecan-1) GTATAGACCAAAGCC C0155 H4A3 0155 anti-human CD107a (LAMP-1) CAGCCCACTGCAATA C0845 3B2/TA8 0845 anti-human CD99 ACCCGTCCCTAAGAA C0156 DX2 0156 anti-human CD95 (Fas) CCAGCTCATTAGAGC C0853 50C1 0853 anti-human CLEC12A CATTAGAGTCTGCCA C0159 L243 0159 anti-human HLA-DR AATAGCGAGCAAGTA C0856 M7004D06 0856 anti-Tau Phospho (Thr181) CTCGTTTGTAGCAAT C0160 L161 0160 anti-human CD1c GAGCTACTTCACTCG C0863 1D6 0863 anti-human CD257 (BAFF, BLYS) CAGAGCACCCATTAA C0162 10.1 0162 anti-human CD64 AAGTATGCCCTACGA C0867 DX22 0867 anti-human CD94 CTTTCCGGTCCTACA C0163 M80 0163 anti-human CD141 (Thrombomodulin) GGATAACCGCGCTTT C0870 A12 (7D4) 0870 anti-human CD150 (SLAM) GTCATTGTATGTCTG C0164 51.1 0164 anti-human CD1d TCGAGTCGCTTATCA C0894 MHK-49 0894 anti-human Ig light chain κ AGCTCAGCCAGTATG C0165 1D11 0165 anti-human CD314 (NKG2D) CGTGTTTGTTCCTCA C0895 M3/38 0895 anti-mouse/human Mac-2 (Galectin-3) GATGCAATTAGCCGG C0166 6/40c 0166 anti-human CD66b AGCTGTAAGTTTCGG C0896 GHI/75 0896 anti-human CD85j (ILT2) CCTTGTGAGGCTATG C0167 E11 0167 anti-human CD35 ACTTCCGTCGATCTT C0897 EBVCS-5 0897 anti-human CD23 TCTGTATAACCGTCT C0168 QA17A04 0168 anti-human CD57 Recombinant AACTCCCTATGGAGG C0898 MHL-38 0898 anti-human Ig light chain λ CAGCCAGTAAGTCAC C0169 F38-2E2 0169 anti-human CD366 (Tim-3) TGTCCTACCCAACTT C0899 BB7.2 0899 anti-human HLA-A2 GAACATTTCCGACAA C0170 MIH26 0170 anti-human CD272 (BTLA) GTTATTGGACTAAGG C0901 7B11 0901 anti-human GARP (LRRC32) AGGTATGGTAGAGTA C0171 C398.4A 0171 anti-human/mouse/rat CD278 (ICOS) CGCGCACCCATTAAA C0902 6-434 0902 anti-human CD328 (Siglec-7) CTTAGCATTTCACTG C0174 TS2/9 0174 anti-human CD58 (LFA-3) GTTCCTATGGACGAC C0908 H131 0908 anti-human TCR Vβ13.1 TTATGGACGTATGGT C0175 NK92.39 0175 anti-human CD96 (TACTILE) TGGCCTATAAATGGT C0920 ASL-24 0920 anti-human CD82 TCCCACTTCCGCTTT C0176 A1 0176 anti-human CD39 TTACCTGGTATCCGT C0944 BB27 0944 anti-human CD101 (BB27) CTACTTCCCTGTCAA C0177 NOK-1 0177 anti-human CD178 (Fas-L) CCGGTCCTCTGTATT C0985 4B2.9 0985 anti-human CD360 (IL-21R) GAGGATGATGCCATG C0179 K0124E1 0179 anti-human CX3CR1 AGTATCGTCTCTGGG C1046 S5/1 1046 anti-human CD88 (C5aR) GCCGCATGAGAAACA C0180 ML5 0180 anti-human CD24 AGATTCCTTCGTGTT C1047 3D11/HLA-F 1047 anti-human HLA-F GCAACTCTCCTACCT C0181 Bu32 0181 anti-human CD21 AACCTAGTAGTTCGG C1048 8F10B51 1048 anti-human NLRP2 ACGCTTGTGTTAGTT C0185 TS2/4 0185 anti-human CD11a TATATCCTTGTGAGC C1051 mAb 84 1051 anti-human Podocalyxin GAGCCGGTATAATGC C0186 HP6123 0186 anti-human IgA AAGATGTCCGAGCAA C1052 KF29 1052 anti-human CD224 CTGATGAGATGTCAG C0187 CB3-1 0187 anti-human CD79b (Igβ) ATTCTTCAACCGAAG C1055 12.1 1055 anti-c-Met GCTGCTGCGATTTGA C0188 ASL-32 0188 anti-human CD66a/c/e GGGACAGTTCGTTTC C1056 T5-39 1056 anti-human CD258 (LIGHT) ACTTCCCTGTAGAAA C0189 C1.7 0189 anti-human CD244 (2B4) TCGCTTGGATGGTAG C1057 JD3 1057 anti-human DR3 (TRAMP) GAGTTCCCTCAGTTC Extended Data Table 3

Virus_id Virus name link NC_007605.1 EBV1 (Human gammaherpesvirus 4) https://www.ncbi.nlm.nih.gov/nuccore/82503188 NC_009334.1 EBV2 (Human herpesvirus 4) https://www.ncbi.nlm.nih.gov/nuccore/139424470 AF156963 ERVWE1 (syncytin) https://www.ncbi.nlm.nih.gov/nuccore/AF156963 AY101582 ERVWE1 (syncytin) https://www.ncbi.nlm.nih.gov/nuccore/AY101582 AY101583 ERVWE1 (syncytin) https://www.ncbi.nlm.nih.gov/nuccore/AY101583 AY101584 ERVWE1 (syncytin) https://www.ncbi.nlm.nih.gov/nuccore/AY101584 AY101585 ERVWE1 (syncytin) https://www.ncbi.nlm.nih.gov/nuccore/AY101585 AF072498 HERV-W https://www.ncbi.nlm.nih.gov/nuccore/AF072498 AF127228 HERV-W https://www.ncbi.nlm.nih.gov/nuccore/AF127228 AF127229 HERV-W https://www.ncbi.nlm.nih.gov/nuccore/AF127229 AF331500 HERV-W https://www.ncbi.nlm.nih.gov/nuccore/AF331500.1/ NC_001664.4 HHV-6A (Human Herpes Virus 6) https://www.ncbi.nlm.nih.gov/nuccore/1344462938 NC_000898.1 HHV-6B (Human Herpes Virus 6) https://www.ncbi.nlm.nih.gov/nuccore/9633069 NC_001806.2 Herpes Simplex Virus 1 (Human alphaherpesvirus 1) https://www.ncbi.nlm.nih.gov/nuccore/820945227 NC_001798.2 Herpes Simplex Virus 2 (Human alphaherpesvirus 1) https://www.ncbi.nlm.nih.gov/nuccore/820945149 NC_001498.1 Measles morbillivirus https://www.ncbi.nlm.nih.gov/nuccore/9626945 NC_002200.1 Mumps rubulavirus https://www.ncbi.nlm.nih.gov/nuccore/9695415 NC_001545.2 Rubella https://www.ncbi.nlm.nih.gov/nuccore/336284682 NC_001348.1 Varicella Zoster Virus (VZV Human alphaherpesvirus 3) https://www.ncbi.nlm.nih.gov/nuccore/9625875 NC_006273.2 Cytomegalovieus (CMV) https://www.ncbi.nlm.nih.gov/nuccore/155573622 NC_045512.2 SARS-CoV2 https://www.ncbi.nlm.nih.gov/nuccore/1798174254